Citrus Sinensis ID: 008920

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------55
Protein Sequence
MMDKKKSEDNNISAPSSIFTTLFGGIPNESTVASSLFSDSNPFKRQHRESQSAENESIFNPMNSDSLDSNNSELKKIKKTRQEKPNPDLPDAEGAATKTLSLSNKSTKLIYPRSILGFEPNGTIENEIKKEHSSNVGSESYLNRQKQNSNFSVEGKKRSENKKTKKRKRDDVEKDYVEKKYGVIAKEEEGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAPAVNSPPKKFVLDSRTLGSGNRSNSKVAMSYQGLQASKSCTQKKVHSGSSGVVKMKKSRTQKGERPKVQPEKRPAVALRKARAKAPKDVWVSRQAGMKRKMESQTPEISQRKKAKVNER
Secondary Structure (PSIPRED)
cccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccccHHHHHHcccccccccccccccHHHHHHcccccHHHHHHHHHHcccHHHHccccccccccccccccccHHHHHcccccccccccccccEEEEccccccccHHHHHHHHHHcccccEEEEEEccccccccccccccccccccccccccEEEEEEccHHHHHHHHHccccccccEEEEEccccccccccccccccccccccEEEEccccccccHHHHHHHHHHcccccccEEEEEEEEcccccccccEEEEEEccHHHHHHHHHHcccccccEEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccHHHcccccccccccccHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccHHHHHHHccccccccHHHHccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccEEEccccccccHcccccccccccccccccccccccccEEcccccccccccccccccHHHHccccHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHHHcccEEEEEEEEEEcccccccccEEEEEEEccccccccEEEEEEccHHHHHHHHHHcccEEccEEEEEccccccccccccccccccccccEEEEccccccccHHHHHHHHHHccccccEEEEEEEEEcccccccccEEEEEEccHHHHHHHHHHccccccccEEEEEEEccccccccccccccccccccHHHcccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccccHHHHHHcccccccccccccccEEccc
Coil and Loop (DISEMBL)
mmdkkksednnisapssifttlfggipnestvasslfsdsnpfkrqhresqsaenesifnpmnsdsldsnnSELKKIKKTrqekpnpdlpdaegaatktlslsnkstkliyprsilgfepngtieneikkehssnvgsesylnrqkqnsnfsvegkkrsenkktkkrkrddVEKDYVEKKYGVIakeeegkkvgvgekrkkadneTEDMLVHrkeegfddegKLLRTIFVgnlplkvkKKTLIKEFIKfgeidsvrirsvpiidtkiprkGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGgnhirldracpprkklkgedaplydikktvfvgnlpfdvkdEEIYQLFCGLNDLESSVEAVRVIrhphmrvgKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHaqqnctpskrkdvapavnsppkkfvldsrtlgsgnrsnskVAMSYQGlqasksctqkkvhsgssgvvkmkksrtqkgerpkvqpekrPAVALRKARAKAPKDVWVSRQAGmkrkmesqtpeisQRKKAKVNER
Flexible Loop (DISEMBL)
mmdkkksednnisapSSIFTTLFGGIPNESTVASSLFSDSNPFKRQHRESQSaenesifnpmnsdsldsnNSELKKIKKtrqekpnpdlpdaegaatktlslsnkstkliyprsiLGFEPNGTIENEIKKEHssnvgsesylnrqkqnsnfsvegkkrsenkktkkrkrddvekdyvekkygviakeeegkkvgvgekrkkadnetedmlvhrkeegfddegkllrtifvgnlplkvkkkTLIKEFikfgeidsvrirsvpiidtkiprkGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLkgedaplydikktvFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRvirhphmrvgKGIAYVLfktreaanlvikrrnlklrdrELRLshaqqnctpskrkdvapavnsppkkfvldsrtlgsgnrsnSKVAMSYQGLqasksctqkkvhsgssgvvkmkksrtqkgerpkvqpekrpavalrkarakapkdvwvsrqagmkrkmesqtpeisqrkkakvner
Low Complexity Region (SEG)
MMDKKKSEDNNISAPSSIFTTLFGGIPNESTVASSLFSDSNPFKRQHRESQSAENESIFNPMnsdsldsnnsELKKIKKTRQEKPNPDLPDAEGAATKTLSLSNKSTKLIYPRSILGFEPNGTIENEIKKEHSSNVGSESYLNRQKQNSNFSVegkkrsenkktkkrkrddvekdYVEKKYGVIAkeeegkkvgvgekrkkADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAPAVNSPPKKFVLDSRTLGSGNRSNSKVAMSYQGLQASKSCTQkkvhsgssgvvkmkksRTQKGERPKVQPEKRPAVALRKARAKAPKDVWVSRQAGMKRKMESQTPEISQRKKAKVNER
Disordered region (IsUnstruct)
*****************IFTTLFGGI**********************************************************************************LIYPRSILGF******************************************************************************************************EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKL**********************************************************************************************************************************************
Disordered Region (DISOPRED)
*********************LFGGI*********************************************************************************************************************************************************************************************************IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR***ILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIR***********************TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELR****************************************************************************************************************************************
Disordered Region (DISEMBL)
***********ISAPSSIFTTLFGGIPNESTVASSLFSD*****************SIFNPMNSDSLDSNNSELKKIKKTRQEKPNPDLPDAEGAATKTLSLSNKSTKLIYPRSILGFEPNGTIENEIKKEHSSNVGSESYLNR****************************EKDYVEKKYGVIAKEEEGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQ**************NSPPKKFVLDSRTLGSGNRSNSKVAMSYQGLQ******************************************************WVSRQAG***********************
Disordered Region (DISPRO)
*****************IFTTLFGGIPNE*************************************************************************************************************************************************************************************************KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACP**************IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQ**********************************************************************************************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MMDKKKSEDNNISAPSSIFTTLFGGIPNESTVASSLFSDSNPFKRQHRESQSAENESIFNPMNSDSLDSNNSELKKIKKTRQEKPNPDLPDAEGAATKTLSLSNKSTKLIYPRSILGFEPNGTIENEIKKEHSSNVGSESYLNRQKQNSNFSVEGKKRSENKKTKKRKRDDVEKDYVEKKYGVIAKEEEGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAPAVNSPPKKFVLDSRTLGSGNRSNSKVAMSYQGLQASKSCTQKKVHSGSSGVVKMKKSRTQKGERPKVQPEKRPAVALRKARAKAPKDVWVSRQAGMKRKMESQTPEISQRKKAKVNER
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	548	2.2.26 [Sep-21-2011]
Q5M9F1	428	RNA-binding protein 34 OS	yes	no	0.339	0.434	0.367	3e-28
Q5AHI7	454	Nucleolar protein 12 OS=C	N/A	no	0.339	0.409	0.373	5e-28
P42696	430	RNA-binding protein 34 OS	yes	no	0.388	0.495	0.349	8e-27
Q8C5L7	375	RNA-binding protein 34 OS	no	no	0.313	0.458	0.371	1e-26
O13741	438	Nucleolar protein 12 OS=S	yes	no	0.339	0.424	0.345	5e-24
Q6C2Q7	509	Nucleolar protein 12 OS=Y	yes	no	0.273	0.294	0.384	6e-23
Q6BTS9	462	Nucleolar protein 12 OS=D	yes	no	0.339	0.402	0.352	2e-22
Q75BJ7	426	Nucleolar protein 12 OS=A	yes	no	0.308	0.396	0.323	3e-22
Q6FUS6	396	Nucleolar protein 12 OS=C	yes	no	0.410	0.568	0.312	6e-19
Q08208	459	Nucleolar protein 12 OS=S	yes	no	0.489	0.583	0.272	9e-19

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

 Score =  127 bits (319), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 78/212 (36%), Positives = 121/212 (57%), Gaps = 26/212 (12%)

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 A     +           K++VFVGNL
Sbjct: 243 NAYVVFKEERAAAKALQRNGAQIAEGFRIRVDLASETASR----------DKRSVFVGNL 292

Query: 345 PFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR 402
           P+ V +  + + F  CG      S+ AVR++R+P   VG+G  YVLF+  +A +L +K  
Sbjct: 293 PYRVDESALEEHFLDCG------SIVAVRIVRNPLTGVGRGFGYVLFENTDAVHLALKLN 346

Query: 403 NLKLRDRELRLSHA-------QQNCTPSKRKD 427
           N +L  R+LR+  +       QQN  PS +KD
Sbjct: 347 NSELMGRKLRVMRSVNKEKLKQQNSNPSVKKD 378

Rattus norvegicus (taxid: 10116)

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

 Score =  126 bits (316), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 78/209 (37%), Positives = 120/209 (57%), Gaps = 23/209 (11%)

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 VGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN--LV 398
           VGNL F+ K+E +++ F     L+  VE+VR+IR     +GKG A V FK   + N  L+
Sbjct: 269 VGNLDFEEKEETLWKYFNS--KLDQDVESVRIIRDSKTNLGKGFALVQFKDTLSVNKALL 326

Query: 399 IKRRNLKL----RDRELRLSHAQQNCTPS 423
           +  + L+     + R+LR+S A+ N  PS
Sbjct: 327 LNDKPLETGTQKKGRKLRISRAKSNAKPS 355

Involved in pre-25S rRNA processing.

Candida albicans (strain SC5314 / ATCC MYA-2876) (taxid: 237561)

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

 Score =  122 bits (306), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 85/243 (34%), Positives = 134/243 (55%), Gaps = 30/243 (12%)

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 VEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHA-------QQN 419
           + AVR++R     +GKG  YVLF+  ++ +L +K  N +L  R+LR+  +       QQN
Sbjct: 313 IMAVRIVRDKMTGIGKGFGYVLFENTDSVHLALKLNNSELMGRKLRVMRSVNKEKFKQQN 372

Query: 420 CTP 422
             P
Sbjct: 373 SNP 375

Homo sapiens (taxid: 9606)

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

 Score =  121 bits (304), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 71/191 (37%), Positives = 112/191 (58%), Gaps = 19/191 (9%)

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 A     +           K++VFVGNL
Sbjct: 249 NAYVVFKDESAAAKALQRNGAQIAEGFRIRVDLASETASR----------DKRSVFVGNL 298

Query: 345 PFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR 402
           P+ ++D  + + F  CG      S+ AVR++R+P   VG+G  YVLF+  +A +L +K  
Sbjct: 299 PYKIEDSALEEHFLDCG------SIVAVRIVRNPLTGVGRGFGYVLFENTDAVHLALKLN 352

Query: 403 NLKLRDRELRL 413
           N +L  R+LR+
Sbjct: 353 NSELMGRKLRV 363

Mus musculus (taxid: 10090)

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

 Score =  113 bits (282), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 74/214 (34%), Positives = 115/214 (53%), Gaps = 28/214 (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--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
           VGNL F+ ++E +++ F  CG      S++ VR++R P   +GKG AY+ FK     +  
Sbjct: 274 VGNLAFEAEEEPLWRYFGDCG------SIDYVRIVRDPKTNLGKGFAYIQFKDTMGVDKA 327

Query: 399 IKRRNLKLRD-RELRLSHAQ----QNCTPSKRKD 427
           +     K+ + R LR+  A+    ++ T SKR D
Sbjct: 328 LLLNEKKMPEGRTLRIMRAKSTKPKSITRSKRGD 361

Involved in pre-25S rRNA processing.

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

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

 Score =  109 bits (272), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 65/169 (38%), Positives = 92/169 (54%), 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 RDTVNAYIVFKNVKSVKGALTLNGSVFKGFHMRVDSVAHPGAQ---------DHKRCVFV 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|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 =  107 bits (268), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 73/207 (35%), Positives = 113/207 (54%), Gaps = 21/207 (10%)

Query: 226 RTIFVGNLPLKV-----KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINE 280
           RT+FVGN+   V       K   K F ++G+I S+R RS+   D  +PRK A  +K+++ 
Sbjct: 159 RTVFVGNVNASVVGSKPMYKKFKKLFSQYGKIQSIRFRSISF-DDAVPRKVAFAKKKLHS 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 FVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN--L 397
           FVGNL F+ K+E +++ F    D  + VE+VRVIR     VGKG A V FK   + N  L
Sbjct: 269 FVGNLDFEEKEETLWRYFNSKTD--NDVESVRVIRDAKTNVGKGFALVQFKDTLSVNKSL 326

Query: 398 VIKRRNLKL-RDRELRLSHAQQNCTPS 423
           ++  + +   + R+LR+S A+ +  PS
Sbjct: 327 LLNDKPMSAEKKRKLRISKAKAHTKPS 353

Involved in pre-25S rRNA processing.

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

>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 =  107 bits (266), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 69/213 (32%), Positives = 111/213 (52%), Gaps = 44/213 (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 RVGKGIAYVLFKTREAANLVIKRRNLKLRDREL 411
            VGKG AYV F     A+LV   + L L D+++
Sbjct: 297 NVGKGFAYVQF-----ADLVSVNKALLLNDKKM 324

Involved in pre-25S rRNA processing.

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

>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 = 96.3 bits (238), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 88/282 (31%), Positives = 140/282 (49%), Gaps = 57/282 (20%)

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 KGIAYVLFKTREAAN--LVIKRR-----NLKLRDRELRLSHAQQNCTPSKRKDVAPAVNS 434
           KG AYV F   ++ +  L++  +     N  L+ R+LR++     C   ++  V P + S
Sbjct: 269 KGFAYVQFNELQSVSKALLLNEKPMISQNEHLKKRKLRVTR----CKNIRK--VEPTLKS 322

Query: 435 PPKKFVLDS---------RTLGSGNRSNSKVAMSYQGLQASK 467
              K++ D          + L    RS     ++ +G++A+K
Sbjct: 323 G--KYMTDGQKTKLGRAKKILNKAERSKLLKELTVEGIRATK 362

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 = 95.5 bits (236), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 95/348 (27%), Positives = 161/348 (46%), Gaps = 80/348 (22%)

Query: 219 DDEGKLLRTIFVGN-LPLKVKKKTLIKEFIK-FGE------------------------- 251
           D+  K  RT+F+GN L   +  K + KEF K FG                          
Sbjct: 141 DELEKAERTVFIGNILSTVITSKKVYKEFKKLFGTNPIAETEESGNEKEEESSKKSDNNE 200

Query: 252 --IDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-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 VEAVRVIRHPHMRVGKGIAYVLFKTREAAN--LVIKRRNLKL-------------RDREL 411
           +E VR+IR     +GKG AYV FK  ++ N  L++  + +K              + R+L
Sbjct: 305 IEYVRIIRDSKTNMGKGFAYVQFKDLQSVNKALLLNEKPMKSQKQEDENTKKPTKKARKL 364

Query: 412 RLSHA---QQNCTPSKRKDVAPAVNSPPKKFVLDSRTLGSGNRSNSKVAMSYQGLQASKS 468
           R+S     ++  T     D     +S   +     + LG  +R+     ++ +GL+A K 
Sbjct: 365 RVSRCKNMKKGTTIGTGLDRNGLTDSQRTRAGRAKKILGKADRATLGQEITIEGLRAKKG 424

Query: 469 CTQKKVHSGSSGVVKMKKSRTQKGERPKVQPEKRPAVALRKARAKAPK 516
                   GS+  +K KK R+  G   K       ++A +KA+A+  K
Sbjct: 425 -------EGSTH-LKKKKQRSATGRVTK------RSIAFKKAQAEKSK 458

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	548
224071371	491	predicted protein [Populus trichocarpa]	0.848	0.947	0.548	1e-140
224138160	487	predicted protein [Populus trichocarpa]	0.846	0.952	0.534	1e-140
225427165	541	PREDICTED: uncharacterized protein LOC10	0.945	0.957	0.525	1e-121
356529724	519	PREDICTED: nucleolar protein 12-like [Gl	0.864	0.913	0.493	1e-118
356496350	515	PREDICTED: nucleolar protein 12-like [Gl	0.863	0.918	0.489	1e-113
255573457	830	RNA binding protein, putative [Ricinus c	0.582	0.384	0.599	1e-111
449462029	559	PREDICTED: LOW QUALITY PROTEIN: uncharac	0.927	0.908	0.459	1e-106
169219255	566	putative RNA recognition motif-containin	0.914	0.885	0.463	1e-105
449516037	410	PREDICTED: RNA-binding protein 34-like [	0.682	0.912	0.553	1e-100
297742077	421	unnamed protein product [Vitis vinifera]	0.75	0.976	0.481	1e-99

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

 Score =  504 bits (1297), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 298/543 (54%), Positives = 362/543 (66%), Gaps = 78/543 (14%)

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---------------------------LGLEP----- 94

Query: 126 NEIKKEHSSNVGSESYLNRQKQNSNFSVEGKKRSENKKTKKRKRDDVEKDYVEKKYGVIA 185
              K+E + N                          +K KKRKRDD+E +Y  KKYG + 
Sbjct: 95  ---KEEKTLN-----------------------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 SVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQNCTPSKR 425
           S+EAVRVIRHPH+ +GKGIAYVLFKTREAANLVIK+RNLKLRDRELR SHA+Q+ TPSKR
Sbjct: 308 SIEAVRVIRHPHIGLGKGIAYVLFKTREAANLVIKKRNLKLRDRELRASHARQDSTPSKR 367

Query: 426 KD--VAPAVNSPPKKFVLDSRTLGSGNRSNSKVAMSYQGLQASKSCTQKKVHSGS----S 479
           ++       N   KK   DSRT    NR ++K A SYQGL+ASKS  +KKVH+ +    +
Sbjct: 368 RNSFAGETANLSNKKLATDSRTPDRNNRPDTKAAKSYQGLRASKSGIEKKVHAPANAKRN 427

Query: 480 GVVKMKKSRTQKGERPKVQPEKRPAVALRKARAKAPKDVWVSRQAGMKRKMESQTPEISQ 539
           G  K+ KS+TQ+ +R     EKRPAVALRKA+A A KD   S  A  KRK++S+TP+ S 
Sbjct: 428 GTAKV-KSKTQREKR----QEKRPAVALRKAKATALKDGGASGPARQKRKLDSRTPDSSN 482

Query: 540 RKK 542
           RKK
Sbjct: 483 RKK 485

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  504 bits (1297), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 293/548 (53%), Positives = 355/548 (64%), Gaps = 84/548 (15%)

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 DLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQNCT 421
           DL SS+EAVRVIR PH+ +GKGIAYVLFKTREAANLVIK+RNLKLRDRELRLSHA+Q+ T
Sbjct: 300 DLASSIEAVRVIRDPHVGLGKGIAYVLFKTREAANLVIKKRNLKLRDRELRLSHARQDST 359

Query: 422 PSKRKD--VAPAVNSPPKKFVLDSRTLGSGNRSNSKVAMSYQGLQASKSCTQKKVHSGSS 479
           PSKRK+       NSP K+   DSR     NR + K A SYQGL+ASKS  +KKVH+ + 
Sbjct: 360 PSKRKNSFAEETANSPNKRLAPDSRAPYHNNRPDRKAAKSYQGLRASKSGVEKKVHAPAH 419

Query: 480 G----VVKMK-KSRTQKGERPKVQPEKRPAVALRKARAKAPKDVWVSRQAGMKRKMESQT 534
                  KMK K R +K +       KRPAVA RKA+A A KD      A  KRK++S+T
Sbjct: 420 SKRDVAPKMKSKPREEKHQ------GKRPAVAKRKAKATALKDGGALEPARQKRKLDSRT 473

Query: 535 PEISQRKK 542
           P+ S RKK
Sbjct: 474 PDSSNRKK 481

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  441 bits (1135), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 296/563 (52%), Positives = 376/563 (66%), Gaps = 45/563 (7%)

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 DEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDR 409
            EEIYQLFCG++ LESS+EAVRV+R+PH  VGKGIAY+LFKT++AANLV+K+RNLKLRDR
Sbjct: 337 AEEIYQLFCGIDSLESSIEAVRVVRNPHTSVGKGIAYILFKTKDAANLVVKKRNLKLRDR 396

Query: 410 ELRLSHAQ-QNCTPSKRKDVAPAVN--SPPKKFVLDSR-TLGSGNRSNSKVAMSYQGLQA 465
           +LRL HA+  + TPSKR++  PA    SP KK    SR +L S NR  +K  +SYQGLQA
Sbjct: 397 DLRLYHAKPSSTTPSKRRNPTPAEADISPAKKLASGSRISLESSNRLKTKSVISYQGLQA 456

Query: 466 SKSCTQKKVHSGSSGVVKMKKSRTQKGERPKVQPEKRPAVALRKARAKA---PKDVWVSR 522
           SKS   KK    +   VK  KS+ QK    K Q +KRPAVA RKA+  A         S+
Sbjct: 457 SKSGVPKKGRLQTKEAVKF-KSKNQKENTLKEQQKKRPAVAARKAKINAVNAAGGGGGSK 515

Query: 523 QAGMKRKMESQTPEISQR-KKAK 544
           Q G KRK+ESQTPE  +R KKAK
Sbjct: 516 QTGKKRKLESQTPEGGRRSKKAK 538

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  431 bits (1108), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 276/559 (49%), Positives = 360/559 (64%), Gaps = 85/559 (15%)

Query: 7   SEDNNISAPSSIFTTLFGGIP--NESTVASSLFSDSNPFKRQHRESQSAENESIFNPMNS 64
           S+ + +S PSSIF+ LF   P    +T A+SLFSD NPF+R+      + N +  NP + 
Sbjct: 13  SQTDTVSTPSSIFSKLFAIAPERTTATTAASLFSDDNPFRRKPTPLSDSTNRTQ-NPNDG 71

Query: 65  D---SLDSNNSELKKIKKTRQEK-PNPDLPDAEGAATKTLSLSNKSTKLIYPRSILGFEP 120
           D   + DS   + +K  K + +K P P    A       +  S+KS K            
Sbjct: 72  DHPVNTDSGEEKKRKRNKEKTDKTPAP----AIDTVVSVIEASDKSEK------------ 115

Query: 121 NGTIENEIKKEHSSNVGSESYLNRQKQNSNFSVEGKKRSENKKTKKRKRDDVEKDYVEKK 180
                   K++  S+ G +  +                +E    +KRKR +VEKD+ EKK
Sbjct: 116 --------KRKRDSDEGKDLIVG---------------AEASGKRKRKRGEVEKDWEEKK 152

Query: 181 YGVIAKEEEGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKK 240
           YG++ +  E K VG+  KRK  D+   DM+V +  EGFDDE KLLRT+FVGNLPLKVKKK
Sbjct: 153 YGIVEEGLENKTVGI--KRKTLDDPA-DMMVSK--EGFDDEDKLLRTVFVGNLPLKVKKK 207

Query: 241 TLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA 300
           TL+KEF KFGE++SVRIRSVPI DTK PRKGAIL K+IN+ ADSVHAYIVFK+EQS +A+
Sbjct: 208 TLLKEFKKFGEVESVRIRSVPIQDTKKPRKGAILAKKINDAADSVHAYIVFKTEQSAQAS 267

Query: 301 LAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGL 360
           L+ NM+++ GNHIR+DRACPPRKK KGE  PLYD K+TVFVGNLPFDVKDEE+YQLFCG+
Sbjct: 268 LSHNMSLVEGNHIRVDRACPPRKKHKGESTPLYDDKRTVFVGNLPFDVKDEELYQLFCGI 327

Query: 361 NDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQNC 420
           ++LESS+EAVRV+R PH+ VGKGIAYVLFKT+EAA  V+K+RNLKLRDRELRLSHA+ + 
Sbjct: 328 SNLESSIEAVRVVRDPHLNVGKGIAYVLFKTKEAAKFVVKKRNLKLRDRELRLSHAKVDA 387

Query: 421 TPSKRKD----------------VAPAVNSPPKKFVLDSRTLGSGNRSNS---KVAMSYQ 461
           TPSKR +                +A A ++P K+F + SR+  S N  +    K   SYQ
Sbjct: 388 TPSKRPNPSSAHAPSTPAKRPYPLAHAPSTPAKEFSVASRSPSSSNNMSKSNRKTNASYQ 447

Query: 462 GLQASKSCTQKKVHSGSSGVVKMKKSRTQKGERPKVQPEKRPAVALRKARAKAPKDVWVS 521
           GL+A+KS   KK+               Q GE+PK +  KRP+VA RKA+AK  K+  + 
Sbjct: 448 GLRATKSDVHKKI---------------QGGEKPKERMTKRPSVAARKAKAKLGKESDLP 492

Query: 522 RQAGMKRKMESQTPEISQR 540
           +QAGMKRK++S+TP+ + R
Sbjct: 493 KQAGMKRKLDSRTPDSTLR 511

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  414 bits (1065), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 274/560 (48%), Positives = 356/560 (63%), Gaps = 87/560 (15%)

Query: 7   SEDNNISAPSSIFTTLFGGIPNESTV--ASSLFSDSNPFKRQHRESQSAENESIFNPMNS 64
           SE + +S PSSIF+ LF   P ++T   A+SLFSD NPF+R+      + N +  NP N 
Sbjct: 13  SETDAVSTPSSIFSKLFANAPEQTTATAAASLFSDDNPFRRKSAPLSYSTNRTQ-NPNNG 71

Query: 65  D---SLDSNNSELKKIKKTRQEKPNPDLPDAEGAATKTLSLSNKSTKLIYPRSILGFEPN 121
           D   + DS+  + +K  K +   P PD                 +  +I P      EP 
Sbjct: 72  DHPVNTDSSEEKKRKRTKDKTSAPAPD-----------------TVSVIEPLE----EPG 110

Query: 122 GTIENEIKKEHSSNVGSESYLNRQKQNSNFSVEGKKRSENKKTKKRKRDDVEKDYVEKKY 181
              + +  +    +VG+E+   R                     KRKRD+VEK++ EKKY
Sbjct: 111 KKRKRDSDEGKDLSVGAEAIGKR---------------------KRKRDEVEKEWEEKKY 149

Query: 182 GVIAKEEEGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKT 241
           G + +  E K VG+  KRK  D+   DM+V +  EGFD+E KLLRT+FVGNLPLKVKKKT
Sbjct: 150 GAVEEGIENKTVGI--KRKTLDDPA-DMMVSK--EGFDNEDKLLRTVFVGNLPLKVKKKT 204

Query: 242 LIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL 301
           L+KEF KFGE++SVRIRSVPI DTK PRKGAIL K+IN+ ADSVHAYIVFK+EQS +A+L
Sbjct: 205 LLKEFKKFGEVESVRIRSVPIQDTKKPRKGAILAKKINDAADSVHAYIVFKTEQSAQASL 264

Query: 302 AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLN 361
           A NM+++ GNHIR+DRACPPRKK KGE  PLYD K+TVFVGNLPFDVKDEE+Y+LFCG++
Sbjct: 265 AHNMSLVEGNHIRVDRACPPRKKHKGESTPLYDNKRTVFVGNLPFDVKDEELYKLFCGIS 324

Query: 362 DLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQNCT 421
           +LESS+EA+RV+R PH+ VGKGIAYVLFKT+EAA  V+K+RNLKLRDRELRL HA+ + T
Sbjct: 325 NLESSIEAIRVVRDPHLNVGKGIAYVLFKTKEAAKFVVKKRNLKLRDRELRLCHAKADAT 384

Query: 422 PSKRKD----------------VAPAVNSPPKKFVLDSRTLGSGNRSNS---KVAMSYQG 462
           PSKR +                 A A ++P KKF + SR+  S N  +    K   SYQG
Sbjct: 385 PSKRPNPSSAHAPSTPAKRPNPSAHAPSTPAKKFSVASRSPSSSNNMSKSNRKTNTSYQG 444

Query: 463 LQASKSCTQKKVHSGSSGVVKMKKSRTQKGERPKVQPEKRPAVALRKARAKAPKDVWVSR 522
           L+A+KS   KK+               Q GE+PK +  KRP+VA RKA+A   K   + +
Sbjct: 445 LRATKSDVHKKI---------------QGGEKPKERKTKRPSVAARKAKANLVKQSDLPK 489

Query: 523 QAGMKRKMESQTPEISQRKK 542
           QAGMKRK++S+TP+ + R +
Sbjct: 490 QAGMKRKVDSRTPDSTLRNR 509

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  409 bits (1052), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 223/372 (59%), Positives = 262/372 (70%), Gaps = 53/372 (14%)

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 KDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRD 408
           KDEEIYQLF G+ DLESS+EAVRVIR  ++ +G+GIAYVLFKTREA NL +K+RNL +RD
Sbjct: 286 KDEEIYQLFSGIKDLESSIEAVRVIRDSYVGLGRGIAYVLFKTREAVNLALKKRNLNIRD 345

Query: 409 RELRLSHAQQNC--TPSKRKDVAPAVNSPPKKFVLDSRTLGSGNRSNSKVAMSYQGLQAS 466
           RELRLSHA+++   TPSKRK+  PA     KK  LDSR    G + N             
Sbjct: 346 RELRLSHAKKDATSTPSKRKNSFPAETGGTKK--LDSRP-AEGEKRNG------------ 390

Query: 467 KSCTQKKVHSGSSGVVKMKKSRTQKGERPKVQPEKRPAVALRKARAKAPKDVWVSRQAGM 526
                                             KRPAVA RKAR K+ KD    +Q G 
Sbjct: 391 ----------------------------------KRPAVAARKARVKS-KDGSAIKQTGQ 415

Query: 527 KRKMESQTPEIS 538
           KRK++S+TPE S
Sbjct: 416 KRKLDSRTPESS 427

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  390 bits (1003), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 270/587 (45%), Positives = 362/587 (61%), Gaps = 79/587 (13%)

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 FVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVI 399
           FVGNLPFDVKDEE+YQLFCG++++ SSVEAVRVIR P + VGKG AYV FKTREAAN V+
Sbjct: 332 FVGNLPFDVKDEELYQLFCGIDNMGSSVEAVRVIRDPKVNVGKGFAYVFFKTREAANSVV 391

Query: 400 KRRNLKLRDRELRLSHAQQN--CTPSKRKDVAP--AVNSPPKKFVLDSRTLGSGNRSNSK 455
             + L+LR R LRL H + N   TP K+++  P  A  +P KK  +DS   G G   +SK
Sbjct: 392 NNQLLELRGRTLRLFHTKTNPTSTPFKKRNRPPTEADRTPAKKKYVDS---GLGTPDSSK 448

Query: 456 ------VAMSYQGLQASKSCTQKKVHS-GSSGVVKMKKSRTQKGERP-----KVQPE--- 500
                   +SYQGL+ASKS +QKK+H+ GSS   K  KS +   E+P     +  PE   
Sbjct: 449 RVTPKATNVSYQGLRASKSGSQKKIHTKGSS--TKWPKSHSNSKEKPIDHKKRRGPEKTS 506

Query: 501 ----KRPAVALRKARAKAPKD-VWVSRQAGMKRKMESQTPEISQRKK 542
               KRPAVA RKA A A K+ +   +Q G+KRK +S++P  S R K
Sbjct: 507 ERKGKRPAVANRKAVAMATKNGIATPKQTGLKRKSDSRSPGSSHRNK 553

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 =  387 bits (995), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 269/580 (46%), Positives = 357/580 (61%), Gaps = 79/580 (13%)

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 DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKL 406
           DVKDEE+YQLFCG++++ SSVEAVRVIR P + VGKG AYV FKTREAAN V+  + L+L
Sbjct: 346 DVKDEELYQLFCGIDNMGSSVEAVRVIRDPKVNVGKGFAYVFFKTREAANSVVNNQLLEL 405

Query: 407 RDRELRLSHAQQN--CTPSKRKDVAP--AVNSPPKKFVLDSRTLGSGNRSNSK------V 456
           R R LRL H + N   TP K+++  P  A  +P KK  +DS   G G   +SK       
Sbjct: 406 RGRTLRLFHTKTNPTSTPFKKRNRPPTEADRTPAKKKYVDS---GLGTPDSSKRVTPKAT 462

Query: 457 AMSYQGLQASKSCTQKKVHS-GSSGVVKMKKSRTQKGERP-----KVQPE-------KRP 503
            +SYQGL+ASKS +QKK+H+ GSS   K  KS +   E+P     +  PE       KRP
Sbjct: 463 NVSYQGLRASKSGSQKKIHTKGSS--TKWPKSHSNSKEKPIDHKKRRGPEKTSERKGKRP 520

Query: 504 AVALRKARAKAPKD-VWVSRQAGMKRKMESQTPEISQRKK 542
           AVA RKA A A K+ +   +Q G+KRK +S++P  S R K
Sbjct: 521 AVANRKAVAMATKNGIATPKQTGLKRKSDSRSPGSSHRNK 560

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449516037|ref|XP_004165054.1| PREDICTED: RNA-binding protein 34-like [Cucumis sativus]

 Score =  372 bits (954), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 227/410 (55%), Positives = 290/410 (70%), Gaps = 36/410 (8%)

Query: 162 KKTKKRKRDDVEKDYVEKKYGV--IAKEE-EGKKVGVGEKRKKADNETEDMLVHRKEEGF 218
           K+ KKRKRD++E++Y  KKYGV  +A++E EG    V  K++KA ++  +MLV +  EGF
Sbjct: 2   KERKKRKRDELEREYEAKKYGVSDVAEDEVEGSGGNVVGKKRKALDDPSEMLVTK--EGF 59

Query: 219 DDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPI--IDTKIPRKGAILQK 276
           DDE KLLRT+FVGNLPLKVKKK L KEF +FGEIDSVRIRSVPI   ++K PRKGAI+ K
Sbjct: 60  DDESKLLRTVFVGNLPLKVKKKALAKEFSQFGEIDSVRIRSVPIDIANSKKPRKGAIISK 119

Query: 277 QINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIK 336
           ++NE ADS HAY+VFK+E+S +A+L+ NMAV  GNHIR+DRACPP +KLK  + P+YD K
Sbjct: 120 KLNEAADSSHAYVVFKTEESAQASLSHNMAVFAGNHIRVDRACPPHEKLKVGNGPIYDPK 179

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           +TVFVGNLPFDVKDEE+YQLFCG++++ SSVEAVRVIR P + VGKG AYV FKTREAAN
Sbjct: 180 RTVFVGNLPFDVKDEELYQLFCGIDNMGSSVEAVRVIRDPKVNVGKGFAYVFFKTREAAN 239

Query: 397 LVIKRRNLKLRDRELRLSHAQQN--CTPSKRKDVAP--AVNSPPKKFVLDSRTLGSGNRS 452
            V+  + L+LR R LRL H + N   TP K+++  P  A  +P KK  +DS   G G   
Sbjct: 240 SVVNNQLLELRGRTLRLFHTKTNPTSTPFKKRNRPPTEADRTPAKKKYVDS---GLGTPD 296

Query: 453 NSK------VAMSYQGLQASKSCTQKKVHS-GSSGVVKMKKSRTQKGERP-----KVQPE 500
           +SK        +SYQGL+ASKS +QKK+H+ GSS   K  KS +   E+P     +  PE
Sbjct: 297 SSKRVTPKATNVSYQGLRASKSGSQKKIHTKGSS--TKWPKSHSNSKEKPIDHKKRRGPE 354

Query: 501 -------KRPAVALRKARAKAPKD-VWVSRQAGMKRKMESQTPEISQRKK 542
                  KRPAVA RKA A A K+ +   +Q G+KRK +S++P  S R K
Sbjct: 355 KTSERKGKRPAVANRKAVAMATKNGIATPKQTGLKRKSDSRSPGSSHRNK 404

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297742077|emb|CBI33864.3| unnamed protein product [Vitis vinifera]

 Score =  370 bits (949), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 250/519 (48%), Positives = 314/519 (60%), Gaps = 108/519 (20%)

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  NPMNSDSLDSNNSELKKIKKTRQEKPNPDLPDAEGAATKTLSLSNKSTKLIYPRSILGFE 119
           NP   DS      E+KK K+T +              ++TL  + K+  L+ P+      
Sbjct: 54  NPSIPDS------EVKKRKRTEETD----------ETSQTLEDAPKAQHLVEPK------ 91

Query: 120 PNGTIENEIKKEHSSNVGSESYLNRQKQNSNFSVEGKKRSENKKTKKRKRDDVEKDYVEK 179
                +++  K  + N+GSES  N +  NS                              
Sbjct: 92  -----KSKNDKLRNPNLGSES--NEELLNS------------------------------ 114

Query: 180 KYGVIAKEEEGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKK 239
                             KRK   N  E MLV +  EGFDDE KLLRT+FVGNLPLK+KK
Sbjct: 115 ------------------KRKSVVNPAE-MLVSK--EGFDDESKLLRTVFVGNLPLKIKK 153

Query: 240 KTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA 299
           K L+KEF  FGE+ SVRIRSVPI+D+K PRKGAI+ K+IN++ DSVHAYIVFK+E+S + 
Sbjct: 154 KALLKEFSVFGEVQSVRIRSVPILDSKKPRKGAIISKKINDSVDSVHAYIVFKTEESAQT 213

Query: 300 ALAFNMAVIGGNHIRLDRACPPRKKLKGE-DAPLYDIKKTVFVGNLPFDVKDEEIYQLFC 358
           +L+ NM+VIGGNHIR+DRACPPRKKLKGE DA LYD K+TVFVGNLPFDVK EEIYQLFC
Sbjct: 214 SLSHNMSVIGGNHIRVDRACPPRKKLKGENDASLYDNKRTVFVGNLPFDVKAEEIYQLFC 273

Query: 359 GLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQ- 417
           G++ LESS+EAVRV+R+PH  VGKGIAY+LFKT++AANLV+K+RNLKLRDR+LRL HA+ 
Sbjct: 274 GIDSLESSIEAVRVVRNPHTSVGKGIAYILFKTKDAANLVVKKRNLKLRDRDLRLYHAKP 333

Query: 418 QNCTPSKRKDVAPAVN--SPPKKFVLDSR-TLGSGNRSNSKVAMSYQGLQASKSCTQKKV 474
            + TPSKR++  PA    SP KK    SR +L S NR  +K  +SYQGLQASKS      
Sbjct: 334 SSTTPSKRRNPTPAEADISPAKKLASGSRISLESSNRLKTKSVISYQGLQASKS------ 387

Query: 475 HSGSSGVVKMKKSRTQKGERPKVQPEKRPAVALRKARAK 513
             G +G  K +  R   G R       +P    RK RAK
Sbjct: 388 -GGKNGSWKARPQRVGGGAR-------KPRNFGRKIRAK 418

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	548
TAIR|locus:2172937	501	AT5G46840 [Arabidopsis thalian	0.613	0.670	0.556	9.7e-99
ZFIN|ZDB-GENE-040718-77	411	rbm34 "RNA binding motif prote	0.381	0.508	0.364	3.5e-29
DICTYBASE|DDB_G0289941	481	DDB_G0289941 "Nucleolar protei	0.381	0.434	0.343	2.4e-27
MGI|MGI:1098653	375	Rbm34 "RNA binding motif prote	0.333	0.488	0.368	6e-26
RGD|1310161	428	Rbm34 "RNA binding motif prote	0.339	0.434	0.372	7.4e-26
CGD|CAL0002615	454	orf19.809 [Candida albicans (t	0.416	0.502	0.339	9.1e-26
UNIPROTKB|F1NIM5	392	RBM34 "Uncharacterized protein	0.372	0.520	0.345	1e-25
UNIPROTKB|F1RGW8	424	RBM34 "Uncharacterized protein	0.410	0.530	0.342	3.2e-25
UNIPROTKB|P42696	430	RBM34 "RNA-binding protein 34"	0.397	0.506	0.348	6.3e-25
UNIPROTKB|E2R3E1	429	RBM34 "Uncharacterized protein	0.406	0.519	0.329	3e-24

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

 Score = 909 (325.0 bits), Expect = 9.7e-99, Sum P(2) = 9.7e-99
 Identities = 197/354 (55%), Positives = 248/354 (70%)

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 GIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAPAVNSPPKKFVLD 442
             GIAYVLFKTREAANLV+K+  LKLR+RELR+S  + + TPSKRK       SP +K +  
Sbjct:   329 GIAYVLFKTREAANLVLKKGYLKLRERELRISRVKPD-TPSKRKSNPSEAYSPAQKRLQK 387

Query:   443 SRTLGSGNRSNSKVAMSYQGLQASKSCTQXXXXXXXXXXXXXXXXR-------TQKGERP 495
              + +        K  +SYQG++ASKS                   R        + G   
Sbjct:   388 DKVVTP--TPTGKANLSYQGVRASKSGDDKKTPYQKSSAQTKMRPRGSSSNDNKKSGNNS 445

Query:   496 --KVQPEKRPAVALRKARA--KAPKDVWVSRQAGMKRKMESQTPE-ISQRKKAK 544
               K + +KRPAVA RKA+A  K  K+    R AG KRK E++TPE  S++KK K
Sbjct:   446 ASKERSQKRPAVAARKAKANAKGSKESGGKRFAGTKRKQENRTPESFSKKKKTK 499

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 = 325 (119.5 bits), Expect = 3.5e-29, P = 3.5e-29
 Identities = 85/233 (36%), Positives = 131/233 (56%)

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 MRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHA----QQNCTPSKRK 426
               +GKG  YVLF++ ++  L +K     L+ R++R+  +    ++  TP  RK
Sbjct:   289 SGMGKGFGYVLFESPDSVMLALKLNGSTLQQRKIRVKRSVKKEKEKKTPPGRK 341

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 = 314 (115.6 bits), Expect = 2.4e-27, Sum P(2) = 2.4e-27
 Identities = 80/233 (34%), Positives = 129/233 (55%)

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 LPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN 403
             +P++ ++EE++ +F   +     V +VR+IR  H  +GKG  YV F T E A+  I +++
Sbjct:   369 IPYETEEEELFLIF---DKTFGDVVSVRIIRDSHTNIGKGFGYVNFSTDETASTAIAQKS 425

Query:   404 LKLRDRELRLSHAQQNCTPSKRKDVAPAVNSPPKKFVLDSR--TLG-SGNRSN 453
             ++   RE+R+   ++N  P K K +        KK +L+ +  T G S N+SN
Sbjct:   426 IQFGKREIRIFPTKEN--PKKGKTIKE------KKKLLNKKPSTRGASQNKSN 470

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

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

 Score = 297 (109.6 bits), Expect = 6.0e-26, P = 6.0e-26
 Identities = 76/206 (36%), Positives = 120/206 (58%)

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 LFKTREAANLVIKRRNLKLRDRELRL 413
             LF+  +A +L +K  N +L  R+LR+
Sbjct:   338 LFENTDAVHLALKLNNSELMGRKLRV 363

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

RGD|1310161 Rbm34 "RNA binding motif protein 34" [Rattus norvegicus (taxid:10116)]

 Score = 306 (112.8 bits), Expect = 7.4e-26, P = 7.4e-26
 Identities = 79/212 (37%), Positives = 122/212 (57%)

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 A     +    D      K++VFVGNL
Sbjct:   243 NAYVVFKEERAAAKALQRNGAQIAEGFRIRVDLA----SETASRD------KRSVFVGNL 292

Query:   345 PFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR 402
             P+ V +  + + F  CG      S+ AVR++R+P   VG+G  YVLF+  +A +L +K  
Sbjct:   293 PYRVDESALEEHFLDCG------SIVAVRIVRNPLTGVGRGFGYVLFENTDAVHLALKLN 346

Query:   403 NLKLRDRELRLSHA-------QQNCTPSKRKD 427
             N +L  R+LR+  +       QQN  PS +KD
Sbjct:   347 NSELMGRKLRVMRSVNKEKLKQQNSNPSVKKD 378

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005730 "nucleolus" evidence=IEA;ISO

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

 Score = 309 (113.8 bits), Expect = 9.1e-26, P = 9.1e-26
 Identities = 87/256 (33%), Positives = 139/256 (54%)

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 VGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN--LV 398
             VGNL F+ K+E +++ F   + L+  VE+VR+IR     +GKG A V FK   + N  L+
Sbjct:   269 VGNLDFEEKEETLWKYFN--SKLDQDVESVRIIRDSKTNLGKGFALVQFKDTLSVNKALL 326

Query:   399 IKRRNLKL----RDRELRLSHAQQNCTPSKRKDVAPA-VNSPPKKFVLDSRTLGSGNRSN 453
             +  + L+     + R+LR+S A+ N  PS    ++P   ++  KKF          +   
Sbjct:   327 LNDKPLETGTQKKGRKLRISRAKSNAKPSL---MSPNHFDNQKKKFAAGKSQQKLNDNQK 383

Query:   454 SKVAMSYQGL-QASKS 468
             +K+  +   L +A +S
Sbjct:   384 TKIGRAQSTLGKADRS 399

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

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

 Score = 295 (108.9 bits), Expect = 1.0e-25, P = 1.0e-25
 Identities = 77/223 (34%), Positives = 121/223 (54%)

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 FKTREAANLVIKRRNLKLRDRELRLSHA-QQNCTPSKRKDVAP 430
             F+  +A +L +K  N  L  R+LR+    ++   P +     P
Sbjct:   300 FENTDAVHLALKLNNSDLMGRKLRVKRCVEKGRAPQRSTTSRP 342

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

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

 Score = 301 (111.0 bits), Expect = 3.2e-25, P = 3.2e-25
 Identities = 90/263 (34%), Positives = 143/263 (54%)

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 GKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHA------QQNCTP-----SKRKDVA 429
             G+G  YVLF+  +A +L +K  N +L  R+LR+  +      +QN  P     +K KD  
Sbjct:   323 GRGFGYVLFENTDAVHLALKLNNSELMGRKLRVMRSIHKEKLKQNSNPGLKNVNKSKD-- 380

Query:   430 PAVNSPPKKFVLDSRTLGSGNRS 452
               +N P K  V  S++L  G ++
Sbjct:   381 -GLNFPSKN-VQRSKSLYVGEKA 401

GO:0005730 "nucleolus" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

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

 Score = 300 (110.7 bits), Expect = 6.3e-25, P = 6.3e-25
 Identities = 85/244 (34%), Positives = 138/244 (56%)

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 HMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAPAVN--S 434
                +GKG  YVLF+  ++ +L +K  N +L  R+LR+  +  N    K+++  P +   S
Sbjct:   323 MTGIGKGFGYVLFENTDSVHLALKLNNSELMGRKLRVMRSV-NKEKFKQQNSNPRLKNVS 381

Query:   435 PPKK 438
              PK+
Sbjct:   382 KPKQ 385

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|E2R3E1 RBM34 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 295 (108.9 bits), Expect = 3.0e-24, P = 3.0e-24
 Identities = 82/249 (32%), Positives = 136/249 (54%)

Query:   204 NETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPII 263
             N+ + + ++++EE   +E    RT+FVGNLP+   KK L   F ++G+IDSVR RS+   
Sbjct:   167 NQRKKIEINQEEEKLKNE----RTVFVGNLPVTCNKKKLKSFFREYGQIDSVRFRSLIPA 222

Query:   264 DTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIG-GNHIRLDRACPPR 322
             +  + +K A ++++I+ +   ++AY+VFK E S   AL  N A I  G  IR+D A    
Sbjct:   223 EGTLSKKLAAIKRKIHPDQKYINAYVVFKDESSATKALKRNGAQIADGFRIRVDLA---- 278

Query:   323 KKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRV 380
              +    D      K++VFVGNLP+ V++  + + F  CG      S+ AVR++R     V
Sbjct:   279 SETSSRD------KRSVFVGNLPYKVEESAVEEHFLDCG------SIVAVRIVRDRVTGV 326

Query:   381 GKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHA--QQNCTPSKRKDVAPAVNSPPKK 438
             G+G  YVLF+  +A +L +K  N +L  R+LR+  +  ++   P+    +   V  P + 
Sbjct:   327 GRGFGYVLFENTDAVHLALKLNNSELMGRKLRVMRSVNKEKLKPNSNPSLKN-VGKPKEG 385

Query:   439 FVLDSRTLG 447
                 S+ +G
Sbjct:   386 LNSASKNVG 394

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

Your Input: fgenesh4_pg.C_LG_III000731 hypothetical protein (491 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	548
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	6e-31
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	1e-26
cd12669	105	cd12669, RRM1_Nop12p_like, RNA recognition motif 1	1e-18
smart00360	73	smart00360, RRM, RNA recognition motif	5e-13
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-12
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	8e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-09
smart00360	73	smart00360, RRM, RNA recognition motif	2e-09
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-09
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	4e-09
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	6e-09
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	2e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-08
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	1e-07
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-07
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-07
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	4e-07
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	8e-07
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	1e-06
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	2e-06
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	5e-06
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	7e-06
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	8e-06
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	8e-06
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	8e-06
cd12508	80	cd12508, RRM2_ESRPs_Fusilli, RNA recognition motif	2e-05
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-05
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	4e-05
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	6e-05
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	7e-05
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	8e-05
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	8e-05
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	1e-04
cd12294	102	cd12294, RRM_Rrp7A, RNA recognition motif in ribos	1e-04
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-04
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	2e-04
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-04
cd12420	79	cd12420, RRM_RBPMS_like, RNA recognition motif in	3e-04
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	4e-04
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	4e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	5e-04
cd12514	73	cd12514, RRM4_RBM12_like, RNA recognition motif 4	6e-04
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	6e-04
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	6e-04
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	6e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	7e-04
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	8e-04
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	0.001
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	0.001
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	0.001
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	0.001
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	0.001
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	0.002
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	0.002
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	0.002
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	0.002
cd12445	81	cd12445, RRM2_CPEBs, RNA recognition motif 2 in cy	0.002
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.002
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	0.002
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	0.002
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	0.003
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	0.003
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	0.003
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.004
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	0.004
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	0.004
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	0.004

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

 Score =  115 bits (289), Expect = 6e-31
 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|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score =  102 bits (257), Expect = 1e-26
 Identities = 35/79 (44%), Positives = 53/79 (67%), Gaps = 8/79 (10%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
           +VFVGNLPFD+++EE+ + F  CG       VEAVR++R     +GKG  YVLFKT+++ 
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCG------DVEAVRIVRDRKTGIGKGFGYVLFKTKDSV 54

Query: 396 NLVIKRRNLKLRDRELRLS 414
            L +K   +KL+ R++R+ 
Sbjct: 55  ALALKLNGIKLKGRKIRVK 73

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

 Score = 80.9 bits (200), Expect = 1e-18
 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|214636 smart00360, RRM, RNA recognition motif

 Score = 63.8 bits (156), Expect = 5e-13
 Identities = 28/77 (36%), Positives = 43/77 (55%), Gaps = 5/77 (6%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
           T+FVGNLP D  +EE+ +LF     +ES    VR++R       KG A+V F++ E A  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVES----VRLVRDKETGKSKGFAFVEFESEEDAEK 56

Query: 398 VIKRRN-LKLRDRELRL 413
            ++  N  +L  R L++
Sbjct: 57  ALEALNGKELDGRPLKV 73

Length = 73

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

 Score = 61.8 bits (151), Expect = 3e-12
 Identities = 28/86 (32%), Positives = 46/86 (53%), Gaps = 10/86 (11%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           +TVF+ NLPFD  +EE+ +LF    +    V+  R+++       KG A+V FKT+E+A 
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGE----VKYARIVKDKLTGHSKGTAFVKFKTKESAQ 56

Query: 397 LVIKRRN------LKLRDRELRLSHA 416
             ++  +      L L  R L ++ A
Sbjct: 57  KCLEAADNAEDSGLSLDGRRLIVTLA 82

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

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

 Score = 55.0 bits (133), Expect = 8e-10
 Identities = 26/79 (32%), Positives = 45/79 (56%), Gaps = 10/79 (12%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           +FVGNLP D  +E++ +LF   G       +E+VR++R    +  KG A+V F++ E A 
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFG------EIESVRIVRDKDGK-SKGFAFVEFESPEDAE 53

Query: 397 LVIKR-RNLKLRDRELRLS 414
             ++     +L  R+L++S
Sbjct: 54  KALEALNGKELDGRKLKVS 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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 54.1 bits (131), Expect = 1e-09
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 7/75 (9%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
           ++V NLP  V +E++ + F         VE VR++R+      +G A+V F + E A   
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGK----VEGVRLVRNKDR--PRGFAFVEFASPEDAEAA 54

Query: 399 IKRRN-LKLRDRELR 412
           +K+ N L L  R LR
Sbjct: 55  LKKLNGLVLDGRTLR 69

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

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

 Score = 53.8 bits (130), Expect = 2e-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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 52.7 bits (127), Expect = 4e-09
 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|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 53.0 bits (127), Expect = 4e-09
 Identities = 32/84 (38%), Positives = 48/84 (57%), Gaps = 11/84 (13%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           VFVGNL F+  +E ++++F  CG       +E VR++R P   VGKG AYV FK   A  
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCG------GIEYVRIVRDPKTNVGKGFAYVQFKDENAVE 55

Query: 397 ---LVIKRRNLKLRDRELRLSHAQ 417
              L+ +++   +  RELR+S  +
Sbjct: 56  KALLLNEKKFPPMLPRELRVSRCK 79

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 52.2 bits (126), Expect = 6e-09
 Identities = 28/77 (36%), Positives = 42/77 (54%), Gaps = 10/77 (12%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           +FVGNLP D  +E++  LF   G       +E++R++R    R  KG A+V F+  E A 
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFG------PIESIRIVRDETGR-SKGFAFVEFEDEEDAE 53

Query: 397 LVIKRRN-LKLRDRELR 412
             ++  N  +L  RELR
Sbjct: 54  KALEALNGKELGGRELR 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|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 = 51.0 bits (123), Expect = 2e-08
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 4/77 (5%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            V +  LPF   +E+I   F GL+      + + ++     R   G AYV F + E A  
Sbjct: 1   VVRLRGLPFSATEEDIRDFFSGLDIPP---DGIHIVYDDDGR-PTGEAYVEFASPEDARR 56

Query: 398 VIKRRNLKLRDRELRLS 414
            +++ N K+  R + + 
Sbjct: 57  ALRKHNNKMGGRYIEVF 73

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

 Score = 51.1 bits (123), Expect = 2e-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|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 48.5 bits (116), Expect = 1e-07
 Identities = 26/78 (33%), Positives = 45/78 (57%), Gaps = 8/78 (10%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP--HMRVGKGIAYVLFKTREAA 395
           T ++GNLP+DV +E+I + F GLN     V +VR+ R P    R+ +G  Y  F+ R++ 
Sbjct: 3   TAYLGNLPYDVTEEDIKEFFRGLN-----VSSVRLPREPGDPGRL-RGFGYAEFEDRDSL 56

Query: 396 NLVIKRRNLKLRDRELRL 413
              +   +  L++R +R+
Sbjct: 57  LQALSLNDESLKNRRIRV 74

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

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 4/57 (7%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
           +FVGNL FD  ++ IY+ F         + +VR+   P     KG  YV F ++EAA
Sbjct: 1   LFVGNLSFDADEDSIYEAFGE----YGEISSVRLPTDPDSGRPKGFGYVEFSSQEAA 53

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

 Score = 47.7 bits (114), Expect = 3e-07
 Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 5/82 (6%)

Query: 335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
           I   +FVG +P D  +EE+   F        SV+ V++I      V KG  +V F+T+E 
Sbjct: 1   IPNRIFVGGIPPDTTEEELRDFFSRF----GSVKDVKIITD-RAGVSKGYGFVTFETQED 55

Query: 395 ANLVIKRRNLKLRDRELRLSHA 416
           A  ++   NL  R ++L +  A
Sbjct: 56  AEKILAMGNLNFRGKKLNIGPA 77

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

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

 Score = 47.3 bits (113), Expect = 4e-07
 Identities = 28/82 (34%), Positives = 45/82 (54%), Gaps = 5/82 (6%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
           K TV+V NLPF + + +++++F         V  V +++    R  KG+A++LF  RE A
Sbjct: 1   KSTVYVSNLPFSLTNNDLHKIFSKY----GKVVKVTIVKDKETRKSKGVAFILFLDREDA 56

Query: 396 NLVIKRRNLK-LRDRELRLSHA 416
           +  +K  N K L  R L+ S A
Sbjct: 57  HKCVKALNNKELFGRTLKCSIA 78

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

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

 Score = 46.5 bits (111), Expect = 8e-07
 Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 9/83 (10%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
           T+FVGNL +  + +++ + F  CG       V  VR+ +    R  KG  +V F T E A
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECG------EVVDVRIAQDDDGR-SKGFGHVEFATEEGA 53

Query: 396 NLVIKRRNLKLRDRELRLSHAQQ 418
              +++   +L  RE+R+  A +
Sbjct: 54  QKALEKSGEELLGREIRVDLATE 76

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

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 9/81 (11%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
           VFVGN+P+D  +E++ ++F  +      V + R++        KG  +  F+  E A   
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGP----VVSFRLVTDRDTGKPKGYGFCEFEDIETAASA 56

Query: 399 IKRRNL---KLRDRELRLSHA 416
           I  RNL   +   R LR+  A
Sbjct: 57  I--RNLNGYEFNGRALRVDFA 75

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

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

 Score = 45.2 bits (108), Expect = 2e-06
 Identities = 27/81 (33%), Positives = 41/81 (50%), Gaps = 17/81 (20%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGK------GIAYVLFKTR 392
           ++VGNL F   +E+IY+LF    D++      R+I    M + +      G  +V + TR
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIK------RII----MGLDRFTKTPCGFCFVEYYTR 50

Query: 393 EAANLVIKRRN-LKLRDRELR 412
           E A   +K  N  KL DR +R
Sbjct: 51  EDAENAVKYLNGTKLDDRIIR 71

This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. . Length = 78

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

 Score = 44.2 bits (105), Expect = 5e-06
 Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 15/76 (19%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
           TVFV NL + V ++E+ +LF  CG       +  VR++++   +  KG AYV F+  E+ 
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCG------EITDVRLVKNYKGKS-KGYAYVEFENEESV 53

Query: 396 NLVIKRRNLKLRDREL 411
              +K       DREL
Sbjct: 54  QEALK------LDREL 63

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

 Score = 43.7 bits (104), Expect = 7e-06
 Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 8/64 (12%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
           TVFV  L   V++ ++Y+ F   G       V  VR+IR  + R  KG+AYV F   E+ 
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAG------KVRDVRIIRDRNSRRSKGVAYVEFYDEESV 54

Query: 396 NLVI 399
            L +
Sbjct: 55  PLAL 58

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

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

 Score = 43.7 bits (104), Expect = 8e-06
 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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 48.0 bits (114), Expect = 8e-06
 Identities = 61/274 (22%), Positives = 104/274 (37%), Gaps = 35/274 (12%)

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-KTREAANLVIKRRNLKLRDRELRLSHAQ 417
            ++ F    EA   +      +L  R +++ +AQ
Sbjct: 231 GFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ 264

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

 Score = 43.8 bits (104), Expect = 8e-06
 Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 5/81 (6%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            ++VGNLP++V +E++  LF         V + RVI        +G  +V  +T E AN 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQ----FGEVTSARVITDRETGRSRGFGFVEMETAEEANA 56

Query: 398 VIKRRN-LKLRDRELRLSHAQ 417
            I++ N      R L ++ A+
Sbjct: 57  AIEKLNGTDFGGRTLTVNEAR 77

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

>gnl|CDD|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 = 42.7 bits (101), Expect = 2e-05
 Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 1/71 (1%)

Query: 344 LPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN 403
           LP+     +I   F GL  +    + +  +  P  R   G A+VLF+T E A   + +  
Sbjct: 9   LPYSATAADILAFFGGLCPVVGGPDGILFVTGPDGR-PTGDAFVLFETEEDAQRALGKHK 67

Query: 404 LKLRDRELRLS 414
             L  R + L 
Sbjct: 68  ENLGSRYIELF 78

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

 Score = 42.5 bits (101), Expect = 2e-05
 Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 4/62 (6%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
           +FVG LP    +E++  LF        ++E V +IR       KG A+V F +RE A   
Sbjct: 2   LFVGQLPKTATEEDVRALFEEY----GNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKA 57

Query: 399 IK 400
           I+
Sbjct: 58  IE 59

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

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

 Score = 41.8 bits (99), Expect = 3e-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|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 = 4e-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|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 41.2 bits (97), Expect = 6e-05
 Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 5/76 (6%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
           T FVGNLPF+    ++  +F  L     SV++VR++R       KG  YV F+  E+   
Sbjct: 3   TAFVGNLPFNTVQGDLDAIFKDL-----SVKSVRLVRDKETDKFKGFCYVEFEDVESLKE 57

Query: 398 VIKRRNLKLRDRELRL 413
            ++       DR LR+
Sbjct: 58  ALEYDGALFDDRSLRV 73

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

 Score = 41.1 bits (97), Expect = 7e-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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 40.6 bits (96), Expect = 8e-05
 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|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 40.8 bits (96), Expect = 8e-05
 Identities = 23/83 (27%), Positives = 47/83 (56%), Gaps = 15/83 (18%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
            T+++G+L   V +E++  LF   G       ++++ +I  P     +G AYV  +TR+ 
Sbjct: 3   TTLWIGHLSKKVTEEDLKNLFEEYG------EIQSIDMI-PP-----RGCAYVCMETRQD 50

Query: 395 AN-LVIKRRNLKLRDRELRLSHA 416
           A+  + K RN+KL  ++++++ A
Sbjct: 51  AHRALQKLRNVKLAGKKIKVAWA 73

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

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

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 23/89 (25%), Positives = 38/89 (42%), Gaps = 13/89 (14%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLES-------------SVEAVRVIRHPHMRVGKG 383
           +TVFVGNLP   K +++ +LF     +ES               +   + +  H +    
Sbjct: 1   RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNV 60

Query: 384 IAYVLFKTREAANLVIKRRNLKLRDRELR 412
            AYV+FK  E+A   +K    +     +R
Sbjct: 61  NAYVVFKEEESAEKALKLNGTEFEGHHIR 89

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

>gnl|CDD|240740 cd12294, RRM_Rrp7A, RNA recognition motif in ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar proteins

 Score = 41.1 bits (97), Expect = 1e-04
 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|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 23/62 (37%), Positives = 31/62 (50%), Gaps = 10/62 (16%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
           TV+VGNLP  + +EE+ + F       S   A+  +R       KG A+V F T EAA  
Sbjct: 2   TVYVGNLPHGLTEEELQRTF-------SPFGAIEEVRVFKD---KGYAFVRFDTHEAAAT 51

Query: 398 VI 399
            I
Sbjct: 52  AI 53

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

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 4/64 (6%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
             +FVG LP+   D+ + + F    ++E   EAV VI        +G  +V FK +E+A 
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIE---EAV-VITDRQTGKSRGYGFVTFKDKESAE 56

Query: 397 LVIK 400
              K
Sbjct: 57  RACK 60

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

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

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 26/80 (32%), Positives = 36/80 (45%), Gaps = 9/80 (11%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
            +FV NLP D  +  ++QLF   G      +V  V+VIR       KG  +V     E A
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFG------AVTNVKVIRDLTTNKCKGYGFVTMTNYEEA 56

Query: 396 NLVIKRRN-LKLRDRELRLS 414
              I   N  +L  R L++S
Sbjct: 57  YSAIASLNGYRLGGRVLQVS 76

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

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 4/66 (6%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            +FV  L     ++E+  LF         VE V +++ P     +G  +V F++ E A+ 
Sbjct: 3   KLFVSGLSTRTTEKELEALFSK----FGRVEEVLLMKDPETGESRGFGFVTFESVEDADA 58

Query: 398 VIKRRN 403
            I+  N
Sbjct: 59  AIRDLN 64

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

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

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 5/60 (8%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG-IAYVLFKTREAAN 396
           T+FV  LP DVK+ E+  LF      E+S    R++        K  + +V F + + A 
Sbjct: 2   TLFVSGLPSDVKERELAHLFRPFPGYEAS----RLVFKEKKGGEKQPVGFVDFSSAQCAA 57

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|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 38.7 bits (91), Expect = 4e-04
 Identities = 21/79 (26%), Positives = 42/79 (53%), Gaps = 6/79 (7%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            + V NL +DV +E++ +LF  + +++     V+ I +      +G A V+F+ RE A  
Sbjct: 2   RLRVSNLHYDVTEEDLEELFGRVGEVKK----VK-INYDRSGRSEGTADVVFEKREDAER 56

Query: 398 VIKRRN-LKLRDRELRLSH 415
            IK+ N + L  + +++  
Sbjct: 57  AIKQFNGVLLDGQPMQVEL 75

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

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

 Score = 38.8 bits (91), Expect = 4e-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|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 38.5 bits (90), Expect = 5e-04
 Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 8/59 (13%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
            +FVGNLP+D   E++   F   G         +VR++        KG A+V F T EA
Sbjct: 2   ILFVGNLPYDTTAEDLLAHFKNAGAPP------SVRLLTDKKTGKSKGCAFVEFDTAEA 54

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|240958 cd12514, RRM4_RBM12_like, RNA recognition motif 4 in RNA-binding protein RBM12, RBM12B and similar proteins

 Score = 38.1 bits (89), Expect = 6e-04
 Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 8/74 (10%)

Query: 343 NLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGI--AYVLFKTREAANLVIK 400
           N+PFDV   E+   F G+   E  +  +      + + GK +  AYV F + E A    +
Sbjct: 6   NIPFDVTKGEVLAFFAGIAIAEQGIHIL------YDKTGKTLGEAYVEFVSEEDAMRAER 59

Query: 401 RRNLKLRDRELRLS 414
               KL+ RE+ L 
Sbjct: 60  LHRKKLKGREILLR 73

This subfamily corresponds to the RRM4 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear. . Length = 73

>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 = 6e-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|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 38.5 bits (90), Expect = 6e-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|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 38.1 bits (89), Expect = 6e-04
 Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 8/59 (13%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
           V+VG +P+   ++EI   F  CG       +E + ++  P     +GIA++ FKT EAA
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCG------EIEELDLMTFPDTGRFRGIAFITFKTEEAA 53

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

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

 Score = 38.3 bits (90), Expect = 7e-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 = 8e-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|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 37.6 bits (88), 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|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 37.5 bits (87), Expect = 0.001
 Identities = 26/84 (30%), Positives = 39/84 (46%), Gaps = 11/84 (13%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK----TRE 393
           T+FV NL F V  E++   F  +  ++ +V    V+  P     +G  +V F      +E
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAV----VVTDPETGESRGYGFVTFAMLEDAQE 56

Query: 394 AANLVIKRRNLKLRDRELRLSHAQ 417
           A     K +N KL  R LRL  A+
Sbjct: 57  ALA---KLKNKKLHGRILRLDIAE 77

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

>gnl|CDD|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 = 0.001
 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|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 37.2 bits (87), Expect = 0.001
 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|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 11/85 (12%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVR---VIRHPHMRVGKGIAYVLFKTREA 394
           T+FV NLP+D  DE++ + F       S V  ++   V++    +  +G  YV F   E 
Sbjct: 1   TLFVRNLPYDTTDEQLEEFF-------SEVGPIKRCFVVKDKGSKKCRGFGYVTFALEED 53

Query: 395 ANLVIKR-RNLKLRDRELRLSHAQQ 418
           A   ++  +  K   R++ +  A++
Sbjct: 54  AKRALEEKKKTKFGGRKIHVEFAKK 78

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

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

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           +FVGNL F+  ++E+   F   G       +  VR++        KG A+V F+  E A 
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVG------RIRRVRMMTFEDSGKCKGFAFVDFEEIEFAT 54

Query: 397 LVIKRRNLKLRD 408
             +K ++L  R 
Sbjct: 55  NALKGKHLNGRA 66

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 37.2 bits (87), Expect = 0.002
 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|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 37.3 bits (87), 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|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 36.9 bits (86), 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|240891 cd12445, RRM2_CPEBs, RNA recognition motif 2 in cytoplasmic polyadenylation element-binding protein CPEB-1, CPEB-2, CPEB-3, CPEB-4 and similar protiens

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 17/70 (24%), Positives = 27/70 (38%), Gaps = 3/70 (4%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           +TVFVG LP  +   E+  +   L  L   V  V +          G A V F   ++  
Sbjct: 1   RTVFVGGLPLPLTAAELAAI---LERLYGGVCYVEIDTDEFYLYPTGCARVTFNNEQSYI 57

Query: 397 LVIKRRNLKL 406
             +    ++L
Sbjct: 58  KAVSEVFVEL 67

This subfamily corresponds to the RRM2 of CPEB family of proteins that bind to defined groups of mRNAs and act as either translational repressors or activators to regulate their translation. CPEB proteins are well conserved in both, vertebrates and invertebrates. Based on sequence similarity, RNA-binding specificity, and functional regulation of translation, the CPEB proteins has been classified into two subfamilies. The first subfamily includes CPEB-1 and related proteins. CPEB-1 is an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. Otherwise, it may function as a translational inhibitor when dephosphorylated and bound to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm. The second subfamily includes CPEB-2, CPEB-3, CPEB-4, and related protiens. Due to the high sequence similarity, members in this subfamily may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. Moreover, CPEB-2 impedes target RNA translation at elongation. It directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All CPEB proteins are nucleus-cytoplasm shuttling proteins. They contain an N-terminal unstructured region, followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. CPEB-2, -3, and -4 have conserved nuclear export signals that are not present in CPEB-1. . Length = 81

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

 Score = 40.6 bits (95), Expect = 0.002
 Identities = 44/220 (20%), Positives = 84/220 (38%), Gaps = 57/220 (25%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH 286
           +++VG+L   V +  L   F  FG + SVR+            + ++ ++ +       +
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRV-----------CRDSVTRRSLG------Y 44

Query: 287 AYIVFKSEQSTEAAL-AFNMAVIGGNHIRL---DRACPPRKKLKGEDAPLYDIKKTVFVG 342
            Y+ F++    E AL   N   +GG  IR+    R    R+   G           +FV 
Sbjct: 45  GYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDPSLRRSGVG----------NIFVK 94

Query: 343 NLPFDVKDEEIYQLF--------CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
           NL   V ++ ++  F        C +   E+                +G  +V F+  E+
Sbjct: 95  NLDKSVDNKALFDTFSKFGNILSCKVATDENGKS-------------RGYGFVHFEKEES 141

Query: 395 ANLVIKRRN-LKLRDRELRLSHAQQNCTPSKRKDVAPAVN 433
           A   I++ N + L D+E+ +    +       ++ AP   
Sbjct: 142 AKAAIQKVNGMLLNDKEVYVGRFIKK----HEREAAPLKK 177

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

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

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 4/57 (7%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
           +FV NLP+  K++++ +LF    +L      V V         KG AYVLF   E A
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSE----VHVAIDKKSGKSKGFAYVLFLDPEDA 57

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

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

 Score = 39.9 bits (92), Expect = 0.002
 Identities = 40/235 (17%), Positives = 77/235 (32%), Gaps = 11/235 (4%)

Query: 261 PIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACP 320
                ++  +    + +   +  S    +  + ++  E  +        G     +    
Sbjct: 40  EANSKELNLEVNSRKIESEISPPSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELF 99

Query: 321 PRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV 380
              +         +   T+FVGNLP+DV +E++ +LF         V+ VR++R      
Sbjct: 100 RSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKF----GPVKRVRLVRDRETGK 155

Query: 381 GKGIAYVLFKTREAANLVIKRRNLK-LRDRELRLSHAQQNCTPSKRKDVAPAVNSPPKKF 439
            +G A+V F++ E+A   I+  N K L  R LR+  AQ    P          +   K  
Sbjct: 156 SRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLS 215

Query: 440 VLDSRTLGSGNRSNSKVAMSYQGLQASKSCTQKKVHSGSSGVVKMKKSRTQKGER 494
              +              +    L    +  +      S G +        K  +
Sbjct: 216 RGKA------LLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGK 264

Length = 306

>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 = 36.5 bits (85), Expect = 0.003
 Identities = 22/86 (25%), Positives = 36/86 (41%), Gaps = 13/86 (15%)

Query: 334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT-- 391
           D   T+FVG L     +E + ++F    D    +  +R++R       KG A+V ++   
Sbjct: 1   DPYLTLFVGRLSLQTTEETLREVFSRYGD----IRRLRLVRDIVTGFSKGYAFVEYEHER 56

Query: 392 ------REAANLVIKRRNLKLRDREL 411
                 R+A  LVI    +   D E 
Sbjct: 57  DALRAYRDAHKLVIDGSEI-FVDFER 81

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

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 4/65 (6%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
           +F+ +LP +  D+++YQLF    ++ S+    +V    +    K   +V +   E+A   
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISA----KVFVDKNTGQSKCFGFVSYDNPESAQAA 56

Query: 399 IKRRN 403
           IK  N
Sbjct: 57  IKAMN 61

This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. . Length = 73

>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
           TV++GNL +D+ ++++ + F G       + +VR+         KG  +V F   E+ + 
Sbjct: 1   TVYIGNLAWDITEDDVREFFKG-----CEITSVRLATDKETGEFKGFGHVDFADEESLDA 55

Query: 398 VIKRRNLKLRDRELRLS 414
            +K     L  R +R++
Sbjct: 56  ALKLDGTVLCGRPIRIA 72

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 39.4 bits (92), Expect = 0.004
 Identities = 39/171 (22%), Positives = 73/171 (42%), Gaps = 30/171 (17%)

Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV-H 286
           IFV NL   V  K L   F KFG I S ++ +                   +EN  S  +
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVAT-------------------DENGKSRGY 131

Query: 287 AYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLP 345
            ++ F+ E+S +AA+   N  ++    + + R    + + +      +     ++V NL 
Sbjct: 132 GFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFI-KKHEREAAPLKKF---TNLYVKNLD 187

Query: 346 FDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
             V ++++ +LF    ++ S+     V++    R  +G A+V F+  E A 
Sbjct: 188 PSVNEDKLRELFAKFGEITSAA----VMKDGSGRS-RGFAFVNFEKHEDAA 233

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

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

 Score = 36.4 bits (84), Expect = 0.004
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 4/82 (4%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESS-VEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           T+FV NL F   ++ +   F  L+    + V+     + P   +  G  +V FKT+E A 
Sbjct: 2   TLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQ 61

Query: 397 LVIKRRNLKLRDR---ELRLSH 415
             +K  +  + D     ++ SH
Sbjct: 62  AALKAMDGFVLDGHTLVVKFSH 83

This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 84

>gnl|CDD|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

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

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 10/82 (12%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLE-SSV----EAVRVIRHPHMRVGKGIAYVLFKTR 392
            V++ NL +   +E++ +    L D E  SV    + VR  R   +R   GIAY  F + 
Sbjct: 1   RVYISNLSYSSSEEDLEEF---LKDFEPVSVLIPSQTVRGFRSRRVR-PLGIAYAEFSSP 56

Query: 393 EAANLVIKRRNLK-LRDRELRL 413
           E A  V+K  N K  ++R+L +
Sbjct: 57  EQAEKVVKDLNGKVFKNRKLFV 78

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	548
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.97
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.95
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.95
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.94
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.94
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.92
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.92
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.92
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.91
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.9
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.9
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.9
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.9
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.89
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.89
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.88
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.88
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.88
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.87
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.86
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.86
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.85
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.84
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.84
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.83
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.81
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.81
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.81
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.77
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.74
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.73
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.7
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.7
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.69
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.66
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.65
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.64
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.64
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.63
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.53
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.52
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.5
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.5
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.48
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.48
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.47
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.42
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.42
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.39
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.38
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.38
PLN03120	260	nucleic acid binding protein; Provisional	99.36
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.36
KOG0122	270	consensus Translation initiation factor 3, subunit	99.34
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.33
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.32
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.31
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.3
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.27
PLN03120	260	nucleic acid binding protein; Provisional	99.27
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.27
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.27
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.26
PLN03121	243	nucleic acid binding protein; Provisional	99.26
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.24
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.24
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.24
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.22
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.19
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.19
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.17
smart00362	72	RRM_2 RNA recognition motif.	99.16
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.16
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.15
PLN03213	759	repressor of silencing 3; Provisional	99.14
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.14
PLN03121	243	nucleic acid binding protein; Provisional	99.13
smart00360	71	RRM RNA recognition motif.	99.13
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.12
KOG0122	270	consensus Translation initiation factor 3, subunit	99.12
smart00362	72	RRM_2 RNA recognition motif.	99.12
PLN03213	759	repressor of silencing 3; Provisional	99.12
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.11
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.11
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.09
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.07
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.07
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.07
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.07
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.06
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.05
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.05
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.04
smart00360	71	RRM RNA recognition motif.	99.03
KOG4210	285	consensus Nuclear localization sequence binding pr	99.03
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.01
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.97
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.95
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.92
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.9
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.88
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.88
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.87
smart00361	70	RRM_1 RNA recognition motif.	98.86
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.84
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.79
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.77
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.76
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.72
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.71
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.69
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.66
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.63
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.62
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.61
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.6
smart00361	70	RRM_1 RNA recognition motif.	98.6
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.59
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.59
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.53
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.42
KOG0151	877	consensus Predicted splicing regulator, contains R	98.41
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.39
KOG0226	290	consensus RNA-binding proteins [General function p	98.38
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.38
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.35
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.34
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.3
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.28
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.26
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.24
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.21
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.2
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.13
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.13
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.08
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.06
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.0
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.98
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.76
KOG0151	877	consensus Predicted splicing regulator, contains R	97.73
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.7
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	97.69
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.59
KOG4660	549	consensus Protein Mei2, essential for commitment t	97.59
KOG0226	290	consensus RNA-binding proteins [General function p	97.52
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.5
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.49
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.17
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.05
KOG4210	285	consensus Nuclear localization sequence binding pr	97.05
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.89
KOG1995	351	consensus Conserved Zn-finger protein [General fun	96.89
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	96.88
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.86
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.79
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.72
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.68
PF12220	94	U1snRNP70_N: U1 small nuclear ribonucleoprotein of	96.6
KOG1995	351	consensus Conserved Zn-finger protein [General fun	96.59
KOG3152	278	consensus TBP-binding protein, activator of basal	96.26
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.24
KOG1855	484	consensus Predicted RNA-binding protein [General f	95.76
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	95.65
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	95.63
KOG2314	698	consensus Translation initiation factor 3, subunit	95.62
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	95.57
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	95.33
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	95.2
COG5175	480	MOT2 Transcriptional repressor [Transcription]	95.13
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	95.07
KOG2314	698	consensus Translation initiation factor 3, subunit	94.99
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	94.94
KOG3152	278	consensus TBP-binding protein, activator of basal	94.68
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	94.62
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	94.58
KOG1996	378	consensus mRNA splicing factor [RNA processing and	94.45
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	94.31
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	94.2
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	94.08
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	93.96
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	93.69
KOG1996	378	consensus mRNA splicing factor [RNA processing and	93.53
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	93.03
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	92.42
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	92.37
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	91.68
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	91.59
KOG2135	526	consensus Proteins containing the RNA recognition	91.34
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	90.46
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	90.32
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	89.79
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	89.72
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	88.79
KOG2068	327	consensus MOT2 transcription factor [Transcription	88.78
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	87.12
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	85.5
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	85.2
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	83.81
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	82.5
KOG2591	684	consensus c-Mpl binding protein, contains La domai	82.22
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	80.52
KOG2135	526	consensus Proteins containing the RNA recognition	80.01

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.97  E-value=9.2e-29  Score=258.94  Aligned_cols=169  Identities=21%  Similarity=0.321  Sum_probs=149.7

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...++|||+|||+++|+++|+++|+.||.|.+|+|+.+.                 .++.++|||||+|.++++|..|| 
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~-----------------~tg~srGyaFVeF~~~e~A~~Ai~  167 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDY-----------------KTGYSFGYAFVDFGSEADSQRAIK  167 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC-----------------CCCccCcEEEEEEccHHHHHHHHH
Confidence            346899999999999999999999999999999996654                 24558899999999999999999 


Q ss_pred             HhcceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCC
Q 008920          302 AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVG  381 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~s  381 (548)
                      .||+..|.++.|.|.++.+...         .....+|||+|||+.+++++|+++|+.|    |.|..|.|++|..++.+
T Consensus       168 ~LnG~~l~gr~i~V~~a~p~~~---------~~~~~~lfV~nLp~~vtee~L~~~F~~f----G~V~~v~i~~d~~tg~~  234 (346)
T TIGR01659       168 NLNGITVRNKRLKVSYARPGGE---------SIKDTNLYVTNLPRTITDDQLDTIFGKY----GQIVQKNILRDKLTGTP  234 (346)
T ss_pred             HcCCCccCCceeeeeccccccc---------ccccceeEEeCCCCcccHHHHHHHHHhc----CCEEEEEEeecCCCCcc
Confidence            6999999999999999864321         1235689999999999999999999999    89999999999989999


Q ss_pred             ceEEEEEECCHHHHHHHHHHcC-CccCC--eEEEEEeeecCCC
Q 008920          382 KGIAYVLFKTREAANLVIKRRN-LKLRD--RELRLSHAQQNCT  421 (548)
Q Consensus       382 rG~AFV~F~~~e~A~~Al~~ln-~~l~G--r~I~V~~Ak~~~~  421 (548)
                      +|||||+|.+.++|+.||..|+ ..|.|  ++|.|.++.....
T Consensus       235 kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~~  277 (346)
T TIGR01659       235 RGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGK  277 (346)
T ss_pred             ceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCcccc
Confidence            9999999999999999999998 66655  7999999987643

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=99.95  E-value=3.5e-27  Score=259.87  Aligned_cols=175  Identities=18%  Similarity=0.358  Sum_probs=150.8

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||+.+++++|+++|..||.|.+|+|+.++.                 +|.++|||||+|.+.++|+.|| .
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            457999999999999999999999999999999976542                 3558899999999999999999 5


Q ss_pred             hcceeecCceeEeecCCCcccccC--CCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCC
Q 008920          303 FNMAVIGGNHIRLDRACPPRKKLK--GEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV  380 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~~k~~~--~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~  380 (548)
                      |||..|.|+.|.|.+.........  ..........++|||+|||+++++++|+++|+.|    |.|..|+|++|+.+|.
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            999999999999987543211100  0001112245799999999999999999999999    9999999999999999


Q ss_pred             CceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          381 GKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       381 srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      ++|||||+|.+.++|..||..|| ..|+|+.|+|.++..+
T Consensus       245 sKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~p  284 (612)
T TIGR01645       245 HKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTP  284 (612)
T ss_pred             cCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCC
Confidence            99999999999999999999998 9999999999999865

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.

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

Probab=99.95  E-value=7.9e-27  Score=253.10  Aligned_cols=179  Identities=24%  Similarity=0.368  Sum_probs=153.4

Q ss_pred             cCCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHH
Q 008920          220 DEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (548)
Q Consensus       220 ~~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~  299 (548)
                      +.+...++|||+|||+.+++++|.++|+.||.|..|+|+.+..                 ++.++|||||+|.+.++|.+
T Consensus        84 ~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~-----------------~~~skg~afVeF~~~e~A~~  146 (457)
T TIGR01622        84 EAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRN-----------------SRRSKGVAYVEFYDVESVIK  146 (457)
T ss_pred             ccccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCC-----------------CCCcceEEEEEECCHHHHHH
Confidence            3455678999999999999999999999999999999966432                 34578999999999999999


Q ss_pred             HHHhcceeecCceeEeecCCCcccccCC---CCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecC
Q 008920          300 ALAFNMAVIGGNHIRLDRACPPRKKLKG---EDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP  376 (548)
Q Consensus       300 Al~lng~~~~gr~I~V~~a~~~~k~~~~---~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~  376 (548)
                      ||.|+|..|.|+.|.|.++.........   ..........+|||+|||+.+++++|.++|..|    |.|..|.|+.+.
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            9999999999999999886543221110   001112336899999999999999999999999    899999999999


Q ss_pred             CCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          377 HMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       377 ~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      .+|.++|||||+|.+.++|..||..|+ ..|.|+.|.|.|+...
T Consensus       223 ~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~  266 (457)
T TIGR01622       223 ETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDS  266 (457)
T ss_pred             CCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccCC
Confidence            999999999999999999999999888 9999999999998743

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=99.94  E-value=4.3e-26  Score=238.85  Aligned_cols=165  Identities=18%  Similarity=0.331  Sum_probs=146.8

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      ..+|||+|||+.+++++|.++|+.||+|.+|+|+.+..                 +|.++|||||+|.+.++|..|| .|
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            47999999999999999999999999999999976542                 3558899999999999999999 59


Q ss_pred             cceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCce
Q 008920          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG  383 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG  383 (548)
                      ||..|.|+.|.|.++.+...         .....+|||+|||..+++++|..+|..|    |.|..+.|+.+..++.++|
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            99999999999999865321         2235689999999999999999999999    8999999999988899999


Q ss_pred             EEEEEECCHHHHHHHHHHcC-CccCC--eEEEEEeeecC
Q 008920          384 IAYVLFKTREAANLVIKRRN-LKLRD--RELRLSHAQQN  419 (548)
Q Consensus       384 ~AFV~F~~~e~A~~Al~~ln-~~l~G--r~I~V~~Ak~~  419 (548)
                      ||||+|.+.++|..||..|+ ..+.|  ..|.|.|+...
T Consensus       133 ~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~  171 (352)
T TIGR01661       133 VGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNP  171 (352)
T ss_pred             EEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCC
Confidence            99999999999999998888 76666  67899998754

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.94  E-value=1.4e-25  Score=234.94  Aligned_cols=174  Identities=24%  Similarity=0.338  Sum_probs=145.7

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      .++|||+|||..+++++|..+|..||.|..+.|+.+..                 ++.++|||||+|.+.++|+.|| .|
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            46899999999999999999999999999999865442                 2347799999999999999999 69


Q ss_pred             cceeecC--ceeEeecCCCcccccCC--------------C---------------------------------------
Q 008920          304 NMAVIGG--NHIRLDRACPPRKKLKG--------------E---------------------------------------  328 (548)
Q Consensus       304 ng~~~~g--r~I~V~~a~~~~k~~~~--------------~---------------------------------------  328 (548)
                      ||..+.|  ..|.|.++..+......              .                                       
T Consensus       152 ~g~~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  231 (352)
T TIGR01661       152 NGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQ  231 (352)
T ss_pred             CCCccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhh
Confidence            9999887  57888887543210000              0                                       


Q ss_pred             ------------CC------------------CcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCC
Q 008920          329 ------------DA------------------PLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM  378 (548)
Q Consensus       329 ------------~~------------------~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~t  378 (548)
                                  ..                  .......+|||+|||+.+++++|+++|+.|    |.|..|+|++|..+
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                  000112369999999999999999999999    99999999999999


Q ss_pred             CCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          379 RVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       379 g~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      |.++|||||+|.+.++|..||..|| ..|.|+.|+|.|+..+
T Consensus       308 ~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~  349 (352)
T TIGR01661       308 NQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNK  349 (352)
T ss_pred             CCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCC
Confidence            9999999999999999999999888 9999999999998765

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

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

Probab=99.92  E-value=2.5e-24  Score=236.45  Aligned_cols=173  Identities=19%  Similarity=0.381  Sum_probs=143.1

Q ss_pred             cCCCcccEEEEcCCCCCCcHHHHHHHhhhcC------------CeeEEEEeeecccCCCCCccchhhhhhhccCCCcceE
Q 008920          220 DEGKLLRTIFVGNLPLKVKKKTLIKEFIKFG------------EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHA  287 (548)
Q Consensus       220 ~~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG------------~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~A  287 (548)
                      ......++|||||||+.+|+++|.+||..|+            .|..|.+                       +..+|||
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            4456779999999999999999999999852            3333333                       2366999


Q ss_pred             EEEecCHHHHHHHHHhcceeecCceeEeecCCCccccc-------CC-------------CCCCcCCCccEEEEeCCCCC
Q 008920          288 YIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKL-------KG-------------EDAPLYDIKKTVFVGNLPFD  347 (548)
Q Consensus       288 FV~F~s~e~A~~Al~lng~~~~gr~I~V~~a~~~~k~~-------~~-------------~~~~~~~~~~tLfV~NLp~~  347 (548)
                      ||+|.+.++|..||+|+|..|.|+.|.|.+........       ..             ......+..++|||+|||+.
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            99999999999999999999999999997643211000       00             00112344679999999999


Q ss_pred             CCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          348 VKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       348 ~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      +++++|.++|..|    |.|..|.|+.+..+|.++|||||+|.+.++|..||..|+ ..|+|+.|.|.++...
T Consensus       307 ~~~~~l~~~f~~~----G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~  375 (509)
T TIGR01642       307 LGEDQIKELLESF----GDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVG  375 (509)
T ss_pred             CCHHHHHHHHHhc----CCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccC
Confidence            9999999999999    899999999999999999999999999999999999888 9999999999999754

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

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

Probab=99.92  E-value=3.9e-24  Score=238.29  Aligned_cols=164  Identities=23%  Similarity=0.389  Sum_probs=144.4

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhcc
Q 008920          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (548)
Q Consensus       227 tVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng  305 (548)
                      +|||+|||.++|+++|.++|+.||.|.+|+|+.+..                 ++.+.|||||+|.+.++|+.|| .+|+
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-----------------TRRSLGYGYVNFQNPADAERALETMNF   64 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC-----------------CCCcceEEEEEECCHHHHHHHHHHhCC
Confidence            799999999999999999999999999999977653                 3457899999999999999999 5899


Q ss_pred             eeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEE
Q 008920          306 AVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIA  385 (548)
Q Consensus       306 ~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~A  385 (548)
                      ..|.|+.|+|.|+.....       .......+|||+|||.++++++|+++|+.|    |.|..|.|+.+ .+|.++|||
T Consensus        65 ~~i~gk~i~i~~s~~~~~-------~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~----G~i~~~~i~~~-~~g~skg~a  132 (562)
T TIGR01628        65 KRLGGKPIRIMWSQRDPS-------LRRSGVGNIFVKNLDKSVDNKALFDTFSKF----GNILSCKVATD-ENGKSRGYG  132 (562)
T ss_pred             CEECCeeEEeeccccccc-------ccccCCCceEEcCCCccCCHHHHHHHHHhc----CCcceeEeeec-CCCCcccEE
Confidence            999999999999753211       112234689999999999999999999999    89999999998 478899999


Q ss_pred             EEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          386 YVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       386 FV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      ||.|.+.++|..|+..++ ..+.|+.|.|.+....
T Consensus       133 fV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~  167 (562)
T TIGR01628       133 FVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKK  167 (562)
T ss_pred             EEEECCHHHHHHHHHHhcccEecCceEEEeccccc
Confidence            999999999999998888 9999999999876543

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

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

Probab=99.92  E-value=3.8e-24  Score=209.04  Aligned_cols=169  Identities=24%  Similarity=0.411  Sum_probs=148.5

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      ..-|||+.|...++-++|++.|.+||+|..++|++|.                 ++++++||+||.|-..++|+.|| .|
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~-----------------~T~KsKGYgFVSf~~k~dAEnAI~~M  124 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDM-----------------NTGKSKGYGFVSFPNKEDAENAIQQM  124 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecc-----------------cCCcccceeEEeccchHHHHHHHHHh
Confidence            4679999999999999999999999999999996654                 46679999999999999999999 69


Q ss_pred             cceeecCceeEeecCCCcccccCCCC-------CCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecC
Q 008920          304 NMAVIGGNHIRLDRACPPRKKLKGED-------APLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP  376 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~k~~~~~~-------~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~  376 (548)
                      ||..|++|.|+..|+..+........       .......++|||+|++..+++++|++.|+.|    |.|..|||..+ 
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            99999999999999986542111111       2334567899999999999999999999999    99999999998 


Q ss_pred             CCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecCC
Q 008920          377 HMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQNC  420 (548)
Q Consensus       377 ~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~~  420 (548)
                           +||+||.|.+.|+|..||..+| ..|.|+.+++.|.+...
T Consensus       200 -----qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~  239 (321)
T KOG0148|consen  200 -----QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGD  239 (321)
T ss_pred             -----cceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCC
Confidence                 6899999999999999997777 99999999999998753

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

Probab=99.91  E-value=1.9e-23  Score=232.68  Aligned_cols=173  Identities=24%  Similarity=0.371  Sum_probs=148.8

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||.++|+++|.++|+.||.|.+|.|+.+.                  +|.++|||||.|.+.++|..|+ .
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------------------SGRSRGFAFVNFEKHEDAAKAVEE  238 (562)
T ss_pred             CCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECC------------------CCCcccEEEEEECCHHHHHHHHHH
Confidence            45789999999999999999999999999999986543                  3457899999999999999999 5


Q ss_pred             hcceeec----CceeEeecCCCcccccCC---------CCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEE
Q 008920          303 FNMAVIG----GNHIRLDRACPPRKKLKG---------EDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEA  369 (548)
Q Consensus       303 lng~~~~----gr~I~V~~a~~~~k~~~~---------~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~  369 (548)
                      |++..|.    |+.|.|.++.........         ..........+|||+||++.+++++|+++|+.|    |.|.+
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    999999988654221000         001112345789999999999999999999999    99999


Q ss_pred             EEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          370 VRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       370 VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      |.|+.| .+|.++|||||+|.+.++|.+||..++ ..|+|+.|.|.||...
T Consensus       315 ~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k  364 (562)
T TIGR01628       315 AKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRK  364 (562)
T ss_pred             EEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCc
Confidence            999999 789999999999999999999998888 9999999999999864

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

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

Probab=99.90  E-value=1.1e-23  Score=195.76  Aligned_cols=170  Identities=25%  Similarity=0.412  Sum_probs=149.0

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-  302 (548)
                      ...||||+||+..++++.|+++|-++|+|.+|.|+.+..+                 ..++|||||+|.++++|+.|+. 
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~-----------------~~~qGygF~Ef~~eedadYAiki   70 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVT-----------------QKHQGYGFAEFRTEEDADYAIKI   70 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhc-----------------ccccceeEEEEechhhhHHHHHH
Confidence            3579999999999999999999999999999999665543                 2477999999999999999996 


Q ss_pred             hcceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEE-EEEeecCCCCCC
Q 008920          303 FNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEA-VRVIRHPHMRVG  381 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~-VrI~~d~~tg~s  381 (548)
                      ||+..|.|++|+|..+...        ....+.+..|||+||.+.+++..|+.+|+.|    |.|.. ..|++++.||.+
T Consensus        71 ln~VkLYgrpIrv~kas~~--------~~nl~vganlfvgNLd~~vDe~~L~dtFsaf----G~l~~~P~i~rd~~tg~~  138 (203)
T KOG0131|consen   71 LNMVKLYGRPIRVNKASAH--------QKNLDVGANLFVGNLDPEVDEKLLYDTFSAF----GVLISPPKIMRDPDTGNP  138 (203)
T ss_pred             HHHHHhcCceeEEEecccc--------cccccccccccccccCcchhHHHHHHHHHhc----cccccCCcccccccCCCC
Confidence            8999999999999998622        1223455889999999999999999999999    66654 478999999999


Q ss_pred             ceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecCCCC
Q 008920          382 KGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQNCTP  422 (548)
Q Consensus       382 rG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~~~~  422 (548)
                      +|||||.|.+.+.+.+|+..++ ..++.++|+|.|+......
T Consensus       139 ~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~k  180 (203)
T KOG0131|consen  139 KGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTK  180 (203)
T ss_pred             CCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCCC
Confidence            9999999999999999999998 8899999999999876443

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

Probab=99.90  E-value=1.1e-23  Score=216.72  Aligned_cols=176  Identities=21%  Similarity=0.377  Sum_probs=149.2

Q ss_pred             CcCCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHH
Q 008920          219 DDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (548)
Q Consensus       219 ~~~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~  298 (548)
                      +..+.+.-.+|||-||..++|.+|+.+|++||.|.+|.|+.|..                 ++.++|||||.|.+.++|.
T Consensus        28 d~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~-----------------t~~s~gcCFv~~~trk~a~   90 (510)
T KOG0144|consen   28 DNPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKS-----------------TGQSKGCCFVKYYTRKEAD   90 (510)
T ss_pred             CCCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccc-----------------cCcccceEEEEeccHHHHH
Confidence            33344556799999999999999999999999999999977664                 3568899999999999999


Q ss_pred             HHH-Hh-cceeecCc--eeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEee
Q 008920          299 AAL-AF-NMAVIGGN--HIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIR  374 (548)
Q Consensus       299 ~Al-~l-ng~~~~gr--~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~  374 (548)
                      +|+ +| |...|.|.  +|.|.++......        ....++|||+-|+..++|.+|+++|+.|    |.|++|.|++
T Consensus        91 ~a~~Alhn~ktlpG~~~pvqvk~Ad~E~er--------~~~e~KLFvg~lsK~~te~evr~iFs~f----G~Ied~~ilr  158 (510)
T KOG0144|consen   91 EAINALHNQKTLPGMHHPVQVKYADGERER--------IVEERKLFVGMLSKQCTENEVREIFSRF----GHIEDCYILR  158 (510)
T ss_pred             HHHHHhhcccccCCCCcceeecccchhhhc--------cccchhhhhhhccccccHHHHHHHHHhh----Cccchhhhee
Confidence            999 56 45667774  7788887643221        2346889999999999999999999999    9999999999


Q ss_pred             cCCCCCCceEEEEEECCHHHHHHHHHHcC--CccCC--eEEEEEeeecCCCCCC
Q 008920          375 HPHMRVGKGIAYVLFKTREAANLVIKRRN--LKLRD--RELRLSHAQQNCTPSK  424 (548)
Q Consensus       375 d~~tg~srG~AFV~F~~~e~A~~Al~~ln--~~l~G--r~I~V~~Ak~~~~~~~  424 (548)
                      |. .+.++|||||.|.+.+.|..||+.||  ..|.|  .+|.|.||.+......
T Consensus       159 d~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~~  211 (510)
T KOG0144|consen  159 DP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKDG  211 (510)
T ss_pred             cc-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCchH
Confidence            95 69999999999999999999999998  88888  6899999987644333

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

Probab=99.90  E-value=1.6e-22  Score=221.39  Aligned_cols=164  Identities=21%  Similarity=0.257  Sum_probs=136.4

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH--
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA--  302 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~--  302 (548)
                      +++|||+|||+++++++|.++|+.||.|.+|.|+.                       ++|||||+|.+.++|+.||.  
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~-----------------------~k~~afVef~~~e~A~~Ai~~~   58 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLP-----------------------GKRQALVEFEDEESAKACVNFA   58 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEEC-----------------------CCCEEEEEeCchHHHHHHHHHh
Confidence            58999999999999999999999999999998842                       45899999999999999995  


Q ss_pred             -hcceeecCceeEeecCCCcccccCCC---CCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCC
Q 008920          303 -FNMAVIGGNHIRLDRACPPRKKLKGE---DAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM  378 (548)
Q Consensus       303 -lng~~~~gr~I~V~~a~~~~k~~~~~---~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~t  378 (548)
                       +++..|.|+.|.|.++..........   .........+|||+||++.+++++|.++|+.|    |.|..|.|+++.. 
T Consensus        59 ~~~~~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~----G~V~~v~i~~~~~-  133 (481)
T TIGR01649        59 TSVPIYIRGQPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPY----GKVLRIVTFTKNN-  133 (481)
T ss_pred             hcCCceEcCeEEEEEecCCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhcc----CCEEEEEEEecCC-
Confidence             47899999999999986543111110   01111233579999999999999999999999    9999999987642 


Q ss_pred             CCCceEEEEEECCHHHHHHHHHHcC-CccCC--eEEEEEeeecC
Q 008920          379 RVGKGIAYVLFKTREAANLVIKRRN-LKLRD--RELRLSHAQQN  419 (548)
Q Consensus       379 g~srG~AFV~F~~~e~A~~Al~~ln-~~l~G--r~I~V~~Ak~~  419 (548)
                         .|+|||+|.+.++|.+|+..|| ..|.|  +.|+|.|+++.
T Consensus       134 ---~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~  174 (481)
T TIGR01649       134 ---VFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKPT  174 (481)
T ss_pred             ---ceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecCC
Confidence               4799999999999999999888 77754  68999999864

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).

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

Probab=99.90  E-value=5.5e-23  Score=216.38  Aligned_cols=172  Identities=22%  Similarity=0.324  Sum_probs=148.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~ln  304 (548)
                      .||||++||+.++.++|.++|+.+|+|..+.+.+++    +             .+.++||+||.|.-.++++.|| +++
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~----g-------------s~~~RGfgfVtFam~ED~qrA~~e~~   68 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNK----G-------------SSEKRGFGFVTFAMEEDVQRALAETE   68 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCC----C-------------cccccCccceeeehHhHHHHHHHHhh
Confidence            699999999999999999999999999999885533    2             3358899999999999999999 589


Q ss_pred             ceeecCceeEeecCCCcccccCCCC-----------------CCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCe
Q 008920          305 MAVIGGNHIRLDRACPPRKKLKGED-----------------APLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSV  367 (548)
Q Consensus       305 g~~~~gr~I~V~~a~~~~k~~~~~~-----------------~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I  367 (548)
                      +..|.|+.|+|+.+...........                 .....+...|.|+||||.+...+|..+|+.|    |.|
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            9999999999999976432221000                 1112336789999999999999999999999    999


Q ss_pred             EEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          368 EAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       368 ~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      ..|.|++..+.+.+ |||||+|....+|..||+.+| ..|.||+|-|.||.+.
T Consensus       145 ~Ei~IP~k~dgklc-GFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~K  196 (678)
T KOG0127|consen  145 VEIVIPRKKDGKLC-GFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDK  196 (678)
T ss_pred             EEEEcccCCCCCcc-ceEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccc
Confidence            99999988776666 999999999999999999999 9999999999999876

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

Probab=99.89  E-value=1.5e-22  Score=213.03  Aligned_cols=173  Identities=31%  Similarity=0.433  Sum_probs=146.6

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-h
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-F  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-l  303 (548)
                      ...|+|+||||.|.+.+|..+|+.||.|..|.|++..                  +|.-+|||||.|....+|..||+ +
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~------------------dgklcGFaFV~fk~~~dA~~Al~~~  178 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK------------------DGKLCGFAFVQFKEKKDAEKALEFF  178 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC------------------CCCccceEEEEEeeHHHHHHHHHhc
Confidence            4679999999999999999999999999999984322                  45577999999999999999995 9


Q ss_pred             cceeecCceeEeecCCCccccc---------------------------------------------CC---------CC
Q 008920          304 NMAVIGGNHIRLDRACPPRKKL---------------------------------------------KG---------ED  329 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~k~~---------------------------------------------~~---------~~  329 (548)
                      |+..|.||+|-|+|+.+...-.                                             .+         ..
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            9999999999999986531100                                             00         00


Q ss_pred             ---------C------------------CcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCc
Q 008920          330 ---------A------------------PLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGK  382 (548)
Q Consensus       330 ---------~------------------~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~sr  382 (548)
                               .                  .......+|||+||||++|+++|.++|++|    |.|.++.|+.++.|+++.
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                     0                  000113799999999999999999999999    999999999999999999


Q ss_pred             eEEEEEECCHHHHHHHHHHc------C-CccCCeEEEEEeeecC
Q 008920          383 GIAYVLFKTREAANLVIKRR------N-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       383 G~AFV~F~~~e~A~~Al~~l------n-~~l~Gr~I~V~~Ak~~  419 (548)
                      |.|||.|.+..+|+.||.+.      + ..|.||.|.|..|..+
T Consensus       335 GtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~R  378 (678)
T KOG0127|consen  335 GTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTR  378 (678)
T ss_pred             cceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccch
Confidence            99999999999999999876      2 6789999999999875

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

Probab=99.89  E-value=1.5e-22  Score=223.04  Aligned_cols=160  Identities=22%  Similarity=0.333  Sum_probs=134.8

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||.++++++|.++|+.||.|.+|+|+.+.                  +|.++|||||+|.+.++|+.|| .
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~------------------sG~sRGfaFV~F~~~e~A~~Ai~~  118 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDF------------------SGQNRGYAFVTFCGKEEAKEAVKL  118 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECC------------------CCCccceEEEEeCCHHHHHHHHHH
Confidence            34899999999999999999999999999999996652                  3568899999999999999999 5


Q ss_pred             hcceeec-CceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEe-ecCCCCC
Q 008920          303 FNMAVIG-GNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVI-RHPHMRV  380 (548)
Q Consensus       303 lng~~~~-gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~-~d~~tg~  380 (548)
                      ||+..|. |+.|.|.++.               ..++|||+|||..+++++|.++|..++   ..|+.+.|+ .....+.
T Consensus       119 lng~~i~~Gr~l~V~~S~---------------~~~rLFVgNLP~~~TeeeL~eeFskv~---egvv~vIv~~~~~~kgK  180 (578)
T TIGR01648       119 LNNYEIRPGRLLGVCISV---------------DNCRLFVGGIPKNKKREEILEEFSKVT---EGVVDVIVYHSAADKKK  180 (578)
T ss_pred             cCCCeecCCccccccccc---------------cCceeEeecCCcchhhHHHHHHhhccc---CCceEEEEeccccccCc
Confidence            8988885 7888777653               257899999999999999999999984   234454443 3334677


Q ss_pred             CceEEEEEECCHHHHHHHHHHcC---CccCCeEEEEEeeecC
Q 008920          381 GKGIAYVLFKTREAANLVIKRRN---LKLRDRELRLSHAQQN  419 (548)
Q Consensus       381 srG~AFV~F~~~e~A~~Al~~ln---~~l~Gr~I~V~~Ak~~  419 (548)
                      ++|||||+|.++++|..|+..+.   ..|.|+.|.|.|+.+.
T Consensus       181 nRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~  222 (578)
T TIGR01648       181 NRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPE  222 (578)
T ss_pred             cCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeeccc
Confidence            89999999999999999997664   5789999999999875

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=99.88  E-value=9e-22  Score=215.54  Aligned_cols=169  Identities=17%  Similarity=0.238  Sum_probs=138.5

Q ss_pred             CcccEEEEcCCCC-CCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          223 KLLRTIFVGNLPL-KVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~-~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ...++|||+|||+ .+|+++|.++|+.||.|..|.|+.+                      .+|||||+|.+.++|..||
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            3568999999998 6999999999999999999998542                      2489999999999999999


Q ss_pred             -HhcceeecCceeEeecCCCcccccC-------------CC-C--------------CCcCCCccEEEEeCCCCCCCHHH
Q 008920          302 -AFNMAVIGGNHIRLDRACPPRKKLK-------------GE-D--------------APLYDIKKTVFVGNLPFDVKDEE  352 (548)
Q Consensus       302 -~lng~~~~gr~I~V~~a~~~~k~~~-------------~~-~--------------~~~~~~~~tLfV~NLp~~~teed  352 (548)
                       .|||..|.|+.|.|.++........             .. .              .....+..+|||+|||+.+++++
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             5999999999999998754211000             00 0              01123567999999999999999


Q ss_pred             HHHHHhccCCCCCC--eEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeE------EEEEeeecC
Q 008920          353 IYQLFCGLNDLESS--VEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE------LRLSHAQQN  419 (548)
Q Consensus       353 L~~~F~~~g~~~G~--I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~------I~V~~Ak~~  419 (548)
                      |+++|..|    |.  |..|.+.... ++ .+|||||+|.+.++|..||..|+ ..|.|+.      |+|+|++++
T Consensus       411 L~~lF~~~----G~~~i~~ik~~~~~-~~-~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       411 LKELFAEN----GVHKVKKFKFFPKD-NE-RSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             HHHHHHhc----CCccceEEEEecCC-CC-cceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccCC
Confidence            99999999    76  8888876543 33 57999999999999999999888 8999885      999999764

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

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

Probab=99.88  E-value=8.9e-22  Score=216.34  Aligned_cols=174  Identities=19%  Similarity=0.250  Sum_probs=141.5

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||+.+|+++|.++|..||.|..|.|+.+.                 .+|.++|||||+|.+.++|..|| .
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~-----------------~~g~~~g~afv~f~~~~~a~~A~~~  356 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDI-----------------ATGLSKGYAFCEYKDPSVTDVAIAA  356 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC-----------------CCCCcCeEEEEEECCHHHHHHHHHH
Confidence            45799999999999999999999999999999986543                 24568899999999999999999 5


Q ss_pred             hcceeecCceeEeecCCCcccccCCCC-------------------CCcCCCccEEEEeCCCCCC----------CHHHH
Q 008920          303 FNMAVIGGNHIRLDRACPPRKKLKGED-------------------APLYDIKKTVFVGNLPFDV----------KDEEI  353 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~~k~~~~~~-------------------~~~~~~~~tLfV~NLp~~~----------teedL  353 (548)
                      |||..|.|+.|.|.++...........                   .....++.+|+|.||....          ..++|
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                   0012256789999996421          23689


Q ss_pred             HHHHhccCCCCCCeEEEEEeecC---CCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeec
Q 008920          354 YQLFCGLNDLESSVEAVRVIRHP---HMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQ  418 (548)
Q Consensus       354 ~~~F~~~g~~~G~I~~VrI~~d~---~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~  418 (548)
                      +++|+.|    |.|..|.|+++.   .++.+.|+|||+|.+.++|..||..|| ..|.|+.|.|.|...
T Consensus       437 ~~~f~~~----G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       437 KTEFSKY----GPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             HHHHHhc----CCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCH
Confidence            9999999    999999998752   345678999999999999999999998 999999999999864

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

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

Probab=99.88  E-value=5.2e-22  Score=205.24  Aligned_cols=165  Identities=24%  Similarity=0.391  Sum_probs=144.8

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...+-||||.||.++.|++|.-||+..|+|-.++||.+++                 +|.++|||||.|.+.+.|+.|+ 
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~-----------------sG~nRGYAFVtf~~Ke~Aq~Aik  143 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPF-----------------SGDNRGYAFVTFCTKEEAQEAIK  143 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeeccc-----------------CCCCcceEEEEeecHHHHHHHHH
Confidence            3457899999999999999999999999999999998875                 4568899999999999999999 


Q ss_pred             Hhcceee-cCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecC-CCC
Q 008920          302 AFNMAVI-GGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP-HMR  379 (548)
Q Consensus       302 ~lng~~~-~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~-~tg  379 (548)
                      .||+..| .|+.|.|+.+.               ..+.|||+|+|...++++|.+.|...+.   -|++|.|...+ +..
T Consensus       144 ~lnn~Eir~GK~igvc~Sv---------------an~RLFiG~IPK~k~keeIlee~~kVte---GVvdVivy~~p~dk~  205 (506)
T KOG0117|consen  144 ELNNYEIRPGKLLGVCVSV---------------ANCRLFIGNIPKTKKKEEILEEMKKVTE---GVVDVIVYPSPDDKT  205 (506)
T ss_pred             HhhCccccCCCEeEEEEee---------------ecceeEeccCCccccHHHHHHHHHhhCC---CeeEEEEecCccccc
Confidence            5898887 68999999875               3588999999999999999999999853   47788777666 457


Q ss_pred             CCceEEEEEECCHHHHHHHHHHc-C--CccCCeEEEEEeeecCCCC
Q 008920          380 VGKGIAYVLFKTREAANLVIKRR-N--LKLRDRELRLSHAQQNCTP  422 (548)
Q Consensus       380 ~srG~AFV~F~~~e~A~~Al~~l-n--~~l~Gr~I~V~~Ak~~~~~  422 (548)
                      +++|||||+|.++..|..|-+.| +  +.|+|+.|.|+||.+...+
T Consensus       206 KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~  251 (506)
T KOG0117|consen  206 KNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEP  251 (506)
T ss_pred             cccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCcccCC
Confidence            89999999999999999997554 4  9999999999999987444

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

Probab=99.87  E-value=7e-22  Score=192.08  Aligned_cols=167  Identities=19%  Similarity=0.308  Sum_probs=150.3

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...+.|.|.-||.++|+++|+.+|...|+|++|.|++|.+                 +|++-||+||.|.++++|++|+ 
T Consensus        39 ~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKi-----------------tGqSLGYGFVNYv~p~DAe~Ain  101 (360)
T KOG0145|consen   39 ESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKI-----------------TGQSLGYGFVNYVRPKDAEKAIN  101 (360)
T ss_pred             cccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccc-----------------cccccccceeeecChHHHHHHHh
Confidence            3457899999999999999999999999999999988774                 4678999999999999999999 


Q ss_pred             HhcceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCC
Q 008920          302 AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVG  381 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~s  381 (548)
                      .|||..+....|.|.++.+..         .......|||.+||..+|..+|.++|++|    |.|..-+|+.|..+|.+
T Consensus       102 tlNGLrLQ~KTIKVSyARPSs---------~~Ik~aNLYvSGlPktMtqkelE~iFs~f----GrIItSRiL~dqvtg~s  168 (360)
T KOG0145|consen  102 TLNGLRLQNKTIKVSYARPSS---------DSIKDANLYVSGLPKTMTQKELEQIFSPF----GRIITSRILVDQVTGLS  168 (360)
T ss_pred             hhcceeeccceEEEEeccCCh---------hhhcccceEEecCCccchHHHHHHHHHHh----hhhhhhhhhhhccccee
Confidence            699999999999999997642         23345789999999999999999999999    89999999999999999


Q ss_pred             ceEEEEEECCHHHHHHHHHHcC-CccCC--eEEEEEeeecC
Q 008920          382 KGIAYVLFKTREAANLVIKRRN-LKLRD--RELRLSHAQQN  419 (548)
Q Consensus       382 rG~AFV~F~~~e~A~~Al~~ln-~~l~G--r~I~V~~Ak~~  419 (548)
                      +|.|||.|....+|+.||..+| ..--|  -+|.|.||..+
T Consensus       169 rGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannP  209 (360)
T KOG0145|consen  169 RGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNP  209 (360)
T ss_pred             cceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCc
Confidence            9999999999999999999998 55545  68999999765

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

Probab=99.86  E-value=1.2e-20  Score=208.02  Aligned_cols=167  Identities=24%  Similarity=0.336  Sum_probs=133.7

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCC-eeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGE-IDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~-I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      .++|||+|||.++++++|.++|+.|+. |..+.+...+ .               ..+.++|||||+|.++++|..|+ .
T Consensus       138 ~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~-~---------------~kgKnRGFAFVeF~s~edAa~Airk  201 (578)
T TIGR01648       138 NCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSA-A---------------DKKKNRGFAFVEYESHRAAAMARRK  201 (578)
T ss_pred             CceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccc-c---------------ccCccCceEEEEcCCHHHHHHHHHH
Confidence            579999999999999999999999864 4444432111 1               12347899999999999999999 4


Q ss_pred             hc--ceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCC
Q 008920          303 FN--MAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV  380 (548)
Q Consensus       303 ln--g~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~  380 (548)
                      |+  ...+.|+.|.|.|+.+.....    ........+|||+||++.+++++|+++|+.|..  |.|+.|.+++      
T Consensus       202 L~~gki~l~Gr~I~VdwA~p~~~~d----~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~--G~I~rV~~~r------  269 (578)
T TIGR01648       202 LMPGRIQLWGHVIAVDWAEPEEEVD----EDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKP--GKVERVKKIR------  269 (578)
T ss_pred             hhccceEecCceEEEEeeccccccc----ccccccccEEEEeCCCCCCCHHHHHHHHHhcCC--CceEEEEeec------
Confidence            53  356889999999987543211    112334578999999999999999999999832  6899998764      


Q ss_pred             CceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecCCC
Q 008920          381 GKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQNCT  421 (548)
Q Consensus       381 srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~~~  421 (548)
                        +||||+|.+.++|.+||..|| ..|.|+.|.|.|+.+...
T Consensus       270 --gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       270 --DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDK  309 (578)
T ss_pred             --CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCCc
Confidence              499999999999999999888 999999999999988643

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.

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

Probab=99.86  E-value=4.4e-21  Score=186.51  Aligned_cols=172  Identities=26%  Similarity=0.342  Sum_probs=146.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~ln  304 (548)
                      ..|||.+||..+|..+|..+|++||.|..-+|+.+..                 +|.++|.+||.|....+|+.|| .||
T Consensus       128 aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqv-----------------tg~srGVgFiRFDKr~EAe~AIk~lN  190 (360)
T KOG0145|consen  128 ANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQV-----------------TGLSRGVGFIRFDKRIEAEEAIKGLN  190 (360)
T ss_pred             cceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcc-----------------cceecceeEEEecchhHHHHHHHhcc
Confidence            5799999999999999999999999998877754432                 4678899999999999999999 599


Q ss_pred             ceeecCc--eeEeecCCCcccccCCC-------------C----------------------------------------
Q 008920          305 MAVIGGN--HIRLDRACPPRKKLKGE-------------D----------------------------------------  329 (548)
Q Consensus       305 g~~~~gr--~I~V~~a~~~~k~~~~~-------------~----------------------------------------  329 (548)
                      |+.-.|.  +|.|.++..+.......             .                                        
T Consensus       191 G~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~  270 (360)
T KOG0145|consen  191 GQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVN  270 (360)
T ss_pred             CCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeec
Confidence            9988774  89999987552210000             0                                        


Q ss_pred             -CCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccC
Q 008920          330 -APLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLR  407 (548)
Q Consensus       330 -~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~  407 (548)
                       ........||||-||..+++|.-||++|.+|    |.|..|.|++|..|..++|||||.+.+.++|..||..|| ..|+
T Consensus       271 lp~~~~~g~ciFvYNLspd~de~~LWQlFgpF----GAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg  346 (360)
T KOG0145|consen  271 LPGGPGGGWCIFVYNLSPDADESILWQLFGPF----GAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLG  346 (360)
T ss_pred             cCCCCCCeeEEEEEecCCCchHhHHHHHhCcc----cceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCcccc
Confidence             0111125799999999999999999999999    999999999999999999999999999999999999998 9999


Q ss_pred             CeEEEEEeeec
Q 008920          408 DRELRLSHAQQ  418 (548)
Q Consensus       408 Gr~I~V~~Ak~  418 (548)
                      ++.|.|.|-..
T Consensus       347 ~rvLQVsFKtn  357 (360)
T KOG0145|consen  347 DRVLQVSFKTN  357 (360)
T ss_pred             ceEEEEEEecC
Confidence            99999999654

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

Probab=99.85  E-value=1.2e-21  Score=197.60  Aligned_cols=174  Identities=18%  Similarity=0.359  Sum_probs=150.6

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      -+.||||.|.+.+.++.|+..|..||+|.+|.|-+|+.+                 ++++|||||+|+-++.|+.|+ .|
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T-----------------~kHKgFAFVEYEvPEaAqLAlEqM  175 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPAT-----------------GKHKGFAFVEYEVPEAAQLALEQM  175 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeeccccccc-----------------ccccceEEEEEeCcHHHHHHHHHh
Confidence            478999999999999999999999999999999888754                 568899999999999999999 59


Q ss_pred             cceeecCceeEeecCCCcccccCCCC--CCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCC
Q 008920          304 NMAVIGGNHIRLDRACPPRKKLKGED--APLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVG  381 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~k~~~~~~--~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~s  381 (548)
                      ||.+++||.|.|.+...-.......+  .......+.|||..+..+++++||+.+|..|    |.|..|.+.+++.++.+
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            99999999999997643211000000  0111235789999999999999999999999    99999999999999999


Q ss_pred             ceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          382 KGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       382 rG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      +|||||+|.+..+...||..|| +.|+|..|+|..+..+
T Consensus       252 kGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vTP  290 (544)
T KOG0124|consen  252 KGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTP  290 (544)
T ss_pred             cceeeEEeccccchHHHhhhcchhhcccceEecccccCC
Confidence            9999999999999999999999 9999999999998754

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

Probab=99.84  E-value=1.4e-19  Score=196.53  Aligned_cols=169  Identities=17%  Similarity=0.260  Sum_probs=137.1

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      .++|||+|||+.+|+++|.++|+.||.|..|.|+.++.                 +|.++|||||+|.+.++|..|| .|
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            68999999999999999999999999999999965442                 3457899999999999999999 59


Q ss_pred             cceeecCceeEeecCCCccccc--------------------------------CCC-----------------------
Q 008920          304 NMAVIGGNHIRLDRACPPRKKL--------------------------------KGE-----------------------  328 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~k~~--------------------------------~~~-----------------------  328 (548)
                      ||..|.|+.|.|.++.......                                ...                       
T Consensus       249 ~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  328 (457)
T TIGR01622       249 NGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRD  328 (457)
T ss_pred             CCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhcccccc
Confidence            9999999999999954210000                                000                       


Q ss_pred             -----C---------------------CCcCCCccEEEEeCCCCCCC----------HHHHHHHHhccCCCCCCeEEEEE
Q 008920          329 -----D---------------------APLYDIKKTVFVGNLPFDVK----------DEEIYQLFCGLNDLESSVEAVRV  372 (548)
Q Consensus       329 -----~---------------------~~~~~~~~tLfV~NLp~~~t----------eedL~~~F~~~g~~~G~I~~VrI  372 (548)
                           .                     ........+|+|.||....+          .+||++.|..|    |.|+.|.|
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                 0                     00123567899999955443          36899999999    89999988


Q ss_pred             eecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeec
Q 008920          373 IRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQ  418 (548)
Q Consensus       373 ~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~  418 (548)
                      ...    ...|++||.|.+.++|..|+..|+ ..|+|+.|.|.|...
T Consensus       405 ~~~----~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~  447 (457)
T TIGR01622       405 DTK----NSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVN  447 (457)
T ss_pred             eCC----CCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcH
Confidence            643    357999999999999999999998 999999999999864

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.

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

Probab=99.84  E-value=1.6e-20  Score=203.57  Aligned_cols=175  Identities=23%  Similarity=0.351  Sum_probs=147.4

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhcc
Q 008920          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (548)
Q Consensus       227 tVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng  305 (548)
                      +|||.||++++|.++|..+|..+|.|.+|.|...+.     |.         +--.+.|||||+|.++++|+.|+ .|+|
T Consensus       517 ~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd-----~~---------~k~lSmGfgFVEF~~~e~A~~a~k~lqg  582 (725)
T KOG0110|consen  517 KLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKD-----PA---------NKYLSMGFGFVEFAKPESAQAALKALQG  582 (725)
T ss_pred             hhhhhcCCcccchhHHHHHHHhcCeEEEEEEecccc-----cc---------ccccccceeEEEecCHHHHHHHHHHhcC
Confidence            399999999999999999999999999998844221     11         01237899999999999999999 5899


Q ss_pred             eeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEE
Q 008920          306 AVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIA  385 (548)
Q Consensus       306 ~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~A  385 (548)
                      +.|.|+.|.|.++........+...+.......|+|+|||+..+-.+|+.+|+.|    |.|.+|+|+.-...+.++|||
T Consensus       583 tvldGH~l~lk~S~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aF----GqlksvRlPKK~~k~a~rGF~  658 (725)
T KOG0110|consen  583 TVLDGHKLELKISENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAF----GQLKSVRLPKKIGKGAHRGFG  658 (725)
T ss_pred             ceecCceEEEEeccCccccccccccccccccceeeeeccchHHHHHHHHHHHhcc----cceeeeccchhhcchhhccce
Confidence            9999999999998722222222122223346799999999999999999999999    999999999876677889999


Q ss_pred             EEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          386 YVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       386 FV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      ||.|-++.+|..|+..|+ ..|.||.|.+.||...
T Consensus       659 Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d  693 (725)
T KOG0110|consen  659 FVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSD  693 (725)
T ss_pred             eeeccCcHHHHHHHHhhcccceechhhheehhccc
Confidence            999999999999999998 9999999999999875

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

Probab=99.83  E-value=4.4e-20  Score=191.07  Aligned_cols=168  Identities=24%  Similarity=0.322  Sum_probs=139.1

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCC-eeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGE-IDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~-I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ..++.|||||||.+.++++|.+.|++.++ |..|.|...+..                ..+++|||||+|.++..|..|-
T Consensus       162 van~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~d----------------k~KNRGFaFveYe~H~~Aa~aR  225 (506)
T KOG0117|consen  162 VANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDD----------------KTKNRGFAFVEYESHRAAAMAR  225 (506)
T ss_pred             eecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccc----------------cccccceEEEEeecchhHHHHH
Confidence            35688999999999999999999999874 566666433311                2348899999999999999987


Q ss_pred             -H-hc-ceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCC
Q 008920          302 -A-FN-MAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM  378 (548)
Q Consensus       302 -~-ln-g~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~t  378 (548)
                       . ++ ...+.|..|.|+|+.+.....    ......-..|||+||+.++|++.|..+|..|    |.|+.|..++|   
T Consensus       226 rKl~~g~~klwgn~~tVdWAep~~e~d----ed~ms~VKvLYVRNL~~~tTeE~lk~~F~~~----G~veRVkk~rD---  294 (506)
T KOG0117|consen  226 RKLMPGKIKLWGNAITVDWAEPEEEPD----EDTMSKVKVLYVRNLMESTTEETLKKLFNEF----GKVERVKKPRD---  294 (506)
T ss_pred             hhccCCceeecCCcceeeccCcccCCC----hhhhhheeeeeeeccchhhhHHHHHHHHHhc----cceEEeecccc---
Confidence             4 34 457899999999998653211    1122335689999999999999999999999    99999998877   


Q ss_pred             CCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecCCCC
Q 008920          379 RVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQNCTP  422 (548)
Q Consensus       379 g~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~~~~  422 (548)
                           ||||.|.+.++|.+||+.+| ..|.|..|.|.+|+|....
T Consensus       295 -----YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~  334 (506)
T KOG0117|consen  295 -----YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKK  334 (506)
T ss_pred             -----eeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhh
Confidence                 99999999999999999998 9999999999999987433

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

Probab=99.81  E-value=1.9e-20  Score=198.38  Aligned_cols=184  Identities=20%  Similarity=0.317  Sum_probs=156.4

Q ss_pred             CCCcCCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHH
Q 008920          217 GFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQS  296 (548)
Q Consensus       217 ~~~~~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~  296 (548)
                      ....++++.+|||+--|+..++.-+|.+||+.+|.|..|+|+.+.+                 ++.++|.|||+|.+.++
T Consensus       171 ~l~~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~-----------------s~rskgi~Yvef~D~~s  233 (549)
T KOG0147|consen  171 ILSPEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRN-----------------SRRSKGIAYVEFCDEQS  233 (549)
T ss_pred             cCCchHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeecccc-----------------chhhcceeEEEEecccc
Confidence            3445677889999999999999999999999999999999977653                 34588999999999999


Q ss_pred             HHHHHHhcceeecCceeEeecCCCcccccCCCC-----CCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEE
Q 008920          297 TEAALAFNMAVIGGNHIRLDRACPPRKKLKGED-----APLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVR  371 (548)
Q Consensus       297 A~~Al~lng~~~~gr~I~V~~a~~~~k~~~~~~-----~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~Vr  371 (548)
                      +..||.|.|..+.|.+|.|..............     .....+-..|||+||.+.+++++|+.+|..|    |.|+.|.
T Consensus       234 Vp~aiaLsGqrllg~pv~vq~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepf----g~Ie~v~  309 (549)
T KOG0147|consen  234 VPLAIALSGQRLLGVPVIVQLSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPF----GKIENVQ  309 (549)
T ss_pred             hhhHhhhcCCcccCceeEecccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCc----ccceeee
Confidence            999999999999999999998764332211111     0111122339999999999999999999999    9999999


Q ss_pred             EeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecCCC
Q 008920          372 VIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQNCT  421 (548)
Q Consensus       372 I~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~~~  421 (548)
                      ++.|..||.++|||||+|.+.++|..|+..|| +.|.|+.|+|........
T Consensus       310 l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~  360 (549)
T KOG0147|consen  310 LTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERVD  360 (549)
T ss_pred             eccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeecc
Confidence            99998899999999999999999999998888 999999999999877633

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

Probab=99.81  E-value=3.9e-19  Score=187.65  Aligned_cols=150  Identities=23%  Similarity=0.414  Sum_probs=136.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~ln  304 (548)
                      ..||||   +++|+..|.++|+.+|+|.+|+++++. +                   +.|||||.|.++.+|..|| ++|
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            368999   899999999999999999999997654 2                   6699999999999999999 699


Q ss_pred             ceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceE
Q 008920          305 MAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGI  384 (548)
Q Consensus       305 g~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~  384 (548)
                      ...+.|++|+|.|+....              ..|||.||+.+++..+|.++|+.|    |.|++|.|..+. .| ++||
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            999999999999986421              229999999999999999999999    999999999995 45 9999


Q ss_pred             EEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          385 AYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       385 AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                       ||+|.+.++|..||.++| ..+.|..|.|......
T Consensus       119 -FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~  153 (369)
T KOG0123|consen  119 -FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERK  153 (369)
T ss_pred             -EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccch
Confidence             999999999999999988 8999999999988764

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

Probab=99.81  E-value=1e-19  Score=179.66  Aligned_cols=145  Identities=17%  Similarity=0.342  Sum_probs=134.4

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-hcc
Q 008920          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-FNM  305 (548)
Q Consensus       227 tVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-lng  305 (548)
                      .|||||||..+++.+|+.+|++||.|..|.|+                         +.||||..++...+.-||. |||
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDIv-------------------------KNYgFVHiEdktaaedairNLhg   58 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDIV-------------------------KNYGFVHIEDKTAAEDAIRNLHG   58 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeeee-------------------------cccceEEeecccccHHHHhhccc
Confidence            59999999999999999999999999999993                         2599999999999999995 999


Q ss_pred             eeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEE
Q 008920          306 AVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIA  385 (548)
Q Consensus       306 ~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~A  385 (548)
                      ..|.|..|.|+.+...           ...+.+|+|+||.+.++..+|+..|++|    |.|..|.|++|        |+
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            9999999999998643           3356889999999999999999999999    99999999977        99


Q ss_pred             EEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          386 YVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       386 FV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      ||.|.-.++|..|+..|+ ..|.|.+|+|..+..+
T Consensus       116 fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen  116 FVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             EEEEeeccchHHHHhcccccccccceeeeeeeccc
Confidence            999999999999998887 9999999999998876

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

Probab=99.77  E-value=1.4e-18  Score=178.11  Aligned_cols=173  Identities=18%  Similarity=0.334  Sum_probs=153.9

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      +.+.|||++|++.++++.|+.+|.+||+|..|.++.++.+                 ++++||+||+|.+++.+..+|..
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t-----------------~rsrgFgfv~f~~~~~v~~vl~~   67 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPST-----------------GRSRGFGFVTFATPEGVDAVLNA   67 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCC-----------------CCcccccceecCCCcchheeecc
Confidence            4689999999999999999999999999999999877643                 45889999999999999999987


Q ss_pred             cceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCce
Q 008920          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG  383 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG  383 (548)
                      ..+.|.|+.|.+..+.+.......   ........|||++||.++++++|+++|.+|    |.|..+.++.|..+...+|
T Consensus        68 ~~h~~dgr~ve~k~av~r~~~~~~---~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~----g~v~~~~~~~d~~~~~~rg  140 (311)
T KOG4205|consen   68 RTHKLDGRSVEPKRAVSREDQTKV---GRHLRTKKIFVGGLPPDTTEEDFKDYFEQF----GKVADVVIMYDKTTSRPRG  140 (311)
T ss_pred             cccccCCccccceeccCccccccc---ccccceeEEEecCcCCCCchHHHhhhhhcc----ceeEeeEEeeccccccccc
Confidence            788899999999999875433222   112257799999999999999999999999    8999999999999999999


Q ss_pred             EEEEEECCHHHHHHHHHHcCCccCCeEEEEEeeecCC
Q 008920          384 IAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQNC  420 (548)
Q Consensus       384 ~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~Ak~~~  420 (548)
                      |+||.|.+.+.+..++....+.|+|+.+.|..|.|+.
T Consensus       141 Fgfv~~~~e~sVdkv~~~~f~~~~gk~vevkrA~pk~  177 (311)
T KOG4205|consen  141 FGFVTFDSEDSVDKVTLQKFHDFNGKKVEVKRAIPKE  177 (311)
T ss_pred             ceeeEeccccccceecccceeeecCceeeEeeccchh
Confidence            9999999999999999888899999999999999873

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

Probab=99.74  E-value=1.6e-17  Score=175.34  Aligned_cols=167  Identities=26%  Similarity=0.402  Sum_probs=145.4

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhcc
Q 008920          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (548)
Q Consensus       227 tVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng  305 (548)
                      .|||.||+.+++..+|..+|+.||.|.+|++.++.                  .| ++|| ||+|.++++|.+|+ .+||
T Consensus        78 ~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~------------------~g-~kg~-FV~f~~e~~a~~ai~~~ng  137 (369)
T KOG0123|consen   78 LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE------------------NG-SKGY-FVQFESEESAKKAIEKLNG  137 (369)
T ss_pred             eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC------------------CC-ceee-EEEeCCHHHHHHHHHHhcC
Confidence            39999999999999999999999999999997654                  22 7799 99999999999999 5899


Q ss_pred             eeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEE
Q 008920          306 AVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIA  385 (548)
Q Consensus       306 ~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~A  385 (548)
                      ..+.|..|.|............... ....-..+||.|++.+++++.|..+|..|    |.|.++.|+.+. .|.++|||
T Consensus       138 ~ll~~kki~vg~~~~~~er~~~~~~-~~~~~t~v~vk~~~~~~~~~~l~~~f~~~----g~i~s~~v~~~~-~g~~~~~g  211 (369)
T KOG0123|consen  138 MLLNGKKIYVGLFERKEEREAPLGE-YKKRFTNVYVKNLEEDSTDEELKDLFSAY----GSITSVAVMRDS-IGKSKGFG  211 (369)
T ss_pred             cccCCCeeEEeeccchhhhcccccc-hhhhhhhhheeccccccchHHHHHhhccc----CcceEEEEeecC-CCCCCCcc
Confidence            9999999999998765433322222 33445789999999999999999999999    999999999994 67799999


Q ss_pred             EEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          386 YVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       386 FV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      ||.|.++++|..|+..++ ..+.|..+.|..+...
T Consensus       212 fv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqkk  246 (369)
T KOG0123|consen  212 FVNFENPEDAKKAVETLNGKIFGDKELYVGRAQKK  246 (369)
T ss_pred             ceeecChhHHHHHHHhccCCcCCccceeecccccc
Confidence            999999999999999999 7778899999988763

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

Probab=99.73  E-value=1.4e-17  Score=163.30  Aligned_cols=137  Identities=26%  Similarity=0.422  Sum_probs=117.3

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      ..+||||+||..++||+-|..||.++|.|..+.|+.+                                           
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            3589999999999999999999999999998887321                                           


Q ss_pred             cceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCce
Q 008920          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG  383 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG  383 (548)
                              .|.|.++..+..+.    .+.....-.|||+.|...++-++|++.|.+|    |.|.+++|++|..|++++|
T Consensus        42 --------e~~v~wa~~p~nQs----k~t~~~hfhvfvgdls~eI~~e~lr~aF~pF----GevS~akvirD~~T~KsKG  105 (321)
T KOG0148|consen   42 --------ELKVNWATAPGNQS----KPTSNQHFHVFVGDLSPEIDNEKLREAFAPF----GEVSDAKVIRDMNTGKSKG  105 (321)
T ss_pred             --------hhccccccCcccCC----CCccccceeEEehhcchhcchHHHHHHhccc----cccccceEeecccCCcccc
Confidence                    45666665542211    2222235679999999999999999999999    9999999999999999999


Q ss_pred             EEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          384 IAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       384 ~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      ||||.|...++|+.||..|| ..|++|.|+-.||.-+
T Consensus       106 YgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRK  142 (321)
T KOG0148|consen  106 YGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRK  142 (321)
T ss_pred             eeEEeccchHHHHHHHHHhCCeeeccceeeccccccC
Confidence            99999999999999999998 9999999999999754

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

Probab=99.70  E-value=8.2e-17  Score=166.29  Aligned_cols=84  Identities=17%  Similarity=0.346  Sum_probs=78.0

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLS  414 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~  414 (548)
                      ...|||.+||.+.-+.+|-..|..|    |.|.+..|..|..|+.++.|+||.|++..+|..||..|| ..|++.+|.|.
T Consensus       424 GanlfiyhlPqefgdq~l~~~f~pf----G~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQ  499 (510)
T KOG0144|consen  424 GANLFIYHLPQEFGDQDLIATFQPF----GGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQ  499 (510)
T ss_pred             ccceeeeeCchhhhhHHHHHHhccc----cceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEE
Confidence            4579999999999999999999999    899999999999999999999999999999999999998 99999999999


Q ss_pred             eeecCCCCC
Q 008920          415 HAQQNCTPS  423 (548)
Q Consensus       415 ~Ak~~~~~~  423 (548)
                      ....+..+.
T Consensus       500 lk~~~~np~  508 (510)
T KOG0144|consen  500 LKRDRNNPY  508 (510)
T ss_pred             eeeccCCCC
Confidence            988765543

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

Probab=99.70  E-value=7.9e-16  Score=143.65  Aligned_cols=153  Identities=21%  Similarity=0.338  Sum_probs=125.1

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...++|||+|||.++-+.+|..+|.+||.|..|.|-..+    +                .-.||||+|+++.+|+.|| 
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~----g----------------~ppfafVeFEd~RDAeDAiy   63 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP----G----------------PPPFAFVEFEDPRDAEDAIY   63 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC----C----------------CCCeeEEEecCccchhhhhh
Confidence            346899999999999999999999999999999882211    1                2369999999999999999 


Q ss_pred             HhcceeecCceeEeecCCCcccccCC-----------------CCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCC
Q 008920          302 AFNMAVIGGNHIRLDRACPPRKKLKG-----------------EDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLE  364 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~~k~~~~-----------------~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~  364 (548)
                      ..+|..+.|..|+|+++..-......                 ...+.......|.|.+||...+|+||++++..-    
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            58999999999999998643211000                 002333445789999999999999999999998    


Q ss_pred             CCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-Ccc
Q 008920          365 SSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKL  406 (548)
Q Consensus       365 G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l  406 (548)
                      |.|....|.+|       |++.|.|...++..-||..|. ..+
T Consensus       140 GdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~  175 (241)
T KOG0105|consen  140 GDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKF  175 (241)
T ss_pred             CCeeeeeeecc-------cceeeeeeehhhHHHHHHhhccccc
Confidence            89999999888       489999999999999998776 443

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

Probab=99.69  E-value=1.6e-16  Score=155.44  Aligned_cols=175  Identities=19%  Similarity=0.315  Sum_probs=145.0

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      +.+.||||-|...-.|+|++.+|..||.|.+|.+.+.+                  +|.++|||||.|.+..+|+.|| .
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            34789999999999999999999999999999996644                  5668999999999999999999 6


Q ss_pred             hccee-ecC--ceeEeecCCCcccc-------------------------------------------------------
Q 008920          303 FNMAV-IGG--NHIRLDRACPPRKK-------------------------------------------------------  324 (548)
Q Consensus       303 lng~~-~~g--r~I~V~~a~~~~k~-------------------------------------------------------  324 (548)
                      |||.. +.|  ..|.|.++.....+                                                       
T Consensus        80 LHgSqTmpGASSSLVVK~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~  159 (371)
T KOG0146|consen   80 LHGSQTMPGASSSLVVKFADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFA  159 (371)
T ss_pred             hcccccCCCCccceEEEeccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhH
Confidence            88764 444  36777776421000                                                       


Q ss_pred             -------------------------------------------------------cCCCC--------------------
Q 008920          325 -------------------------------------------------------LKGED--------------------  329 (548)
Q Consensus       325 -------------------------------------------------------~~~~~--------------------  329 (548)
                                                                             ..+..                    
T Consensus       160 ~~~mQ~~aA~~angl~A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~v  239 (371)
T KOG0146|consen  160 AAQMQQMAALNANGLAAAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTV  239 (371)
T ss_pred             HHHHHHHHHHhhcccccCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccc
Confidence                                                                   00000                    


Q ss_pred             ---------------------------------------CCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEE
Q 008920          330 ---------------------------------------APLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAV  370 (548)
Q Consensus       330 ---------------------------------------~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~V  370 (548)
                                                             ....+..+.|||-.||....+.+|.++|-.|    |.|++.
T Consensus       240 a~~lq~a~~g~~~Y~Aaypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PF----GhivSa  315 (371)
T KOG0146|consen  240 ADPLQQAYAGVQQYAAAYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPF----GHIVSA  315 (371)
T ss_pred             cchhhhhhhhHHHHhhhcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccc----cceeee
Confidence                                                   0012346899999999999999999999999    999999


Q ss_pred             EEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecCC
Q 008920          371 RVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQNC  420 (548)
Q Consensus       371 rI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~~  420 (548)
                      .|..|+.|+.+++||||.|.++.+|+.||..|| +.|+-++|.|..-+|+.
T Consensus       316 KVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkd  366 (371)
T KOG0146|consen  316 KVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPKD  366 (371)
T ss_pred             eeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcCccc
Confidence            999999999999999999999999999999998 99999999999877653

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

Probab=99.66  E-value=2e-15  Score=158.67  Aligned_cols=167  Identities=22%  Similarity=0.342  Sum_probs=134.5

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhc
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~ln  304 (548)
                      ..-|-+.+|||.||+++|.+||+.|+ |+++.+.+                   .+|+.+|-|||+|.+.+++++||+.+
T Consensus        10 ~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r-------------------~~Gr~sGeA~Ve~~seedv~~Alkkd   69 (510)
T KOG4211|consen   10 AFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR-------------------RNGRPSGEAYVEFTSEEDVEKALKKD   69 (510)
T ss_pred             ceEEEecCCCccccHHHHHHHHhcCc-eeEEEEec-------------------cCCCcCcceEEEeechHHHHHHHHhh
Confidence            35689999999999999999999998 77776632                   13567899999999999999999999


Q ss_pred             ceeecCceeEeecCCCcccc--cCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEE--EEEeecCCCCC
Q 008920          305 MAVIGGNHIRLDRACPPRKK--LKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEA--VRVIRHPHMRV  380 (548)
Q Consensus       305 g~~~~gr~I~V~~a~~~~k~--~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~--VrI~~d~~tg~  380 (548)
                      ...+..+.|.|-.+......  ..........+...|-+++|||.||++||.+||+..     .|..  |.++.+ ..++
T Consensus        70 R~~mg~RYIEVf~~~~~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL-----~Iv~~gi~l~~d-~rgR  143 (510)
T KOG4211|consen   70 RESMGHRYIEVFTAGGAEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGL-----EIVPDGILLPMD-QRGR  143 (510)
T ss_pred             HHHhCCceEEEEccCCccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCC-----cccccceeeecc-CCCC
Confidence            99999999999887543211  111111111355789999999999999999999987     3333  445666 4678


Q ss_pred             CceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEeee
Q 008920          381 GKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQ  417 (548)
Q Consensus       381 srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~Ak  417 (548)
                      +.|-|||+|.+.+.|+.||......|+.|-|.|..+.
T Consensus       144 ~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  144 PTGEAFVQFESQESAEIALGRHRENIGHRYIEVFRSS  180 (510)
T ss_pred             cccceEEEecCHHHHHHHHHHHHHhhccceEEeehhH
Confidence            9999999999999999999988889999999998775

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

Probab=99.65  E-value=3.1e-15  Score=138.52  Aligned_cols=85  Identities=21%  Similarity=0.388  Sum_probs=79.1

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|..|.|+.|..++.++|||||+|.+.++|+.||..++ ..|.|+.|
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~----G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l  106 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHF----GDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHI  106 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcC----CCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            4456899999999999999999999999    999999999999999999999999999999999998887 99999999


Q ss_pred             EEEeeecCCC
Q 008920          412 RLSHAQQNCT  421 (548)
Q Consensus       412 ~V~~Ak~~~~  421 (548)
                      .|.|+.++..
T Consensus       107 ~V~~a~~~~~  116 (144)
T PLN03134        107 RVNPANDRPS  116 (144)
T ss_pred             EEEeCCcCCC
Confidence            9999987543

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

Probab=99.64  E-value=1.7e-15  Score=150.61  Aligned_cols=169  Identities=21%  Similarity=0.267  Sum_probs=113.2

Q ss_pred             ccccccccCccCCCCCCCCchhhHhhhccCCCCCchhhhhhhhcCC--ccccccccchhhhhhhhhhhhhhHHHHHHhhc
Q 008920          105 KSTKLIYPRSILGFEPNGTIENEIKKEHSSNVGSESYLNRQKQNSN--FSVEGKKRSENKKTKKRKRDDVEKDYVEKKYG  182 (548)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~k~~~~--~~~~~e~~~~~kKkkKrK~~e~eee~e~~~~~  182 (548)
                      +--.||.|+|||+|.||.|++..++++. -.+++..|+.--....+  .....+. ..++....+  .+..+..... ..
T Consensus         8 nllaLF~pRpPl~y~pP~d~~p~kr~~~-~~tGvA~~~~~~~~~~d~p~~~p~~t-~~e~~er~~--~~k~e~~~~~-~~   82 (335)
T KOG0113|consen    8 NLLALFAPRPPLPYLPPTDKLPHKRKTN-PYTGVAQYLSTFEDPKDAPPKFPVET-PEEPLERGR--REKTEKIPHK-LE   82 (335)
T ss_pred             cHHHhcCCCCCcccCCccccChhhccCC-CcccHHHHHHhhcCcccCCCcCcccc-hhhHHHhhh--hhhhhhhHHH-HH
Confidence            4457999999999999999999999888 58887666655333322  1122222 111111111  1111110000 00


Q ss_pred             chhhhhcccccccccccccccchhhhhhhccccCCCCcCCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecc
Q 008920          183 VIAKEEEGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPI  262 (548)
Q Consensus       183 ~~~~e~e~e~~~~~kKrK~~~~~e~~~~~~~~~e~~~~~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~  262 (548)
                      .-..-               -++..+         ...-....+||||+-|+++++|..|...|+.||+|..|+|+.+.+
T Consensus        83 ~~l~~---------------wdP~~d---------p~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~v  138 (335)
T KOG0113|consen   83 RRLKL---------------WDPNND---------PNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKV  138 (335)
T ss_pred             HHHHh---------------cCCCCC---------CcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecc
Confidence            00000               111111         111123468999999999999999999999999999999977653


Q ss_pred             cCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-HhcceeecCceeEeecCC
Q 008920          263 IDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       263 ~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng~~~~gr~I~V~~a~  319 (548)
                                       +|.++|||||+|.++.++..|. ..+|..|+|+.|.|+.-.
T Consensus       139 -----------------TgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvER  179 (335)
T KOG0113|consen  139 -----------------TGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVER  179 (335)
T ss_pred             -----------------cCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEecc
Confidence                             4568899999999999999999 589999999999999853

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

Probab=99.64  E-value=1.3e-14  Score=160.88  Aligned_cols=80  Identities=20%  Similarity=0.402  Sum_probs=71.4

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||+++++++|.++|+.||.|.+|+|..++.                 ++.++|||||+|.+.++|..|| .
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~-----------------tgksKGfGFVeFe~~e~A~kAI~a  265 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPT-----------------GRGHKGYGFIEYNNLQSQSEAIAS  265 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCC-----------------CCCcCCeEEEEECCHHHHHHHHHH
Confidence            457999999999999999999999999999999966542                 3457899999999999999999 6


Q ss_pred             hcceeecCceeEeecCCC
Q 008920          303 FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~  320 (548)
                      ||+..|+|+.|+|.++..
T Consensus       266 mNg~elgGr~LrV~kAi~  283 (612)
T TIGR01645       266 MNLFDLGGQYLRVGKCVT  283 (612)
T ss_pred             hCCCeeCCeEEEEEecCC
Confidence            999999999999988653

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.

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

Probab=99.63  E-value=5.7e-15  Score=142.53  Aligned_cols=165  Identities=24%  Similarity=0.371  Sum_probs=134.3

Q ss_pred             cccEEEEcCCCCCCcHHHHHH----HhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHH
Q 008920          224 LLRTIFVGNLPLKVKKKTLIK----EFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~----~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~  299 (548)
                      .+.||||.||+..+..++|+.    +|++||.|..|....                    +...+|-|||+|.+.+.|-.
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            345999999999999999888    999999999988732                    23478999999999999999


Q ss_pred             HH-HhcceeecCceeEeecCCCcccccCC--------------------------CC---------------CCcCCCcc
Q 008920          300 AL-AFNMAVIGGNHIRLDRACPPRKKLKG--------------------------ED---------------APLYDIKK  337 (548)
Q Consensus       300 Al-~lng~~~~gr~I~V~~a~~~~k~~~~--------------------------~~---------------~~~~~~~~  337 (548)
                      |+ .|+|..|.|..|+|+++.........                          ..               .....+..
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 69999999999999998753111000                          00               12245678


Q ss_pred             EEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccC-CeEEEEEe
Q 008920          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLR-DRELRLSH  415 (548)
Q Consensus       338 tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~-Gr~I~V~~  415 (548)
                      .||+.|||..++.+.|..+|++|    .....|+++...     .++|||+|.+...|..|...++ ..+. ...|.|.+
T Consensus       148 ilf~~niP~es~~e~l~~lf~qf----~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~  218 (221)
T KOG4206|consen  148 ILFLTNIPSESESEMLSDLFEQF----PGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITF  218 (221)
T ss_pred             EEEEecCCcchhHHHHHHHHhhC----cccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEecc
Confidence            99999999999999999999999    567778877653     5799999999999999988776 5554 88899988


Q ss_pred             ee
Q 008920          416 AQ  417 (548)
Q Consensus       416 Ak  417 (548)
                      +.
T Consensus       219 a~  220 (221)
T KOG4206|consen  219 AK  220 (221)
T ss_pred             cC
Confidence            75

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

Probab=99.53  E-value=3.7e-14  Score=137.98  Aligned_cols=152  Identities=18%  Similarity=0.374  Sum_probs=126.9

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhcc
Q 008920          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (548)
Q Consensus       227 tVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng  305 (548)
                      .||||+||+.+.+.+|..||..||.|..|.|                         ..||+||+|.+..+|..|+ .+|+
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~m-------------------------k~gf~fv~fed~rda~Dav~~l~~   57 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADM-------------------------KNGFGFVEFEDPRDADDAVHDLDG   57 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhcccccccee-------------------------ecccceeccCchhhhhcccchhcC
Confidence            5999999999999999999999999999988                         3489999999999999999 7999


Q ss_pred             eeecCceeEeecCCCccccc----CC-------CCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEee
Q 008920          306 AVIGGNHIRLDRACPPRKKL----KG-------EDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIR  374 (548)
Q Consensus       306 ~~~~gr~I~V~~a~~~~k~~----~~-------~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~  374 (548)
                      ..|.|..+.|.++.......    .+       .-.......+.|+|.||+..+.+.+|.++|+.+    |.+..+.+  
T Consensus        58 ~~l~~e~~vve~~r~~~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~----g~~~~~~~--  131 (216)
T KOG0106|consen   58 KELCGERLVVEHARGKRRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPA----GEVTYVDA--  131 (216)
T ss_pred             ceecceeeeeecccccccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhccc----CCCchhhh--
Confidence            99999889898887421111    00       001223346788999999999999999999999    78755443  


Q ss_pred             cCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEe
Q 008920          375 HPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSH  415 (548)
Q Consensus       375 d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~  415 (548)
                            ..+++||+|.+.++|..||..++ ..|.|+.|.|.+
T Consensus       132 ------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen  132 ------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             ------hccccceeehhhhhhhhcchhccchhhcCceeeecc
Confidence                  35699999999999999999998 999999999943

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

Probab=99.52  E-value=7.8e-14  Score=152.05  Aligned_cols=173  Identities=22%  Similarity=0.328  Sum_probs=135.8

Q ss_pred             CCcCCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHH
Q 008920          218 FDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQST  297 (548)
Q Consensus       218 ~~~~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A  297 (548)
                      +...++..+.|+|+|||..+..++|..+|..||.|..|.|+  +                     .-.-|+|+|.++.+|
T Consensus       378 F~~~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp--~---------------------~G~~aiv~fl~p~eA  434 (725)
T KOG0110|consen  378 FSQAERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLP--P---------------------GGTGAIVEFLNPLEA  434 (725)
T ss_pred             chhhhhhcceeeeccCccccccHHHHHHhhcccccceeecC--c---------------------ccceeeeeecCccch
Confidence            33356667899999999999999999999999999998551  1                     112499999999999


Q ss_pred             HHHH-HhcceeecCceeEeecCCCcccc------------------------cCCCC------C-----------CcCCC
Q 008920          298 EAAL-AFNMAVIGGNHIRLDRACPPRKK------------------------LKGED------A-----------PLYDI  335 (548)
Q Consensus       298 ~~Al-~lng~~~~gr~I~V~~a~~~~k~------------------------~~~~~------~-----------~~~~~  335 (548)
                      +.|+ .|..+.+...+|.+.|+......                        ...+.      .           .....
T Consensus       435 r~Afrklaysr~k~~plyle~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~  514 (725)
T KOG0110|consen  435 RKAFRKLAYSRFKSAPLYLEWAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEET  514 (725)
T ss_pred             HHHHHHhchhhhccCccccccChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhcccc
Confidence            9999 58888888888877775321000                        00000      0           00111


Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCC---CCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM---RVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~t---g~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      .+.|||.||+|+++.++|..+|..+    |.|.+|.|...++.   -.+.|||||+|.+.++|+.|++.|+ ..|.|+.|
T Consensus       515 ~t~lfvkNlnf~Tt~e~l~~~F~k~----G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l  590 (725)
T KOG0110|consen  515 ETKLFVKNLNFDTTLEDLEDLFSKQ----GTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKL  590 (725)
T ss_pred             chhhhhhcCCcccchhHHHHHHHhc----CeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceE
Confidence            2349999999999999999999998    89999988876532   2456999999999999999999998 99999999


Q ss_pred             EEEeee
Q 008920          412 RLSHAQ  417 (548)
Q Consensus       412 ~V~~Ak  417 (548)
                      .|.++.
T Consensus       591 ~lk~S~  596 (725)
T KOG0110|consen  591 ELKISE  596 (725)
T ss_pred             EEEecc
Confidence            999998

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

Probab=99.50  E-value=9.2e-14  Score=148.01  Aligned_cols=166  Identities=19%  Similarity=0.262  Sum_probs=129.0

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhcc
Q 008920          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (548)
Q Consensus       227 tVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng  305 (548)
                      .||||||-+++++++|..+|+.||.|+.|.++.+.                 .+|.++||+||+|.+.++|.+|+ .|||
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~-----------------~tG~skgfGfi~f~~~~~ar~a~e~lng  342 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDS-----------------ETGRSKGFGFITFVNKEDARKALEQLNG  342 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeecccc-----------------ccccccCcceEEEecHHHHHHHHHHhcc
Confidence            39999999999999999999999999999985432                 25678999999999999999998 6999


Q ss_pred             eeecCceeEeecCCCcccccC--------------------CC-------------------------------------
Q 008920          306 AVIGGNHIRLDRACPPRKKLK--------------------GE-------------------------------------  328 (548)
Q Consensus       306 ~~~~gr~I~V~~a~~~~k~~~--------------------~~-------------------------------------  328 (548)
                      ..|.|+.|.|......-....                    ..                                     
T Consensus       343 felAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~  422 (549)
T KOG0147|consen  343 FELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFN  422 (549)
T ss_pred             ceecCceEEEEEeeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhc
Confidence            999999999987542200000                    00                                     


Q ss_pred             ------C-CC------cCCCccEEEEeCCCC--CCC--------HHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEE
Q 008920          329 ------D-AP------LYDIKKTVFVGNLPF--DVK--------DEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIA  385 (548)
Q Consensus       329 ------~-~~------~~~~~~tLfV~NLp~--~~t--------eedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~A  385 (548)
                            . .+      ...++.|+.+.||-.  ..|        .+||.+.+..|    |.|..|.|..+     +-|+.
T Consensus       423 ~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~----g~v~hi~vd~n-----s~g~V  493 (549)
T KOG0147|consen  423 GVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKH----GKVCHIFVDKN-----SAGCV  493 (549)
T ss_pred             CCcCccccCccccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhc----CCeeEEEEccC-----CCceE
Confidence                  0 00      013356777777722  222        36777888888    89988877544     34899


Q ss_pred             EEEECCHHHHHHHHHHcC-CccCCeEEEEEeeec
Q 008920          386 YVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQ  418 (548)
Q Consensus       386 FV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~  418 (548)
                      ||.|.+.++|..|+..|| .+|.|+.|.+.|-..
T Consensus       494 Yvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~~  527 (549)
T KOG0147|consen  494 YVRCPSAEAAGTAVKALHGRWFAGRMITAKYLPL  527 (549)
T ss_pred             EEecCcHHHHHHHHHHHhhhhhccceeEEEEeeh
Confidence            999999999999999998 999999999999754

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

Probab=99.50  E-value=1.3e-13  Score=127.71  Aligned_cols=81  Identities=20%  Similarity=0.393  Sum_probs=72.5

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||+++++++|+++|.+||.|.+|.|+.+..                 ++.++|||||+|.+.++|+.|| .
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~-----------------tg~~kGfaFV~F~~~e~A~~Al~~   95 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRE-----------------TGRSRGFGFVNFNDEGAATAAISE   95 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCC-----------------CCCcceEEEEEECCHHHHHHHHHH
Confidence            457899999999999999999999999999999966542                 3457899999999999999999 5


Q ss_pred             hcceeecCceeEeecCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~  321 (548)
                      ||+..|.|+.|.|.++...
T Consensus        96 lng~~i~Gr~l~V~~a~~~  114 (144)
T PLN03134         96 MDGKELNGRHIRVNPANDR  114 (144)
T ss_pred             cCCCEECCEEEEEEeCCcC
Confidence            9999999999999998654

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

Probab=99.48  E-value=9.1e-13  Score=133.57  Aligned_cols=184  Identities=23%  Similarity=0.285  Sum_probs=136.9

Q ss_pred             CCCcCCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHH
Q 008920          217 GFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQS  296 (548)
Q Consensus       217 ~~~~~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~  296 (548)
                      .+.-+...++.|||.|||.++|.+++.++|+.||.|.     +++  +++.|+   +.+..-+.|+.+|-|.|.|...++
T Consensus       126 ~~~~~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~-----~d~--~t~epk---~KlYrd~~G~lKGDaLc~y~K~ES  195 (382)
T KOG1548|consen  126 WFNPEPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIM-----RDP--QTGEPK---VKLYRDNQGKLKGDALCCYIKRES  195 (382)
T ss_pred             ccCcccccCceEEecCCCCcccHHHHHHHHHhcceEe-----ccC--CCCCee---EEEEecCCCCccCceEEEeecccH
Confidence            4444556677899999999999999999999999662     222  334444   112223568899999999999999


Q ss_pred             HHHHHH-hcceeecCceeEeecCCCcccc-------cC----------------------CCCCCcCCCccEEEEeCCCC
Q 008920          297 TEAALA-FNMAVIGGNHIRLDRACPPRKK-------LK----------------------GEDAPLYDIKKTVFVGNLPF  346 (548)
Q Consensus       297 A~~Al~-lng~~~~gr~I~V~~a~~~~k~-------~~----------------------~~~~~~~~~~~tLfV~NLp~  346 (548)
                      +..|+. |++..|.|+.|+|..|.-..+.       ..                      ..........++|.|.||-.
T Consensus       196 VeLA~~ilDe~~~rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ft  275 (382)
T KOG1548|consen  196 VELAIKILDEDELRGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFT  275 (382)
T ss_pred             HHHHHHHhCcccccCcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCC
Confidence            999995 8999999999999998632110       00                      00012223457899999832


Q ss_pred             ----CCC-------HHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEE
Q 008920          347 ----DVK-------DEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLS  414 (548)
Q Consensus       347 ----~~t-------eedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~  414 (548)
                          ..+       .++|.+-+..|    |.|..|.|.-    ..+.|.+-|.|.+.++|..||+.|+ ..|.||.|...
T Consensus       276 p~~~~~~~~l~~dlkedl~eec~K~----G~v~~vvv~d----~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~  347 (382)
T KOG1548|consen  276 PEDFEKNPDLLNDLKEDLTEECEKF----GQVRKVVVYD----RHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTAS  347 (382)
T ss_pred             HHHhccCHHHHHHHHHHHHHHHHHh----CCcceEEEec----cCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEE
Confidence                223       46677778888    8999986652    2467899999999999999999998 99999999988


Q ss_pred             eeec
Q 008920          415 HAQQ  418 (548)
Q Consensus       415 ~Ak~  418 (548)
                      ....
T Consensus       348 i~DG  351 (382)
T KOG1548|consen  348 IWDG  351 (382)
T ss_pred             EeCC
Confidence            7654

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

Probab=99.48  E-value=8.3e-13  Score=136.84  Aligned_cols=170  Identities=20%  Similarity=0.287  Sum_probs=138.0

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhh-hcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFI-KFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs-~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ..+.|||.||||++.+++|+.||. ..|+|+.|.|..|.                  .|+.+|||.|+|.+++.+++|++
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~------------------~GK~rGcavVEFk~~E~~qKa~E  104 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE------------------SGKARGCAVVEFKDPENVQKALE  104 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc------------------CCCcCCceEEEeeCHHHHHHHHH
Confidence            356799999999999999999998 58999999996544                  46688999999999999999995


Q ss_pred             -hcceeecCceeEeecCCCcccc-----------------------------------------cCCCC-----------
Q 008920          303 -FNMAVIGGNHIRLDRACPPRKK-----------------------------------------LKGED-----------  329 (548)
Q Consensus       303 -lng~~~~gr~I~V~~a~~~~k~-----------------------------------------~~~~~-----------  329 (548)
                       ||.+.+.||.|.|.........                                         ....+           
T Consensus       105 ~lnk~~~~GR~l~vKEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~  184 (608)
T KOG4212|consen  105 KLNKYEVNGRELVVKEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTM  184 (608)
T ss_pred             HhhhccccCceEEEeccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCcccc
Confidence             9999999999999775431000                                         00000           


Q ss_pred             --------------------CC----cCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEE
Q 008920          330 --------------------AP----LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIA  385 (548)
Q Consensus       330 --------------------~~----~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~A  385 (548)
                                          .+    ..+-...+||.||.+.+....|.+.|.-.    |.|+.|.+-.|+ .|.++|||
T Consensus       185 ~~~~~~~~~~~lfgl~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmA----Gkv~~vdf~idK-eG~s~G~~  259 (608)
T KOG4212|consen  185 SNDYNNSSNYNLFGLSASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMA----GKVQSVDFSIDK-EGNSRGFA  259 (608)
T ss_pred             ccccccchhhhcccchhhhhhhccCCCCCccceeeeeccccccchHHHHHHhccc----eeeeeeceeecc-ccccCCee
Confidence                                00    01124689999999999999999999987    899999999996 47999999


Q ss_pred             EEEECCHHHHHHHHHHcC-CccCCeEEEEEee
Q 008920          386 YVLFKTREAANLVIKRRN-LKLRDRELRLSHA  416 (548)
Q Consensus       386 FV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~A  416 (548)
                      .++|..+-.|..||.+++ .-+..+++.|...
T Consensus       260 vi~y~hpveavqaIsml~~~g~~~~~~~~Rl~  291 (608)
T KOG4212|consen  260 VIEYDHPVEAVQAISMLDRQGLFDRRMTVRLD  291 (608)
T ss_pred             EEEecchHHHHHHHHhhccCCCccccceeecc
Confidence            999999999999999998 6667777777664

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

Probab=99.47  E-value=5.4e-13  Score=130.86  Aligned_cols=153  Identities=27%  Similarity=0.408  Sum_probs=114.6

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      .++|||+|||+.+|+++|..+|..||.|..|.|..+.                 .++.++|||||+|.+.++|..|+ .+
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~-----------------~~~~~~g~~~v~f~~~~~~~~a~~~~  177 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDR-----------------ETGKSRGFAFVEFESEESAEKAIEEL  177 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeecc-----------------ccCccCceEEEEecCHHHHHHHHHHc
Confidence            5899999999999999999999999999999986543                 13568899999999999999999 58


Q ss_pred             cceeecCceeEeecCCC----ccccc-----------CCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeE
Q 008920          304 NMAVIGGNHIRLDRACP----PRKKL-----------KGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVE  368 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~----~~k~~-----------~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~  368 (548)
                      ++..|.|+.|.|.+...    .....           .............+++.+++..++..++..+|..+    |.+.
T Consensus       178 ~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~  253 (306)
T COG0724         178 NGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSR----GDIV  253 (306)
T ss_pred             CCCeECCceeEeeccccccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhcccc----ccce
Confidence            99999999999999642    11111           00012234456789999999999999999999999    7886


Q ss_pred             EEEEeecCCCCCCceEEEEEECCHHHHHHH
Q 008920          369 AVRVIRHPHMRVGKGIAYVLFKTREAANLV  398 (548)
Q Consensus       369 ~VrI~~d~~tg~srG~AFV~F~~~e~A~~A  398 (548)
                      .+.+...........+.++.+.....+..+
T Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  283 (306)
T COG0724         254 RASLPPSKDGKIPKSRSFVGNEASKDALES  283 (306)
T ss_pred             eeeccCCCCCcccccccccchhHHHhhhhh
Confidence            666665543333443444444434433333

>PF00076 RRM_1: RNA recognition motif

Probab=99.42  E-value=7.5e-13  Score=105.42  Aligned_cols=69  Identities=35%  Similarity=0.591  Sum_probs=62.2

Q ss_pred             EEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-hcce
Q 008920          228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-FNMA  306 (548)
Q Consensus       228 VfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-lng~  306 (548)
                      |||+|||.++|+++|.++|+.||.|..+.+....                  .+..+|||||+|.+.++|..|++ ++|.
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------------------SGKSKGYAFVEFESEEDAEKALEELNGK   62 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEET------------------TSSEEEEEEEEESSHHHHHHHHHHHTTE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccc------------------cccccceEEEEEcCHHHHHHHHHHcCCC
Confidence            8999999999999999999999999999996541                  23477999999999999999995 9999


Q ss_pred             eecCceeE
Q 008920          307 VIGGNHIR  314 (548)
Q Consensus       307 ~~~gr~I~  314 (548)
                      .|.|+.|+
T Consensus        63 ~~~~~~ir   70 (70)
T PF00076_consen   63 KINGRKIR   70 (70)
T ss_dssp             EETTEEEE
T ss_pred             EECccCcC
Confidence            99999885

(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 ....

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

Probab=99.42  E-value=2e-12  Score=124.18  Aligned_cols=160  Identities=23%  Similarity=0.324  Sum_probs=114.9

Q ss_pred             cCCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHH
Q 008920          220 DEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (548)
Q Consensus       220 ~~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~  299 (548)
                      ++...-+||||.+||.++..-+|..+|..|.-.+.+.|....   .+             +...+-+|||+|.+.+.|..
T Consensus        29 ~~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Ts---k~-------------~~~~~pvaFatF~s~q~A~a   92 (284)
T KOG1457|consen   29 DEPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTS---KG-------------DQVCKPVAFATFTSHQFALA   92 (284)
T ss_pred             ccccccceeeeccCCcccCHHHHHHHhccCCCccceeeeecc---CC-------------CccccceEEEEecchHHHHH
Confidence            334456999999999999999999999999878877774322   11             11245799999999999999


Q ss_pred             HH-Hhcceeec---CceeEeecCCCcccccCCCC----------------------------------------------
Q 008920          300 AL-AFNMAVIG---GNHIRLDRACPPRKKLKGED----------------------------------------------  329 (548)
Q Consensus       300 Al-~lng~~~~---gr~I~V~~a~~~~k~~~~~~----------------------------------------------  329 (548)
                      |+ .|||..|+   +..|+|+++....+......                                              
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 79999996   46788888754311100000                                              


Q ss_pred             -------------------------------CCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCC
Q 008920          330 -------------------------------APLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM  378 (548)
Q Consensus       330 -------------------------------~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~t  378 (548)
                                                     ........+|||-||...++|++|+.+|+.|.   | ..-++|. .   
T Consensus       173 ~~~~~t~~~~l~a~~~~~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~---g-f~~l~~~-~---  244 (284)
T KOG1457|consen  173 KENDTTKSEALSAPDSKAPSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYP---G-FHILKIR-A---  244 (284)
T ss_pred             CCccccchhhhhhhhhcCCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCC---C-ceEEEEe-c---
Confidence                                           00001134899999999999999999999994   3 2222322 1   


Q ss_pred             CCCceEEEEEECCHHHHHHHHHHcC
Q 008920          379 RVGKGIAYVLFKTREAANLVIKRRN  403 (548)
Q Consensus       379 g~srG~AFV~F~~~e~A~~Al~~ln  403 (548)
                      ..+...|||.|++.+.|..||..|.
T Consensus       245 ~~g~~vaf~~~~~~~~at~am~~lq  269 (284)
T KOG1457|consen  245 RGGMPVAFADFEEIEQATDAMNHLQ  269 (284)
T ss_pred             CCCcceEeecHHHHHHHHHHHHHhh
Confidence            2235589999999999999987664

>PF00076 RRM_1: RNA recognition motif

Probab=99.39  E-value=1.8e-12  Score=103.18  Aligned_cols=69  Identities=35%  Similarity=0.658  Sum_probs=65.3

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       339 LfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      |||+|||.++++++|+++|..|    |.|..+.|..+ .++..+|||||+|.+.++|..|+..++ ..|.|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~----g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQF----GKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTT----STEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHh----hhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            7999999999999999999999    89999999998 688999999999999999999999777 999999985

(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 ....

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.38  E-value=1.5e-12  Score=137.01  Aligned_cols=83  Identities=27%  Similarity=0.474  Sum_probs=78.1

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+++++++|+++|..|    |.|+.|+|+.|..++.++|||||+|.+.++|..||..|+ ..|.+++|
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~~----G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i  179 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRTI----GPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRL  179 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCcee
Confidence            3457899999999999999999999999    899999999999999999999999999999999998888 99999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      .|.|+.+.
T Consensus       180 ~V~~a~p~  187 (346)
T TIGR01659       180 KVSYARPG  187 (346)
T ss_pred             eeeccccc
Confidence            99999764

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).

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

Probab=99.38  E-value=7.9e-13  Score=117.12  Aligned_cols=80  Identities=20%  Similarity=0.343  Sum_probs=70.4

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      +.++|||||||++-++|++|.+||+.||+|..|.|-.+.+                 +...+|||||+|.+.++|..||.
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            3468999999999999999999999999999998844332                 23478999999999999999996


Q ss_pred             -hcceeecCceeEeecCC
Q 008920          303 -FNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       303 -lng~~~~gr~I~V~~a~  319 (548)
                       ++++.|..+.|+|+|..
T Consensus        97 yisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   97 YISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             HhccCcccccceeeeccc
Confidence             89999999999999964

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.36  E-value=2.2e-12  Score=128.67  Aligned_cols=76  Identities=30%  Similarity=0.395  Sum_probs=69.3

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhc
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~ln  304 (548)
                      .++|||+|||+.+|+++|++||+.||.|.+|.|+.+.                    ..+|||||+|.++++|..||.||
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~--------------------~~~GfAFVtF~d~eaAe~AllLn   63 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN--------------------ERSQIAYVTFKDPQGAETALLLS   63 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC--------------------CCCCEEEEEeCcHHHHHHHHHhc
Confidence            4799999999999999999999999999999996532                    14589999999999999999999


Q ss_pred             ceeecCceeEeecCCC
Q 008920          305 MAVIGGNHIRLDRACP  320 (548)
Q Consensus       305 g~~~~gr~I~V~~a~~  320 (548)
                      |..|.|+.|.|.++..
T Consensus        64 G~~l~gr~V~Vt~a~~   79 (260)
T PLN03120         64 GATIVDQSVTITPAED   79 (260)
T ss_pred             CCeeCCceEEEEeccC
Confidence            9999999999999863

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

Probab=99.36  E-value=4.7e-12  Score=120.48  Aligned_cols=86  Identities=23%  Similarity=0.353  Sum_probs=80.8

Q ss_pred             CCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCC
Q 008920          330 APLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRD  408 (548)
Q Consensus       330 ~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~G  408 (548)
                      .+..+....|.|-||-+.++.++|+.+|..|    |.|-+|.|++|+.|+.++|||||.|.+..+|+.||++|+ .+|+|
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekY----G~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldg   82 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKY----GRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDG   82 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHh----CcccceecccccccccccceeEEEeeecchHHHHHHhhcceeecc
Confidence            4556777899999999999999999999999    899999999999999999999999999999999999998 99999


Q ss_pred             eEEEEEeeecC
Q 008920          409 RELRLSHAQQN  419 (548)
Q Consensus       409 r~I~V~~Ak~~  419 (548)
                      +.|+|++|.-.
T Consensus        83 RelrVq~aryg   93 (256)
T KOG4207|consen   83 RELRVQMARYG   93 (256)
T ss_pred             ceeeehhhhcC
Confidence            99999999754

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

Probab=99.34  E-value=3.4e-12  Score=124.30  Aligned_cols=83  Identities=27%  Similarity=0.402  Sum_probs=78.8

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      .+..++|-|.||+.++++++|.++|..|    |.|..|.|.+|..||.++|||||.|.+.++|.+||..|| .-+..-.|
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~f----g~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LIL  261 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPF----GPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLIL  261 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhcc----CccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEE
Confidence            4467899999999999999999999999    899999999999999999999999999999999999998 88999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      +|.|++|.
T Consensus       262 rvEwskP~  269 (270)
T KOG0122|consen  262 RVEWSKPS  269 (270)
T ss_pred             EEEecCCC
Confidence            99999875

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

Probab=99.33  E-value=2.4e-12  Score=124.84  Aligned_cols=82  Identities=23%  Similarity=0.337  Sum_probs=77.1

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEe
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSH  415 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~  415 (548)
                      -.+||||+|+|.+..+.|+.+|++|    |+|+...|+.|+.+|+++|||||+|.+.++|.+||..-+..|+||+..|..
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqf----GeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnl   87 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQF----GEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNL   87 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHh----CceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccch
Confidence            4689999999999999999999999    999999999999999999999999999999999999999999999999998


Q ss_pred             eecCCC
Q 008920          416 AQQNCT  421 (548)
Q Consensus       416 Ak~~~~  421 (548)
                      |.-...
T Consensus        88 A~lg~~   93 (247)
T KOG0149|consen   88 ASLGGK   93 (247)
T ss_pred             hhhcCc
Confidence            875433

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

Probab=99.32  E-value=2e-11  Score=129.77  Aligned_cols=181  Identities=23%  Similarity=0.354  Sum_probs=124.4

Q ss_pred             CCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       221 ~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      ...-++.||||+||++++|+.|...|..||.+ .|............|.+|           +-||+|+.|+++.+++..
T Consensus       255 ~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkG-----------s~~YvflvFe~E~sV~~L  322 (520)
T KOG0129|consen  255 SPRYSRKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKG-----------SYGYVFLVFEDERSVQSL  322 (520)
T ss_pred             ccccccceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCC-----------cccEEEEEecchHHHHHH
Confidence            35567899999999999999999999999976 344422111122223222           336999999999998877


Q ss_pred             H-Hhc----ceee-------cCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeE
Q 008920          301 L-AFN----MAVI-------GGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVE  368 (548)
Q Consensus       301 l-~ln----g~~~-------~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~  368 (548)
                      | +..    ...|       ....+.|..+......--.+.....++.+|||||+||.-++.++|..+|...   +|.|.
T Consensus       323 l~aC~~~~~~~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~l---yGgV~  399 (520)
T KOG0129|consen  323 LSACSEGEGNYYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDL---FGGVL  399 (520)
T ss_pred             HHHHhhcccceEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHh---cCceE
Confidence            6 321    1111       1122222222111100011124557889999999999999999999999843   39999


Q ss_pred             EEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccC----CeEEEEEee
Q 008920          369 AVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLR----DRELRLSHA  416 (548)
Q Consensus       369 ~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~----Gr~I~V~~A  416 (548)
                      .|-|-.|++-+.++|-|-|+|.+..+..+||.+--..|.    .+.|.|..-
T Consensus       400 yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsarFvql~h~d~~KRVEIkPY  451 (520)
T KOG0129|consen  400 YVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISARFVQLDHTDIDKRVEIKPY  451 (520)
T ss_pred             EEEeccCcccCCCCCcceeeecccHHHHHHHhhheEEEeccccceeeeecce
Confidence            999999999999999999999999999999976543332    235555543

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.31  E-value=1e-11  Score=99.85  Aligned_cols=69  Identities=30%  Similarity=0.577  Sum_probs=63.8

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       339 LfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      |||+|||+.+++++|.++|+.|    |.|..|.+..+.. +.++|+|||+|.+.++|..|+..++ ..|.|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~----g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRF----GPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTS----SBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhc----CCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            7999999999999999999999    8999999999976 9999999999999999999999998 999999884

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 ....

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

Probab=99.30  E-value=3.8e-11  Score=119.91  Aligned_cols=91  Identities=18%  Similarity=0.326  Sum_probs=82.5

Q ss_pred             cCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeE
Q 008920          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE  410 (548)
Q Consensus       332 ~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~  410 (548)
                      ..++.+||||+-|+++++|..|+..|..|    |.|..|+||.|..||.++|||||+|.+.-+...|.+..+ ..|+|+.
T Consensus        97 ~gDPy~TLFv~RLnydT~EskLrreF~~Y----G~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrr  172 (335)
T KOG0113|consen   97 IGDPYKTLFVARLNYDTSESKLRREFEKY----GPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRR  172 (335)
T ss_pred             cCCccceeeeeeccccccHHHHHHHHHhc----CcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcE
Confidence            35788999999999999999999999999    999999999999999999999999999999999997766 9999999


Q ss_pred             EEEEeeecCCCCCCCC
Q 008920          411 LRLSHAQQNCTPSKRK  426 (548)
Q Consensus       411 I~V~~Ak~~~~~~~rr  426 (548)
                      |.|.+-.....+.-..
T Consensus       173 i~VDvERgRTvkgW~P  188 (335)
T KOG0113|consen  173 ILVDVERGRTVKGWLP  188 (335)
T ss_pred             EEEEeccccccccccc
Confidence            9999988765544443

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.27  E-value=2.1e-11  Score=98.02  Aligned_cols=69  Identities=28%  Similarity=0.527  Sum_probs=58.6

Q ss_pred             EEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-hcce
Q 008920          228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-FNMA  306 (548)
Q Consensus       228 VfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-lng~  306 (548)
                      |||+|||+++++++|.++|+.||.|..|.+....                  .+..+|+|||+|.+.++|..|+. +++.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~------------------~~~~~~~a~v~f~~~~~a~~al~~~~~~   62 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNK------------------DGQSRGFAFVEFSSEEDAKRALELLNGK   62 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEEST------------------TSSEEEEEEEEESSHHHHHHHHHHHTTE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeee------------------ccccCCEEEEEeCCHHHHHHHHHHCCCc
Confidence            7999999999999999999999999999985422                  13467999999999999999996 5669


Q ss_pred             eecCceeE
Q 008920          307 VIGGNHIR  314 (548)
Q Consensus       307 ~~~gr~I~  314 (548)
                      .|.|++|+
T Consensus        63 ~~~g~~l~   70 (70)
T PF14259_consen   63 EIDGRKLR   70 (70)
T ss_dssp             EETTEEEE
T ss_pred             EECCEEcC
Confidence            99999884

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 ....

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.27  E-value=2.3e-11  Score=121.53  Aligned_cols=77  Identities=22%  Similarity=0.335  Sum_probs=70.5

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEe
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSH  415 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~  415 (548)
                      .++|||+|||+.+++++|+++|+.|    |.|.+|.|+.+..   .+|||||+|.+.++|..||.+.+..|.|+.|.|.+
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~----G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~   76 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFS----GDIEYVEMQSENE---RSQIAYVTFKDPQGAETALLLSGATIVDQSVTITP   76 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEe
Confidence            5799999999999999999999999    9999999999853   47899999999999999997556999999999999


Q ss_pred             eecC
Q 008920          416 AQQN  419 (548)
Q Consensus       416 Ak~~  419 (548)
                      +..-
T Consensus        77 a~~~   80 (260)
T PLN03120         77 AEDY   80 (260)
T ss_pred             ccCC
Confidence            8754

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

Probab=99.27  E-value=1.3e-11  Score=115.75  Aligned_cols=134  Identities=20%  Similarity=0.237  Sum_probs=98.0

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      ..++|||+|||.++-+.+|.++|.+|    |.|..|.|..-+   .+.+||||+|+++-+|+.||..-+ ..+.|..|+|
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKy----g~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRV   77 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKY----GRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRV   77 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhh----cceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEE
Confidence            56899999999999999999999999    899999886542   346799999999999999998877 9999999999


Q ss_pred             EeeecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccccCcCCCccccccCCC
Q 008920          414 SHAQQNCTPSKRKDVAPAVNSPPKKFVLDSRTLGSGNRSNSKVAMSYQGLQASKSCTQKKVHSGSS  479 (548)
Q Consensus       414 ~~Ak~~~~~~~rr~~~~~~~g~~~k~~~~~r~~~~~~~~~~~~~~~~~G~ras~s~~~kr~~~~~~  479 (548)
                      .|+..-.. ...++..-..+|+.+...++.   .......+.......|+.+|.||..-+.|.+..
T Consensus        78 Efprggr~-s~~~~G~y~gggrgGgg~gg~---rgppsrrSe~RVvVsGLp~SgSWQDLKDHmRea  139 (241)
T KOG0105|consen   78 EFPRGGRS-SSDRRGSYSGGGRGGGGGGGR---RGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREA  139 (241)
T ss_pred             EeccCCCc-ccccccccCCCCCCCCCCCcc---cCCcccccceeEEEecCCCCCchHHHHHHHHhh
Confidence            99876431 111111111122221112222   222333346778899999999999999886433

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

Probab=99.27  E-value=1e-10  Score=120.81  Aligned_cols=164  Identities=20%  Similarity=0.285  Sum_probs=130.0

Q ss_pred             ccEEEEcCCC-CCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          225 LRTIFVGNLP-LKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       225 ~rtVfVgNLP-~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ...|.|.||. ..+|.+.|..+|.-||.|..|.|+...                      +-.|+|+|.+...|+.|+ .
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk----------------------kd~ALIQmsd~~qAqLA~~h  354 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK----------------------KDNALIQMSDGQQAQLAMEH  354 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC----------------------CcceeeeecchhHHHHHHHH
Confidence            5789999995 468999999999999999999995422                      247999999999999999 5


Q ss_pred             hcceeecCceeEeecCCCcccccCCCC--------------------------CCcCCCccEEEEeCCCCCCCHHHHHHH
Q 008920          303 FNMAVIGGNHIRLDRACPPRKKLKGED--------------------------APLYDIKKTVFVGNLPFDVKDEEIYQL  356 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~~k~~~~~~--------------------------~~~~~~~~tLfV~NLp~~~teedL~~~  356 (548)
                      |+|..+.|+.|+|.++....-....+.                          ...++++.+|++.|+|.++++++|..+
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            999999999999999875422211110                          123456789999999999999999999


Q ss_pred             HhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCC-eEEEEEeeec
Q 008920          357 FCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRD-RELRLSHAQQ  418 (548)
Q Consensus       357 F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~G-r~I~V~~Ak~  418 (548)
                      |..-|   |.|....+.     +..+-+|++.+.+.++|..|+-.++ +.+++ .-|+|+|++.
T Consensus       435 f~~~g---~~vkafkff-----~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  435 FQEPG---GQVKAFKFF-----QKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             hhcCC---ceEEeeeec-----CCCcceeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence            99884   444444332     2235599999999999999987776 77776 4899999875

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

Probab=99.26  E-value=1.1e-12  Score=122.43  Aligned_cols=86  Identities=21%  Similarity=0.527  Sum_probs=79.5

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      +-.+.-|||||||+.+|+.||..+|++|    |.|++|.|++|..||.++||||+.|++.-+...|+..+| ..|.||.|
T Consensus        32 YkdsA~Iyiggl~~~LtEgDil~VFSqy----Ge~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRti  107 (219)
T KOG0126|consen   32 YKDSAYIYIGGLPYELTEGDILCVFSQY----GEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTI  107 (219)
T ss_pred             cccceEEEECCCcccccCCcEEEEeecc----CceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeE
Confidence            4567889999999999999999999999    999999999999999999999999999999999998888 99999999


Q ss_pred             EEEeeecCCCC
Q 008920          412 RLSHAQQNCTP  422 (548)
Q Consensus       412 ~V~~Ak~~~~~  422 (548)
                      +|.+...-..|
T Consensus       108 rVDHv~~Yk~p  118 (219)
T KOG0126|consen  108 RVDHVSNYKKP  118 (219)
T ss_pred             EeeecccccCC
Confidence            99998755444

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.26  E-value=1.9e-11  Score=120.33  Aligned_cols=76  Identities=26%  Similarity=0.264  Sum_probs=69.0

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhc
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~ln  304 (548)
                      ..||||+||++.+|+++|++||+.||.|.+|.|+++.                    ...|||||+|.++++|..||.|+
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            4799999999999999999999999999999996532                    24579999999999999999999


Q ss_pred             ceeecCceeEeecCCC
Q 008920          305 MAVIGGNHIRLDRACP  320 (548)
Q Consensus       305 g~~~~gr~I~V~~a~~  320 (548)
                      |..|.++.|.|..+..
T Consensus        65 Ga~l~d~~I~It~~~~   80 (243)
T PLN03121         65 GATIVDQRVCITRWGQ   80 (243)
T ss_pred             CCeeCCceEEEEeCcc
Confidence            9999999999998753

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

Probab=99.24  E-value=1.2e-11  Score=119.97  Aligned_cols=79  Identities=24%  Similarity=0.358  Sum_probs=71.1

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhc
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~ln  304 (548)
                      .+.||||+|+|.+..+.|+.+|++||+|....|++|.                 .+|+++||+||+|.+.++|..|++-.
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~-----------------~t~rskGyGfVTf~d~~aa~rAc~dp   74 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDK-----------------NTGRSKGYGFVTFRDAEAATRACKDP   74 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEecc-----------------CCccccceeeEEeecHHHHHHHhcCC
Confidence            4689999999999999999999999999999997765                 35679999999999999999999877


Q ss_pred             ceeecCceeEeecCCC
Q 008920          305 MAVIGGNHIRLDRACP  320 (548)
Q Consensus       305 g~~~~gr~I~V~~a~~  320 (548)
                      .-+|+||...|.++.-
T Consensus        75 ~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   75 NPIIDGRKANCNLASL   90 (247)
T ss_pred             CCcccccccccchhhh
Confidence            7889999999988764

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

Probab=99.24  E-value=1.5e-11  Score=114.44  Aligned_cols=75  Identities=27%  Similarity=0.464  Sum_probs=68.2

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      .+.||||||+..+++.+|..+|..||+|.+|+|-..|                      -|||||+|+++.+|..|+ .|
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            5789999999999999999999999999999994432                      389999999999999999 69


Q ss_pred             cceeecCceeEeecCCCc
Q 008920          304 NMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~  321 (548)
                      +|..|.|..|.|+++...
T Consensus        68 DG~~~cG~r~rVE~S~G~   85 (195)
T KOG0107|consen   68 DGKDICGSRIRVELSTGR   85 (195)
T ss_pred             CCccccCceEEEEeecCC
Confidence            999999999999998643

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

Probab=99.24  E-value=1.6e-11  Score=108.85  Aligned_cols=80  Identities=25%  Similarity=0.434  Sum_probs=75.3

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      .++||||+||++.++|++|+++|+.+    |+|..|.+-.|+.+..+-|||||+|.+.++|..||.-++ ..|..++|+|
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~c----G~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~  110 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKC----GDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRI  110 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhc----cchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceee
Confidence            47899999999999999999999999    999999998999899999999999999999999999988 9999999999


Q ss_pred             Eeeec
Q 008920          414 SHAQQ  418 (548)
Q Consensus       414 ~~Ak~  418 (548)
                      .|..-
T Consensus       111 D~D~G  115 (153)
T KOG0121|consen  111 DWDAG  115 (153)
T ss_pred             ecccc
Confidence            99653

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

Probab=99.22  E-value=1.6e-10  Score=107.68  Aligned_cols=76  Identities=22%  Similarity=0.371  Sum_probs=70.6

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      ..+.|||+||+..++..+|..+|..|    |.|..|.|...+     .|||||+|+++-+|..|+..|+ ..|+|..|+|
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~y----G~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rV   79 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKY----GPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRV   79 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhc----CcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEE
Confidence            46899999999999999999999999    899999988764     7999999999999999999998 9999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      .++.-.
T Consensus        80 E~S~G~   85 (195)
T KOG0107|consen   80 ELSTGR   85 (195)
T ss_pred             EeecCC
Confidence            998754

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

Probab=99.19  E-value=5.3e-11  Score=120.11  Aligned_cols=85  Identities=21%  Similarity=0.359  Sum_probs=76.7

Q ss_pred             cCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeE
Q 008920          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE  410 (548)
Q Consensus       332 ~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~  410 (548)
                      ..+..+.|+|.||||..-+-||+.+|.+|    |.|.+|.|+.+.  ..++|||||+|++.++|++|-..|+ ..+.||+
T Consensus        92 s~~~pkRLhVSNIPFrFRdpDL~aMF~kf----G~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRk  165 (376)
T KOG0125|consen   92 SKDTPKRLHVSNIPFRFRDPDLRAMFEKF----GKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRK  165 (376)
T ss_pred             CCCCCceeEeecCCccccCccHHHHHHhh----CceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceE
Confidence            34556899999999999999999999999    999999999883  4589999999999999999998888 9999999


Q ss_pred             EEEEeeecCCCC
Q 008920          411 LRLSHAQQNCTP  422 (548)
Q Consensus       411 I~V~~Ak~~~~~  422 (548)
                      |.|..|..+...
T Consensus       166 IEVn~ATarV~n  177 (376)
T KOG0125|consen  166 IEVNNATARVHN  177 (376)
T ss_pred             EEEeccchhhcc
Confidence            999999887433

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

Probab=99.19  E-value=2.2e-11  Score=124.80  Aligned_cols=171  Identities=18%  Similarity=0.268  Sum_probs=131.1

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhc----CCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKF----GEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~f----G~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      .-.|-+++||+++++.++..||..-    |-.+.|.+++.+                  +|+..|-|||.|..+++|+.|
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            3578899999999999999999742    234566664433                  456789999999999999999


Q ss_pred             HHhcceeecCceeEeecCCCccc----------cc------------CCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHh
Q 008920          301 LAFNMAVIGGNHIRLDRACPPRK----------KL------------KGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFC  358 (548)
Q Consensus       301 l~lng~~~~gr~I~V~~a~~~~k----------~~------------~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~  358 (548)
                      |..|...|+-|.|.+-++....-          ..            .....+......||.+++||+..+-++|..||.
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            98888888888877766431100          00            000022233478999999999999999999999


Q ss_pred             ccCCCCCCeEE--EEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeee
Q 008920          359 GLNDLESSVEA--VRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQ  417 (548)
Q Consensus       359 ~~g~~~G~I~~--VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak  417 (548)
                      .|.   -.|..  |.++.+ ..|++.|-|||+|.+.+.|..|....+ ..+.+|.|.|-.+.
T Consensus       303 dFa---~~i~f~gVHmv~N-~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S  360 (508)
T KOG1365|consen  303 DFA---TDIRFQGVHMVLN-GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCS  360 (508)
T ss_pred             HHh---hhcccceeEEEEc-CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeecc
Confidence            984   34544  888888 569999999999999999999987776 66679999998775

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

Probab=99.17  E-value=2.5e-11  Score=116.40  Aligned_cols=83  Identities=22%  Similarity=0.373  Sum_probs=79.7

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||++|...+++.-|...|-+|    |.|.+|.++.|..+++++|||||+|...++|.+||..|| ..|.||.|
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPF----GDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~Grti   82 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPF----GDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTI   82 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccc----cchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeE
Confidence            4567999999999999999999999999    999999999999999999999999999999999999999 99999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      +|.||.|.
T Consensus        83 rVN~AkP~   90 (298)
T KOG0111|consen   83 RVNLAKPE   90 (298)
T ss_pred             EEeecCCc
Confidence            99999986

>smart00362 RRM_2 RNA recognition motif

Probab=99.16  E-value=1.7e-10  Score=90.55  Aligned_cols=71  Identities=39%  Similarity=0.659  Sum_probs=65.9

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEE
Q 008920          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLS  414 (548)
Q Consensus       338 tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~  414 (548)
                      +|||+|||..+++++|+++|..|    |.|..+.++.+.  +.+.|+|||+|.+.++|..|+..++ ..+.|+.|.|.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~----g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKF----GPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhc----CCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999    899999999885  7788999999999999999999888 99999999873

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

Probab=99.16  E-value=1.1e-10  Score=100.16  Aligned_cols=79  Identities=19%  Similarity=0.348  Sum_probs=70.0

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...+.|||.|||+++|.+++.++|..||.|..|+|-.                    +...+|.|||+|++..+|.+|+ 
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~--------------------~k~TrGTAFVVYedi~dAk~A~d   75 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGN--------------------TKETRGTAFVVYEDIFDAKKACD   75 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecC--------------------ccCcCceEEEEehHhhhHHHHHH
Confidence            3468999999999999999999999999999999822                    2236799999999999999999 


Q ss_pred             HhcceeecCceeEeecCCCc
Q 008920          302 AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~  321 (548)
                      .|+|..+.++.|.|.+.++.
T Consensus        76 hlsg~n~~~ryl~vlyyq~~   95 (124)
T KOG0114|consen   76 HLSGYNVDNRYLVVLYYQPE   95 (124)
T ss_pred             HhcccccCCceEEEEecCHH
Confidence            59999999999999998754

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

Probab=99.15  E-value=1.2e-10  Score=104.23  Aligned_cols=85  Identities=16%  Similarity=0.184  Sum_probs=79.6

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ......|||.++...+++++|.+.|+.|    |.|.++.|-.|+.||..+|||+|+|.+..+|+.|+..+| ..|.|..|
T Consensus        69 SVEGwIi~VtgvHeEatEedi~d~F~dy----GeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v  144 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEEDIHDKFADY----GEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNV  144 (170)
T ss_pred             ceeeEEEEEeccCcchhHHHHHHHHhhc----ccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCce
Confidence            3456789999999999999999999999    999999999999999999999999999999999999999 99999999


Q ss_pred             EEEeeecCCC
Q 008920          412 RLSHAQQNCT  421 (548)
Q Consensus       412 ~V~~Ak~~~~  421 (548)
                      .|.||.....
T Consensus       145 ~VDw~Fv~gp  154 (170)
T KOG0130|consen  145 SVDWCFVKGP  154 (170)
T ss_pred             eEEEEEecCC
Confidence            9999987543

>PLN03213 repressor of silencing 3; Provisional

Probab=99.14  E-value=1.2e-10  Score=122.57  Aligned_cols=77  Identities=22%  Similarity=0.385  Sum_probs=71.0

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCH--HHHHHHHHHcC-CccCCeEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR--EAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~--e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ...+||||||++.+++++|..+|..|    |.|..|.|++  .+|  +|||||+|.+.  .++.+||..|| ..+.|+.|
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeF----GsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~L   80 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPM----GTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRL   80 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhc----CCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCcee
Confidence            45789999999999999999999999    9999999994  467  99999999987  78999999888 99999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      +|..|++.
T Consensus        81 KVNKAKP~   88 (759)
T PLN03213         81 RLEKAKEH   88 (759)
T ss_pred             EEeeccHH
Confidence            99999886

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

Probab=99.14  E-value=1.9e-10  Score=112.81  Aligned_cols=79  Identities=38%  Similarity=0.665  Sum_probs=76.1

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLS  414 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~  414 (548)
                      ..+|||+|||+.+++++|..+|..|    |.|..|.|+.+..++.++|||||.|.+.++|..|+..++ ..|.|+.|.|.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~----g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~  190 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKF----GPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQ  190 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhc----CceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEee
Confidence            6999999999999999999999999    899999999998899999999999999999999999998 99999999999


Q ss_pred             eeec
Q 008920          415 HAQQ  418 (548)
Q Consensus       415 ~Ak~  418 (548)
                      ++.+
T Consensus       191 ~~~~  194 (306)
T COG0724         191 KAQP  194 (306)
T ss_pred             cccc
Confidence            9764

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.13  E-value=3e-10  Score=111.93  Aligned_cols=77  Identities=23%  Similarity=0.276  Sum_probs=70.4

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLS  414 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~  414 (548)
                      ...+|||+||++.+|+++|++||+.|    |.|.+|.|++|.   ...|||||+|.+.++|..||.+.+..|.|+.|.|.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~----G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It   76 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHC----GAIEHVEIIRSG---EYACTAYVTFKDAYALETAVLLSGATIVDQRVCIT   76 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhc----CCeEEEEEecCC---CcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEE
Confidence            45899999999999999999999999    999999999984   44589999999999999999877799999999999


Q ss_pred             eeec
Q 008920          415 HAQQ  418 (548)
Q Consensus       415 ~Ak~  418 (548)
                      .+..
T Consensus        77 ~~~~   80 (243)
T PLN03121         77 RWGQ   80 (243)
T ss_pred             eCcc
Confidence            8764

>smart00360 RRM RNA recognition motif

Probab=99.13  E-value=2.6e-10  Score=89.09  Aligned_cols=70  Identities=37%  Similarity=0.629  Sum_probs=65.5

Q ss_pred             EeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEE
Q 008920          341 VGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLS  414 (548)
Q Consensus       341 V~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~  414 (548)
                      |+|||..+++++|+.+|..|    |.|..|.+..+..++.++|||||+|.+.++|..|+..++ ..+.|+.|.|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~----g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKF----GKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhh----CCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            68999999999999999999    899999999988789999999999999999999999998 88999998873

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

Probab=99.12  E-value=1e-11  Score=116.20  Aligned_cols=82  Identities=23%  Similarity=0.380  Sum_probs=73.6

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      -+++.-|||||||+..|+.+|.-+|++||+|..|.|+++.                 .+|.++||||+.|++..+...|+
T Consensus        32 YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk-----------------~TGKSKGFaFLcYEDQRSTILAV   94 (219)
T KOG0126|consen   32 YKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDK-----------------KTGKSKGFAFLCYEDQRSTILAV   94 (219)
T ss_pred             cccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecC-----------------CCCcccceEEEEecCccceEEEE
Confidence            3456789999999999999999999999999999997765                 35779999999999999999999


Q ss_pred             -HhcceeecCceeEeecCCC
Q 008920          302 -AFNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       302 -~lng~~~~gr~I~V~~a~~  320 (548)
                       .|||..|.||.|+|+....
T Consensus        95 DN~NGiki~gRtirVDHv~~  114 (219)
T KOG0126|consen   95 DNLNGIKILGRTIRVDHVSN  114 (219)
T ss_pred             eccCCceecceeEEeeeccc
Confidence             5999999999999998753

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

Probab=99.12  E-value=1.6e-10  Score=112.67  Aligned_cols=80  Identities=21%  Similarity=0.262  Sum_probs=72.9

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      +..+|-|.|||.++++.+|.+||..||.|..|.|..+.                 .+|.++|||||.|.+.++|.+|| .
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK-----------------~TG~~kGFAFVtF~sRddA~rAI~~  250 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDK-----------------ETGLSKGFAFVTFESRDDAARAIAD  250 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEcc-----------------ccCcccceEEEEEecHHHHHHHHHH
Confidence            56799999999999999999999999999999996544                 35778899999999999999999 5


Q ss_pred             hcceeecCceeEeecCCC
Q 008920          303 FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~  320 (548)
                      |||.-++.--|+|.|+.|
T Consensus       251 LnG~gyd~LILrvEwskP  268 (270)
T KOG0122|consen  251 LNGYGYDNLILRVEWSKP  268 (270)
T ss_pred             ccCcccceEEEEEEecCC
Confidence            999999999999999875

>smart00362 RRM_2 RNA recognition motif

Probab=99.12  E-value=3.3e-10  Score=88.87  Aligned_cols=71  Identities=39%  Similarity=0.662  Sum_probs=62.3

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhcc
Q 008920          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (548)
Q Consensus       227 tVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng  305 (548)
                      +|||+|||..++.++|..+|..||.|..+.+...+                   +.+.|+|||+|.+.++|..|+ .+++
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~-------------------~~~~~~~~v~f~~~~~a~~a~~~~~~   61 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT-------------------GKSKGFAFVEFESEEDAEKAIEALNG   61 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-------------------CCCCceEEEEeCCHHHHHHHHHHhCC
Confidence            59999999999999999999999999999885432                   236699999999999999999 5899


Q ss_pred             eeecCceeEee
Q 008920          306 AVIGGNHIRLD  316 (548)
Q Consensus       306 ~~~~gr~I~V~  316 (548)
                      ..+.|+.|.|.
T Consensus        62 ~~~~~~~i~v~   72 (72)
T smart00362       62 TKLGGRPLRVE   72 (72)
T ss_pred             cEECCEEEeeC
Confidence            99999998873

>PLN03213 repressor of silencing 3; Provisional

Probab=99.12  E-value=1.9e-10  Score=121.09  Aligned_cols=76  Identities=28%  Similarity=0.413  Sum_probs=67.6

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCH--HHHHHHH-
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSE--QSTEAAL-  301 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~--e~A~~Al-  301 (548)
                      ..+||||||++.+++++|..+|..||.|..|.|++    .               +|  +|||||+|.+.  .++.+|| 
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR----E---------------TG--RGFAFVEMssdddaEeeKAIS   68 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR----T---------------KG--RSFAYIDFSPSSTNSLTKLFS   68 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec----c---------------cC--CceEEEEecCCcHHHHHHHHH
Confidence            36899999999999999999999999999999952    1               22  69999999988  6789999 


Q ss_pred             HhcceeecCceeEeecCCCc
Q 008920          302 AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~  321 (548)
                      .|||..+.|+.|+|..+.+.
T Consensus        69 aLNGAEWKGR~LKVNKAKP~   88 (759)
T PLN03213         69 TYNGCVWKGGRLRLEKAKEH   88 (759)
T ss_pred             HhcCCeecCceeEEeeccHH
Confidence            69999999999999998753

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

Probab=99.11  E-value=4.4e-10  Score=121.38  Aligned_cols=174  Identities=20%  Similarity=0.277  Sum_probs=131.5

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-  302 (548)
                      ....+||++||...++.++.++...||++....+..+.                 .+|.++||||.+|.++--...|++ 
T Consensus       288 ~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~-----------------~~g~skg~af~ey~dpsvtd~A~ag  350 (500)
T KOG0120|consen  288 SPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDS-----------------ATGNSKGFAFCEYCDPSVTDQAIAG  350 (500)
T ss_pred             ccchhhhccCcCccCHHHHHHHHHhcccchhheeeccc-----------------ccccccceeeeeeeCCcchhhhhcc
Confidence            34579999999999999999999999999998885544                 235688999999999999999995 


Q ss_pred             hcceeecCceeEeecCCCcccccCCCCC---------------CcCCCccEEEEeCC--CCCC-CH-------HHHHHHH
Q 008920          303 FNMAVIGGNHIRLDRACPPRKKLKGEDA---------------PLYDIKKTVFVGNL--PFDV-KD-------EEIYQLF  357 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~~k~~~~~~~---------------~~~~~~~tLfV~NL--p~~~-te-------edL~~~F  357 (548)
                      |||..+++..|.|..+............               ....++..|++.|+  |.++ .+       ++|+.-+
T Consensus       351 LnGm~lgd~~lvvq~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec  430 (500)
T KOG0120|consen  351 LNGMQLGDKKLVVQRAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTEC  430 (500)
T ss_pred             cchhhhcCceeEeehhhccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHh
Confidence            9999999999999998754322111111               11122344444443  1111 11       4556666


Q ss_pred             hccCCCCCCeEEEEEeec-C--CCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeec
Q 008920          358 CGLNDLESSVEAVRVIRH-P--HMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQ  418 (548)
Q Consensus       358 ~~~g~~~G~I~~VrI~~d-~--~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~  418 (548)
                      ..|    |.|..|.|+++ .  .-.-+.|-.||+|.+.++|+.|+..|+ ..|.||.|...|..+
T Consensus       431 ~k~----g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  431 AKF----GAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             ccc----CceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence            777    89999999887 2  234456778999999999999999998 999999999999764

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

Probab=99.11  E-value=9.7e-11  Score=109.79  Aligned_cols=80  Identities=30%  Similarity=0.483  Sum_probs=76.8

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      +...+|||+||+..++++.|+++|-+.    |.|++++|++|..++...|||||+|.+.++|+-|++.|| ..|.|++|+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqa----gpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIr   82 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQA----GPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIR   82 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhc----CceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeE
Confidence            456899999999999999999999999    999999999999999999999999999999999999999 999999999


Q ss_pred             EEeee
Q 008920          413 LSHAQ  417 (548)
Q Consensus       413 V~~Ak  417 (548)
                      |..+.
T Consensus        83 v~kas   87 (203)
T KOG0131|consen   83 VNKAS   87 (203)
T ss_pred             EEecc
Confidence            99887

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

Probab=99.09  E-value=1.3e-09  Score=111.19  Aligned_cols=80  Identities=21%  Similarity=0.414  Sum_probs=70.9

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      +....|||..+-++.+++||+..|+.||+|..|.|-+.+.                 .+.++||+||+|.+..+...|+ 
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            4457899999999999999999999999999999966552                 2358899999999999999999 


Q ss_pred             HhcceeecCceeEeecCC
Q 008920          302 AFNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~  319 (548)
                      .||-..++|..|+|..+.
T Consensus       271 sMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  271 SMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             hcchhhcccceEeccccc
Confidence            599999999999998864

>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=99.07  E-value=1e-09  Score=86.58  Aligned_cols=73  Identities=40%  Similarity=0.661  Sum_probs=66.9

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEe
Q 008920          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSH  415 (548)
Q Consensus       338 tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~  415 (548)
                      +|+|+|||..+++++|+++|..|    |.|..+.+..+..+ .+.|+|||+|.+.++|..|+..++ ..+.|+.|.|.|
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~----g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKF----GKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhc----CCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            48999999999999999999999    89999999988654 778999999999999999999888 769999999875

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).

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

Probab=99.07  E-value=2.8e-09  Score=111.03  Aligned_cols=72  Identities=22%  Similarity=0.292  Sum_probs=65.6

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLS  414 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~  414 (548)
                      .++|||+|||+++||..|++-|..|    |.|.++.|+   ..|.++|  .|.|.++++|+.|+.+++ ..|.||.|.|.
T Consensus       536 a~qIiirNlP~dfTWqmlrDKfre~----G~v~yadim---e~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~  606 (608)
T KOG4212|consen  536 ACQIIIRNLPFDFTWQMLRDKFREI----GHVLYADIM---ENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVT  606 (608)
T ss_pred             ccEEEEecCCccccHHHHHHHHHhc----cceehhhhh---ccCCccc--eEEecCHHHHHHHHHHhccCcccCceeeee
Confidence            4689999999999999999999999    899999884   3477776  899999999999999998 99999999999


Q ss_pred             ee
Q 008920          415 HA  416 (548)
Q Consensus       415 ~A  416 (548)
                      |.
T Consensus       607 y~  608 (608)
T KOG4212|consen  607 YF  608 (608)
T ss_pred             eC
Confidence            84

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

Probab=99.07  E-value=2.2e-10  Score=115.79  Aligned_cols=78  Identities=21%  Similarity=0.386  Sum_probs=70.5

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      .+.|+|.|||+..-+-||+.+|.+||.|.+|.|+..                   +..++||+||+|++.++|++|- +|
T Consensus        96 pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN-------------------ERGSKGFGFVTmen~~dadRARa~L  156 (376)
T KOG0125|consen   96 PKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN-------------------ERGSKGFGFVTMENPADADRARAEL  156 (376)
T ss_pred             CceeEeecCCccccCccHHHHHHhhCceeeEEEEec-------------------cCCCCccceEEecChhhHHHHHHHh
Confidence            368999999999999999999999999999999542                   2338899999999999999999 69


Q ss_pred             cceeecCceeEeecCCCc
Q 008920          304 NMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~  321 (548)
                      ||+.+.||.|.|..+...
T Consensus       157 Hgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen  157 HGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             hcceeeceEEEEeccchh
Confidence            999999999999998753

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

Probab=99.07  E-value=2.8e-09  Score=112.95  Aligned_cols=169  Identities=19%  Similarity=0.228  Sum_probs=128.4

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeE-EEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDS-VRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~s-Vri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...+|-+++||+.||+++|.+||+..-.|.. |.|+.++                  .++.+|-|||+|++.+.|+.||.
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            3468999999999999999999998776655 3332221                  34578999999999999999998


Q ss_pred             hcceeecCceeEeecCCCcc------------------cc---cCC----------------------------------
Q 008920          303 FNMAVIGGNHIRLDRACPPR------------------KK---LKG----------------------------------  327 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~~------------------k~---~~~----------------------------------  327 (548)
                      .|...|.-|.|.|..+....                  ..   ...                                  
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            88888888888887753110                  00   000                                  


Q ss_pred             C--C---------------------------CCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCC
Q 008920          328 E--D---------------------------APLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM  378 (548)
Q Consensus       328 ~--~---------------------------~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~t  378 (548)
                      .  .                           .........|+.++||+..++.+|..+|+..     ....|.|-.. .+
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-----NPYRVHIEIG-PD  317 (510)
T ss_pred             ccccccccccccccccCCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCC-----CceeEEEEeC-CC
Confidence            0  0                           0000112688999999999999999999986     5557777777 46


Q ss_pred             CCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEee
Q 008920          379 RVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHA  416 (548)
Q Consensus       379 g~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~A  416 (548)
                      |+..|-|+|+|.+.++|..|+...+..|..+-|.+..-
T Consensus       318 Gr~TGEAdveF~t~edav~Amskd~anm~hrYVElFln  355 (510)
T KOG4211|consen  318 GRATGEADVEFATGEDAVGAMGKDGANMGHRYVELFLN  355 (510)
T ss_pred             CccCCcceeecccchhhHhhhccCCcccCcceeeeccc
Confidence            99999999999999999999988888888887776543

>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=99.06  E-value=9.6e-10  Score=86.70  Aligned_cols=73  Identities=38%  Similarity=0.601  Sum_probs=63.8

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhcc
Q 008920          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (548)
Q Consensus       227 tVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng  305 (548)
                      +|+|+|||..+++++|.++|..||.|..+.+...+..                  ...|+|||+|.+.++|..|+ .+++
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            4899999999999999999999999999998654321                  25689999999999999999 5899


Q ss_pred             eeecCceeEeec
Q 008920          306 AVIGGNHIRLDR  317 (548)
Q Consensus       306 ~~~~gr~I~V~~  317 (548)
                      ..+.|+.|.|.+
T Consensus        63 ~~~~~~~~~v~~   74 (74)
T cd00590          63 KELGGRPLRVEF   74 (74)
T ss_pred             CeECCeEEEEeC
Confidence            999999998864

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).

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

Probab=99.05  E-value=3.4e-10  Score=121.45  Aligned_cols=79  Identities=28%  Similarity=0.556  Sum_probs=76.7

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEe
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSH  415 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~  415 (548)
                      +.|||||+|+++++++|..+|+..    |.|.+++++.|+.||.++||||++|.+.++|..|++.|| ..+.||+|+|.|
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~----g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~   94 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGV----GPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNY   94 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhcc----CccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeec
Confidence            899999999999999999999999    899999999999999999999999999999999999999 999999999999


Q ss_pred             eecC
Q 008920          416 AQQN  419 (548)
Q Consensus       416 Ak~~  419 (548)
                      +...
T Consensus        95 ~~~~   98 (435)
T KOG0108|consen   95 ASNR   98 (435)
T ss_pred             cccc
Confidence            9764

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

Probab=99.05  E-value=2.6e-10  Score=108.78  Aligned_cols=78  Identities=26%  Similarity=0.419  Sum_probs=71.9

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      ..+|.|-||.+-++.++|..+|++||.|-.|.|..+.+                 +..++|||||.|....+|+.|| +|
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            47899999999999999999999999999999977764                 4568899999999999999999 69


Q ss_pred             cceeecCceeEeecCC
Q 008920          304 NMAVIGGNHIRLDRAC  319 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~  319 (548)
                      +|.+|+|+.|.|++|.
T Consensus        76 DG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   76 DGAVLDGRELRVQMAR   91 (256)
T ss_pred             cceeeccceeeehhhh
Confidence            9999999999999985

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

Probab=99.04  E-value=8.8e-10  Score=94.60  Aligned_cols=79  Identities=22%  Similarity=0.461  Sum_probs=71.7

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      +..+-|||+|||+.+|.+++.++|..|    |.|..|+|-..+.   .+|.|||.|++..+|..|++.|. ..+.++.|.
T Consensus        16 evnriLyirNLp~~ITseemydlFGky----g~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~   88 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKY----GTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLV   88 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcc----cceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhcccccCCceEE
Confidence            346889999999999999999999999    9999999876654   58999999999999999999888 999999999


Q ss_pred             EEeeecC
Q 008920          413 LSHAQQN  419 (548)
Q Consensus       413 V~~Ak~~  419 (548)
                      |-|..+.
T Consensus        89 vlyyq~~   95 (124)
T KOG0114|consen   89 VLYYQPE   95 (124)
T ss_pred             EEecCHH
Confidence            9998764

>smart00360 RRM RNA recognition motif

Probab=99.03  E-value=9.9e-10  Score=85.74  Aligned_cols=70  Identities=36%  Similarity=0.544  Sum_probs=60.7

Q ss_pred             EcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhcceee
Q 008920          230 VGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVI  308 (548)
Q Consensus       230 VgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng~~~  308 (548)
                      |+|||..+++++|..+|..||.|..|.+...+.                 ++.++|||||+|.+.++|..|+ .+++..+
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            689999999999999999999999998854331                 2347799999999999999999 5899999


Q ss_pred             cCceeEee
Q 008920          309 GGNHIRLD  316 (548)
Q Consensus       309 ~gr~I~V~  316 (548)
                      .|+.|.|.
T Consensus        64 ~~~~~~v~   71 (71)
T smart00360       64 DGRPLKVK   71 (71)
T ss_pred             CCcEEEeC
Confidence            99998873

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=99.03  E-value=3.1e-10  Score=116.32  Aligned_cols=177  Identities=21%  Similarity=0.223  Sum_probs=137.2

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      ...++|++++.+.+.+.++..+|..+|.+..+.+..                 ..+...++|+++|.|...+.+..||.+
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~-----------------~~~~~~sk~~~s~~f~~ks~~~~~l~~  149 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSS-----------------LEDSLSSKGGLSVHFAGKSQFFAALEE  149 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhh-----------------hccccccccceeeccccHHHHHHHHHh
Confidence            468999999999999999999999999776665522                 123445889999999999999999987


Q ss_pred             cce-eecCceeEeecCCCcccccCCCC-CCcCCCccEEE-EeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCC
Q 008920          304 NMA-VIGGNHIRLDRACPPRKKLKGED-APLYDIKKTVF-VGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV  380 (548)
Q Consensus       304 ng~-~~~gr~I~V~~a~~~~k~~~~~~-~~~~~~~~tLf-V~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~  380 (548)
                      .+. .+.++.+................ ........++| |+||++.+++++|+.+|..+    |.|..|+++.+..++.
T Consensus       150 s~~~~~~~~~~~~dl~~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~----~~i~~~r~~~~~~s~~  225 (285)
T KOG4210|consen  150 SGSKVLDGNKGEKDLNTRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSS----GEITSVRLPTDEESGD  225 (285)
T ss_pred             hhccccccccccCcccccccccccchhcccccCccccceeecccccccchHHHhhhccCc----CcceeeccCCCCCccc
Confidence            775 55566555554432221100000 11122334455 99999999999999999998    8999999999999999


Q ss_pred             CceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEeeecCCC
Q 008920          381 GKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQNCT  421 (548)
Q Consensus       381 srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~Ak~~~~  421 (548)
                      +.|||||.|.....+..++...+..+.++++.|.+..+...
T Consensus       226 ~kg~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  266 (285)
T KOG4210|consen  226 SKGFAYVDFSAGNSKKLALNDQTRSIGGRPLRLEEDEPRPK  266 (285)
T ss_pred             hhhhhhhhhhhchhHHHHhhcccCcccCcccccccCCCCcc
Confidence            99999999999999999998833999999999999887643

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

Probab=99.01  E-value=6.8e-10  Score=119.92  Aligned_cols=173  Identities=21%  Similarity=0.415  Sum_probs=140.1

Q ss_pred             cCCCcccEEEEcCCCCCCcHHHHHHHhhhc-----------C-CeeEEEEeeecccCCCCCccchhhhhhhccCCCcceE
Q 008920          220 DEGKLLRTIFVGNLPLKVKKKTLIKEFIKF-----------G-EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHA  287 (548)
Q Consensus       220 ~~~~~~rtVfVgNLP~~~tee~L~~~Fs~f-----------G-~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~A  287 (548)
                      ....+.+.++|+++|+.++++.+..+|..-           | .|.+|.|                       .....||
T Consensus       170 ~~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~-----------------------n~~~nfa  226 (500)
T KOG0120|consen  170 QATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQL-----------------------NLEKNFA  226 (500)
T ss_pred             chhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeee-----------------------cccccce
Confidence            334567889999999999999999999853           1 2344444                       1255799


Q ss_pred             EEEecCHHHHHHHHHhcceeecCceeEeecCCCcccc--------------cCCCCCCcCCCccEEEEeCCCCCCCHHHH
Q 008920          288 YIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKK--------------LKGEDAPLYDIKKTVFVGNLPFDVKDEEI  353 (548)
Q Consensus       288 FV~F~s~e~A~~Al~lng~~~~gr~I~V~~a~~~~k~--------------~~~~~~~~~~~~~tLfV~NLp~~~teedL  353 (548)
                      ||+|.+.+.|..|+.+++..|.|+.+.+.........              .........+....+||++||..+++.++
T Consensus       227 ~ie~~s~~~at~~~~~~~~~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~  306 (500)
T KOG0120|consen  227 FIEFRSISEATEAMALDGIIFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQV  306 (500)
T ss_pred             eEEecCCCchhhhhcccchhhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHH
Confidence            9999999999999999999999987777554321100              00011233445678999999999999999


Q ss_pred             HHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          354 YQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       354 ~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      .+++..|    |.+....++.|..+|.++||||.+|.+......|+..+| ..+++..|.|..|-..
T Consensus       307 ~Ell~~f----g~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g  369 (500)
T KOG0120|consen  307 KELLDSF----GPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVG  369 (500)
T ss_pred             HHHHHhc----ccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhcc
Confidence            9999999    899999999999999999999999999999999999998 8899999999999765

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

Probab=98.97  E-value=1.3e-08  Score=105.59  Aligned_cols=167  Identities=19%  Similarity=0.251  Sum_probs=127.1

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcce-EEEEecCHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH-AYIVFKSEQSTEAA  300 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~-AFV~F~s~e~A~~A  300 (548)
                      ...--.++|+|+-+-++-+-|..+|+.||.|..|.-    ++                  ++.|| |+|+|.+.+.|+.|
T Consensus       147 ~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiT----F~------------------Knn~FQALvQy~d~~sAq~A  204 (492)
T KOG1190|consen  147 PNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLKIIT----FT------------------KNNGFQALVQYTDAVSAQAA  204 (492)
T ss_pred             CceeEEEEeccceeeeEHHHHHHHHhhcceeEEEEE----Ee------------------cccchhhhhhccchhhHHHH
Confidence            334457889999999999999999999999977644    21                  12344 99999999999999


Q ss_pred             H-HhcceeecC--ceeEeecCCCc----------ccc------cCCC-----------------------C---------
Q 008920          301 L-AFNMAVIGG--NHIRLDRACPP----------RKK------LKGE-----------------------D---------  329 (548)
Q Consensus       301 l-~lng~~~~g--r~I~V~~a~~~----------~k~------~~~~-----------------------~---------  329 (548)
                      - .|+|..|..  ..|+|+++.-.          ...      ..++                       .         
T Consensus       205 K~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a  284 (492)
T KOG1190|consen  205 KLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGA  284 (492)
T ss_pred             HHhccCCcccCceeEEEeehhhcccceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhh
Confidence            7 788887643  46777765311          000      0000                       0         


Q ss_pred             ----CCcCCC--ccEEEEeCCCC-CCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHc
Q 008920          330 ----APLYDI--KKTVFVGNLPF-DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR  402 (548)
Q Consensus       330 ----~~~~~~--~~tLfV~NLp~-~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~l  402 (548)
                          .....+  ...|.|.||.. .+|.+-|..+|+-|    |+|..|.|+.+..     --|.|+|.+...|+.|+..|
T Consensus       285 ~~a~~~~~~~~~n~vllvsnln~~~VT~d~LftlFgvY----GdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL  355 (492)
T KOG1190|consen  285 NAADGKIESPSANVVLLVSNLNEEAVTPDVLFTLFGVY----GDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHL  355 (492)
T ss_pred             cccccccccCCCceEEEEecCchhccchhHHHHHHhhh----cceEEEEeeecCC-----cceeeeecchhHHHHHHHHh
Confidence                000111  46788888865 58999999999999    9999999998852     47999999999999999999


Q ss_pred             C-CccCCeEEEEEeeecC
Q 008920          403 N-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       403 n-~~l~Gr~I~V~~Ak~~  419 (548)
                      + ..|.|+.|+|.+++-.
T Consensus       356 ~g~~l~gk~lrvt~SKH~  373 (492)
T KOG1190|consen  356 EGHKLYGKKLRVTLSKHT  373 (492)
T ss_pred             hcceecCceEEEeeccCc
Confidence            8 9999999999999865

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

Probab=98.95  E-value=5.3e-10  Score=125.01  Aligned_cols=161  Identities=20%  Similarity=0.272  Sum_probs=132.0

Q ss_pred             cCCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHH
Q 008920          220 DEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (548)
Q Consensus       220 ~~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~  299 (548)
                      |+....+|||+|||+..+++.+|+..|..+|.|..|.|-+..                  -++..-||||.|.+...+..
T Consensus       367 DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~------------------~~~esa~~f~~~~n~dmtp~  428 (975)
T KOG0112|consen  367 DDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH------------------IKTESAYAFVSLLNTDMTPS  428 (975)
T ss_pred             cchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC------------------CCcccchhhhhhhccccCcc
Confidence            456778999999999999999999999999999999983322                  12355799999999999999


Q ss_pred             HH-HhcceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCC
Q 008920          300 AL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM  378 (548)
Q Consensus       300 Al-~lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~t  378 (548)
                      |+ ++.+..|..-.+.+.+..+           .......|+|++|+.++....|...|..|    |.|..|.+-     
T Consensus       429 ak~e~s~~~I~~g~~r~glG~~-----------kst~ttr~~sgglg~w~p~~~l~r~fd~f----Gpir~Idy~-----  488 (975)
T KOG0112|consen  429 AKFEESGPLIGNGTHRIGLGQP-----------KSTPTTRLQSGGLGPWSPVSRLNREFDRF----GPIRIIDYR-----  488 (975)
T ss_pred             cchhhcCCccccCccccccccc-----------ccccceeeccCCCCCCChHHHHHHHhhcc----Ccceeeecc-----
Confidence            87 7887777666666655532           24467889999999999999999999999    888876542     


Q ss_pred             CCCceEEEEEECCHHHHHHHHHHcC-CccCC--eEEEEEeeecC
Q 008920          379 RVGKGIAYVLFKTREAANLVIKRRN-LKLRD--RELRLSHAQQN  419 (548)
Q Consensus       379 g~srG~AFV~F~~~e~A~~Al~~ln-~~l~G--r~I~V~~Ak~~  419 (548)
                       +.-.||||.|.+...|+.|+..+- ..|+|  +.|+|.|+.+.
T Consensus       489 -hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~~  531 (975)
T KOG0112|consen  489 -HGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASPP  531 (975)
T ss_pred             -cCCcceeeecccCccchhhHHHHhcCcCCCCCcccccccccCC
Confidence             224599999999999999996654 88877  78999999876

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

Probab=98.92  E-value=1.4e-09  Score=97.41  Aligned_cols=78  Identities=19%  Similarity=0.298  Sum_probs=69.8

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      ...|||.++-..+|+++|...|..||+|.+|.|-.+.                 .+|-.+|||+|+|.+...|+.|+ .+
T Consensus        72 GwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDR-----------------RtGy~KGYaLvEYet~keAq~A~~~~  134 (170)
T KOG0130|consen   72 GWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDR-----------------RTGYVKGYALVEYETLKEAQAAIDAL  134 (170)
T ss_pred             eEEEEEeccCcchhHHHHHHHHhhcccccceeecccc-----------------ccccccceeeeehHhHHHHHHHHHhc
Confidence            4689999999999999999999999999999883222                 35567899999999999999999 69


Q ss_pred             cceeecCceeEeecCC
Q 008920          304 NMAVIGGNHIRLDRAC  319 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~  319 (548)
                      ||..|.|..|.|+|+.
T Consensus       135 Ng~~ll~q~v~VDw~F  150 (170)
T KOG0130|consen  135 NGAELLGQNVSVDWCF  150 (170)
T ss_pred             cchhhhCCceeEEEEE
Confidence            9999999999999985

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

Probab=98.90  E-value=9.6e-10  Score=105.67  Aligned_cols=83  Identities=28%  Similarity=0.460  Sum_probs=73.9

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..+|||||+|...+++.-|...|-+||.|..|.|+.+                 +.+++++|||||+|...++|.+|| .
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlD-----------------yesqkHRgFgFVefe~aEDAaaAiDN   71 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLD-----------------YESQKHRGFGFVEFEEAEDAAAAIDN   71 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccc-----------------hhcccccceeEEEeeccchhHHHhhc
Confidence            3589999999999999999999999999999998543                 334568999999999999999999 5


Q ss_pred             hcceeecCceeEeecCCCccc
Q 008920          303 FNMAVIGGNHIRLDRACPPRK  323 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~~k  323 (548)
                      ||+..|.|+.|+|.++.|...
T Consensus        72 MnesEL~GrtirVN~AkP~ki   92 (298)
T KOG0111|consen   72 MNESELFGRTIRVNLAKPEKI   92 (298)
T ss_pred             CchhhhcceeEEEeecCCccc
Confidence            999999999999999987643

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

Probab=98.88  E-value=3.2e-09  Score=114.02  Aligned_cols=78  Identities=24%  Similarity=0.399  Sum_probs=71.6

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-hc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-FN  304 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-ln  304 (548)
                      +.|||||||+++++++|..+|+..|.|.++++..|+.                 +|..+||||++|.+.+.|..|++ ||
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~-----------------tG~~~G~~f~~~~~~~~~~~a~~~lN   81 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRE-----------------TGKPKGFGFCEFTDEETAERAIRNLN   81 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeeccccc-----------------CCCcCceeeEecCchhhHHHHHHhcC
Confidence            7899999999999999999999999999999976652                 45677999999999999999995 99


Q ss_pred             ceeecCceeEeecCCC
Q 008920          305 MAVIGGNHIRLDRACP  320 (548)
Q Consensus       305 g~~~~gr~I~V~~a~~  320 (548)
                      |..+.|+.|+|.|+..
T Consensus        82 g~~~~gr~l~v~~~~~   97 (435)
T KOG0108|consen   82 GAEFNGRKLRVNYASN   97 (435)
T ss_pred             CcccCCceEEeecccc
Confidence            9999999999999864

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

Probab=98.88  E-value=6.1e-09  Score=106.17  Aligned_cols=86  Identities=19%  Similarity=0.303  Sum_probs=78.7

Q ss_pred             cCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHc-CCccCCeE
Q 008920          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR-NLKLRDRE  410 (548)
Q Consensus       332 ~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~l-n~~l~Gr~  410 (548)
                      ..++.+.|||--|.+.++++||.-+|+.|    |.|.+|.|++|..||.+-.||||+|.+.++++.|.-.| |..|.++.
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrF----G~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrR  310 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRF----GKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRR  310 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhc----ccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccce
Confidence            34567899999999999999999999999    99999999999999999999999999999999997555 59999999


Q ss_pred             EEEEeeecCCC
Q 008920          411 LRLSHAQQNCT  421 (548)
Q Consensus       411 I~V~~Ak~~~~  421 (548)
                      |+|.|++..+.
T Consensus       311 IHVDFSQSVsk  321 (479)
T KOG0415|consen  311 IHVDFSQSVSK  321 (479)
T ss_pred             EEeehhhhhhh
Confidence            99999987643

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

Probab=98.87  E-value=3.8e-10  Score=125.67  Aligned_cols=152  Identities=26%  Similarity=0.309  Sum_probs=127.5

Q ss_pred             cCCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHH
Q 008920          220 DEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (548)
Q Consensus       220 ~~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~  299 (548)
                      ++-++..++||.||++.+.+.+|...|..+|.|..|++.                 ...+.+..+|+|||+|..++++.+
T Consensus       662 n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~-----------------~h~n~~~~rG~~Y~~F~~~~~~~a  724 (881)
T KOG0128|consen  662 NEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIV-----------------IHKNEKRFRGKAYVEFLKPEHAGA  724 (881)
T ss_pred             hHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHH-----------------HHhhccccccceeeEeecCCchhh
Confidence            334567799999999999999999999999998888773                 112345677999999999999999


Q ss_pred             HHHhcceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCC
Q 008920          300 ALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMR  379 (548)
Q Consensus       300 Al~lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg  379 (548)
                      ||.+....+.|                         ...|||.|+|+..|.+.|+.+|..+    |.+.+++++..+ .|
T Consensus       725 aV~f~d~~~~g-------------------------K~~v~i~g~pf~gt~e~~k~l~~~~----gn~~~~~~vt~r-~g  774 (881)
T KOG0128|consen  725 AVAFRDSCFFG-------------------------KISVAISGPPFQGTKEELKSLASKT----GNVTSLRLVTVR-AG  774 (881)
T ss_pred             hhhhhhhhhhh-------------------------hhhhheeCCCCCCchHHHHhhcccc----CCccccchhhhh-cc
Confidence            99877666656                         2348999999999999999999999    899999988884 69


Q ss_pred             CCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeec
Q 008920          380 VGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQ  418 (548)
Q Consensus       380 ~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~  418 (548)
                      .++|.|||.|.+..++..++.... ..+.-+.+.|..+.|
T Consensus       775 kpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  775 KPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             ccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            999999999999999999987666 666666777776555

>smart00361 RRM_1 RNA recognition motif

Probab=98.86  E-value=9.1e-09  Score=83.38  Aligned_cols=60  Identities=20%  Similarity=0.262  Sum_probs=53.9

Q ss_pred             HHHHHHHHh----ccCCCCCCeEEEE-EeecCCC--CCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          350 DEEIYQLFC----GLNDLESSVEAVR-VIRHPHM--RVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       350 eedL~~~F~----~~g~~~G~I~~Vr-I~~d~~t--g~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      +++|+++|.    .|    |.|..|. |+.+..+  +.++|||||.|.+.++|..|+..|+ ..+.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~f----G~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYF----GEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhc----CCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578899998    88    8999995 7777666  8999999999999999999999888 9999999986

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

Probab=98.84  E-value=6e-10  Score=107.12  Aligned_cols=137  Identities=22%  Similarity=0.276  Sum_probs=112.4

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-h
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-F  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-l  303 (548)
                      .+||||+||...++++-|.++|-+-|+|..|.|+.+..                  +..+ ||||.|.++-++..|+. +
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------------------QEQK-FAYVFFPNENSVQLAGQLE   69 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc------------------CCCc-eeeeecccccchhhhhhhc
Confidence            38999999999999999999999999999999865432                  2233 99999999999999996 6


Q ss_pred             cceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCce
Q 008920          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG  383 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG  383 (548)
                      ||..+.++.|.|.+-+...          .        .-|...++++.+...|+.-    |.+..+++.++.+ |+++.
T Consensus        70 ng~~l~~~e~q~~~r~G~s----------h--------apld~r~~~ei~~~v~s~a----~p~~~~R~~~~~d-~rnrn  126 (267)
T KOG4454|consen   70 NGDDLEEDEEQRTLRCGNS----------H--------APLDERVTEEILYEVFSQA----GPIEGVRIPTDND-GRNRN  126 (267)
T ss_pred             ccchhccchhhcccccCCC----------c--------chhhhhcchhhheeeeccc----CCCCCcccccccc-CCccC
Confidence            9999999998887754210          0        0155668999999999988    8999999999965 88999


Q ss_pred             EEEEEECCHHHHHHHHHHcC
Q 008920          384 IAYVLFKTREAANLVIKRRN  403 (548)
Q Consensus       384 ~AFV~F~~~e~A~~Al~~ln  403 (548)
                      ++||.+....+.-.++....
T Consensus       127 ~~~~~~qr~~~~P~~~~~y~  146 (267)
T KOG4454|consen  127 FGFVTYQRLCAVPFALDLYQ  146 (267)
T ss_pred             ccchhhhhhhcCcHHhhhhc
Confidence            99999988777777776543

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

Probab=98.79  E-value=2.3e-08  Score=102.93  Aligned_cols=176  Identities=16%  Similarity=0.186  Sum_probs=128.7

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      .+...|-.++||+..++.+|..||.-.....-.+.+                 .....|...|+|.|.|.+++.-..|++
T Consensus        58 ~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aK-----------------OG~~qgrRnge~lvrf~d~e~Rdlalk  120 (508)
T KOG1365|consen   58 DDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRAL-----------------CLNAQGRRNGEALVRFVDPEGRDLALK  120 (508)
T ss_pred             CcceEEEecCCCCCcccCCHHHHHhhhhccccceee-----------------eehhhhccccceEEEecCchhhhhhhH
Confidence            345677889999999999999999854322221211                 112235567999999999999999999


Q ss_pred             hcceeecCceeEeecCCCcccccCCCC-------CCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeec
Q 008920          303 FNMAVIGGNHIRLDRACPPRKKLKGED-------APLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRH  375 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~~k~~~~~~-------~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d  375 (548)
                      .|...+.++.|.|..+.....-.-...       -....+.-.|.+++||+++++.|+..||...+.+-|.++.|-++..
T Consensus       121 Rhkhh~g~ryievYka~ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r  200 (508)
T KOG1365|consen  121 RHKHHMGTRYIEVYKATGEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR  200 (508)
T ss_pred             hhhhhccCCceeeeccCchhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC
Confidence            888899999999988865422111000       1111234567778999999999999999755444467778877776


Q ss_pred             CCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEee
Q 008920          376 PHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHA  416 (548)
Q Consensus       376 ~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~A  416 (548)
                      + .|+..|-|||.|...++|+.||...-..|+-|.|.|-.+
T Consensus       201 p-dgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElFRS  240 (508)
T KOG1365|consen  201 P-DGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELFRS  240 (508)
T ss_pred             C-CCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence            4 589999999999999999999987766676677666554

>PF13893 RRM_5: RNA recognition motif

Probab=98.77  E-value=2e-08  Score=77.43  Aligned_cols=55  Identities=27%  Similarity=0.458  Sum_probs=47.4

Q ss_pred             HHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-HhcceeecCceeEeecC
Q 008920          242 LIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRA  318 (548)
Q Consensus       242 L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng~~~~gr~I~V~~a  318 (548)
                      |.++|++||.|..|.+...                      ..++|||+|.+.++|..|+ .||+..|.|+.|.|.++
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            6899999999999998321                      1389999999999999999 59999999999999874

(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 ....

>PF13893 RRM_5: RNA recognition motif

Probab=98.76  E-value=3.5e-08  Score=76.08  Aligned_cols=55  Identities=29%  Similarity=0.579  Sum_probs=49.3

Q ss_pred             HHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEee
Q 008920          353 IYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHA  416 (548)
Q Consensus       353 L~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~A  416 (548)
                      |..+|+.|    |.|..|.+....     .|+|||+|.+.++|..|+..++ ..+.|++|+|.||
T Consensus         1 L~~~f~~f----G~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKF----GEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTT----S-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCc----ccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999    999999987763     5899999999999999999888 9999999999996

(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 ....

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=98.72  E-value=2.3e-07  Score=95.47  Aligned_cols=162  Identities=17%  Similarity=0.222  Sum_probs=123.7

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-  302 (548)
                      .+-.|.|++|-..+++.+|.+.++.||+|.-|.++.                       .+..|.|+|++.+.|..|+. 
T Consensus        30 ~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P-----------------------~~r~alvefedi~~akn~Vnf   86 (494)
T KOG1456|consen   30 PSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMP-----------------------HKRQALVEFEDIEGAKNCVNF   86 (494)
T ss_pred             CCceEEEeccccccchhHHHHHHhcCCceEEEEecc-----------------------ccceeeeeeccccchhhheeh
Confidence            456899999999999999999999999998887732                       34589999999999999984 


Q ss_pred             --hcceeecCceeEeecCCCcccccCCCCCCcCCCccEEE--EeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCC
Q 008920          303 --FNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVF--VGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM  378 (548)
Q Consensus       303 --lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLf--V~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~t  378 (548)
                        -+...+.|..-.+.++........+.. . ..+...|.  |-|--+.+|-+-|..++..+    |.|..|.|+..  +
T Consensus        87 aa~n~i~i~gq~Al~NyStsq~i~R~g~e-s-~~pN~VLl~TIlNp~YpItvDVly~Icnp~----GkVlRIvIfkk--n  158 (494)
T KOG1456|consen   87 AADNQIYIAGQQALFNYSTSQCIERPGDE-S-ATPNKVLLFTILNPQYPITVDVLYTICNPQ----GKVLRIVIFKK--N  158 (494)
T ss_pred             hccCcccccCchhhcccchhhhhccCCCC-C-CCCCeEEEEEeecCccccchhhhhhhcCCC----CceEEEEEEec--c
Confidence              356677888777777754322222211 1 12223333  44555678999999999998    99999887765  3


Q ss_pred             CCCceEEEEEECCHHHHHHHHHHcC-Ccc-CC-eEEEEEeeecC
Q 008920          379 RVGKGIAYVLFKTREAANLVIKRRN-LKL-RD-RELRLSHAQQN  419 (548)
Q Consensus       379 g~srG~AFV~F~~~e~A~~Al~~ln-~~l-~G-r~I~V~~Ak~~  419 (548)
                      |.   .|.|+|++.+.|++|-..|| ..| -| .+|.|.||+|.
T Consensus       159 gV---QAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~  199 (494)
T KOG1456|consen  159 GV---QAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPT  199 (494)
T ss_pred             ce---eeEEeechhHHHHHHHhhcccccccccceeEEEEecCcc
Confidence            43   79999999999999999988 444 34 79999999986

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

Probab=98.71  E-value=2.4e-08  Score=110.38  Aligned_cols=76  Identities=28%  Similarity=0.418  Sum_probs=69.8

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      -.++|||||.|+..+++.+|..+|+.||.|.+|.|+-                       .+|||||.+...++|.+|| 
T Consensus       419 V~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~-----------------------~R~cAfI~M~~RqdA~kalq  475 (894)
T KOG0132|consen  419 VCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP-----------------------PRGCAFIKMVRRQDAEKALQ  475 (894)
T ss_pred             EeeeeeeeccccchhhHHHHHHHHHhcccceeEeecc-----------------------CCceeEEEEeehhHHHHHHH
Confidence            3578999999999999999999999999999999832                       6699999999999999999 


Q ss_pred             HhcceeecCceeEeecCCCc
Q 008920          302 AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~  321 (548)
                      +|+...+.+..|.|.|+...
T Consensus       476 kl~n~kv~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  476 KLSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             HHhcccccceeeEEeeeccC
Confidence            79999999999999999754

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

Probab=98.69  E-value=3.6e-08  Score=100.63  Aligned_cols=76  Identities=28%  Similarity=0.547  Sum_probs=68.3

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      +....||||++|-..+++.+|++||.+||+|.+|++..                       ..++|||+|.+.++|+.|.
T Consensus       225 D~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~-----------------------~~~CAFv~ftTR~aAE~Aa  281 (377)
T KOG0153|consen  225 DTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILP-----------------------RKGCAFVTFTTREAAEKAA  281 (377)
T ss_pred             ccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeec-----------------------ccccceeeehhhHHHHHHH
Confidence            45578999999988999999999999999999999832                       4579999999999999998


Q ss_pred             H--hcceeecCceeEeecCCC
Q 008920          302 A--FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       302 ~--lng~~~~gr~I~V~~a~~  320 (548)
                      +  ++...|.|..|.|.|..+
T Consensus       282 e~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  282 EKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             HhhcceeeecceEEEEEeCCC
Confidence            4  788999999999999876

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.66  E-value=7.3e-08  Score=92.36  Aligned_cols=86  Identities=24%  Similarity=0.388  Sum_probs=77.7

Q ss_pred             CcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCe
Q 008920          331 PLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDR  409 (548)
Q Consensus       331 ~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr  409 (548)
                      +.......+||..+|..+.+..|..+|.+|+   |.|..+++.++..||.++|||||+|++.+.|.-|-+.|| ..|.|+
T Consensus        44 p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~---g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~  120 (214)
T KOG4208|consen   44 PEQEIEGVVYVDHIPHGFFETEILNYFRQFG---GTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEH  120 (214)
T ss_pred             CccCCccceeecccccchhHHHHhhhhhhcC---CeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhh
Confidence            3345567899999999999999999999996   899999999999999999999999999999999999888 888899


Q ss_pred             EEEEEeeecC
Q 008920          410 ELRLSHAQQN  419 (548)
Q Consensus       410 ~I~V~~Ak~~  419 (548)
                      .|.|.+-.|.
T Consensus       121 lL~c~vmppe  130 (214)
T KOG4208|consen  121 LLECHVMPPE  130 (214)
T ss_pred             eeeeEEeCch
Confidence            9999987765

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.63  E-value=1.1e-08  Score=105.39  Aligned_cols=171  Identities=18%  Similarity=0.172  Sum_probs=124.7

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhcc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNM  305 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~lng  305 (548)
                      ..|.|.||.+.+|.++++.||.-+|.|..++|... +.+...|             .....|||.|.+...+..|..|..
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~-~~d~~~p-------------v~sRtcyVkf~d~~sv~vaQhLtn   73 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPN-VDDSKIP-------------VISRTCYVKFLDSQSVTVAQHLTN   73 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCC-CCCccCc-------------ceeeeEEEeccCCcceeHHhhhcc
Confidence            48999999999999999999999999999998331 1222222             255789999999999999999989


Q ss_pred             eeecCceeEeecCCCcccc-----------------cCCCC--------------------CCc----------CCCccE
Q 008920          306 AVIGGNHIRLDRACPPRKK-----------------LKGED--------------------APL----------YDIKKT  338 (548)
Q Consensus       306 ~~~~gr~I~V~~a~~~~k~-----------------~~~~~--------------------~~~----------~~~~~t  338 (548)
                      ++|-++-|.|-++......                 +..+.                    .|.          ....++
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            9999998888775432100                 00000                    000          112368


Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEeeec
Q 008920          339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQ  418 (548)
Q Consensus       339 LfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~Ak~  418 (548)
                      |+|.+|+..+...++.+.|..+    |.|.+.++..    +...-||-|.|........|+.+++..+.-+..++..-.|
T Consensus       154 ~~v~sl~~~~~l~e~~e~f~r~----Gev~ya~~as----k~~s~~c~~sf~~qts~~halr~~gre~k~qhsr~ai~kP  225 (479)
T KOG4676|consen  154 REVQSLISAAILPESGESFERK----GEVSYAHTAS----KSRSSSCSHSFRKQTSSKHALRSHGRERKRQHSRRAIIKP  225 (479)
T ss_pred             hhhhcchhhhcchhhhhhhhhc----chhhhhhhhc----cCCCcchhhhHhhhhhHHHHHHhcchhhhhhhhhhhhcCc
Confidence            9999999999999999999999    7887766543    3345588899999999999999988655543333333333

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

Probab=98.62  E-value=4.6e-08  Score=99.87  Aligned_cols=81  Identities=22%  Similarity=0.277  Sum_probs=72.7

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      .+...|||.-|.+-+|.++|.-+|+.||.|.+|.++++.                 .+|-+-.||||+|.+.+++++|. 
T Consensus       237 PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~-----------------ktgdsLqyaFiEFen~escE~AyF  299 (479)
T KOG0415|consen  237 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDR-----------------KTGDSLQYAFIEFENKESCEQAYF  299 (479)
T ss_pred             CCcceEEEEecCCcccccchhhHHhhcccceeeeEEecc-----------------cccchhheeeeeecchhhHHHHHh
Confidence            345789999999999999999999999999999996654                 35567789999999999999998 


Q ss_pred             HhcceeecCceeEeecCCC
Q 008920          302 AFNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~  320 (548)
                      .|+...|.++.|.|++++.
T Consensus       300 KMdNvLIDDrRIHVDFSQS  318 (479)
T KOG0415|consen  300 KMDNVLIDDRRIHVDFSQS  318 (479)
T ss_pred             hhcceeeccceEEeehhhh
Confidence            8999999999999999864

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

Probab=98.61  E-value=6e-08  Score=96.99  Aligned_cols=75  Identities=20%  Similarity=0.412  Sum_probs=69.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEe
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSH  415 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~  415 (548)
                      ..|||+|||..+++.+|+.+|++|    |.|..|.|+.+        ||||..++...|..||..|+ ..|+|..|.|.-
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~y----gkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVea   70 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQY----GKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEA   70 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhh----CceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEe
Confidence            469999999999999999999999    99999999977        99999999999999999877 999999999999


Q ss_pred             eecCCCCC
Q 008920          416 AQQNCTPS  423 (548)
Q Consensus       416 Ak~~~~~~  423 (548)
                      ++.++++.
T Consensus        71 SksKsk~s   78 (346)
T KOG0109|consen   71 SKSKSKAS   78 (346)
T ss_pred             ccccCCCc
Confidence            98774443

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

Probab=98.60  E-value=1.2e-07  Score=92.10  Aligned_cols=80  Identities=21%  Similarity=0.424  Sum_probs=71.5

Q ss_pred             CccEEEEeCCCCCCCHHHHHH----HHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCe
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQ----LFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDR  409 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~----~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr  409 (548)
                      +..||||.||+..+..++|+.    +|++|    |.|..|....   +...+|.|||.|.+.+.|-.|+..|+ ..+.|.
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqf----G~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK   80 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQF----GKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGK   80 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhh----CCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCc
Confidence            344999999999999998888    99999    8999887764   46789999999999999999999887 999999


Q ss_pred             EEEEEeeecCCC
Q 008920          410 ELRLSHAQQNCT  421 (548)
Q Consensus       410 ~I~V~~Ak~~~~  421 (548)
                      +|+|.||+.++.
T Consensus        81 ~mriqyA~s~sd   92 (221)
T KOG4206|consen   81 PMRIQYAKSDSD   92 (221)
T ss_pred             hhheecccCccc
Confidence            999999998744

>smart00361 RRM_1 RNA recognition motif

Probab=98.60  E-value=1.7e-07  Score=75.90  Aligned_cols=62  Identities=23%  Similarity=0.386  Sum_probs=50.2

Q ss_pred             HHHHHHHhh----hcCCeeEEE-EeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-HhcceeecCce
Q 008920          239 KKTLIKEFI----KFGEIDSVR-IRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNH  312 (548)
Q Consensus       239 ee~L~~~Fs----~fG~I~sVr-i~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng~~~~gr~  312 (548)
                      +++|.++|+    .||.|.+|. |..++.+.               .+.++|||||.|.+.++|..|+ .|||..+.|+.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~---------------~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~   66 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGY---------------ENHKRGNVYITFERSEDAARAIVDLNGRYFDGRT   66 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCC---------------CCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            578899998    999999985 53322110               1447799999999999999999 59999999999


Q ss_pred             eEe
Q 008920          313 IRL  315 (548)
Q Consensus       313 I~V  315 (548)
                      |.+
T Consensus        67 l~~   69 (70)
T smart00361       67 VKA   69 (70)
T ss_pred             EEe
Confidence            976

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

Probab=98.59  E-value=4e-08  Score=101.45  Aligned_cols=84  Identities=24%  Similarity=0.445  Sum_probs=78.9

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLS  414 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~  414 (548)
                      ..++|||++|+|+++++.|+..|.+|    |.|..|.|++|+.+++++||+||+|.+.+....+|....+.|.|+.|.+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~----Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k   80 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQF----GEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPK   80 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhccc----CceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccce
Confidence            56899999999999999999999999    99999999999999999999999999999999999888899999999999


Q ss_pred             eeecCCCC
Q 008920          415 HAQQNCTP  422 (548)
Q Consensus       415 ~Ak~~~~~  422 (548)
                      .|.++...
T Consensus        81 ~av~r~~~   88 (311)
T KOG4205|consen   81 RAVSREDQ   88 (311)
T ss_pred             eccCcccc
Confidence            99887433

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=98.59  E-value=1.8e-06  Score=88.97  Aligned_cols=160  Identities=13%  Similarity=0.147  Sum_probs=124.4

Q ss_pred             CCcccEEEEcCCCCC-CcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLK-VKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~-~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      ..+.+.+.|-+|... ++-+.|.++|-.||.|+.|.++...                      -|.|.|++.+..+++.|
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            345678999999865 6778899999999999999996532                      37899999999999999


Q ss_pred             H-HhcceeecCceeEeecCCCccccc------CC----------------------CCCCcCCCccEEEEeCCCCCCCHH
Q 008920          301 L-AFNMAVIGGNHIRLDRACPPRKKL------KG----------------------EDAPLYDIKKTVFVGNLPFDVKDE  351 (548)
Q Consensus       301 l-~lng~~~~gr~I~V~~a~~~~k~~------~~----------------------~~~~~~~~~~tLfV~NLp~~~tee  351 (548)
                      + .||+..+.|.+|.|+.+...--..      ..                      .......+++.|+.-|.|..+||+
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 599999999999999876431100      00                      002334578899999999999999


Q ss_pred             HHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCC
Q 008920          352 EIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRD  408 (548)
Q Consensus       352 dL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~G  408 (548)
                      .|..+|...+.   ....|+|..-+ +.++ --|.++|++.++|..||..+| ..|.+
T Consensus       422 ~l~~i~nek~v---~~~svkvFp~k-serS-ssGllEfe~~s~Aveal~~~NH~pi~~  474 (494)
T KOG1456|consen  422 QLIGICNEKDV---PPTSVKVFPLK-SERS-SSGLLEFENKSDAVEALMKLNHYPIEG  474 (494)
T ss_pred             HHHHHhhhcCC---CcceEEeeccc-cccc-ccceeeeehHHHHHHHHHHhccccccC
Confidence            99999988742   35667776554 3333 368999999999999998888 66655

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

Probab=98.53  E-value=7.5e-08  Score=95.18  Aligned_cols=97  Identities=22%  Similarity=0.336  Sum_probs=82.5

Q ss_pred             CceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEE
Q 008920          310 GNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLF  389 (548)
Q Consensus       310 gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F  389 (548)
                      .|.|.|..+.....         ....++||||-|...-.|+|++.+|..|    |.|..|.|.+.+ .|.++|+|||.|
T Consensus         2 nrpiqvkpadsesr---------g~~drklfvgml~kqq~e~dvrrlf~pf----G~~~e~tvlrg~-dg~sKGCAFVKf   67 (371)
T KOG0146|consen    2 NRPIQVKPADSESR---------GGDDRKLFVGMLNKQQSEDDVRRLFQPF----GNIEECTVLRGP-DGNSKGCAFVKF   67 (371)
T ss_pred             CCCccccccccccC---------CccchhhhhhhhcccccHHHHHHHhccc----CCcceeEEecCC-CCCCCCceEEEe
Confidence            46777877754321         2246899999999999999999999999    999999999986 599999999999


Q ss_pred             CCHHHHHHHHHHcC--CccCC--eEEEEEeeecCC
Q 008920          390 KTREAANLVIKRRN--LKLRD--RELRLSHAQQNC  420 (548)
Q Consensus       390 ~~~e~A~~Al~~ln--~~l~G--r~I~V~~Ak~~~  420 (548)
                      .+..+|+.||..|+  ..|-|  -.|.|.|+....
T Consensus        68 ~s~~eAqaAI~aLHgSqTmpGASSSLVVK~ADTdk  102 (371)
T KOG0146|consen   68 SSHAEAQAAINALHGSQTMPGASSSLVVKFADTDK  102 (371)
T ss_pred             ccchHHHHHHHHhcccccCCCCccceEEEeccchH
Confidence            99999999999887  77877  689999997653

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

Probab=98.42  E-value=5.8e-07  Score=92.02  Aligned_cols=76  Identities=28%  Similarity=0.462  Sum_probs=68.0

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHH-HcC-CccCCeE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIK-RRN-LKLRDRE  410 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~-~ln-~~l~Gr~  410 (548)
                      ...-.+|||++|...+++.+|+++|.+|    |.|.+|+++..      .|+|||+|.+.++|+.|.. .++ ..|.|+.
T Consensus       225 D~~I~tLyIg~l~d~v~e~dIrdhFyqy----Geirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~R  294 (377)
T KOG0153|consen  225 DTSIKTLYIGGLNDEVLEQDIRDHFYQY----GEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFR  294 (377)
T ss_pred             ccceeEEEecccccchhHHHHHHHHhhc----CCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceE
Confidence            3346899999999999999999999999    99999998866      5699999999999999974 455 8999999


Q ss_pred             EEEEeeec
Q 008920          411 LRLSHAQQ  418 (548)
Q Consensus       411 I~V~~Ak~  418 (548)
                      |.|.|+.+
T Consensus       295 l~i~Wg~~  302 (377)
T KOG0153|consen  295 LKIKWGRP  302 (377)
T ss_pred             EEEEeCCC
Confidence            99999987

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.41  E-value=4.7e-07  Score=99.55  Aligned_cols=89  Identities=22%  Similarity=0.393  Sum_probs=75.2

Q ss_pred             CCCcCCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHH
Q 008920          217 GFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQS  296 (548)
Q Consensus       217 ~~~~~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~  296 (548)
                      .+|+.+...+.|||+||++.++++.|...|..||+|.+|+|+... ++...             ....-||||.|.+..+
T Consensus       166 sfDdgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpR-tEeEk-------------~r~r~cgfvafmnR~D  231 (877)
T KOG0151|consen  166 SFDDGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPR-TEEEK-------------RRERNCGFVAFMNRAD  231 (877)
T ss_pred             cCCCCCCcccceeeecCCccccHHHHHHHhcccCcccceeeeccc-chhhh-------------ccccccceeeehhhhh
Confidence            455667778899999999999999999999999999999997633 22221             2255799999999999


Q ss_pred             HHHHH-HhcceeecCceeEeecCC
Q 008920          297 TEAAL-AFNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       297 A~~Al-~lng~~~~gr~I~V~~a~  319 (548)
                      |+.|+ .|+|..+.+..|.+.|+.
T Consensus       232 ~era~k~lqg~iv~~~e~K~gWgk  255 (877)
T KOG0151|consen  232 AERALKELQGIIVMEYEMKLGWGK  255 (877)
T ss_pred             HHHHHHHhcceeeeeeeeeecccc
Confidence            99999 599999999999999983

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

Probab=98.39  E-value=5.5e-07  Score=99.92  Aligned_cols=75  Identities=20%  Similarity=0.506  Sum_probs=69.8

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      .++|||||.|+..+++.||..+|..|    |.|.+|.++..      +|+|||.+....+|.+||.+|. ..+.++.|+|
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feef----GeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki  489 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEF----GEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKI  489 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhc----ccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEE
Confidence            46899999999999999999999999    99999988755      7899999999999999998887 9999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      .||...
T Consensus       490 ~Wa~g~  495 (894)
T KOG0132|consen  490 AWAVGK  495 (894)
T ss_pred             eeeccC
Confidence            999865

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.38  E-value=3.2e-07  Score=90.39  Aligned_cols=165  Identities=19%  Similarity=0.218  Sum_probs=115.4

Q ss_pred             cEEEEcCCCCCCcHHH-H--HHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          226 RTIFVGNLPLKVKKKT-L--IKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       226 rtVfVgNLP~~~tee~-L--~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...|++|+-..+..+- |  ...|+.|-.+....+..+                  ..+.-.+++|+.|........+- 
T Consensus        97 f~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~------------------~p~~~~~~~~~~~k~s~a~~k~~~  158 (290)
T KOG0226|consen   97 FRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRD------------------RPQPIRPEAFESFKASDALLKAET  158 (290)
T ss_pred             ccccccccccccCCCCCCcchhhhccchhhhhhhhhhc------------------CCCccCcccccCcchhhhhhhhcc
Confidence            3566777666655444 2  456665554433333211                  12346689999999877666665 


Q ss_pred             HhcceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCC
Q 008920          302 AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVG  381 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~s  381 (548)
                      +-++..+.-..|++.....-....   .....+....||.+.|..+++++-|-..|..|    -......+++|..||.+
T Consensus       159 ~~~~Kki~~~~VR~a~gtswedPs---l~ew~~~DfRIfcgdlgNevnd~vl~raf~Kf----psf~~akviRdkRTgKS  231 (290)
T KOG0226|consen  159 EKEKKKIGKPPVRLAAGTSWEDPS---LAEWDEDDFRIFCGDLGNEVNDDVLARAFKKF----PSFQKAKVIRDKRTGKS  231 (290)
T ss_pred             ccccccccCcceeeccccccCCcc---cccCccccceeecccccccccHHHHHHHHHhc----cchhhcccccccccccc
Confidence            345666655666655543221110   02223456789999999999999999999999    45667889999999999


Q ss_pred             ceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEe
Q 008920          382 KGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSH  415 (548)
Q Consensus       382 rG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~  415 (548)
                      +||+||.|.+..++..|+..|+ ..++.++|.+.-
T Consensus       232 kgygfVSf~~pad~~rAmrem~gkyVgsrpiklRk  266 (290)
T KOG0226|consen  232 KGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRK  266 (290)
T ss_pred             ccceeeeecCHHHHHHHHHhhcccccccchhHhhh
Confidence            9999999999999999998887 888888887653

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.38  E-value=7.2e-07  Score=95.79  Aligned_cols=80  Identities=16%  Similarity=0.308  Sum_probs=75.7

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLS  414 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~  414 (548)
                      .+.|||.+|...+-..||+.+|+.|    |.|+...|+.+..+...++||||++.+.++|.+||..|+ ..|.|+.|.|.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKy----GKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVE  480 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKY----GKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVE  480 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHh----cceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeee
Confidence            5789999999999999999999999    899999999998888889999999999999999999999 99999999999


Q ss_pred             eeecC
Q 008920          415 HAQQN  419 (548)
Q Consensus       415 ~Ak~~  419 (548)
                      .++..
T Consensus       481 kaKNE  485 (940)
T KOG4661|consen  481 KAKNE  485 (940)
T ss_pred             ecccC
Confidence            99864

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.35  E-value=2.9e-06  Score=91.00  Aligned_cols=80  Identities=19%  Similarity=0.285  Sum_probs=69.0

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEe
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSH  415 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~  415 (548)
                      ..+|||+|||++++..+|.++|..|    |.|....|..-...+...+||||+|.+.++++.||.+.-..|+|++|.|.-
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~F----G~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Vee  363 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQF----GPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEE  363 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhc----ccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEe
Confidence            3459999999999999999999999    899998877643234444899999999999999999988999999999997


Q ss_pred             eecC
Q 008920          416 AQQN  419 (548)
Q Consensus       416 Ak~~  419 (548)
                      -++.
T Consensus       364 k~~~  367 (419)
T KOG0116|consen  364 KRPG  367 (419)
T ss_pred             cccc
Confidence            7664

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.34  E-value=1.1e-06  Score=84.32  Aligned_cols=79  Identities=16%  Similarity=0.308  Sum_probs=67.2

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhc-CCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKF-GEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~f-G~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ...+||..||..+.+..|..+|.+| |.|..+++-+                 +..+|.++|||||+|.+++.|.-|. .
T Consensus        49 ~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsR-----------------nkrTGNSKgYAFVEFEs~eVA~IaAET  111 (214)
T KOG4208|consen   49 EGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSR-----------------NKRTGNSKGYAFVEFESEEVAKIAAET  111 (214)
T ss_pred             ccceeecccccchhHHHHhhhhhhcCCeeEEEEeec-----------------ccccCCcCceEEEEeccHHHHHHHHHH
Confidence            4579999999999999999999998 6777777622                 1237789999999999999999888 5


Q ss_pred             hcceeecCceeEeecCCC
Q 008920          303 FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~  320 (548)
                      ||++.|.|+-|.|....+
T Consensus       112 MNNYLl~e~lL~c~vmpp  129 (214)
T KOG4208|consen  112 MNNYLLMEHLLECHVMPP  129 (214)
T ss_pred             hhhhhhhhheeeeEEeCc
Confidence            999999999999988643

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

Probab=98.30  E-value=4.4e-06  Score=81.08  Aligned_cols=90  Identities=28%  Similarity=0.403  Sum_probs=69.6

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEee-cCCCCCCceEEEEEECCHHHHHHHHHHcC-Ccc---CCe
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIR-HPHMRVGKGIAYVLFKTREAANLVIKRRN-LKL---RDR  409 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~-d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l---~Gr  409 (548)
                      .-+||||.+||.++...+|+.+|..|.   | .+.+.|-. +.....++.+|||+|.+...|..|+.+|| ..|   .+.
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~---G-YEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~s  108 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFH---G-YEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGS  108 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCC---C-ccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCc
Confidence            358999999999999999999999994   3 34444432 33334566899999999999999999998 555   468


Q ss_pred             EEEEEeeecCCCCCCCCCC
Q 008920          410 ELRLSHAQQNCTPSKRKDV  428 (548)
Q Consensus       410 ~I~V~~Ak~~~~~~~rr~~  428 (548)
                      .|+|.+|+.+....+++..
T Consensus       109 tLhiElAKSNtK~kr~k~s  127 (284)
T KOG1457|consen  109 TLHIELAKSNTKRKRRKGS  127 (284)
T ss_pred             eeEeeehhcCcccccCCCC
Confidence            9999999987655544433

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.28  E-value=1.3e-06  Score=93.91  Aligned_cols=81  Identities=15%  Similarity=0.340  Sum_probs=70.3

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...+.|||.+|...+-..+|..||++||.|.-..+++.    ...|-             .+.|+||++.+.++|.+|| 
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTN----aRsPG-------------aRCYGfVTMSts~eAtkCI~  465 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTN----ARSPG-------------ARCYGFVTMSTSAEATKCIE  465 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeec----CCCCC-------------cceeEEEEecchHHHHHHHH
Confidence            35678999999999999999999999999999888543    33332             6689999999999999999 


Q ss_pred             HhcceeecCceeEeecCCC
Q 008920          302 AFNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~  320 (548)
                      .||.+.|.|+.|.|..+..
T Consensus       466 hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  466 HLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             Hhhhhhhcceeeeeeeccc
Confidence            5999999999999999864

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.26  E-value=1.3e-06  Score=94.38  Aligned_cols=164  Identities=20%  Similarity=0.197  Sum_probs=107.7

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      +-..++|+|-|||..++.++|..+|+.||+|..|+..                      -...|.+||+|.+..+|+.|+
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t----------------------~~~~~~~~v~FyDvR~A~~Al  129 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRET----------------------PNKRGIVFVEFYDVRDAERAL  129 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcc----------------------cccCceEEEEEeehHhHHHHH
Confidence            3456899999999999999999999999999997761                      125689999999999999999


Q ss_pred             -HhcceeecCceeEeecCCCcccccCCCC-------------CCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCe
Q 008920          302 -AFNMAVIGGNHIRLDRACPPRKKLKGED-------------APLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSV  367 (548)
Q Consensus       302 -~lng~~~~gr~I~V~~a~~~~k~~~~~~-------------~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I  367 (548)
                       +|++..|.|+.|................             .+..-+...+| +.|++..+..-+..+|.-+    |.+
T Consensus       130 k~l~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~-g~l~P~~s~~~~~~~~~~~----~~~  204 (549)
T KOG4660|consen  130 KALNRREIAGKRIKRPGGARRAMGLQSGTSFLNHFGSPLANSPPGGWPRGQLF-GMLSPTRSSILLEHISSVD----GSS  204 (549)
T ss_pred             HHHHHHHhhhhhhcCCCcccccchhcccchhhhhccchhhcCCCCCCcCCcce-eeeccchhhhhhhcchhcc----Ccc
Confidence             6999999998887222211100000000             11111122333 3488887776666666666    555


Q ss_pred             EEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEeeec
Q 008920          368 EAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQ  418 (548)
Q Consensus       368 ~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~Ak~  418 (548)
                      .. +     .++.-.-.-||.|.+..++..++..++..+.+....+.++.+
T Consensus       205 ~~-~-----~~~~~~hq~~~~~~~~~s~a~~~~~~G~~~s~~~~v~t~S~~  249 (549)
T KOG4660|consen  205 PG-R-----ETPLLNHQRFVEFADNRSYAFSEPRGGFLISNSSGVITFSGP  249 (549)
T ss_pred             cc-c-----cccchhhhhhhhhccccchhhcccCCceecCCCCceEEecCC
Confidence            43 2     222222356788888888855555344666666666666655

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.24  E-value=2.5e-06  Score=93.68  Aligned_cols=172  Identities=12%  Similarity=0.040  Sum_probs=125.2

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhc
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~ln  304 (548)
                      .+-|-+.++++++...++++||...- |.++.|..                 +.-.+...|.+||.|....++++|+..|
T Consensus       311 ~~y~~~~gm~fn~~~nd~rkfF~g~~-~~~~~l~~-----------------~~v~~~~tG~~~v~f~~~~~~q~A~~rn  372 (944)
T KOG4307|consen  311 KYYNNYKGMEFNNDFNDGRKFFPGRN-AQSTDLSE-----------------NRVAPPQTGRKTVMFTPQAPFQNAFTRN  372 (944)
T ss_pred             hheeeecccccccccchhhhhcCccc-ccccchhh-----------------hhcCCCcCCceEEEecCcchHHHHHhcC
Confidence            35677789999999999999987422 22333311                 1111224789999999999999999989


Q ss_pred             ceeecCceeEeecCCCcccccCC--------------C--------------C--CCcCCCccEEEEeCCCCCCCHHHHH
Q 008920          305 MAVIGGNHIRLDRACPPRKKLKG--------------E--------------D--APLYDIKKTVFVGNLPFDVKDEEIY  354 (548)
Q Consensus       305 g~~~~gr~I~V~~a~~~~k~~~~--------------~--------------~--~~~~~~~~tLfV~NLp~~~teedL~  354 (548)
                      .+.+-.|.|.|..+.........              .              .  ........+|||..||+.+++.++.
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            99888999888776422110000              0              0  0112346799999999999999999


Q ss_pred             HHHhccCCCCCCeEE-EEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          355 QLFCGLNDLESSVEA-VRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       355 ~~F~~~g~~~G~I~~-VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      .+|...    -.|++ |.|.+.+ ++..++.|||.|...+++..|+.... +.++.|.|+|.-....
T Consensus       453 ~~f~~~----~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~~  514 (944)
T KOG4307|consen  453 NKFMGA----AAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIADY  514 (944)
T ss_pred             hhhhhh----hhhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEeechhhH
Confidence            999876    46766 5555554 68889999999999999988876666 7888899999876544

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.21  E-value=3.5e-06  Score=84.13  Aligned_cols=80  Identities=23%  Similarity=0.363  Sum_probs=69.2

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      -..+|+|.|||+.++.++|.+||..||.+..+-|..++                  .|.+.|.|-|.|...++|..|+ .
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~------------------~G~s~Gta~v~~~r~~DA~~avk~  143 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR------------------AGRSLGTADVSFNRRDDAERAVKK  143 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC------------------CCCCCccceeeecchHhHHHHHHH
Confidence            34789999999999999999999999988777774433                  4567899999999999999999 5


Q ss_pred             hcceeecCceeEeecCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~  321 (548)
                      +|+..+.|+.|.+.....+
T Consensus       144 ~~gv~ldG~~mk~~~i~~~  162 (243)
T KOG0533|consen  144 YNGVALDGRPMKIEIISSP  162 (243)
T ss_pred             hcCcccCCceeeeEEecCc
Confidence            9999999999999887643

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.20  E-value=4.3e-06  Score=83.52  Aligned_cols=79  Identities=27%  Similarity=0.414  Sum_probs=73.6

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLS  414 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~  414 (548)
                      ...|+|.|||+.++++||.++|..|    |.+..+-|.++ ..|.+.|.|-|.|...++|..|++.++ ..|.|+.|.+.
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~----~~~~r~~vhy~-~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~  157 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEF----GELKRVAVHYD-RAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIE  157 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHh----ccceEEeeccC-CCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeE
Confidence            4789999999999999999999999    88999999999 479999999999999999999999988 99999999999


Q ss_pred             eeecC
Q 008920          415 HAQQN  419 (548)
Q Consensus       415 ~Ak~~  419 (548)
                      ...+.
T Consensus       158 ~i~~~  162 (243)
T KOG0533|consen  158 IISSP  162 (243)
T ss_pred             EecCc
Confidence            88765

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.13  E-value=4.9e-06  Score=89.27  Aligned_cols=81  Identities=21%  Similarity=0.312  Sum_probs=66.7

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      .....+|||+|||++++..+|.++|..||.|....|.....                 .+..-+||||+|.+..+++.||
T Consensus       285 ~~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~-----------------~~~~~~fgFV~f~~~~~~~~~i  347 (419)
T KOG0116|consen  285 RADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSP-----------------GGKNPCFGFVEFENAAAVQNAI  347 (419)
T ss_pred             eecccceEeecCCCCCCHHHHHHHHhhcccccccceEEecc-----------------CCCcCceEEEEEeecchhhhhh
Confidence            34556799999999999999999999999999888844221                 1123389999999999999999


Q ss_pred             HhcceeecCceeEeecCC
Q 008920          302 AFNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~  319 (548)
                      .-+-..++++.|.|..-.
T Consensus       348 ~Asp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  348 EASPLEIGGRKLNVEEKR  365 (419)
T ss_pred             hcCccccCCeeEEEEecc
Confidence            888888999999998743

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.13  E-value=2.8e-06  Score=84.74  Aligned_cols=80  Identities=21%  Similarity=0.257  Sum_probs=70.1

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      -+.+.|||+|+.+.+|.++|..+|+.||.|..|.|..+.+                 .++++|||||+|.+.+.++.||.
T Consensus        99 ~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~-----------------~~~~k~~~yvef~~~~~~~~ay~  161 (231)
T KOG4209|consen   99 VDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKF-----------------RGHPKGFAYVEFSSYELVEEAYK  161 (231)
T ss_pred             cCCceEEEeccccccccchhhheeeccCCccceeeecccc-----------------CCCcceeEEEecccHhhhHHHhh
Confidence            3457899999999999999999999999999888855442                 34477999999999999999999


Q ss_pred             hcceeecCceeEeecCC
Q 008920          303 FNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~  319 (548)
                      |++..|.|+.|.|.+..
T Consensus       162 l~gs~i~~~~i~vt~~r  178 (231)
T KOG4209|consen  162 LDGSEIPGPAIEVTLKR  178 (231)
T ss_pred             cCCcccccccceeeeee
Confidence            99999999999998864

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.08  E-value=1e-05  Score=80.79  Aligned_cols=83  Identities=23%  Similarity=0.246  Sum_probs=76.1

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELR  412 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~  412 (548)
                      ......|||+|+.+.++.+.+..+|..|    |.|..|.|+.|..++.++||+||+|.+.+.+..|+.+.+..|.|+.|.
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~C----g~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~  173 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESC----GGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIE  173 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeecc----CCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCCcccccccce
Confidence            3456789999999999999999999999    899999999999999999999999999999999999555999999999


Q ss_pred             EEeeecC
Q 008920          413 LSHAQQN  419 (548)
Q Consensus       413 V~~Ak~~  419 (548)
                      |.+..-+
T Consensus       174 vt~~r~~  180 (231)
T KOG4209|consen  174 VTLKRTN  180 (231)
T ss_pred             eeeeeee
Confidence            9998866

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

Probab=98.06  E-value=2.5e-05  Score=67.52  Aligned_cols=80  Identities=21%  Similarity=0.192  Sum_probs=68.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccC----CeEE
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLR----DREL  411 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~----Gr~I  411 (548)
                      +||.|+|+|...+.++|.+++....  .|..-.+.++.|..++-+.|||||.|.+++.|.......+ ..+.    .+..
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~--~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc   79 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHF--KGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVC   79 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhc--cCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEE
Confidence            6899999999999999999997653  3888889999999999999999999999999999987766 4433    3677


Q ss_pred             EEEeeec
Q 008920          412 RLSHAQQ  418 (548)
Q Consensus       412 ~V~~Ak~  418 (548)
                      .|.||.-
T Consensus        80 ~i~yAri   86 (97)
T PF04059_consen   80 EISYARI   86 (97)
T ss_pred             EEehhHh
Confidence            8888864

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

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.00  E-value=1.3e-06  Score=91.21  Aligned_cols=151  Identities=17%  Similarity=0.269  Sum_probs=118.9

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-hcc
Q 008920          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-FNM  305 (548)
Q Consensus       227 tVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-lng  305 (548)
                      .+|++||...++..+|..+|...-.-.+-.|                +.       ..|||||.+.+..+|.+|++ ++|
T Consensus         3 klyignL~p~~~psdl~svfg~ak~~~~g~f----------------l~-------k~gyafvd~pdq~wa~kaie~~sg   59 (584)
T KOG2193|consen    3 KLYIGNLSPQVTPSDLESVFGDAKIPGSGQF----------------LV-------KSGYAFVDCPDQQWANKAIETLSG   59 (584)
T ss_pred             cccccccCCCCChHHHHHHhccccCCCCcce----------------ee-------ecceeeccCCchhhhhhhHHhhch
Confidence            5899999999999999999985421111111                11       45899999999999999995 665


Q ss_pred             e-eecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEe-ecCCCCCCce
Q 008920          306 A-VIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVI-RHPHMRVGKG  383 (548)
Q Consensus       306 ~-~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~-~d~~tg~srG  383 (548)
                      . .+.|..+.|....+.           ....+.+-|+|+|....|+.|..++..|    |.|+.|.++ .+..+    -
T Consensus        60 k~elqGkr~e~~~sv~k-----------kqrsrk~Qirnippql~wevld~Ll~qy----g~ve~~eqvnt~~et----a  120 (584)
T KOG2193|consen   60 KVELQGKRQEVEHSVPK-----------KQRSRKIQIRNIPPQLQWEVLDSLLAQY----GTVENCEQVNTDSET----A  120 (584)
T ss_pred             hhhhcCceeeccchhhH-----------HHHhhhhhHhcCCHHHHHHHHHHHHhcc----CCHhHhhhhccchHH----H
Confidence            4 688999999887653           2345679999999999999999999999    899998654 34332    2


Q ss_pred             EEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          384 IAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       384 ~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      ..-|+|...+.+..||..++ ..|....+.|.|-...
T Consensus       121 vvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiPde  157 (584)
T KOG2193|consen  121 VVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIPDE  157 (584)
T ss_pred             HHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCchh
Confidence            34578999999999999888 9999999999997543

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

Probab=97.98  E-value=1.8e-05  Score=81.25  Aligned_cols=79  Identities=27%  Similarity=0.408  Sum_probs=70.4

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeE--------EEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-Ccc
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVE--------AVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKL  406 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~--------~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l  406 (548)
                      ...|||.|||.++|.+++.++|+.|    |.|.        .|.|.++. .|..+|=|.+.|...+++..||..|+ ..|
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKc----GiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~  208 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKC----GIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDEL  208 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhc----ceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccc
Confidence            4569999999999999999999999    5553        27788884 59999999999999999999999999 999


Q ss_pred             CCeEEEEEeeecC
Q 008920          407 RDRELRLSHAQQN  419 (548)
Q Consensus       407 ~Gr~I~V~~Ak~~  419 (548)
                      .|+.|+|..|+-.
T Consensus       209 rg~~~rVerAkfq  221 (382)
T KOG1548|consen  209 RGKKLRVERAKFQ  221 (382)
T ss_pred             cCcEEEEehhhhh
Confidence            9999999999754

>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=97.76  E-value=0.00011  Score=61.39  Aligned_cols=69  Identities=23%  Similarity=0.287  Sum_probs=47.0

Q ss_pred             cEEEEeCCCCCCCHH----HHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          337 KTVFVGNLPFDVKDE----EIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       337 ~tLfV~NLp~~~tee----dL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ..|||.|||.+.+..    -|++++..||   |.|..|.          .|.|+|.|.+.+.|..|++.|. ..+.|+.|
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCG---GkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI   69 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCG---GKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKI   69 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT-----EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccC---CEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceE
Confidence            469999999998865    5667777887   8888772          3689999999999999997776 99999999


Q ss_pred             EEEeeec
Q 008920          412 RLSHAQQ  418 (548)
Q Consensus       412 ~V~~Ak~  418 (548)
                      .|.|...
T Consensus        70 ~v~~~~~   76 (90)
T PF11608_consen   70 SVSFSPK   76 (90)
T ss_dssp             EEESS--
T ss_pred             EEEEcCC
Confidence            9999853

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

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=97.73  E-value=5.3e-05  Score=83.84  Aligned_cols=81  Identities=19%  Similarity=0.351  Sum_probs=72.5

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecC---CCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP---HMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE  410 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~---~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~  410 (548)
                      .+..|||+||+..++++.|...|+.|    |.|.+|.|+.-+   .....+.+|||.|-+..+|++|+..|+ ..+.+..
T Consensus       173 ~TTNlyv~Nlnpsv~E~~ll~tfGrf----gPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e  248 (877)
T KOG0151|consen  173 QTTNLYVGNLNPSVDENFLLRTFGRF----GPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYE  248 (877)
T ss_pred             cccceeeecCCccccHHHHHHHhccc----CcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeee
Confidence            46789999999999999999999999    899999988654   345667799999999999999998888 9999999


Q ss_pred             EEEEeeecC
Q 008920          411 LRLSHAQQN  419 (548)
Q Consensus       411 I~V~~Ak~~  419 (548)
                      |++.|++..
T Consensus       249 ~K~gWgk~V  257 (877)
T KOG0151|consen  249 MKLGWGKAV  257 (877)
T ss_pred             eeecccccc
Confidence            999999765

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

Probab=97.70  E-value=4e-05  Score=75.25  Aligned_cols=71  Identities=20%  Similarity=0.476  Sum_probs=63.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEe
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSH  415 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~  415 (548)
                      ..|||++||+.+.+.+|..||..|    |.|..|.+.        .||+||+|.+.-+|..|+..++ ..|+|-.+.|.|
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~y----g~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~   69 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGY----GKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEH   69 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhc----cccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeec
Confidence            358999999999999999999999    889888764        4599999999999999998887 888887799999


Q ss_pred             eecC
Q 008920          416 AQQN  419 (548)
Q Consensus       416 Ak~~  419 (548)
                      +...
T Consensus        70 ~r~~   73 (216)
T KOG0106|consen   70 ARGK   73 (216)
T ss_pred             cccc
Confidence            8854

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

Probab=97.69  E-value=1.8e-05  Score=76.68  Aligned_cols=79  Identities=23%  Similarity=0.271  Sum_probs=69.7

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      .+..++|||+||-..++++-|.++|-+-    |.|..|.|+.+. .+..+ ||||.|.+.....-|++++| ..|.++.|
T Consensus         6 ae~drtl~v~n~~~~v~eelL~Elfiqa----GPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~   79 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQA----GPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEE   79 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhcc----CceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchh
Confidence            3456899999999999999999999998    899999988875 45666 99999999999999999998 99999888


Q ss_pred             EEEeee
Q 008920          412 RLSHAQ  417 (548)
Q Consensus       412 ~V~~Ak  417 (548)
                      .|.+-.
T Consensus        80 q~~~r~   85 (267)
T KOG4454|consen   80 QRTLRC   85 (267)
T ss_pred             hccccc
Confidence            887754

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

Probab=97.59  E-value=4.6e-06  Score=93.83  Aligned_cols=162  Identities=19%  Similarity=0.164  Sum_probs=123.2

Q ss_pred             cEEEEcCCCCCCcHH-HHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhc
Q 008920          226 RTIFVGNLPLKVKKK-TLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (548)
Q Consensus       226 rtVfVgNLP~~~tee-~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~ln  304 (548)
                      +...+.|+.+..... .+...|..+|.|+.|++.-..     .         +-|   ...++|+++....+++.|....
T Consensus       572 ~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g-----~---------k~h---~q~~~~~~~s~~~~~esat~pa  634 (881)
T KOG0128|consen  572 REKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRG-----F---------KAH---EQPQQQKVQSKHGSAESATVPA  634 (881)
T ss_pred             hhhcccCCCcchhhHHhhHHHhhcccccccccCcccc-----c---------ccc---ccchhhhhhccccchhhccccc
Confidence            346677777776655 567889999999999872210     0         001   2228999999999999999988


Q ss_pred             ceeecCceeEeecCCCcccccCCCCC-CcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCce
Q 008920          305 MAVIGGNHIRLDRACPPRKKLKGEDA-PLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG  383 (548)
Q Consensus       305 g~~~~gr~I~V~~a~~~~k~~~~~~~-~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG  383 (548)
                      +..+.++.+.|..+.+.......... .......++||+||+..+.+.+|...|..+    |.+..|+|......+..+|
T Consensus       635 ~~~~a~~~~av~~ad~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~----~~~e~vqi~~h~n~~~~rG  710 (881)
T KOG0128|consen  635 GGALANRSAAVGLADAEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPS----GTIEVVQIVIHKNEKRFRG  710 (881)
T ss_pred             ccccCCccccCCCCCchhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCcc----chhhhHHHHHHhhcccccc
Confidence            99999999999988765422111111 112235689999999999999999999999    7888887776667899999


Q ss_pred             EEEEEECCHHHHHHHHHHcCCccCC
Q 008920          384 IAYVLFKTREAANLVIKRRNLKLRD  408 (548)
Q Consensus       384 ~AFV~F~~~e~A~~Al~~ln~~l~G  408 (548)
                      +|||.|...+.+.+||......+.|
T Consensus       711 ~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  711 KAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             ceeeEeecCCchhhhhhhhhhhhhh
Confidence            9999999999999999988755555

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=97.59  E-value=5.7e-05  Score=81.89  Aligned_cols=71  Identities=21%  Similarity=0.346  Sum_probs=63.6

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ..+.++|+|-|||..+++++|..+|+.|    |+|..|+.     +-..+|.+||+|.|.-+|+.|++.++ ..|.|+.|
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~y----Geir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~  142 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAY----GEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRI  142 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhh----cchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhh
Confidence            4567999999999999999999999999    89988764     44458999999999999999999999 99999887


Q ss_pred             E
Q 008920          412 R  412 (548)
Q Consensus       412 ~  412 (548)
                      .
T Consensus       143 k  143 (549)
T KOG4660|consen  143 K  143 (549)
T ss_pred             c
Confidence            7

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=97.52  E-value=0.00011  Score=72.73  Aligned_cols=79  Identities=19%  Similarity=0.298  Sum_probs=66.6

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      +...||+|.|..+++.+.|...|.+|-.....+++++.                 .+|+++||+||.|.+..++..|+ +
T Consensus       189 ~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdk-----------------RTgKSkgygfVSf~~pad~~rAmre  251 (290)
T KOG0226|consen  189 DDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDK-----------------RTGKSKGYGFVSFRDPADYVRAMRE  251 (290)
T ss_pred             ccceeecccccccccHHHHHHHHHhccchhhccccccc-----------------cccccccceeeeecCHHHHHHHHHh
Confidence            34689999999999999999999999766555553332                 46789999999999999999999 7


Q ss_pred             hcceeecCceeEeecCC
Q 008920          303 FNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~  319 (548)
                      |+|..++.+.|.+..+.
T Consensus       252 m~gkyVgsrpiklRkS~  268 (290)
T KOG0226|consen  252 MNGKYVGSRPIKLRKSE  268 (290)
T ss_pred             hcccccccchhHhhhhh
Confidence            99999999988876653

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

Probab=97.50  E-value=0.00067  Score=58.73  Aligned_cols=76  Identities=21%  Similarity=0.249  Sum_probs=56.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhc--CCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKF--GEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~f--G~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      +||.|+|||...|.++|.+++...  |...-+-|+.|                 +.++.+.|||||.|.+++.|.... .
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiD-----------------f~~~~N~GYAFVNf~~~~~~~~F~~~   64 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPID-----------------FKNKCNLGYAFVNFTSPQAAIRFYKA   64 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeee-----------------ccCCCceEEEEEEcCCHHHHHHHHHH
Confidence            799999999999999999998863  44333444322                 334568899999999999999887 5


Q ss_pred             hcceeecC----ceeEeecC
Q 008920          303 FNMAVIGG----NHIRLDRA  318 (548)
Q Consensus       303 lng~~~~g----r~I~V~~a  318 (548)
                      ++|..+..    ....|.+|
T Consensus        65 f~g~~w~~~~s~Kvc~i~yA   84 (97)
T PF04059_consen   65 FNGKKWPNFNSKKVCEISYA   84 (97)
T ss_pred             HcCCccccCCCCcEEEEehh
Confidence            88887743    34555555

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

>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=97.49  E-value=0.00039  Score=58.13  Aligned_cols=67  Identities=21%  Similarity=0.239  Sum_probs=45.9

Q ss_pred             cEEEEcCCCCCCcHHHHH----HHhhhcC-CeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          226 RTIFVGNLPLKVKKKTLI----KEFIKFG-EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~----~~Fs~fG-~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      ..|||.|||.+.+...|.    +++..|| .|.+|                           +.+.|+|.|.+.+.|..|
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            469999999998876655    5666786 45443                           237899999999999999


Q ss_pred             H-HhcceeecCceeEeecCC
Q 008920          301 L-AFNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       301 l-~lng~~~~gr~I~V~~a~  319 (548)
                      + .|+|..+.|+.|.|.+..
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 599999999999999974

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_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=97.17  E-value=0.001  Score=58.46  Aligned_cols=68  Identities=28%  Similarity=0.349  Sum_probs=43.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC------CccCCeE
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN------LKLRDRE  410 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln------~~l~Gr~  410 (548)
                      ..|+|.+++..++.++|+++|..|    |.|..|.+....      ..|||.|.+.+.|+.|+..+.      ..|.+..
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~----g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~   71 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQF----GEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKE   71 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS------EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSS
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhc----CCcceEEecCCC------CEEEEEECCcchHHHHHHHHHhccCCceEEcCce
Confidence            468999999999999999999999    899999887652      389999999999999987654      4566655


Q ss_pred             EEEE
Q 008920          411 LRLS  414 (548)
Q Consensus       411 I~V~  414 (548)
                      +.+.
T Consensus        72 ~~~~   75 (105)
T PF08777_consen   72 VTLE   75 (105)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            5554

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.05  E-value=0.0006  Score=72.00  Aligned_cols=82  Identities=28%  Similarity=0.320  Sum_probs=62.1

Q ss_pred             CCCCcCCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeee---cccCCCCCccchhhhhhhccCCCcceEEEEec
Q 008920          216 EGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSV---PIIDTKIPRKGAILQKQINENADSVHAYIVFK  292 (548)
Q Consensus       216 e~~~~~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~---~~~~~~~prkga~~~~~~~~g~skG~AFV~F~  292 (548)
                      ..+++++-..+||.+-|||.+-.-+-|.++|..||.|.+|+|+..   +....+.|+       .+..-..+-||||+|.
T Consensus       222 p~~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~-------~~~~~~tk~~AlvEye  294 (484)
T KOG1855|consen  222 PEFDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPK-------KYFELQTKECALVEYE  294 (484)
T ss_pred             CCccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCc-------cchhhhhhhhhhhhhh
Confidence            345566678899999999999999999999999999999999653   222222222       1222234678999999


Q ss_pred             CHHHHHHHHHhc
Q 008920          293 SEQSTEAALAFN  304 (548)
Q Consensus       293 s~e~A~~Al~ln  304 (548)
                      ..+.|.+|.++.
T Consensus       295 ~~~~A~KA~e~~  306 (484)
T KOG1855|consen  295 EVEAARKARELL  306 (484)
T ss_pred             hhHHHHHHHHhh
Confidence            999999999754

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.05  E-value=0.00039  Score=71.62  Aligned_cols=80  Identities=33%  Similarity=0.515  Sum_probs=67.1

Q ss_pred             ccEEE-EcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          225 LRTIF-VGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       225 ~rtVf-VgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      ..++| |+||++.++.++|..+|..+|.|..|+++.++  .               .+...|||||.|.....+..++..
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~--~---------------s~~~kg~a~~~~~~~~~~~~~~~~  246 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDE--E---------------SGDSKGFAYVDFSAGNSKKLALND  246 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCCC--C---------------ccchhhhhhhhhhhchhHHHHhhc
Confidence            34566 99999999999999999999999999985543  1               345779999999999999998854


Q ss_pred             cceeecCceeEeecCCCc
Q 008920          304 NMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~  321 (548)
                      +...+.++++.|....+.
T Consensus       247 ~~~~~~~~~~~~~~~~~~  264 (285)
T KOG4210|consen  247 QTRSIGGRPLRLEEDEPR  264 (285)
T ss_pred             ccCcccCcccccccCCCC
Confidence            778889999999987643

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.89  E-value=0.0011  Score=67.97  Aligned_cols=113  Identities=12%  Similarity=0.296  Sum_probs=74.4

Q ss_pred             cEEEEcCCCCCCcHHHH------HHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcce--EEEEecCHHHH
Q 008920          226 RTIFVGNLPLKVKKKTL------IKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH--AYIVFKSEQST  297 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L------~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~--AFV~F~s~e~A  297 (548)
                      .-|||-+||+.+..+++      .++|.+||.|..|.+-.  -+    +-        .+  ...+.  .||.|.+.++|
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNk--kt----~s--------~n--st~~h~gvYITy~~kedA  178 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNK--KT----SS--------LN--STASHAGVYITYSTKEDA  178 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecc--cc----cc--------cc--cccccceEEEEecchHHH
Confidence            46999999998876662      27999999998887711  11    10        01  11223  39999999999


Q ss_pred             HHHH-HhcceeecCceeEeecCCCccc--ccCCCCCCcCCCccEEEEeCCCC---CCCHHHHHHHH
Q 008920          298 EAAL-AFNMAVIGGNHIRLDRACPPRK--KLKGEDAPLYDIKKTVFVGNLPF---DVKDEEIYQLF  357 (548)
Q Consensus       298 ~~Al-~lng~~~~gr~I~V~~a~~~~k--~~~~~~~~~~~~~~tLfV~NLp~---~~teedL~~~F  357 (548)
                      ..|| +.+|..++|+.|...+.....=  -..   ....++..|+|+.--..   ..+.++|...-
T Consensus       179 arcIa~vDgs~~DGr~lkatYGTTKYCtsYLR---n~~CpNp~CMyLHEpg~e~Ds~tK~el~n~q  241 (480)
T COG5175         179 ARCIAEVDGSLLDGRVLKATYGTTKYCTSYLR---NAVCPNPDCMYLHEPGPEKDSLTKDELCNSQ  241 (480)
T ss_pred             HHHHHHhccccccCceEeeecCchHHHHHHHc---CCCCCCCCeeeecCCCcccccccHHHHhhhh
Confidence            9999 6899999999999988643200  000   12234556777754333   24677776544

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=96.89  E-value=0.00077  Score=69.96  Aligned_cols=83  Identities=18%  Similarity=0.233  Sum_probs=73.5

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeE--------EEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVE--------AVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-  403 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~--------~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-  403 (548)
                      .....+|||-+||..+++.+|.++|.++    |.|.        .|.|.+|.+|+.++|-|.|.|.+...|+.||.-++ 
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qc----g~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~ag  138 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQC----GVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAG  138 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhc----ceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcc
Confidence            3345789999999999999999999999    5552        36788899999999999999999999999999888 


Q ss_pred             CccCCeEEEEEeeecC
Q 008920          404 LKLRDRELRLSHAQQN  419 (548)
Q Consensus       404 ~~l~Gr~I~V~~Ak~~  419 (548)
                      ..|.|..|.|..|...
T Consensus       139 kdf~gn~ikvs~a~~r  154 (351)
T KOG1995|consen  139 KDFCGNTIKVSLAERR  154 (351)
T ss_pred             ccccCCCchhhhhhhc
Confidence            9999999999998765

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=96.88  E-value=0.0016  Score=67.13  Aligned_cols=80  Identities=13%  Similarity=0.189  Sum_probs=68.3

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      ...++||+||-|.+|++||.+.+...|.  ..+.++.+..++.+|.++|||+|...+..+....++.|. ..|.|..-.|
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~--~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGL--AQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhH--HHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            3578999999999999999999987742  367788888898999999999999999999999999998 8999975555


Q ss_pred             Eee
Q 008920          414 SHA  416 (548)
Q Consensus       414 ~~A  416 (548)
                      .-+
T Consensus       157 ~~~  159 (498)
T KOG4849|consen  157 LSY  159 (498)
T ss_pred             ecc
Confidence            443

>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=96.86  E-value=0.003  Score=55.50  Aligned_cols=54  Identities=20%  Similarity=0.394  Sum_probs=35.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      +.|+|.+++..++.++|+.+|+.||.|..|.+..                       ....|||.|.+++.|+.|+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~-----------------------G~~~g~VRf~~~~~A~~a~~   55 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSR-----------------------GDTEGYVRFKTPEAAQKALE   55 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--T-----------------------T-SEEEEEESS---HHHHHH
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecC-----------------------CCCEEEEEECCcchHHHHHH
Confidence            4789999999999999999999999998888721                       22479999999999999994

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.79  E-value=0.0027  Score=48.79  Aligned_cols=52  Identities=27%  Similarity=0.496  Sum_probs=42.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      +.|-|.+.|.+..+ .|..+|..||+|..+.+..                       ..-+.||.|.+..+|+.||
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~-----------------------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPE-----------------------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCC-----------------------CCcEEEEEECCHHHHHhhC
Confidence            57889999988775 4556999999999988720                       2358999999999999986

>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=96.72  E-value=0.007  Score=52.76  Aligned_cols=82  Identities=16%  Similarity=0.164  Sum_probs=51.6

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEE-EeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVR-IRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVr-i~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      .+.|.|=+.|.. ....|..+|++||.|.... +......-...|           ......+..|.|.++.+|.+||..
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~-----------~~~~~NWi~I~Y~~~~~A~rAL~~   73 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYP-----------IPSGGNWIHITYDNPLSAQRALQK   73 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG---------------------E-CCTTEEEEEESSHHHHHHHHTT
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeeccccccccccccc-----------CCCCCCEEEEECCCHHHHHHHHHh
Confidence            356888899988 4568889999999997664 100000000000           012446899999999999999999


Q ss_pred             cceeecCceeE-eecC
Q 008920          304 NMAVIGGNHIR-LDRA  318 (548)
Q Consensus       304 ng~~~~gr~I~-V~~a  318 (548)
                      ||..|.|..|. |.++
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            99999987544 5554

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.68  E-value=0.0041  Score=69.17  Aligned_cols=75  Identities=27%  Similarity=0.419  Sum_probs=63.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEe
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSH  415 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~  415 (548)
                      +.|-+.|+|++++-+||.+||..|-.   ..-+|++-++ +.|...|-|.|.|++.++|..|...++ ..|..|.|.|..
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~---~p~sI~~r~n-d~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEP---DPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhccccc---CCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            47889999999999999999999931   2234555555 789999999999999999999988887 999999998764

>PF12220 U1snRNP70_N: U1 small nuclear ribonucleoprotein of 70kDa MW N terminal; InterPro: IPR022023 This domain is found in eukaryotes

Probab=96.60  E-value=0.0023  Score=55.08  Aligned_cols=44  Identities=23%  Similarity=0.270  Sum_probs=40.2

Q ss_pred             ccccccCccCCCCCCCCchhhHhhhccCCCCCchhhhhhhhcCCc
Q 008920          107 TKLIYPRSILGFEPNGTIENEIKKEHSSNVGSESYLNRQKQNSNF  151 (548)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~k~~~~~  151 (548)
                      .+||.|+|||+|.+|.+|+.+++++.. ++|+++|++.-..+.+.
T Consensus        10 l~LF~PRPPL~y~pP~d~~p~~r~t~~-itGvs~~l~~~~~~~~~   53 (94)
T PF12220_consen   10 LALFAPRPPLPYLPPIDYPPEKRKTPP-ITGVSQYLSEFEDYKDE   53 (94)
T ss_pred             HHHcCCCCCCCCCCccccCcccccCCC-CCcHHHHHHHHhccccC
Confidence            579999999999999999999998888 99999999998888753

This domain is about 90 amino acids in length. This domain is found associated with PF00076 from PFAM. This domain is part of U1 snRNP, which is the pre-mRNA binding protein of the penta-snRNP spliceosome complex. It extends over a distance of 180 A from its RNA binding domain, wraps around the core domain of U1 snRNP consisting of the seven Sm proteins and finally contacts U1-C, which is crucial for 5'-splice-site recognition.

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=96.59  E-value=0.0026  Score=66.09  Aligned_cols=89  Identities=22%  Similarity=0.218  Sum_probs=70.3

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...-+|||-+||..+++.+|..+|.+||.|..       ...+..|+.  .+-++..++..+|-|.|.|.+...|+.|+.
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikr-------nK~t~kPki--~~y~dkeT~~~KGeatvS~~D~~~akaai~  134 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKR-------NKRTGKPKI--KIYTDKETGAPKGEATVSYEDPPAAKAAIE  134 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceecc-------CCCCCCcch--hccccccccCcCCceeeeecChhhhhhhhh
Confidence            34568999999999999999999999997632       112223331  122345778899999999999999999996


Q ss_pred             -hcceeecCceeEeecCCC
Q 008920          303 -FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 -lng~~~~gr~I~V~~a~~  320 (548)
                       +++..|.+..|.|.++..
T Consensus       135 ~~agkdf~gn~ikvs~a~~  153 (351)
T KOG1995|consen  135 WFAGKDFCGNTIKVSLAER  153 (351)
T ss_pred             hhccccccCCCchhhhhhh
Confidence             899999999999988764

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.26  E-value=0.0038  Score=62.20  Aligned_cols=84  Identities=21%  Similarity=0.305  Sum_probs=58.4

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..-.||+++||+.+...-|+++|+.||.|-.|.|-..  ..+.  + .+-.....+.+..-.-|.|+|.+...|..+. .
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE--~~s~--~-~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~  147 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPE--DDSK--R-AARKRKGGNYKKLYSEGWVEFISKRVAKRIAEL  147 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecch--hhHH--H-HHHhhcCCCccccchhHHHHHHHHHHHHHHHHH
Confidence            3468999999999999999999999999999988221  1110  0 0000000111222234789999999999877 5


Q ss_pred             hcceeecCce
Q 008920          303 FNMAVIGGNH  312 (548)
Q Consensus       303 lng~~~~gr~  312 (548)
                      ||+..|+|+.
T Consensus       148 Lnn~~Iggkk  157 (278)
T KOG3152|consen  148 LNNTPIGGKK  157 (278)
T ss_pred             hCCCccCCCC
Confidence            8999999874

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.24  E-value=0.0088  Score=59.69  Aligned_cols=102  Identities=17%  Similarity=0.136  Sum_probs=83.8

Q ss_pred             HHHHH-HhcceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeec
Q 008920          297 TEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRH  375 (548)
Q Consensus       297 A~~Al-~lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d  375 (548)
                      |..|- +|++....|+.|+|.++..                ..|||.||...+.-+.|.+-|..|    |.|....++.|
T Consensus         7 ae~ak~eLd~~~~~~~~lr~rfa~~----------------a~l~V~nl~~~~sndll~~~f~~f----g~~e~av~~vD   66 (275)
T KOG0115|consen    7 AEIAKRELDGRFPKGRSLRVRFAMH----------------AELYVVNLMQGASNDLLEQAFRRF----GPIERAVAKVD   66 (275)
T ss_pred             HHHHHHhcCCCCCCCCceEEEeecc----------------ceEEEEecchhhhhHHHHHhhhhc----Cccchheeeec
Confidence            44444 5899999999999999852                679999999999999999999999    89988777777


Q ss_pred             CCCCCCceEEEEEECCHHHHHHHHHHcC-----CccCCeEEEEEeeecC
Q 008920          376 PHMRVGKGIAYVLFKTREAANLVIKRRN-----LKLRDRELRLSHAQQN  419 (548)
Q Consensus       376 ~~tg~srG~AFV~F~~~e~A~~Al~~ln-----~~l~Gr~I~V~~Ak~~  419 (548)
                       +.+.+.+-++|.|...-.|..|+....     ....+++.-|..+...
T Consensus        67 -~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP~eq~  114 (275)
T KOG0115|consen   67 -DRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEPMEQP  114 (275)
T ss_pred             -ccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCChhhcc
Confidence             568889999999999999998887663     5556677777766543

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=95.76  E-value=0.12  Score=55.16  Aligned_cols=66  Identities=26%  Similarity=0.351  Sum_probs=56.2

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeec---CCC--CCC--------ceEEEEEECCHHHHHHHHH
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRH---PHM--RVG--------KGIAYVLFKTREAANLVIK  400 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d---~~t--g~s--------rG~AFV~F~~~e~A~~Al~  400 (548)
                      .+.++|.+-|||.+-.-+-|..+|+.+    |.|..|+|+.-   +.+  +..        +-+|+|+|...+.|.+|.+
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~----G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e  304 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTV----GSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARE  304 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcc----cceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHH
Confidence            368999999999999999999999999    99999999876   322  222        3468999999999999999


Q ss_pred             HcC
Q 008920          401 RRN  403 (548)
Q Consensus       401 ~ln  403 (548)
                      .++
T Consensus       305 ~~~  307 (484)
T KOG1855|consen  305 LLN  307 (484)
T ss_pred             hhc
Confidence            986

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=95.65  E-value=0.027  Score=43.21  Aligned_cols=52  Identities=19%  Similarity=0.392  Sum_probs=41.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHH
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVI  399 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al  399 (548)
                      +.|-|.+.+....+ .|..+|..|    |.|..+.+...      ..+.||.|.+..+|+.||
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~f----GeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASF----GEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhc----CCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            46888888876664 455688899    99999887622      348999999999999985

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

Probab=95.63  E-value=0.034  Score=60.47  Aligned_cols=63  Identities=27%  Similarity=0.355  Sum_probs=52.5

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhh-hcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFI-KFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs-~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ...+|||||+||--++.++|..+|. -||-|..+-|-+|+  +-+-               .+|-|=|.|.+..+-.+||
T Consensus       368 DprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~--k~KY---------------PkGaGRVtFsnqqsYi~AI  430 (520)
T KOG0129|consen  368 DPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDP--KLKY---------------PKGAGRVTFSNQQAYIKAI  430 (520)
T ss_pred             CccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCc--ccCC---------------CCCcceeeecccHHHHHHH
Confidence            3568999999999999999999999 69999999994443  1223               4488999999999999998


Q ss_pred             H
Q 008920          302 A  302 (548)
Q Consensus       302 ~  302 (548)
                      .
T Consensus       431 s  431 (520)
T KOG0129|consen  431 S  431 (520)
T ss_pred             h
Confidence            5

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=95.62  E-value=0.021  Score=62.45  Aligned_cols=77  Identities=19%  Similarity=0.191  Sum_probs=58.1

Q ss_pred             cccEEEEcCCCCCC------cHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHH
Q 008920          224 LLRTIFVGNLPLKV------KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQST  297 (548)
Q Consensus       224 ~~rtVfVgNLP~~~------tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A  297 (548)
                      ....|+|.|+|.--      -...|.++|+.+|+|..+.++-+.                  .|...||.|++|.+..+|
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e------------------~ggtkG~lf~E~~~~~~A  118 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDE------------------EGGTKGYLFVEYASMRDA  118 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCc------------------cCCeeeEEEEEecChhhH
Confidence            34689999999632      234566899999999888874322                  334789999999999999


Q ss_pred             HHHH-HhcceeecCc-eeEeecC
Q 008920          298 EAAL-AFNMAVIGGN-HIRLDRA  318 (548)
Q Consensus       298 ~~Al-~lng~~~~gr-~I~V~~a  318 (548)
                      +.|+ .|||..|+-. .+.|...
T Consensus       119 ~~aVK~l~G~~ldknHtf~v~~f  141 (698)
T KOG2314|consen  119 KKAVKSLNGKRLDKNHTFFVRLF  141 (698)
T ss_pred             HHHHHhcccceecccceEEeehh
Confidence            9999 5999988654 5555543

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=95.57  E-value=0.033  Score=51.61  Aligned_cols=70  Identities=23%  Similarity=0.383  Sum_probs=51.6

Q ss_pred             cEEEEcCCC-----CCCcH----HHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHH
Q 008920          226 RTIFVGNLP-----LKVKK----KTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQS  296 (548)
Q Consensus       226 rtVfVgNLP-----~~~te----e~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~  296 (548)
                      -||.|.=+.     ...-.    .+|.+.|..||.|.-||+.                         -+.-+|+|.+.++
T Consensus        28 aTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv-------------------------~~~mwVTF~dg~s   82 (146)
T PF08952_consen   28 ATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFV-------------------------GDTMWVTFRDGQS   82 (146)
T ss_dssp             -EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEE-------------------------TTCEEEEESSCHH
T ss_pred             ceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEe-------------------------CCeEEEEECccHH
Confidence            577776555     11222    3677889999999888872                         1578999999999


Q ss_pred             HHHHHHhcceeecCceeEeecCCC
Q 008920          297 TEAALAFNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       297 A~~Al~lng~~~~gr~I~V~~a~~  320 (548)
                      |.+|+.++|..+.|+.|.|..-.+
T Consensus        83 ALaals~dg~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   83 ALAALSLDGIQVNGRTLKIRLKTP  106 (146)
T ss_dssp             HHHHHHGCCSEETTEEEEEEE---
T ss_pred             HHHHHccCCcEECCEEEEEEeCCc
Confidence            999999999999999999988654

; PDB: 1UFW_A 2DNR_A.

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

Probab=95.33  E-value=0.021  Score=65.48  Aligned_cols=75  Identities=31%  Similarity=0.442  Sum_probs=64.9

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..+.+||++|+.++....|...|..||.|..|.+..                       ..-||||+|.+...++.|+ .
T Consensus       454 ~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h-----------------------gq~yayi~yes~~~aq~a~~~  510 (975)
T KOG0112|consen  454 PTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH-----------------------GQPYAYIQYESPPAAQAATHD  510 (975)
T ss_pred             cceeeccCCCCCCChHHHHHHHhhccCcceeeeccc-----------------------CCcceeeecccCccchhhHHH
Confidence            456799999999999999999999999999887721                       3469999999999999999 5


Q ss_pred             hcceeecC--ceeEeecCCCc
Q 008920          303 FNMAVIGG--NHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~g--r~I~V~~a~~~  321 (548)
                      |-|..|+|  +.|.|+++..+
T Consensus       511 ~rgap~G~P~~r~rvdla~~~  531 (975)
T KOG0112|consen  511 MRGAPLGGPPRRLRVDLASPP  531 (975)
T ss_pred             HhcCcCCCCCcccccccccCC
Confidence            88888876  67999998764

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=95.20  E-value=0.026  Score=59.39  Aligned_cols=78  Identities=18%  Similarity=0.261  Sum_probs=65.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCC---CCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEE
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPH---MRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRL  413 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~---tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V  413 (548)
                      ..|.|.||.+.++.++++.+|...    |.|..++|+....   -....-.|||.|.+...+..|..+.|..|-|+.|.|
T Consensus         8 ~vIqvanispsat~dqm~tlFg~l----GkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv   83 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNL----GKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIV   83 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhc----cccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEE
Confidence            479999999999999999999998    8999999876432   234455899999999999999999998888887777


Q ss_pred             Eeeec
Q 008920          414 SHAQQ  418 (548)
Q Consensus       414 ~~Ak~  418 (548)
                      -.+-.
T Consensus        84 ~p~~~   88 (479)
T KOG4676|consen   84 RPYGD   88 (479)
T ss_pred             EecCC
Confidence            65543

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=95.13  E-value=0.055  Score=55.95  Aligned_cols=81  Identities=22%  Similarity=0.324  Sum_probs=61.5

Q ss_pred             CccEEEEeCCCCCCCHHHH------HHHHhccCCCCCCeEEEEEeecCCC-CCCce-E-EEEEECCHHHHHHHHHHcC-C
Q 008920          335 IKKTVFVGNLPFDVKDEEI------YQLFCGLNDLESSVEAVRVIRHPHM-RVGKG-I-AYVLFKTREAANLVIKRRN-L  404 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL------~~~F~~~g~~~G~I~~VrI~~d~~t-g~srG-~-AFV~F~~~e~A~~Al~~ln-~  404 (548)
                      ..+-|||-+||..+..+++      .++|++|    |.|..|.|-+...+ ....+ + .||+|.+.++|..||...+ .
T Consensus       113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQy----GkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs  188 (480)
T COG5175         113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQY----GKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGS  188 (480)
T ss_pred             ecceeEEecCCCCCCcccccccccchhhhhhc----cceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccc
Confidence            4577999999998876662      4789999    89988866543211 11112 2 3999999999999998877 9


Q ss_pred             ccCCeEEEEEeeecC
Q 008920          405 KLRDRELRLSHAQQN  419 (548)
Q Consensus       405 ~l~Gr~I~V~~Ak~~  419 (548)
                      .++||.|+..|...+
T Consensus       189 ~~DGr~lkatYGTTK  203 (480)
T COG5175         189 LLDGRVLKATYGTTK  203 (480)
T ss_pred             cccCceEeeecCchH
Confidence            999999999998643

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=95.07  E-value=0.022  Score=59.02  Aligned_cols=77  Identities=16%  Similarity=0.210  Sum_probs=58.9

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCC--eeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGE--IDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~--I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      .-.+|||||-|.+|+++|.+.+...|-  |..+.+    +.             +...|+++|||+|...+..++.+.|+
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKF----FE-------------NR~NGQSKG~AL~~~~SdAa~Kq~Me  142 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKF----FE-------------NRTNGQSKGYALLVLNSDAAVKQTME  142 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhh----hh-------------cccCCcccceEEEEecchHHHHHHHH
Confidence            357999999999999999999988772  333443    11             12357899999999999999888886


Q ss_pred             -hcceeecCceeEeecC
Q 008920          303 -FNMAVIGGNHIRLDRA  318 (548)
Q Consensus       303 -lng~~~~gr~I~V~~a  318 (548)
                       |....|.|..-.|..+
T Consensus       143 iLP~k~iHGQ~P~V~~~  159 (498)
T KOG4849|consen  143 ILPTKTIHGQSPTVLSY  159 (498)
T ss_pred             hcccceecCCCCeeecc
Confidence             6777888876666544

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=94.99  E-value=0.076  Score=58.31  Aligned_cols=77  Identities=14%  Similarity=0.180  Sum_probs=60.5

Q ss_pred             ccEEEEeCCCCCCC------HHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-Ccc-C
Q 008920          336 KKTVFVGNLPFDVK------DEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKL-R  407 (548)
Q Consensus       336 ~~tLfV~NLp~~~t------eedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l-~  407 (548)
                      ..+|+|.|+|---.      ..-|..+|+.+    |.|..+.++.+..+| ++||.|++|.+..+|..|++.+| ..| .
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~----gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldk  132 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKA----GKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDK  132 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhh----ccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecc
Confidence            46889999987432      23566788999    899999999997655 99999999999999999999887 444 4


Q ss_pred             CeEEEEEeee
Q 008920          408 DRELRLSHAQ  417 (548)
Q Consensus       408 Gr~I~V~~Ak  417 (548)
                      .+++.|..-.
T Consensus       133 nHtf~v~~f~  142 (698)
T KOG2314|consen  133 NHTFFVRLFK  142 (698)
T ss_pred             cceEEeehhh
Confidence            5777776443

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=94.94  E-value=0.094  Score=57.92  Aligned_cols=80  Identities=14%  Similarity=0.111  Sum_probs=63.0

Q ss_pred             CcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC--C--cc
Q 008920          331 PLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN--L--KL  406 (548)
Q Consensus       331 ~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln--~--~l  406 (548)
                      .....++.|||.||=.-+|.-+|+.++..-|   |.|+..  ++|.    -+..|||.|.+.++|...+.+|+  .  .-
T Consensus       439 sR~~~SnvlhI~nLvRPFTlgQLkelL~rtg---g~Vee~--WmDk----IKShCyV~yss~eEA~atr~AlhnV~WP~s  509 (718)
T KOG2416|consen  439 SRKEPSNVLHIDNLVRPFTLGQLKELLGRTG---GNVEEF--WMDK----IKSHCYVSYSSVEEAAATREALHNVQWPPS  509 (718)
T ss_pred             CCCCccceEeeecccccchHHHHHHHHhhcc---CchHHH--HHHH----hhcceeEecccHHHHHHHHHHHhccccCCC
Confidence            3455688999999999999999999999664   677666  4453    25689999999999999998876  2  22


Q ss_pred             CCeEEEEEeeecC
Q 008920          407 RDRELRLSHAQQN  419 (548)
Q Consensus       407 ~Gr~I~V~~Ak~~  419 (548)
                      +++.|.|.|+...
T Consensus       510 NPK~L~adf~~~d  522 (718)
T KOG2416|consen  510 NPKHLIADFVRAD  522 (718)
T ss_pred             CCceeEeeecchh
Confidence            4588999998654

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=94.68  E-value=0.021  Score=57.00  Aligned_cols=71  Identities=13%  Similarity=0.185  Sum_probs=57.7

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCC--------CCCceE----EEEEECCHHHHHHHHHHcC
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM--------RVGKGI----AYVLFKTREAANLVIKRRN  403 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~t--------g~srG~----AFV~F~~~e~A~~Al~~ln  403 (548)
                      ...||+++||+.+...-|+++|+.|    |.|-.|.|-....+        |...++    |.|+|.+...|..+...||
T Consensus        74 ~GVvylS~IPp~m~~~rlReil~~y----GeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Ln  149 (278)
T KOG3152|consen   74 TGVVYLSNIPPYMDPVRLREILSQY----GEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLN  149 (278)
T ss_pred             ceEEEeccCCCccCHHHHHHHHHhc----cccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhC
Confidence            3579999999999999999999999    88888887765444        223332    7899999999999988888


Q ss_pred             -CccCCeE
Q 008920          404 -LKLRDRE  410 (548)
Q Consensus       404 -~~l~Gr~  410 (548)
                       ..|+|+.
T Consensus       150 n~~Iggkk  157 (278)
T KOG3152|consen  150 NTPIGGKK  157 (278)
T ss_pred             CCccCCCC
Confidence             8888854

>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=94.62  E-value=0.12  Score=45.12  Aligned_cols=78  Identities=10%  Similarity=0.175  Sum_probs=51.9

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEE-EeecC------CCCCCceEEEEEECCHHHHHHHHHHcCCccCC
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVR-VIRHP------HMRVGKGIAYVLFKTREAANLVIKRRNLKLRD  408 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~Vr-I~~d~------~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~G  408 (548)
                      ...|.|-+.|.. .-..|.++|+.|    |.|.... +.++.      .......+-.|+|.++.+|.+||..++..|.|
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~----G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g   80 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSF----GTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSG   80 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCC----S-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETT
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhc----ceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcC
Confidence            456888888887 566788899999    8887774 11100      01123458999999999999999999988888


Q ss_pred             e-EEEEEeeec
Q 008920          409 R-ELRLSHAQQ  418 (548)
Q Consensus       409 r-~I~V~~Ak~  418 (548)
                      . .+-|.|+.+
T Consensus        81 ~~mvGV~~~~~   91 (100)
T PF05172_consen   81 SLMVGVKPCDP   91 (100)
T ss_dssp             CEEEEEEE-HH
T ss_pred             cEEEEEEEcHH
Confidence            5 555777743

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.

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=94.58  E-value=0.016  Score=57.91  Aligned_cols=61  Identities=26%  Similarity=0.414  Sum_probs=48.1

Q ss_pred             HHHHHHhh-hcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-HhcceeecCceeEeec
Q 008920          240 KTLIKEFI-KFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDR  317 (548)
Q Consensus       240 e~L~~~Fs-~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng~~~~gr~I~V~~  317 (548)
                      ++|...|+ +||+|+.+.+...-                  ...-.|.+||.|...++|++|+ .||+..|.|++|...+
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------------------GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAEL  144 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc------------------chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeee
Confidence            45555556 89999998763211                  1125689999999999999999 5999999999999888


Q ss_pred             C
Q 008920          318 A  318 (548)
Q Consensus       318 a  318 (548)
                      +
T Consensus       145 ~  145 (260)
T KOG2202|consen  145 S  145 (260)
T ss_pred             c
Confidence            6

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=94.45  E-value=0.092  Score=53.46  Aligned_cols=65  Identities=22%  Similarity=0.351  Sum_probs=50.9

Q ss_pred             HHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-HhcceeecCceeEeec
Q 008920          239 KKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDR  317 (548)
Q Consensus       239 ee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng~~~~gr~I~V~~  317 (548)
                      ++++..-+.+||.|..|.|..++    ..|-.            -..-.||+|...++|.+|+ .|||..|+|+.+..++
T Consensus       300 ede~keEceKyg~V~~viifeip----~~p~d------------eavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~F  363 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIP----SQPED------------EAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACF  363 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecC----CCccc------------hhheeeeeeccHHHHHHHHHhcCCceecceeeehee
Confidence            34667788999999999886554    22221            2235799999999999998 7999999999998877


Q ss_pred             CC
Q 008920          318 AC  319 (548)
Q Consensus       318 a~  319 (548)
                      ..
T Consensus       364 yn  365 (378)
T KOG1996|consen  364 YN  365 (378)
T ss_pred             cc
Confidence            64

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=94.31  E-value=0.19  Score=42.22  Aligned_cols=51  Identities=16%  Similarity=0.372  Sum_probs=37.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      +..+|+ .|..+...||.++|+.||.|.--.|                         +-.-|||.....+.|..|+.
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi-------------------------~dTSAfV~l~~r~~~~~v~~   60 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWI-------------------------NDTSAFVALHNRDQAKVVMN   60 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEEEEEE-------------------------CTTEEEEEECCCHHHHHHHH
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEEEEEE-------------------------cCCcEEEEeecHHHHHHHHH
Confidence            456666 9999999999999999999843344                         22579999999999999884

; 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.

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=94.20  E-value=0.016  Score=57.91  Aligned_cols=53  Identities=19%  Similarity=0.199  Sum_probs=45.8

Q ss_pred             CCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeee
Q 008920          364 ESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQ  417 (548)
Q Consensus       364 ~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak  417 (548)
                      +|.|+.+.|..+. .-...|-+||.|...++|++|+..|| .++.|++|...++.
T Consensus        93 ygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   93 YGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             hhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            3999999777653 45668899999999999999999888 99999999999874

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=94.08  E-value=0.036  Score=61.02  Aligned_cols=74  Identities=15%  Similarity=0.150  Sum_probs=57.2

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhh-hcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFI-KFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs-~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      -..+..|+|.||-.-.|.-+|+.|+. .+|.|+..+|  |.                     -+..|||.|.+.+.|.+-
T Consensus       441 ~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--Dk---------------------IKShCyV~yss~eEA~at  497 (718)
T KOG2416|consen  441 KEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--DK---------------------IKSHCYVSYSSVEEAAAT  497 (718)
T ss_pred             CCccceEeeecccccchHHHHHHHHhhccCchHHHHH--HH---------------------hhcceeEecccHHHHHHH
Confidence            34567899999999999999999999 5788888766  22                     225899999999999988


Q ss_pred             H-Hhcceee---cCceeEeecC
Q 008920          301 L-AFNMAVI---GGNHIRLDRA  318 (548)
Q Consensus       301 l-~lng~~~---~gr~I~V~~a  318 (548)
                      + +|||..+   ++++|.|+|.
T Consensus       498 r~AlhnV~WP~sNPK~L~adf~  519 (718)
T KOG2416|consen  498 REALHNVQWPPSNPKHLIADFV  519 (718)
T ss_pred             HHHHhccccCCCCCceeEeeec
Confidence            8 6888765   3345555554

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=93.96  E-value=0.23  Score=46.12  Aligned_cols=74  Identities=20%  Similarity=0.300  Sum_probs=51.6

Q ss_pred             CCccEEEEeCCCC------CCCH---HHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCC
Q 008920          334 DIKKTVFVGNLPF------DVKD---EEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNL  404 (548)
Q Consensus       334 ~~~~tLfV~NLp~------~~te---edL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~  404 (548)
                      ++..||.|.-+..      .+.+   .+|.+.|..|    |.|.-||++-+        .-+|+|.+-..|.+|+.+.+.
T Consensus        25 PpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~----GevvLvRfv~~--------~mwVTF~dg~sALaals~dg~   92 (146)
T PF08952_consen   25 PPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQY----GEVVLVRFVGD--------TMWVTFRDGQSALAALSLDGI   92 (146)
T ss_dssp             -TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCC----S-ECEEEEETT--------CEEEEESSCHHHHHHHHGCCS
T ss_pred             CCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhC----CceEEEEEeCC--------eEEEEECccHHHHHHHccCCc
Confidence            3456666665541      1222   3667777888    88888887755        568999999999999999999


Q ss_pred             ccCCeEEEEEeeecC
Q 008920          405 KLRDRELRLSHAQQN  419 (548)
Q Consensus       405 ~l~Gr~I~V~~Ak~~  419 (548)
                      .++|+.|.|..-.|.
T Consensus        93 ~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   93 QVNGRTLKIRLKTPD  107 (146)
T ss_dssp             EETTEEEEEEE----
T ss_pred             EECCEEEEEEeCCcc
Confidence            999999999987765

; PDB: 1UFW_A 2DNR_A.

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=93.69  E-value=0.059  Score=57.24  Aligned_cols=73  Identities=18%  Similarity=0.300  Sum_probs=58.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC--CccCCeEEEEE
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN--LKLRDRELRLS  414 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln--~~l~Gr~I~V~  414 (548)
                      +.|||+||...++..||..+|.....  | . +-.++.      -.||+||.+.+...|..|++.++  ..+.|..+.|.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~--~-~-~g~fl~------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~   71 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKI--P-G-SGQFLV------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVE   71 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccC--C-C-Ccceee------ecceeeccCCchhhhhhhHHhhchhhhhcCceeecc
Confidence            46899999999999999999976521  1 1 111111      25799999999999999999987  88999999999


Q ss_pred             eeecC
Q 008920          415 HAQQN  419 (548)
Q Consensus       415 ~Ak~~  419 (548)
                      +..+.
T Consensus        72 ~sv~k   76 (584)
T KOG2193|consen   72 HSVPK   76 (584)
T ss_pred             chhhH
Confidence            98765

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=93.53  E-value=0.19  Score=51.27  Aligned_cols=64  Identities=16%  Similarity=0.126  Sum_probs=51.0

Q ss_pred             HHHHHHHHhccCCCCCCeEEEEEeecCCCCCCce-EEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeee
Q 008920          350 DEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG-IAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQ  417 (548)
Q Consensus       350 eedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG-~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak  417 (548)
                      ++++.+.+.+|    |.|..|.|..++....... --||+|...++|.+|+-.|| ..|+||.+...|..
T Consensus       300 ede~keEceKy----g~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKY----GKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhh----cceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            45677888888    8999998887754322222 36999999999999987777 99999999988864

>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=93.03  E-value=0.095  Score=50.33  Aligned_cols=80  Identities=13%  Similarity=0.115  Sum_probs=47.0

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhh-cCCe---eEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIK-FGEI---DSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~-fG~I---~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      ...|.|++||+++|++++++.++. ++..   ..+...   ....  +         +.. ....-|||.|.+.+++...
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~---~~~~--~---------~~~-~~~SRaYi~F~~~~~~~~F   71 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGK---YGKK--S---------FKP-PTYSRAYINFKNPEDLLEF   71 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEE---ES-S--S---------STT-S--EEEEEEESSCHHHHHH
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecC---CCCc--c---------CCC-CcceEEEEEeCCHHHHHHH
Confidence            468999999999999999997776 6654   222210   1100  0         001 1234699999999998887


Q ss_pred             H-HhcceeecCc-----eeEeecCC
Q 008920          301 L-AFNMAVIGGN-----HIRLDRAC  319 (548)
Q Consensus       301 l-~lng~~~~gr-----~I~V~~a~  319 (548)
                      + .++|..|.+.     ...|.+|.
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 5889887553     44455543

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=92.42  E-value=0.5  Score=48.54  Aligned_cols=72  Identities=18%  Similarity=0.205  Sum_probs=55.4

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhcc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNM  305 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~lng  305 (548)
                      .=|-|-++|.... ..|..+|++||.|..+...          .             .-.+-+|.|.+.-+|++||..||
T Consensus       198 ~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~----------~-------------ngNwMhirYssr~~A~KALskng  253 (350)
T KOG4285|consen  198 TWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP----------S-------------NGNWMHIRYSSRTHAQKALSKNG  253 (350)
T ss_pred             ceEEEeccCccch-hHHHHHHHhhCeeeeeecC----------C-------------CCceEEEEecchhHHHHhhhhcC
Confidence            3455667877654 4788999999999877651          1             22589999999999999999999


Q ss_pred             eeecCc-eeEeecCCCc
Q 008920          306 AVIGGN-HIRLDRACPP  321 (548)
Q Consensus       306 ~~~~gr-~I~V~~a~~~  321 (548)
                      .+|.|. .|-|..+..+
T Consensus       254 ~ii~g~vmiGVkpCtDk  270 (350)
T KOG4285|consen  254 TIIDGDVMIGVKPCTDK  270 (350)
T ss_pred             eeeccceEEeeeecCCH
Confidence            999886 5667776543

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=92.37  E-value=0.65  Score=36.95  Aligned_cols=58  Identities=17%  Similarity=0.193  Sum_probs=45.4

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHc
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR  402 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~l  402 (548)
                      ...|+|.++.. ++.+||..+|..|... .....|..+-|.       -|-|.|.+.+.|..||.+|
T Consensus         5 peavhirGvd~-lsT~dI~~y~~~y~~~-~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVDE-LSTDDIKAYFSEYFDE-EGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCCC-CCHHHHHHHHHHhccc-CCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            35799999966 8889999999988211 245567777663       6899999999999999764

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=91.68  E-value=0.63  Score=43.00  Aligned_cols=71  Identities=25%  Similarity=0.270  Sum_probs=53.2

Q ss_pred             ccEEEEcCCCCCC----cHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          225 LRTIFVGNLPLKV----KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       225 ~rtVfVgNLP~~~----tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      -.||.|+=|..++    +...|...++.||+|.+|.+.                        .+--|.|+|.+..+|-.|
T Consensus        86 MsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c------------------------GrqsavVvF~d~~SAC~A  141 (166)
T PF15023_consen   86 MSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC------------------------GRQSAVVVFKDITSACKA  141 (166)
T ss_pred             ceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec------------------------CCceEEEEehhhHHHHHH
Confidence            4688887666554    344556677889999999872                        234799999999999999


Q ss_pred             HHhcceeecCceeEeecCC
Q 008920          301 LAFNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       301 l~lng~~~~gr~I~V~~a~  319 (548)
                      +..-+....|..+.+.|-+
T Consensus       142 v~Af~s~~pgtm~qCsWqq  160 (166)
T PF15023_consen  142 VSAFQSRAPGTMFQCSWQQ  160 (166)
T ss_pred             HHhhcCCCCCceEEeeccc
Confidence            9533446778888888854

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=91.59  E-value=9.2  Score=39.47  Aligned_cols=171  Identities=13%  Similarity=0.160  Sum_probs=103.2

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      +=..|.|.+.||...++-..+...|-.||+|++|.++....    .+.      .+.+.......+.+-|-+.+.|....
T Consensus        12 ~YrTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~----~~~------d~~~~d~~~~SilLSFlsr~~CLdFY   81 (309)
T PF10567_consen   12 EYRTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSND----KPS------DDYNDDKNNQSILLSFLSREICLDFY   81 (309)
T ss_pred             cceeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCC----ccc------ccccccccceEEEEeeechHHHHHHH
Confidence            33457899999999999999999999999999999955332    111      11223345567899999998876553


Q ss_pred             -H----hc--ceeecCceeEeecCCCcccccC--CCC---------------CCcCCCccEEEEeCCCCCCCHHHHHHHH
Q 008920          302 -A----FN--MAVIGGNHIRLDRACPPRKKLK--GED---------------APLYDIKKTVFVGNLPFDVKDEEIYQLF  357 (548)
Q Consensus       302 -~----ln--g~~~~gr~I~V~~a~~~~k~~~--~~~---------------~~~~~~~~tLfV~NLp~~~teedL~~~F  357 (548)
                       .    |.  .+.+....|.|.+..-......  ...               -.....++.|.|.--.....++-|...+
T Consensus        82 NnvLQrLsEfK~~L~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~IeF~~~~~~~dl~~~kL  161 (309)
T PF10567_consen   82 NNVLQRLSEFKTKLKSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIEFKDPVDKDDLIEKKL  161 (309)
T ss_pred             HHHHHHHHHHHHhcCCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEEecCccchhHHHHHhh
Confidence             1    21  2345556666665542111100  000               1112346778876332222333333333


Q ss_pred             hccCCCCC----CeEEEEEeecC--CCCCCceEEEEEECCHHHHHHHHHHcC
Q 008920          358 CGLNDLES----SVEAVRVIRHP--HMRVGKGIAYVLFKTREAANLVIKRRN  403 (548)
Q Consensus       358 ~~~g~~~G----~I~~VrI~~d~--~tg~srG~AFV~F~~~e~A~~Al~~ln  403 (548)
                       +|-...+    -|++|.|+.-.  ...-+..||.++|-+...|...++.+.
T Consensus       162 -~fL~~~~n~RYVlEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk  212 (309)
T PF10567_consen  162 -PFLKNSNNKRYVLESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLK  212 (309)
T ss_pred             -hhhccCCCceEEEEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHH
Confidence             1110012    47888888543  234567799999999999999987665

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=91.34  E-value=0.1  Score=56.22  Aligned_cols=75  Identities=25%  Similarity=0.379  Sum_probs=62.3

Q ss_pred             CcccEEEEcCCCCCC-cHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKV-KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~-tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      .+.+.|-+.-+|+.+ |-.+|..+|.+||.|..|.+..                       +.-.|.|+|.+..+|-.|.
T Consensus       370 ~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~-----------------------~~~~a~vTF~t~aeag~a~  426 (526)
T KOG2135|consen  370 VDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDY-----------------------SSLHAVVTFKTRAEAGEAY  426 (526)
T ss_pred             cccchhhhhccCCCCchHhhhhhhhhhcCccccccccC-----------------------chhhheeeeeccccccchh
Confidence            355677777777775 5688999999999999998832                       1236999999999998899


Q ss_pred             HhcceeecCceeEeecCCC
Q 008920          302 AFNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~  320 (548)
                      ..++..|.++.|.|.|..+
T Consensus       427 ~s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  427 ASHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             ccccceecCceeEEEEecC
Confidence            8999999999999999865

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=90.46  E-value=1.1  Score=41.46  Aligned_cols=74  Identities=18%  Similarity=0.183  Sum_probs=56.5

Q ss_pred             CCccEEEEeCCCCCC----CHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCe
Q 008920          334 DIKKTVFVGNLPFDV----KDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDR  409 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~----teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr  409 (548)
                      .+-.+|.|+=|..++    +-..|...++.|    |.|.+|.+.       ++.-|.|.|.+..+|-.|+.+++....|.
T Consensus        84 pPMsTIVVRWlkknm~~~edl~sV~~~Ls~f----GpI~SVT~c-------GrqsavVvF~d~~SAC~Av~Af~s~~pgt  152 (166)
T PF15023_consen   84 PPMSTIVVRWLKKNMQPTEDLKSVIQRLSVF----GPIQSVTLC-------GRQSAVVVFKDITSACKAVSAFQSRAPGT  152 (166)
T ss_pred             CCceeEEeehhhhcCChHHHHHHHHHHHHhc----CCcceeeec-------CCceEEEEehhhHHHHHHHHhhcCCCCCc
Confidence            345677776555544    334445556778    999999764       24479999999999999999999888899


Q ss_pred             EEEEEeeec
Q 008920          410 ELRLSHAQQ  418 (548)
Q Consensus       410 ~I~V~~Ak~  418 (548)
                      .+.+.|-..
T Consensus       153 m~qCsWqqr  161 (166)
T PF15023_consen  153 MFQCSWQQR  161 (166)
T ss_pred             eEEeecccc
Confidence            999998654

>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=90.32  E-value=0.3  Score=41.61  Aligned_cols=72  Identities=19%  Similarity=0.161  Sum_probs=46.8

Q ss_pred             EEEEecCHHHHHHHHHh--cceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHh
Q 008920          287 AYIVFKSEQSTEAALAF--NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFC  358 (548)
Q Consensus       287 AFV~F~s~e~A~~Al~l--ng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~  358 (548)
                      |+|+|.++.-|+..+.+  +...+.+..+.|....-.........-......++|.|.|||..+.+++|++.+.
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            68999999999999864  5556666655554332111110000111233568999999999999999987664

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>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=89.79  E-value=0.71  Score=44.36  Aligned_cols=81  Identities=17%  Similarity=0.116  Sum_probs=47.7

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhc-cCCCCCCe---EEEEEeecCCC--CCCceEEEEEECCHHHHHHHHHHcC-CccC
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCG-LNDLESSV---EAVRVIRHPHM--RVGKGIAYVLFKTREAANLVIKRRN-LKLR  407 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~-~g~~~G~I---~~VrI~~d~~t--g~srG~AFV~F~~~e~A~~Al~~ln-~~l~  407 (548)
                      ....|.|++||+.+|+++++..+.. +    +.-   ..+.-......  ...-.-|||.|.+.+++...+..++ ..|.
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l----~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~   81 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWL----PDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFV   81 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS------SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhc----ccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEE
Confidence            3468999999999999999997777 4    333   33332222211  1223359999999999888888775 3442


Q ss_pred             C-----eEEEEEeeecC
Q 008920          408 D-----RELRLSHAQQN  419 (548)
Q Consensus       408 G-----r~I~V~~Ak~~  419 (548)
                      +     ....|.+|--.
T Consensus        82 D~kg~~~~~~VE~Apyq   98 (176)
T PF03467_consen   82 DSKGNEYPAVVEFAPYQ   98 (176)
T ss_dssp             -TTS-EEEEEEEE-SS-
T ss_pred             CCCCCCcceeEEEcchh
Confidence            2     45667777544

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.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=89.72  E-value=1.4  Score=35.00  Aligned_cols=51  Identities=16%  Similarity=0.316  Sum_probs=40.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhc----CCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKF----GEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~f----G~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ..|+|.+|. +++.++|..+|..|    ++ ..|..+-+                        .-|=|.|.+.+.|..||
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~-~~IEWIdD------------------------tScNvvf~d~~~A~~AL   59 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGP-FRIEWIDD------------------------TSCNVVFKDEETAARAL   59 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCC-ceEEEecC------------------------CcEEEEECCHHHHHHHH
Confidence            479999995 58889999999998    53 46666332                        25889999999999998


Q ss_pred             H
Q 008920          302 A  302 (548)
Q Consensus       302 ~  302 (548)
                      .
T Consensus        60 ~   60 (62)
T PF10309_consen   60 V   60 (62)
T ss_pred             H
Confidence            3

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=88.79  E-value=2.2  Score=36.08  Aligned_cols=54  Identities=26%  Similarity=0.453  Sum_probs=39.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN  403 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln  403 (548)
                      ...||. +|..+-..||.++|+.|    |.|. |..+.|       .-|||...+.+.|..|+..+.
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspf----G~I~-VsWi~d-------TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPF----GQIY-VSWIND-------TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCC----CCEE-EEEECT-------TEEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccC----CcEE-EEEEcC-------CcEEEEeecHHHHHHHHHHhc
Confidence            445555 99999999999999999    6663 555555       279999999999999988775

; 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.

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=88.78  E-value=0.22  Score=51.76  Aligned_cols=81  Identities=16%  Similarity=0.370  Sum_probs=59.4

Q ss_pred             cEEEEcCCCCCCcHHHHH---HHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          226 RTIFVGNLPLKVKKKTLI---KEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~---~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      .-|||-+|+.....+.+.   ++|.+||.|..|.+..++..  ...           .+.. .-+||.|...++|..|| 
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~--~s~-----------~~~~-~s~yITy~~~eda~rci~  143 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSS--SSS-----------SGGT-CSVYITYEEEEDADRCID  143 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCccc--ccC-----------CCCC-CcccccccchHhhhhHHH
Confidence            458999999887666555   58999999999988554410  000           1111 23899999999999999 


Q ss_pred             HhcceeecCceeEeecCCC
Q 008920          302 AFNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~  320 (548)
                      ..+|..+.|+.|...+...
T Consensus       144 ~v~g~~~dg~~lka~~gtt  162 (327)
T KOG2068|consen  144 DVDGFVDDGRALKASLGTT  162 (327)
T ss_pred             HhhhHHhhhhhhHHhhCCC
Confidence            5899999999877776643

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=87.12  E-value=2.6  Score=45.61  Aligned_cols=67  Identities=15%  Similarity=0.254  Sum_probs=56.3

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhc-CCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKF-GEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~f-G~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      .+.|+|-.+|..+|-.||..|+..| -.|..|+|+++.+.                   ++=.++|.|.+..+|.... .
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            6899999999999999999999865 47889999775532                   3346899999999999998 6


Q ss_pred             hcceeecC
Q 008920          303 FNMAVIGG  310 (548)
Q Consensus       303 lng~~~~g  310 (548)
                      +||..|..
T Consensus       135 fNGk~Fn~  142 (493)
T KOG0804|consen  135 FNGKQFNS  142 (493)
T ss_pred             cCCCcCCC
Confidence            99998865

>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=85.50  E-value=5.7  Score=35.26  Aligned_cols=66  Identities=17%  Similarity=0.174  Sum_probs=45.6

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhc-CCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKF-GEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~f-G~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      ..+.+...|+.++-++|..+.+.+ ..|..++|+++...                   ++=.+.|.|.+.++|.... .+
T Consensus        14 ~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~p-------------------nrymVLikF~~~~~Ad~Fy~~f   74 (110)
T PF07576_consen   14 TLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTP-------------------NRYMVLIKFRDQESADEFYEEF   74 (110)
T ss_pred             eEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCC-------------------ceEEEEEEECCHHHHHHHHHHh
Confidence            345555555666666776666655 45677888664321                   3446899999999999988 68


Q ss_pred             cceeecC
Q 008920          304 NMAVIGG  310 (548)
Q Consensus       304 ng~~~~g  310 (548)
                      ||..|..
T Consensus        75 NGk~Fns   81 (110)
T PF07576_consen   75 NGKPFNS   81 (110)
T ss_pred             CCCccCC
Confidence            9998854

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=85.20  E-value=0.97  Score=45.52  Aligned_cols=75  Identities=16%  Similarity=0.264  Sum_probs=56.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-hc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-FN  304 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-ln  304 (548)
                      ..|||.||+.-+.-+.|..-|+.||+|....+.-|.                  .+...+-++|.|...-.|.+|+. +.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~------------------r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD------------------RGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc------------------cccccccchhhhhcchhHHHHHHHhc
Confidence            469999999999999999999999999876553221                  34567889999999999999984 32


Q ss_pred             -c---eeecCceeEeecC
Q 008920          305 -M---AVIGGNHIRLDRA  318 (548)
Q Consensus       305 -g---~~~~gr~I~V~~a  318 (548)
                       +   ....+++..|...
T Consensus        94 ~~g~~~~~~~~p~~VeP~  111 (275)
T KOG0115|consen   94 EGGFGGTTGGRPVGVEPM  111 (275)
T ss_pred             cCccccCCCCCccCCChh
Confidence             2   2334556555554

>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=83.81  E-value=16  Score=32.39  Aligned_cols=78  Identities=12%  Similarity=0.197  Sum_probs=54.2

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccC---CeE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLR---DRE  410 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~---Gr~  410 (548)
                      ....+.+...|+.++-++|..+...+.   ..|..++|++|..  .++-.+.+.|.+.+.|..-....| ..+.   ...
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~~~---~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fNGk~FnslEpE~   86 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAPFR---EDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFNGKPFNSLEPET   86 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhccc---ccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhCCCccCCCCCce
Confidence            345555666666677777776666663   5788999999842  356679999999999999987776 4443   344


Q ss_pred             EEEEeee
Q 008920          411 LRLSHAQ  417 (548)
Q Consensus       411 I~V~~Ak  417 (548)
                      -+|-|..
T Consensus        87 ChvvfV~   93 (110)
T PF07576_consen   87 CHVVFVK   93 (110)
T ss_pred             eEEEEEE
Confidence            4444443

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=82.50  E-value=3  Score=40.43  Aligned_cols=60  Identities=17%  Similarity=0.170  Sum_probs=42.8

Q ss_pred             cHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhc--ceeecCceeE
Q 008920          238 KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN--MAVIGGNHIR  314 (548)
Q Consensus       238 tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~ln--g~~~~gr~I~  314 (548)
                      ....|..+|..|+.+..+.++.                       +-+-..|.|.+.++|..|. .|+  +..|.|..|+
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~-----------------------sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~   64 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLK-----------------------SFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLR   64 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEET-----------------------TTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-E
T ss_pred             hHHHHHHHHHhcCCceEEEEcC-----------------------CCCEEEEEeCCHHHHHHHHHHhcccccccCCCceE
Confidence            4578999999999887776521                       3456899999999999998 578  8999999999


Q ss_pred             eecCCC
Q 008920          315 LDRACP  320 (548)
Q Consensus       315 V~~a~~  320 (548)
                      |.++..
T Consensus        65 ~yf~~~   70 (184)
T PF04847_consen   65 VYFGQP   70 (184)
T ss_dssp             EE----
T ss_pred             EEEccc
Confidence            998854

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=82.22  E-value=4.3  Score=45.02  Aligned_cols=67  Identities=18%  Similarity=0.226  Sum_probs=50.5

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC---CccCCeEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN---LKLRDREL  411 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln---~~l~Gr~I  411 (548)
                      .+.|.|+-||..+-.++|+.+|..-.  |-.+.+|.+-.+-       -=||+|++..+|+.|...|.   ..|.|++|
T Consensus       175 RcIvilREIpettp~e~Vk~lf~~en--cPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpI  244 (684)
T KOG2591|consen  175 RCIVILREIPETTPIEVVKALFKGEN--CPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPI  244 (684)
T ss_pred             eeEEEEeecCCCChHHHHHHHhccCC--CCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcch
Confidence            45677899999999999999996521  1477888766542       24999999999999987664   56666554

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=80.52  E-value=1.4  Score=49.63  Aligned_cols=70  Identities=19%  Similarity=0.208  Sum_probs=58.4

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      .++..+|||+|+...+..+-+..++..|    |.|.++..+.         |||..|..+.....|+..+. ..++|..+
T Consensus        37 ~~~~~~vfv~~~~~~~s~~~~~~il~~~----g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl  103 (668)
T KOG2253|consen   37 LPPRDTVFVGNISYLVSQEFWKSILAKS----GFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKL  103 (668)
T ss_pred             CCCCceeEecchhhhhhHHHHHHHHhhC----Ccchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchh
Confidence            4567899999999999999999999988    7777664322         99999999999999999888 88888777


Q ss_pred             EEEe
Q 008920          412 RLSH  415 (548)
Q Consensus       412 ~V~~  415 (548)
                      .+.-
T Consensus       104 ~~~~  107 (668)
T KOG2253|consen  104 IENV  107 (668)
T ss_pred             hccc
Confidence            6654

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=80.01  E-value=0.95  Score=49.11  Aligned_cols=74  Identities=20%  Similarity=0.262  Sum_probs=59.7

Q ss_pred             ccEEEEeCCCCCC-CHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEE
Q 008920          336 KKTVFVGNLPFDV-KDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLS  414 (548)
Q Consensus       336 ~~tLfV~NLp~~~-teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~  414 (548)
                      .+.|-+.-.|+.+ +-++|..+|..|    |.|..|.|-...      --|.|+|.+..+|-.|.......|++|.|.|.
T Consensus       372 hs~l~lek~~~glnt~a~ln~hfA~f----G~i~n~qv~~~~------~~a~vTF~t~aeag~a~~s~~avlnnr~iKl~  441 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNTIADLNPHFAQF----GEIENIQVDYSS------LHAVVTFKTRAEAGEAYASHGAVLNNRFIKLF  441 (526)
T ss_pred             cchhhhhccCCCCchHhhhhhhhhhc----CccccccccCch------hhheeeeeccccccchhccccceecCceeEEE
Confidence            3455555566655 578999999999    999999775542      36899999999998888777799999999999


Q ss_pred             eeecC
Q 008920          415 HAQQN  419 (548)
Q Consensus       415 ~Ak~~  419 (548)
                      |-.+.
T Consensus       442 whnps  446 (526)
T KOG2135|consen  442 WHNPS  446 (526)
T ss_pred             EecCC
Confidence            98874

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	548
1wi8_A	104	Solution Structure Of The Rna Binding Domain Of Euk		1e-04
1x4h_A	111	Solution Structure Of Rrm Domain In Rna-Binding Pro		1e-04
2j76_E	100	Solution Structure And Rna Interactions Of The Rna		2e-04
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		3e-04

>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic Initiation Factor 4b Length = 104

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 30/95 (31%), Positives = 48/95 (50%), Gaps = 10/95 (10%)
Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP-HMRVGKGIAYVLFKTREAAN 396
           T F+GNLP+DV +E I + F GLN     + AVR+ R P +    KG  Y  F+  ++  
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLN-----ISAVRLPREPSNPERLKGFGYAEFEDLDSLL 71
Query: 397 LVIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAPA 431
             +      L ++ +R+  A Q    ++ KD  P+
Sbjct: 72  SALSLNEESLGNKRIRVDVADQ----AQDKDSGPS 102

>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28 Length = 111

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 30/95 (31%), Positives = 47/95 (49%), Gaps = 4/95 (4%)
Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           KTVF+ NL FD ++E + ++     DL+     VRV+ HP     KG A+  F T+EAA 
Sbjct: 16  KTVFIRNLSFDSEEEALGEVLQQFGDLKY----VRVVLHPDTEHSKGCAFAQFMTQEAAQ 71
Query: 397 LVIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAPA 431
             +   +L+     L+L   Q     +  +D A +
Sbjct: 72  KCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAAS 106

>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 = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 42/82 (51%), Gaps = 6/82 (7%)
Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP-HMRVGKGIAYVLFKTREAAN 396
           T F+GNLP+DV +E I + F GLN     + AVR+ R P +    KG  Y  F+  ++  
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLN-----ISAVRLPREPSNPERLKGFGYAEFEDLDSLL 75
Query: 397 LVIKRRNLKLRDRELRLSHAQQ 418
             +      L +R +R+  A Q
Sbjct: 76  SALSLNEESLGNRRIRVDVADQ 97

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 46/211 (21%), Positives = 93/211 (44%), Gaps = 36/211 (17%)
Query: 222 GKLLRTIFVGNLPLKVKKKTLIKEF---IKFGEIDSVRIRSVPIIDTKIPRKGAILQKQI 278
           G + R ++VGN+P  + ++ ++  F   ++ G +            T+ P    +L  QI
Sbjct: 1   GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGL------------TQAPGN-PVLAVQI 47
Query: 279 NENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKG--EDAPLY--- 333
           N+  D   A++ F+S   T  A+AF+  +  G  +++ R     + L G  E+  +Y   
Sbjct: 48  NQ--DKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPH-DYQPLPGMSENPSVYVPG 104
Query: 334 -------DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAY 386
                  D    +F+G LP  + D+++ +L      L    +A  +++     + KG A+
Sbjct: 105 VVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPL----KAFNLVKDSATGLSKGYAF 160
Query: 387 VLFKTREAANLVIKRRN-LKLRDRELRLSHA 416
             +      +  I   N ++L D++L +  A
Sbjct: 161 CEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 191

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	548
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	6e-26
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-11
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-25
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-10
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-08
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-22
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-06
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	9e-22
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-22
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-11
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-20
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-11
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-19
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-17
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-19
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-11
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	7e-19
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	6e-07
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-18
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	7e-07
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-17
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	9e-17
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	6e-10
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-16
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-10
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-14
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-10
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	3e-14
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	6e-07
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	5e-14
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-04
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	6e-14
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	4e-06
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	7e-14
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	7e-04
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-13
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	9e-07
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-13
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	3e-06
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	3e-13
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-09
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	4e-13
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	1e-04
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-12
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-06
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-12
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	6e-07
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-12
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	4e-08
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	3e-12
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	4e-12
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	6e-06
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	7e-12
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	8e-04
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	9e-12
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-05
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-11
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-05
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-11
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	3e-11
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	3e-05
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-11
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-04
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	5e-11
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-07
2div_A	99	TRNA selenocysteine associated protein; structural	5e-11
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-10
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	8e-09
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-10
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	4e-07
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-10
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	8e-04
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-10
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	6e-07
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-10
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-08
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	3e-10
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	3e-07
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-10
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-10
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	8e-06
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-10
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-10
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-04
2dis_A	109	Unnamed protein product; structural genomics, RRM	6e-10
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-05
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	6e-10
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	3e-06
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-09
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-07
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	4e-09
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	5e-06
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-09
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	5e-07
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	5e-09
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-06
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	6e-09
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-06
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	8e-09
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	9e-09
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-07
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	9e-09
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	4e-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	1e-08
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-08
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-06
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-08
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-08
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-08
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	5e-04
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-08
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-08
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	4e-08
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	8e-07
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-08
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-08
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-05
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	5e-08
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-04
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-04
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	7e-08
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-05
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	8e-08
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	9e-08
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	4e-07
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	9e-08
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	7e-04
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	9e-08
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	9e-08
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-05
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-07
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	8e-07
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-07
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-07
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-05
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-07
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	4e-06
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-07
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-06
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-07
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-07
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	6e-04
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-07
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-07
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-04
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-07
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-05
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-07
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	6e-06
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-07
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-07
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-07
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	7e-05
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	4e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-04
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	4e-07
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-05
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-07
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-05
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	4e-07
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	5e-07
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-06
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	5e-07
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	6e-07
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	7e-06
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	6e-07
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-04
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-07
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-04
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	8e-07
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-06
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	9e-07
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	9e-07
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-06
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-06
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-06
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-06
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	6e-06
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-06
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-06
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-06
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-06
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-06
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	3e-05
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-06
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-04
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-06
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-06
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-04
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-06
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	3e-06
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	3e-04
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-06
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-06
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-06
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-05
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	4e-06
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	4e-06
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	5e-05
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	4e-06
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	4e-05
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	4e-06
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	4e-06
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	7e-06
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	4e-06
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	7e-05
1x5p_A	97	Negative elongation factor E; structure genomics,	4e-06
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-05
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-06
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-05
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	5e-06
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-04
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	1e-05
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-05
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-05
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-05
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-05
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	8e-04
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-05
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-05
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-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
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-05
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-05
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	3e-05
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-05
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	4e-05
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-04
1x4e_A	85	RNA binding motif, single-stranded interacting pro	5e-05
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	5e-05
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-04
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	6e-05
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-04
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	7e-05
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	5e-04
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	8e-05
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	7e-04
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-04
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-04
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-04
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-04
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-04
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	1e-04
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	2e-04
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-04
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-04
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	5e-04
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-04
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	3e-04
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-04
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	3e-04
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	4e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	4e-04
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	4e-04
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	6e-04
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	7e-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 =  103 bits (259), Expect = 6e-26
 Identities = 35/196 (17%), Positives = 80/196 (40%), Gaps = 34/196 (17%)

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--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKR 401
           LP  + D+++ +L    G       ++A  +++     + KG A+  +      +  I  
Sbjct: 102 LPNYLNDDQVKELLTSFG------PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 155

Query: 402 RN-LKLRDRELRLSHA 416
            N ++L D++L +  A
Sbjct: 156 LNGMQLGDKKLLVQRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 61.5 bits (150), Expect = 2e-11
 Identities = 11/89 (12%), Positives = 33/89 (37%), Gaps = 1/89 (1%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCG-LNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
           + ++VGN+PF + +E +   F   +     +      +    +   K  A++ F++ +  
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 396 NLVIKRRNLKLRDRELRLSHAQQNCTPSK 424
              +    +  + + L++           
Sbjct: 65  TQAMAFDGIIFQGQSLKIRRPHDYQPLPG 93

>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 =  101 bits (254), Expect = 4e-25
 Identities = 37/209 (17%), Positives = 83/209 (39%), Gaps = 36/209 (17%)

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 TREAANLVIKRRN-LKLRDRELRLSHAQQ 418
                +  I   N ++L D++L +  A  
Sbjct: 165 DINVTDQAIAGLNGMQLGDKKLLVQRASV 193

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 60.0 bits (146), Expect = 1e-10
 Identities = 13/101 (12%), Positives = 35/101 (34%), Gaps = 1/101 (0%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAV-RVIRHPHMRVGKGIAYVLFKTREAA 395
           + ++VGN+PF + +E +   F     L    +A    +    +   K  A++ F++ +  
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 396 NLVIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAPAVNSPP 436
              +    +  + + L++             +         
Sbjct: 65  TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGV 105

>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 = 54.3 bits (131), 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

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 93.9 bits (234), Expect = 3e-22
 Identities = 37/207 (17%), Positives = 87/207 (42%), Gaps = 31/207 (14%)

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--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVI 399
            ++  D+ D++I  +F   G       +++  + R P     KG  ++ ++  +++   +
Sbjct: 131 ASVHQDLSDDDIKSVFEAFG------KIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV 184

Query: 400 KRRNLK-LRDRELRLSHAQQNCTPSKR 425
              NL  L  + LR+  A     P   
Sbjct: 185 SSMNLFDLGGQYLRVGKAVTPPMPLLT 211

>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 = 1e-06
 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

>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 = 91.5 bits (228), Expect = 9e-22
 Identities = 38/208 (18%), Positives = 76/208 (36%), Gaps = 39/208 (18%)

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 REAANLVIKRRNLK-LRDRELRLSHAQQ 418
              A   ++ +    +  R + L +  +
Sbjct: 146 EADAEKNLEEKQGAEIDGRSVSLYYTGE 173

>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 = 91.4 bits (228), Expect = 9e-22
 Identities = 39/198 (19%), Positives = 75/198 (37%), Gaps = 37/198 (18%)

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--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKR 401
           L  +V DE +   F          S  +  V+        +G  +V F +++ A   +  
Sbjct: 95  LNVNVDDETLRNAFKDFP------SYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148

Query: 402 RN-LKLRDRELRLSHAQQ 418
                L  R LR++ A +
Sbjct: 149 MQGQDLNGRPLRINWAAK 166

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 61.8 bits (151), Expect = 2e-11
 Identities = 15/95 (15%), Positives = 42/95 (44%), Gaps = 12/95 (12%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
           + ++VGNL   + ++ + Q F   G       +  ++++   + +     A+V +     
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGG------PIANIKIMIDKNNK-NVNYAFVEYHQSHD 53

Query: 395 ANLVIKRRN-LKLRDRELRLSHAQQNCTPSKRKDV 428
           AN+ ++  N  ++ +  ++++ A Q+       D 
Sbjct: 54  ANIALQTLNGKQIENNIVKINWAFQS--QQSSSDD 86

>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 = 88.5 bits (220), Expect = 3e-20
 Identities = 47/216 (21%), Positives = 90/216 (41%), Gaps = 38/216 (17%)

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 PFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNL 404
              + ++ +Y  F        ++ + +V+   +    KG  +V F+T+EAA   I++ N 
Sbjct: 112 DKSIDNKALYDTFSAF----GNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNG 165

Query: 405 K-LRDRELRLSHAQQNCTPSKRKDVAPAVNSPPKKF 439
             L DR++ +   +       RK+    + +  K+F
Sbjct: 166 MLLNDRKVFVGRFK------SRKEREAELGARAKEF 195

>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 = 62.3 bits (152), Expect = 3e-11
 Identities = 25/95 (26%), Positives = 45/95 (47%), Gaps = 11/95 (11%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRE 393
             +++VG+L  DV +  +Y+ F   G       + ++RV R    R   G AYV F+   
Sbjct: 15  MASLYVGDLHPDVTEAMLYEKFSPAG------PILSIRVCRDMITRRSLGYAYVNFQQPA 68

Query: 394 AANLVIKRRN-LKLRDRELRLSHAQQNCTPSKRKD 427
            A   +   N   ++ + +R+  +Q++  PS RK 
Sbjct: 69  DAERALDTMNFDVIKGKPVRIMWSQRD--PSLRKS 101

>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 = 87.7 bits (218), Expect = 2e-19
 Identities = 33/198 (16%), Positives = 72/198 (36%), Gaps = 32/198 (16%)

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-PHMRVGKGIAYVLFKTREAANLVI 399
           L  ++ DE  + + F   G      S+E + +             A+++F+ +++A   +
Sbjct: 218 LSTELLDENLLRESFEGFG------SIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 271

Query: 400 KRRNLKLRDRELRLSHAQ 417
           +     L +RE+ +S A 
Sbjct: 272 QMNRSLLGNREISVSLAD 289

>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 = 81.2 bits (201), Expect = 4e-17
 Identities = 40/226 (17%), Positives = 71/226 (31%), Gaps = 44/226 (19%)

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--KGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQ 418
           P +R    +  AY+   ++E A   +++ N LK+    L    +  
Sbjct: 151 PSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP 196

>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 = 84.2 bits (209), Expect = 3e-19
 Identities = 40/198 (20%), Positives = 75/198 (37%), Gaps = 40/198 (20%)

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--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKR 401
           LP  + D+++  +F   G      S+    ++R       +G+A+V +  RE A   I  
Sbjct: 97  LPRTITDDQLDTIFGKYG------SIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 150

Query: 402 RN---LKLRDRELRLSHA 416
            N    +   + L +  A
Sbjct: 151 LNNVIPEGGSQPLSVRLA 168

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 62.2 bits (152), Expect = 1e-11
 Identities = 24/92 (26%), Positives = 41/92 (44%), Gaps = 9/92 (9%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRE 393
              + V  LP D+ D E+Y LF   G       +   R++R        G A+V F +  
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIG------PINTCRIMRDYKTGYSYGYAFVDFTSEM 56

Query: 394 AANLVIKRRN-LKLRDRELRLSHAQQNCTPSK 424
            +   IK  N + +R++ L++S+A+      K
Sbjct: 57  DSQRAIKVLNGITVRNKRLKVSYARPGGESIK 88

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 83.0 bits (206), Expect = 7e-19
 Identities = 35/194 (18%), Positives = 76/194 (39%), Gaps = 35/194 (18%)

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--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN 403
            DV+ +E  + F   G      ++   +++        +G  +V + + +A + V + + 
Sbjct: 97  PDVRPKEFEEFFSQWG------TIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKF 150

Query: 404 LKLRDRELRLSHAQ 417
           +  +DR++ +  A+
Sbjct: 151 IDFKDRKIEIKRAE 164

>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 = 48.3 bits (116), Expect = 6e-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

>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 = 83.1 bits (206), Expect = 1e-18
 Identities = 30/195 (15%), Positives = 71/195 (36%), Gaps = 28/195 (14%)

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--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR 402
             D ++  +   F   G       +E + ++        +G A+V F   ++ + ++ ++
Sbjct: 113 KEDTEEHHLRDYFEQYG------KIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 166

Query: 403 NLKLRDRELRLSHAQ 417
              +      +  A 
Sbjct: 167 YHTVNGHNCEVRKAL 181

>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 = 7e-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

>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 = 80.8 bits (200), Expect = 4e-17
 Identities = 27/198 (13%), Positives = 57/198 (28%), Gaps = 49/198 (24%)

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--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR 402
           P  +  ++  +L    G      S+E   ++        KG  +  +  +++A       
Sbjct: 104 PPSLTQQQFEELVRPFG------SLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157

Query: 403 N-LKLRDRELRLSHAQQN 419
               L  R L +      
Sbjct: 158 LGKPLGPRTLYVHWTDAG 175

>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 = 80.0 bits (198), Expect = 9e-17
 Identities = 27/197 (13%), Positives = 61/197 (30%), Gaps = 37/197 (18%)

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--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKR 401
           P    D + + +            S    ++      +  KG A + ++T E A    ++
Sbjct: 193 PPGFNDVDALCRALSAVH------SPTFCQLACGQDGQ-LKGFAVLEYETAEMAEEAQQQ 245

Query: 402 RNLK-LRDRELRLSHAQ 417
            +   L    LR+S   
Sbjct: 246 ADGLSLGGSHLRVSFCA 262

>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 = 59.2 bits (144), Expect = 6e-10
 Identities = 21/104 (20%), Positives = 39/104 (37%), Gaps = 16/104 (15%)

Query: 321 PRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHM 378
             +K        +  ++ + +  LP DV ++E++ L     L           V ++   
Sbjct: 7   EIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKY-------CFVDKY--- 56

Query: 379 RVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQNCT 421
              KG A+V     E A   I   +  +LR+REL +     +  
Sbjct: 57  ---KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDAL 97

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 76.8 bits (190), Expect = 1e-16
 Identities = 34/197 (17%), Positives = 68/197 (34%), Gaps = 40/197 (20%)

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--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR 402
           P  +  +E+ QLF   G       +   R++      V +G+ ++ F  R  A   IK  
Sbjct: 97  PKTMTQKELEQLFSQYG------RIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150

Query: 403 N---LKLRDRELRLSHA 416
           N          + +  A
Sbjct: 151 NGQKPSGATEPITVKFA 167

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 58.7 bits (143), Expect = 2e-10
 Identities = 21/93 (22%), Positives = 40/93 (43%), Gaps = 13/93 (13%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
            + V  LP ++  EE   LF   G       +E+ +++R        G  +V +   + A
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIG------EIESCKLVRDKITGQSLGYGFVNYIDPKDA 57

Query: 396 NLVIKRRN-LKLRDRELRLSHAQQNCTPSKRKD 427
              I   N L+L+ + +++S+A+    PS    
Sbjct: 58  EKAINTLNGLRLQTKTIKVSYAR----PSSASI 86

>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 = 68.9 bits (169), Expect = 1e-14
 Identities = 24/100 (24%), Positives = 40/100 (40%), Gaps = 8/100 (8%)

Query: 320 PPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPH 377
            P ++     +P     +TVF   L   ++  ++   F   G       V  VR+I   +
Sbjct: 9   SPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVG------KVRDVRIISDRN 62

Query: 378 MRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQ 417
            R  KGIAYV F   ++  L I     +L    + +  +Q
Sbjct: 63  SRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQ 102

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 57.3 bits (139), Expect = 2e-10
 Identities = 26/132 (19%), Positives = 47/132 (35%), Gaps = 22/132 (16%)

Query: 196 GEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSV 255
           G       +   + + +   E  D      RT+F   L  +++ + L   F   G++  V
Sbjct: 1   GSSGSSGKSPVREPVDNLSPEERDA-----RTVFCMQLAARIRPRDLEDFFSAVGKVRDV 55

Query: 256 RIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRL 315
           RI S    +++   KG               AY+ F   QS   A+      + G  I +
Sbjct: 56  RIISDR--NSRRS-KG--------------IAYVEFCEIQSVPLAIGLTGQRLLGVPIIV 98

Query: 316 DRACPPRKKLKG 327
             +   + +L G
Sbjct: 99  QASQAEKNRLSG 110

>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 = 67.6 bits (166), Expect = 3e-14
 Identities = 30/100 (30%), Positives = 46/100 (46%), Gaps = 10/100 (10%)

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-KGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQ 418
              KG  Y  F+  ++    +      L +R +R+  A Q
Sbjct: 58  ERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQ 97

>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 = 6e-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

>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 = 69.6 bits (171), Expect = 5e-14
 Identities = 33/181 (18%), Positives = 66/181 (36%), Gaps = 30/181 (16%)

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--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR 402
                + +I  +F   G       +E  R++R P     +G A+V F TR  A   IK  
Sbjct: 104 SKKCTENDIRVMFSSFG------QIEECRILRGPDGL-SRGCAFVTFTTRAMAQTAIKAM 156

Query: 403 N 403
           +
Sbjct: 157 H 157

>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 = 41.8 bits (99), 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

>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 = 67.1 bits (164), Expect = 6e-14
 Identities = 21/93 (22%), Positives = 39/93 (41%), Gaps = 6/93 (6%)

Query: 327 GEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAY 386
           G+  P+      V V  +PF   + ++   F GL      V+AV +++    R   G   
Sbjct: 7   GKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR-----VDAVHLLKDHVGR-NNGNGL 60

Query: 387 VLFKTREAANLVIKRRNLKLRDRELRLSHAQQN 419
           V F + +     +KR  + +  R + +S A + 
Sbjct: 61  VKFLSPQDTFEALKRNRMLMIQRYVEVSPATER 93

>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 = 45.1 bits (107), Expect = 4e-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

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 67.6 bits (165), Expect = 7e-14
 Identities = 23/103 (22%), Positives = 37/103 (35%), Gaps = 8/103 (7%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
           +  V +  LPF    EE+   F     +    E +  + +P  R   G A+VLF   E A
Sbjct: 23  QVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRP-TGDAFVLFACEEYA 81

Query: 396 NLVIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAPAVNSPPKK 438
              +++    L  R + L         S   +V   +N     
Sbjct: 82  QNALRKHKDLLGKRYIEL-------FRSTAAEVQQVLNRFSSA 117

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 38.7 bits (90), Expect = 7e-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

>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 = 66.1 bits (162), Expect = 1e-13
 Identities = 27/83 (32%), Positives = 41/83 (49%), Gaps = 6/83 (7%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVG-KGIAYVLFKTREAA 395
            T F+GNLP+DV +E I + F GLN     + AVR+ R P      KG  Y  F+  ++ 
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLN-----ISAVRLPREPSNPERLKGFGYAEFEDLDSL 70

Query: 396 NLVIKRRNLKLRDRELRLSHAQQ 418
              +      L ++ +R+  A Q
Sbjct: 71  LSALSLNEESLGNKRIRVDVADQ 93

>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 = 9e-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

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 65.4 bits (160), Expect = 2e-13
 Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 5/82 (6%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
            T +VGNLPF+    +I  +F  L+     + +VR++R       KG  YV F   ++  
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFKDLS-----IRSVRLVRDKDTDKFKGFCYVEFDEVDSLK 70

Query: 397 LVIKRRNLKLRDRELRLSHAQQ 418
             +      L DR LR+  A+ 
Sbjct: 71  EALTYDGALLGDRSLRVDIAEG 92

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 45.0 bits (107), Expect = 3e-06
 Identities = 25/100 (25%), Positives = 40/100 (40%), Gaps = 22/100 (22%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIID--TKIPRKGAILQKQINENAD 283
            T +VGNLP    +  +   F     I SVR+    + D  T    KG            
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRL----VRDKDTDKF-KG------------ 57

Query: 284 SVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRK 323
               Y+ F    S + AL ++ A++G   +R+D A   ++
Sbjct: 58  --FCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQ 95

>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 = 64.5 bits (158), Expect = 3e-13
 Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 8/86 (9%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRE 393
            ++++VGN+ +    EE+   F  CG      SV  V ++        KG AY+ F  +E
Sbjct: 6   ARSIYVGNVDYGATAEELEAHFHGCG------SVNRVTILCDKFSGHPKGFAYIEFSDKE 59

Query: 394 AANLVIKRRNLKLRDRELRLSHAQQN 419
           +    +       R R++++   + N
Sbjct: 60  SVRTSLALDESLFRGRQIKVIPKRTN 85

>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 = 53.7 bits (130), 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

>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 = 65.2 bits (159), Expect = 4e-13
 Identities = 17/118 (14%), Positives = 49/118 (41%), Gaps = 11/118 (9%)

Query: 321 PRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV 380
           P  + +      ++    V++  LPF+ +++ +   F  L+ +E   +++ +   P+ + 
Sbjct: 10  PSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVE---DSIYIAYGPNGK- 65

Query: 381 GKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAPAVNSPPKK 438
             G  +V F+        + R    + +R +++        P  +K +   ++   K+
Sbjct: 66  ATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVH-------PITKKGMLEKIDMIRKR 116

>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 = 41.0 bits (96), Expect = 1e-04
 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

>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 = 63.6 bits (155), Expect = 1e-12
 Identities = 24/103 (23%), Positives = 40/103 (38%), Gaps = 11/103 (10%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
           K    + N+PF +   ++ Q   G+   E    AV V+   + + G G A V FK  + A
Sbjct: 15  KVCAHITNIPFSITKMDVLQFLEGIPVDE---NAVHVLVDNNGQ-GLGQALVQFKNEDDA 70

Query: 396 NLVIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAPAVNSPPKK 438
               +    KL  RE  +            +D+     +PP +
Sbjct: 71  RKSERLHRKKLNGREAFVH-------VVTLEDMREIEKNPPAQ 106

>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 = 46.7 bits (111), Expect = 1e-06
 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

>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 = 62.7 bits (153), Expect = 1e-12
 Identities = 16/79 (20%), Positives = 31/79 (39%), Gaps = 6/79 (7%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
             TV +   PF+V ++ + +    L        A+R++R+ H     G  +V F   E  
Sbjct: 10  CHTVKLRGAPFNVTEKNVMEFLAPLK-----PVAIRIVRNAHGN-KTGYIFVDFSNEEEV 63

Query: 396 NLVIKRRNLKLRDRELRLS 414
              +K     +  R + + 
Sbjct: 64  KQALKCNREYMGGRYIEVF 82

>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 = 46.5 bits (111), 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

>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 = 67.0 bits (164), Expect = 1e-12
 Identities = 35/180 (19%), Positives = 58/180 (32%), Gaps = 48/180 (26%)

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--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN 403
             V +E + Q F   G       VE   V+     R   G  +V F  +  A   ++R  
Sbjct: 106 PVVSNELLEQAFSQFG------PVEKAVVVVDDRGR-ATGKGFVEFAAKPPARKALERCG 158

>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 = 53.5 bits (129), Expect = 4e-08
 Identities = 25/112 (22%), Positives = 43/112 (38%), Gaps = 22/112 (19%)

Query: 310 GNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSV 367
           G  I +     P +K   +          +FVGNLP D+ +E+  +LF   G        
Sbjct: 3   GFTIDIKSFLKPGEKTYTQRC-------RLFVGNLPTDITEEDFKRLFERYG------EP 49

Query: 368 EAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQ 418
             V + R       +G  ++  ++R  A +     +   L+ R LR+  A  
Sbjct: 50  SEVFINR------DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH 95

>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 = 62.6 bits (152), Expect = 3e-12
 Identities = 16/101 (15%), Positives = 33/101 (32%), Gaps = 9/101 (8%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            V +  LP+    E++          +  V  V  I     R   G A+V  ++ +   L
Sbjct: 19  VVKLRGLPWSCSIEDVQNFLSDCTIHD-GVAGVHFIYTREGR-QSGEAFVELESEDDVKL 76

Query: 398 VIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAPAVNSPPKK 438
            +K+    +  R + +         S R ++   +      
Sbjct: 77  ALKKDRESMGHRYIEVF-------KSHRTEMDWVLKHSGPN 110

>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 = 61.7 bits (150), Expect = 4e-12
 Identities = 21/92 (22%), Positives = 38/92 (41%), Gaps = 4/92 (4%)

Query: 327 GEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAY 386
             ++P       V +  LPF    EEI Q F GL  +      + +      R   G A+
Sbjct: 6   SGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVP---NGMTLPVDFQGR-STGEAF 61

Query: 387 VLFKTREAANLVIKRRNLKLRDRELRLSHAQQ 418
           V F ++E A   +K+   ++  R + +  + +
Sbjct: 62  VQFASQEIAEKALKKHKERIGHRYIEIFKSSR 93

>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 = 6e-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

>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 = 60.8 bits (148), Expect = 7e-12
 Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 5/80 (6%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            + V N+PF V  +EI   F G   +  S   V +  +       G A V F++R+ A  
Sbjct: 17  VIKVQNMPFTVSIDEILDFFYGYQVIPGS---VCLKYNEKGM-PTGEAMVAFESRDEATA 72

Query: 398 VIKRRNLK-LRDRELRLSHA 416
            +   N + +  R+++LS  
Sbjct: 73  AVIDLNDRPIGSRKVKLSGP 92

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 38.1 bits (89), Expect = 8e-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

>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 = 60.8 bits (148), Expect = 9e-12
 Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 5/80 (6%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            + V N+PF V  +EI   F G   +  S   V +  +       G A V F++R+ A  
Sbjct: 17  IIKVQNMPFTVSIDEILDFFYGYQVIPGS---VCLKYNEKGM-PTGEAMVAFESRDEATA 72

Query: 398 VIKRRNLK-LRDRELRLSHA 416
            +   N + +  R+++L   
Sbjct: 73  AVIDLNDRPIGSRKVKLVLG 92

>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 = 42.3 bits (100), 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

>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 = 61.0 bits (148), Expect = 1e-11
 Identities = 21/93 (22%), Positives = 39/93 (41%), Gaps = 4/93 (4%)

Query: 326 KGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIA 385
           +G ++        V +  LPF    EEI Q F GL  +      + +   P  +   G A
Sbjct: 32  RGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVP---NGITLPVDPEGK-ITGEA 87

Query: 386 YVLFKTREAANLVIKRRNLKLRDRELRLSHAQQ 418
           +V F ++E A   + +   ++  R + +  + Q
Sbjct: 88  FVQFASQELAEKALGKHKERIGHRYIEVFKSSQ 120

>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 = 2e-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

>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 = 60.1 bits (146), Expect = 2e-11
 Identities = 23/82 (28%), Positives = 33/82 (40%), Gaps = 8/82 (9%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
             V +  LP+   + +IY  F  LN        V +   P  RV  G A V F T E A 
Sbjct: 16  HCVHMRGLPYRATENDIYNFFSPLN-----PMRVHIEIGPDGRV-TGEADVEFATHEDAV 69

Query: 397 LVIKRRNLKLRDR--ELRLSHA 416
             + +    ++ R  EL L+  
Sbjct: 70  AAMAKDKANMQHRYVELFLNST 91

>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 = 3e-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

>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 = 60.6 bits (147), Expect = 3e-11
 Identities = 23/94 (24%), Positives = 33/94 (35%), Gaps = 6/94 (6%)

Query: 320 PPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMR 379
             R     E          V +  LP+   + +IY  F  LN        V +   P  R
Sbjct: 30  MGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-----PVRVHIEIGPDGR 84

Query: 380 VGKGIAYVLFKTREAANLVIKRRNLKLRDRELRL 413
           V  G A V F T E A   + +    ++ R + L
Sbjct: 85  V-TGEADVEFATHEEAVAAMSKDRANMQHRYIEL 117

>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 = 43.3 bits (102), Expect = 3e-05
 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

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 58.5 bits (142), Expect = 4e-11
 Identities = 14/87 (16%), Positives = 34/87 (39%), Gaps = 7/87 (8%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
            T+ + N+      + I         L   V  +R+I+    +  +G A+V   +   A+
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLA--VNNIRLIKDKQTQQNRGFAFVQLSSAMDAS 67

Query: 397 LVIKRRN-----LKLRDRELRLSHAQQ 418
            +++        LK+  + + +  A+ 
Sbjct: 68  QLLQILQSLHPPLKIDGKTIGVDFAKS 94

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 39.6 bits (93), 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

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 59.3 bits (144), Expect = 5e-11
 Identities = 18/86 (20%), Positives = 38/86 (44%), Gaps = 8/86 (9%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRE 393
           K++V+VGN+ +    +++   F  CG      S+  + ++        KG AY+ F  R 
Sbjct: 36  KRSVYVGNVDYGSTAQDLEAHFSSCG------SINRITILCDKFSGHPKGYAYIEFAERN 89

Query: 394 AANLVIKRRNLKLRDRELRLSHAQQN 419
           + +  +       R R +++   + N
Sbjct: 90  SVDAAVAMDETVFRGRTIKVLPKRTN 115

>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 = 49.7 bits (119), Expect = 1e-07
 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

>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 = 58.5 bits (142), Expect = 5e-11
 Identities = 16/91 (17%), Positives = 40/91 (43%), Gaps = 8/91 (8%)

Query: 334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRE 393
            +  ++++G+L   + +  I + F     +  +V +V++IR+    +  G  +V F    
Sbjct: 7   GMAASLWMGDLEPYMDENFISRAF---ATMGETVMSVKIIRNRLTGIPAGYCFVEFADLA 63

Query: 394 AANLVIKRRNLKL-----RDRELRLSHAQQN 419
            A   + + N K        +  +L++A  +
Sbjct: 64  TAEKCLHKINGKPLPGATPAKRFKLNYATYS 94

>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 = 57.6 bits (140), Expect = 1e-10
 Identities = 23/94 (24%), Positives = 40/94 (42%), Gaps = 14/94 (14%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRE 393
            +T++VGNL  DV +  I QLF   G        ++ ++I            +V F    
Sbjct: 15  PRTLYVGNLSRDVTEVLILQLFSQIG------PCKSCKMIT--EHTSNDPYCFVEFYEHR 66

Query: 394 AANLVIKRRN-LKLRDRELRLSHAQQNCTPSKRK 426
            A   +   N  K+  +E++++ A     PS +K
Sbjct: 67  DAAAALAAMNGRKILGKEVKVNWATT---PSSQK 97

>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 = 8e-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

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 57.4 bits (139), Expect = 2e-10
 Identities = 19/85 (22%), Positives = 32/85 (37%), Gaps = 9/85 (10%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRE 393
            K V    L  +V++  +  +    G       VE V ++ HP  R   G+A VLF +  
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKYG------EVEEVEILLHPRTRKHLGLARVLFTSTR 59

Query: 394 AANLVIKRRNLK-LRDRELRLSHAQ 417
            A   +K  +L  +    +      
Sbjct: 60  GAKETVKNLHLTSVMGNIIHAQLDI 84

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 47.8 bits (114), Expect = 4e-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

>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 = 57.2 bits (138), Expect = 2e-10
 Identities = 11/101 (10%), Positives = 35/101 (34%), Gaps = 9/101 (8%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            +    LP+    E++   F     + +    +  + +   +  +G A +  ++ +    
Sbjct: 13  LIRAQGLPWSCTMEDVLNFFSDCR-IRNGENGIHFLLNRDGKR-RGDALIEMESEQDVQK 70

Query: 398 VIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAPAVNSPPKK 438
            +++  + +  R + +            +DV   + S   K
Sbjct: 71  ALEKHRMYMGQRYVEVY-------EINNEDVDALMKSLQVK 104

>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 = 38.3 bits (89), Expect = 8e-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

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 56.9 bits (138), Expect = 3e-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

>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 = 47.2 bits (113), Expect = 6e-07
 Identities = 24/106 (22%), Positives = 50/106 (47%), Gaps = 17/106 (16%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
             +F+ NL   + ++ +Y  F   G      ++ + +V+   +    KG  +V F+T+EA
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFG------NILSCKVVCDENG--SKGYGFVHFETQEA 57

Query: 395 ANLVIKRRN-LKLRDRELRLSHAQQNCTPSKRKDVAPAVNSPPKKF 439
           A   I++ N + L DR++ +   +       RK+    + +  K+F
Sbjct: 58  AERAIEKMNGMLLNDRKVFVGRFK------SRKEREAELGARAKEF 97

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 56.5 bits (137), Expect = 3e-10
 Identities = 16/80 (20%), Positives = 29/80 (36%), Gaps = 15/80 (18%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
           T ++GN+P    + ++  LF   G       +   +          KG  ++ + T E A
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFG------FILDFKHYP------EKGCCFIKYDTHEQA 76

Query: 396 NLVIKRRN-LKLRDRELRLS 414
            + I        + R LR  
Sbjct: 77  AVCIVALANFPFQGRNLRTG 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 = 51.5 bits (124), Expect = 1e-08
 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

>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 = 55.9 bits (135), Expect = 3e-10
 Identities = 11/77 (14%), Positives = 32/77 (41%), Gaps = 1/77 (1%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCG-LNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
           + ++VGN+PF + +E +   F   +     +      +    +   K  A++ F++ +  
Sbjct: 7   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66

Query: 396 NLVIKRRNLKLRDRELR 412
              +    +  + + L+
Sbjct: 67  TQAMAFDGIIFQGQSLK 83

>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 = 3e-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

>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 = 59.2 bits (143), Expect = 3e-10
 Identities = 36/224 (16%), Positives = 73/224 (32%), Gaps = 60/224 (26%)

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 MRVGKGIAYVLFKTREAANLVIKR-RNLKLRD-RELRLSHAQQN 419
               + +A +   + E A   +    N  L +   LR+S ++  
Sbjct: 188 ---DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 228

>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 = 57.9 bits (140), Expect = 3e-10
 Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 9/84 (10%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
            T++VGNL F   +E+IY+LF   G       ++ + +      +   G  +V + +R  
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSG------DIKKIIMGLDKMKKTACGFCFVEYYSRAD 93

Query: 395 ANLVIKRRN-LKLRDRELRLSHAQ 417
           A   ++  N  +L DR +R     
Sbjct: 94  AENAMRYINGTRLDDRIIRTDWDA 117

>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 = 45.2 bits (107), Expect = 8e-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

>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 = 57.3 bits (138), Expect = 4e-10
 Identities = 14/91 (15%), Positives = 30/91 (32%), Gaps = 9/91 (9%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            V +  LP+    E++         +      V  I     R   G A+V   + +   +
Sbjct: 46  VVKLRGLPWSCSVEDVQNFLSDCT-IHDGAAGVHFIYTREGR-QSGEAFVELGSEDDVKM 103

Query: 398 VIKRRNLKLRDRELRLSHAQQNCTPSKRKDV 428
            +K+    +  R + +         S R ++
Sbjct: 104 ALKKDRESMGHRYIEVF-------KSHRTEM 127

>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 = 55.7 bits (135), Expect = 4e-10
 Identities = 27/94 (28%), Positives = 47/94 (50%), Gaps = 9/94 (9%)

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 IAYVLFKTREAANLVIKRRN-LKLRDRELRLSHA 416
           +A++LF  +++A    +  N  +L  R ++ S A
Sbjct: 60  VAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93

>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 = 40.3 bits (95), 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

>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 = 56.0 bits (135), Expect = 6e-10
 Identities = 21/104 (20%), Positives = 43/104 (41%), Gaps = 9/104 (8%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP-HMRVGKGIAYVLFKTREA 394
              +F+G +P   K EEI +    + +    V  V V          +G A+V +++  A
Sbjct: 8   NCRLFIGGIPKMKKREEILEEIAKVTE---GVLDVIVYASAADKMKNRGFAFVEYESHRA 64

Query: 395 ANLVIKR---RNLKLRDRELRLSHAQQNCTPSKRKDVAPAVNSP 435
           A +  ++     ++L   ++ +  A+        +DV   V+ P
Sbjct: 65  AAMARRKLMPGRIQLWGHQIAVDWAEPE--IDVDEDVMETVSGP 106

>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 = 2e-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

>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 = 55.8 bits (135), Expect = 6e-10
 Identities = 29/90 (32%), Positives = 45/90 (50%), Gaps = 15/90 (16%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
           KTVF+ NL FD ++E + ++    G       ++ VRV+ HP     KG A+  F T+EA
Sbjct: 16  KTVFIRNLSFDSEEEALGEVLQQFG------DLKYVRVVLHPDTEHSKGCAFAQFMTQEA 69

Query: 395 ANLVIKRRN-------LKLRDRELRLSHAQ 417
           A   +   +       LKL  R+L++  A 
Sbjct: 70  AQKCLAAASLEAEGGGLKLDGRQLKVDLAV 99

>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 = 3e-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

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 55.0 bits (133), Expect = 1e-09
 Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 11/81 (13%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
           TV+ G +   + D+ + Q F     +      +RV         KG ++V F T E+A  
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIME----IRVFP------EKGYSFVRFSTHESAAH 76

Query: 398 VIKRRN-LKLRDRELRLSHAQ 417
            I   N   +    ++    +
Sbjct: 77  AIVSVNGTTIEGHVVKCYWGK 97

>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 = 3e-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

>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 = 56.4 bits (136), Expect = 2e-09
 Identities = 36/223 (16%), Positives = 71/223 (31%), Gaps = 60/223 (26%)

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 MRVGKGIAYVLFKTREAANLVIKRRN-LKLRD-RELRLSHAQQ 418
            +  + +A +   + E A   +   +   L +   LR+S ++ 
Sbjct: 154 FQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS 196

>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 = 49.1 bits (117), Expect = 6e-07
 Identities = 25/131 (19%), Positives = 45/131 (34%), Gaps = 18/131 (13%)

Query: 337 KTVFVGNL-PFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
             + V NL P  V  + ++ LF    D    V+ V++     +   K  A V       A
Sbjct: 4   SVLLVSNLNPERVTPQSLFILFGVYGD----VQRVKI-----LFNKKENALVQMADGNQA 54

Query: 396 NLVIKRRN-LKLRDRELRLSHAQQNCTPSKRKDVAPAVNSPPKKFVLDSRTLGSGNRSNS 454
            L +   N  KL  + +R        T SK ++V         + +         +R   
Sbjct: 55  QLAMSHLNGHKLHGKPIR-------ITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKK 107

Query: 455 KVAMSYQGLQA 465
             + ++Q +  
Sbjct: 108 PGSKNFQNIFP 118

>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 = 53.0 bits (128), Expect = 4e-09
 Identities = 19/94 (20%), Positives = 44/94 (46%), Gaps = 9/94 (9%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
           + V++G++P+D  +E+I  L    G       V  ++++  P     KG A++ F+  E+
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVG------PVINLKMMFDPQTGRSKGYAFIEFRDLES 56

Query: 395 ANLVIKRRN-LKLRDRELRLSHAQQNCTPSKRKD 427
           +   ++  N  +L  R L+  ++  +       +
Sbjct: 57  SASAVRNLNGYQLGSRFLKCGYSSNSDISGVSLE 90

>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 = 44.1 bits (105), 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

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 53.1 bits (128), Expect = 4e-09
 Identities = 18/87 (20%), Positives = 45/87 (51%), Gaps = 14/87 (16%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVG--KGIAYVLFKT 391
           K  +F+  LPF    EE+ ++    G      +V+ +R++ +   R G  KG+AYV ++ 
Sbjct: 17  KHKLFISGLPFSCTKEELEEICKAHG------TVKDLRLVTN---RAGKPKGLAYVEYEN 67

Query: 392 REAANLVIKRRN-LKLRDRELRLSHAQ 417
              A+  + + + + +++  ++++ + 
Sbjct: 68  ESQASQAVMKMDGMTIKENIIKVAISN 94

>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 = 5e-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

>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 = 52.6 bits (127), Expect = 5e-09
 Identities = 21/91 (23%), Positives = 39/91 (42%), Gaps = 15/91 (16%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
            +FVGNLP D+ +EE+ +LF   G          V + +       KG  ++  +TR  A
Sbjct: 17  RLFVGNLPPDITEEEMRKLFEKYG------KAGEVFIHK------DKGFGFIRLETRTLA 64

Query: 396 NLVIKRRNLKLRD-RELRLSHAQQNCTPSKR 425
            +     +      ++LR+  A  + + +  
Sbjct: 65  EIAKVELDNMPLRGKQLRVRFACHSASLTSG 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 = 46.1 bits (110), Expect = 1e-06
 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

>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 = 53.1 bits (128), Expect = 6e-09
 Identities = 20/86 (23%), Positives = 39/86 (45%), Gaps = 12/86 (13%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFC--GLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
           + +++ NLP+ +  EE+Y +F   G       +  +RV   P  R   G AYV+++    
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYG------PIRQIRVGNTPETR---GTAYVVYEDIFD 59

Query: 395 ANLVIKRRN-LKLRDRELRLSHAQQN 419
           A   +   +   + +R L + +   N
Sbjct: 60  AKNAVDHLSGFNVSNRYLVVLYYNAN 85

>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 = 45.4 bits (108), 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

>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 = 55.1 bits (132), Expect = 8e-09
 Identities = 14/121 (11%), Positives = 38/121 (31%), Gaps = 7/121 (5%)

Query: 320 PPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPH 377
             +             +  +++GNL +   DE++ +     G+ND+      ++   +  
Sbjct: 52  VGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILE----IKFFENRA 107

Query: 378 MRVGKGIAYVLFKTREAANLVIKRRNLK-LRDRELRLSHAQQNCTPSKRKDVAPAVNSPP 436
               KG A V   +  ++  ++     + L  +   ++   +               S  
Sbjct: 108 NGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQ 167

Query: 437 K 437
            
Sbjct: 168 M 168

>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 = 9e-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 = 48.4 bits (116), Expect = 2e-07
 Identities = 21/86 (24%), Positives = 38/86 (44%), Gaps = 9/86 (10%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRE 393
             TV+VG L   V +  +++LF   G       V    + +       +G  +V F + E
Sbjct: 15  DATVYVGGLDEKVSEPLLWELFLQAG------PVVNTHMPKDRVTGQHQGYGFVEFLSEE 68

Query: 394 AANLVIKRRN-LKLRDRELRLSHAQQ 418
            A+  IK  + +KL  + +R++ A  
Sbjct: 69  DADYAIKIMDMIKLYGKPIRVNKASA 94

>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 = 51.9 bits (125), Expect = 9e-09
 Identities = 17/85 (20%), Positives = 32/85 (37%), Gaps = 5/85 (5%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGL--NDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            T+FV  L  +V  E +   F   G+   + ++    + +         KG A V F   
Sbjct: 14  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73

Query: 393 EAANLVIKRRN-LKLRDRELRLSHA 416
            +A   I   +  +     +++S A
Sbjct: 74  PSAKAAIDWFDGKEFSGNPIKVSFA 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 = 44.6 bits (106), Expect = 4e-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

>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 = 51.5 bits (124), Expect = 1e-08
 Identities = 15/80 (18%), Positives = 36/80 (45%), Gaps = 12/80 (15%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
            T++VG L   + + ++   F    ++ +    + V++       +  A++ F TR+AA 
Sbjct: 13  TTLYVGGLGDTITETDLRNHFYQFGEIRT----ITVVQ------RQQCAFIQFATRQAAE 62

Query: 397 LVIKRR--NLKLRDRELRLS 414
           +  ++    L +  R L + 
Sbjct: 63  VAAEKSFNKLIVNGRRLNVK 82

>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 = 51.1 bits (123), 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

>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 = 51.5 bits (124), Expect = 1e-08
 Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 10/84 (11%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
           +TVFVGNL   V++E +Y+LF   G       +  V + +    +  K   +V FK  E+
Sbjct: 17  RTVFVGNLEARVREEILYELFLQAG------PLTKVTICKDREGK-PKSFGFVCFKHPES 69

Query: 395 ANLVIKRRN-LKLRDRELRLSHAQ 417
            +  I   N ++L  R + +S   
Sbjct: 70  VSYAIALLNGIRLYGRPINVSGPS 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 = 44.5 bits (106), Expect = 4e-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

>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 = 51.9 bits (125), Expect = 1e-08
 Identities = 14/82 (17%), Positives = 30/82 (36%), Gaps = 9/82 (10%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
            +F+GNL  +    E+              +   + V+        +   YV F++ E  
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELF------AKNDLAVVDVRTGT-NRKFGYVDFESAEDL 71

Query: 396 NLVIKRRNLKLRDRELRLSHAQ 417
              ++   LK+   E++L   +
Sbjct: 72  EKALELTGLKVFGNEIKLEKPK 93

>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 = 50.7 bits (122), 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

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 51.7 bits (124), Expect = 1e-08
 Identities = 15/83 (18%), Positives = 36/83 (43%), Gaps = 5/83 (6%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
            ++V++   P D   ++I +           V  +++ R  H +  KG  +V+F + E+A
Sbjct: 11  NRSVYIKGFPTDATLDDIKEWLEDKGQ----VLNIQMRRTLH-KAFKGSIFVVFDSIESA 65

Query: 396 NLVIKRRNLKLRDRELRLSHAQQ 418
              ++    K ++ +L +     
Sbjct: 66  KKFVETPGQKYKETDLLILFKDD 88

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 38.9 bits (91), Expect = 5e-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

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 51.6 bits (124), Expect = 2e-08
 Identities = 17/87 (19%), Positives = 33/87 (37%), Gaps = 5/87 (5%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGL--NDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            T+FV  L  +V  E +   F   G+   + ++    + +         KG A V F   
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67

Query: 393 EAANLVIKRRN-LKLRDRELRLSHAQQ 418
            +A   I   +  +     +++S A +
Sbjct: 68  PSAKAAIDWFDGKEFSGNPIKVSFATR 94

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 42.8 bits (101), 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

>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 = 56.0 bits (134), Expect = 2e-08
 Identities = 79/532 (14%), Positives = 146/532 (27%), Gaps = 185/532 (34%)

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-----DDVEKDYVEKKYGVIAKEEEGKKVGVGEKRK----- 200
            S++ + R    K+K  +       +V+       + +        K+ +  + K     
Sbjct: 229 -SIQAELR-RLLKSKPYENCLLVLLNVQNAKAWNAFNL------SCKILLTTRFKQVTDF 280

Query: 201 -KADNETEDMLVHRKEEGF-DDEGK-LLRTIF---VGNLPLKV----------------- 237
             A   T   L H        DE K LL         +LP +V                 
Sbjct: 281 LSAATTTHISLDHH-SMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRD 339

Query: 238 --------------KKKTLIKEFIKFGEIDSVR--IRSVPII--DTKIP----------- 268
                         K  T+I+  +   E    R     + +      IP           
Sbjct: 340 GLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDV 399

Query: 269 ------------RKGAILQKQINENADSVHA-YIVFKSEQSTEAALAFNMAVIGGNHIRL 315
                        K ++++KQ  E+  S+ + Y+  K +   E AL          H  +
Sbjct: 400 IKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYAL----------HRSI 449

Query: 316 -DRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIR 374
            D                Y+I KT    +L     D+  Y                    
Sbjct: 450 VDH---------------YNIPKTFDSDDLIPPYLDQYFYS------------------- 475

Query: 375 HPHMRVGKGIAYVLFKTREAANLVIKRR---NLKLRDRELRLSHAQQNCTPS 423
           H        I + L        + + R    + +  ++++R      N + S
Sbjct: 476 H--------IGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGS 519

>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 = 50.7 bits (122), Expect = 4e-08
 Identities = 26/95 (27%), Positives = 40/95 (42%), Gaps = 9/95 (9%)

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 IAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQ 417
            A+V F  R  A       +  +L  RELR+  A+
Sbjct: 57  FAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVAR 91

>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 = 46.4 bits (111), Expect = 8e-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

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 52.8 bits (126), Expect = 4e-08
 Identities = 19/205 (9%), Positives = 49/205 (23%), Gaps = 25/205 (12%)

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 REAANLVIKRRN-LKLRDRELRLSH 415
           +  A   +   N  ++++      +
Sbjct: 175 KSDALETLGFLNHYQMKNPNGPYPY 199

>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 = 49.9 bits (120), Expect = 5e-08
 Identities = 17/84 (20%), Positives = 32/84 (38%), Gaps = 9/84 (10%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
             +FV NL +   +E++ +LF   G       +  +        +  KG A+V F   E 
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYG------PLSELHYPIDSLTKKPKGFAFVTFMFPEH 62

Query: 395 ANLVIKRRNLK-LRDRELRLSHAQ 417
           A       + +  + R L +  + 
Sbjct: 63  AVKAYAEVDGQVFQGRMLHVLPST 86

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 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

>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 = 49.5 bits (119), Expect = 5e-08
 Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 5/81 (6%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
           VFVG+L  ++    I   F         +   RV++       KG  +V F  +  A   
Sbjct: 9   VFVGDLSPEITTAAIAAAFAPF----GRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64

Query: 399 IKRRNLK-LRDRELRLSHAQQ 418
           I++   + L  R++R + A +
Sbjct: 65  IQQMGGQWLGGRQIRTNWATR 85

>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 = 39.8 bits (94), 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

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 53.3 bits (127), Expect = 6e-08
 Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 4/84 (4%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
            T+++ NL   +K +E+ +    +      +  + V R   MR   G A+V+FK   +A 
Sbjct: 10  HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIFKEVSSAT 66

Query: 397 LVIKRRN-LKLRDRELRLSHAQQN 419
             ++        D+ +R+ +A+ +
Sbjct: 67  NALRSMQGFPFYDKPMRIQYAKTD 90

>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 = 43.3 bits (101), Expect = 1e-04
 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

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 49.4 bits (118), Expect = 7e-08
 Identities = 23/100 (23%), Positives = 40/100 (40%), Gaps = 13/100 (13%)

Query: 320 PPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMR 379
                  GE APL      V+VGNLP D +  ++ +        E     +R+      +
Sbjct: 6   SGPGSPPGEGAPL---AADVYVGNLPRDARVSDLKRAL-----RELGSVPLRLTW----Q 53

Query: 380 VGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQ 418
             +  A++ +    AA   +     L+L    LR++ A+Q
Sbjct: 54  GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQ 93

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 42.9 bits (101), Expect = 2e-05
 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

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 49.1 bits (118), Expect = 8e-08
 Identities = 20/84 (23%), Positives = 45/84 (53%), Gaps = 8/84 (9%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
            +F+GNL  ++ ++ +Y  F   G       ++  +++R P     KG A++ F + +A+
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFG-----VILQTPKIMRDPDTGNSKGYAFINFASFDAS 61

Query: 396 NLVIKRRNLK-LRDRELRLSHAQQ 418
           +  I+  N + L +R + +S+A +
Sbjct: 62  DAAIEAMNGQYLCNRPITVSYAFK 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 = 49.2 bits (118), Expect = 9e-08
 Identities = 17/90 (18%), Positives = 35/90 (38%), Gaps = 17/90 (18%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFC--GLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
             ++VG L  +     + + F   G      S+  +  ++      G   AY+ +++ +A
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFG------SIRTIDHVK------GDSFAYIQYESLDA 65

Query: 395 ANLVIKRRN---LKLRDRELRLSHAQQNCT 421
           A     +     L   DR LR+  A+   +
Sbjct: 66  AQAACAKMRGFPLGGPDRRLRVDFAKSGPS 95

>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 = 4e-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

>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 = 49.7 bits (119), Expect = 9e-08
 Identities = 24/102 (23%), Positives = 41/102 (40%), Gaps = 9/102 (8%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
            VFVG+L  ++  E+I   F   G       +   RV++       KG  +V F  +  A
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFG------RISDARVVKDMATGKSKGYGFVSFFNKWDA 70

Query: 396 NLVIKRRNLK-LRDRELRLSHAQQNCTPSKRKDVAPAVNSPP 436
              I++   + L  R++R + A +     K    +    S P
Sbjct: 71  ENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGP 112

>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 = 38.5 bits (90), Expect = 7e-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

>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 = 49.2 bits (118), Expect = 9e-08
 Identities = 18/99 (18%), Positives = 43/99 (43%), Gaps = 16/99 (16%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           +F+G +P ++ ++++  LF   G       +  + V++     + KG A++ +  RE+A 
Sbjct: 16  LFIGQIPRNLDEKDLKPLFEEFG------KIYELTVLKDRFTGMHKGCAFLTYCERESAL 69

Query: 397 LVIK----RRNLKLRDRELRLSHAQQNCTPSKRKDVAPA 431
                   ++ L   +R +++  A        R    P+
Sbjct: 70  KAQSALHEQKTLPGMNRPIQVKPAD----SESRGGSGPS 104

>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 = 49.7 bits (119), Expect = 9e-08
 Identities = 14/87 (16%), Positives = 35/87 (40%), Gaps = 5/87 (5%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGL--NDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRE 393
            ++V  L   V  +++   F  CG+   +  +    + +         KG A V ++   
Sbjct: 17  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 76

Query: 394 AANLVIKRRN-LKLRDRELRLSHAQQN 419
            A   ++  +    +  +L++S A++ 
Sbjct: 77  TAKAAVEWFDGKDFQGSKLKVSLARKK 103

>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 = 42.8 bits (101), 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

>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 = 49.2 bits (118), Expect = 1e-07
 Identities = 20/82 (24%), Positives = 33/82 (40%), Gaps = 11/82 (13%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           K ++V NL     +E I + F  +          RV +       +  A+V F  RE A 
Sbjct: 16  KILYVRNLMLSTSEEMIEKEFNNIKPGAV----ERVKKI------RDYAFVHFSNREDAV 65

Query: 397 LVIKRRNLK-LRDRELRLSHAQ 417
             +K  N K L    + ++ A+
Sbjct: 66  EAMKALNGKVLDGSPIEVTLAK 87

>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 = 46.5 bits (111), 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

>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 = 49.2 bits (118), Expect = 1e-07
 Identities = 20/83 (24%), Positives = 35/83 (42%), Gaps = 10/83 (12%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
           TVFV NL + V  +++ ++F   G       V    ++     +  +GI  V F+    A
Sbjct: 17  TVFVANLDYKVGWKKLKEVFSMAG------VVVRADILEDKDGK-SRGIGTVTFEQSIEA 69

Query: 396 NLVIKRRNLK-LRDRELRLSHAQ 417
              I   N + L DR + +   +
Sbjct: 70  VQAISMFNGQLLFDRPMHVKMDE 92

>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 = 48.8 bits (117), Expect = 1e-07
 Identities = 20/84 (23%), Positives = 41/84 (48%), Gaps = 9/84 (10%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
           ++VFVGN+P++  +E++  +F   G       V + R++        KG  +  ++ +E 
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVG------PVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 395 ANLVIKRRN-LKLRDRELRLSHAQ 417
           A   ++  N  +   R LR+ +A 
Sbjct: 63  ALSAMRNLNGREFSGRALRVDNAA 86

>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 = 43.0 bits (102), 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

>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 = 48.3 bits (116), Expect = 1e-07
 Identities = 17/84 (20%), Positives = 36/84 (42%), Gaps = 10/84 (11%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIR-HPHMRVGKGIAYVLFKTREA 394
            V +G L  +V  + I ++F   G       ++ + +     H  + KG AYV F+  + 
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYG------KIKMIDMPVERMHPHLSKGYAYVEFENPDE 59

Query: 395 ANLVIKRRN-LKLRDRELRLSHAQ 417
           A   +K  +  ++  +E+  +   
Sbjct: 60  AEKALKHMDGGQIDGQEITATAVL 83

>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

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 49.8 bits (119), Expect = 1e-07
 Identities = 27/135 (20%), Positives = 50/135 (37%), Gaps = 9/135 (6%)

Query: 285 VHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNL 344
           VH+     S++  E       +V        +R         G        K+ ++VG L
Sbjct: 12  VHSKCENLSDEMYEILSNLPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGL 71

Query: 345 PFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR 402
             +V D+ ++  F   G       +  +++         +G A+V F+  E A   I   
Sbjct: 72  AEEVDDKVLHAAFIPFG------DITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125

Query: 403 N-LKLRDRELRLSHA 416
           N  +L  R +R++ A
Sbjct: 126 NESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 45.9 bits (109), Expect = 3e-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

>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 = 49.0 bits (117), Expect = 1e-07
 Identities = 17/104 (16%), Positives = 25/104 (24%), Gaps = 11/104 (10%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
           K  +   NLP      EI + F               +    +  G   A V F     A
Sbjct: 10  KTVILAKNLPAGTLAAEIQETF----------SRFGSLGRVLLPEGGITAIVEFLEPLEA 59

Query: 396 NLVIKRRNLK-LRDRELRLSHAQQNCTPSKRKDVAPAVNSPPKK 438
               +           L L  A      +  +        P +K
Sbjct: 60  RKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEK 103

>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 = 48.4 bits (116), Expect = 2e-07
 Identities = 14/86 (16%), Positives = 36/86 (41%), Gaps = 12/86 (13%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHP---HMRVGKGIAYVLFKTR 392
            +F+ NL F   +E +  +F   G      ++++  + +      + +  G  +V +K  
Sbjct: 7   GLFIKNLNFSTTEETLKGVFSKVG------AIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60

Query: 393 EAANLVIKRRNLK-LRDRELRLSHAQ 417
           E A   +K+     +   +L +  ++
Sbjct: 61  EQAQKALKQLQGHTVDGHKLEVRISE 86

>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 = 6e-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

>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 = 49.3 bits (118), Expect = 2e-07
 Identities = 17/105 (16%), Positives = 39/105 (37%), Gaps = 10/105 (9%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
            +FV  +  +  +E+I+  F   G       ++ + +         KG   V ++T + A
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYG------EIKNIHLNLDRRTGYLKGYTLVEYETYKEA 77

Query: 396 NLVIKRRN-LKLRDRELRLSHAQ-QNCTPSKRKDVAPAVNSPPKK 438
              ++  N   L  + + +     +     KR+       SP ++
Sbjct: 78  QAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRSPDRR 122

>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 = 48.4 bits (116), Expect = 2e-07
 Identities = 18/90 (20%), Positives = 40/90 (44%), Gaps = 9/90 (10%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           KT+ + NL +   +E + ++F            ++V ++ + +  KG A++ F + E A 
Sbjct: 16  KTLVLSNLSYSATEETLQEVF-------EKATFIKVPQNQNGK-SKGYAFIEFASFEDAK 67

Query: 397 LVIKRRN-LKLRDRELRLSHAQQNCTPSKR 425
             +   N  ++  R +RL       +P+  
Sbjct: 68  EALNSCNKREIEGRAIRLELQGPRGSPNSG 97

>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 = 39.6 bits (93), Expect = 2e-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

>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 = 49.0 bits (117), Expect = 2e-07
 Identities = 18/101 (17%), Positives = 38/101 (37%), Gaps = 9/101 (8%)

Query: 320 PPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPH 377
             R      +    D    + V  L     + ++ ++F   G       +  V ++    
Sbjct: 30  MGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYG------PIADVSIVYDQQ 83

Query: 378 MRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQ 417
            R  +G A+V F+  + A    +R N ++L  R +R+  + 
Sbjct: 84  SRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSI 124

>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 = 43.9 bits (104), Expect = 1e-05
 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

>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 = 47.5 bits (114), Expect = 2e-07
 Identities = 20/91 (21%), Positives = 40/91 (43%), Gaps = 9/91 (9%)

Query: 330 APLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYV 387
             +   K+ ++VG L  +V D+ ++  F   G       +  +++         +G A+V
Sbjct: 1   GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFG------DITDIQIPLDYETEKHRGFAFV 54

Query: 388 LFKTREAANLVIKRRN-LKLRDRELRLSHAQ 417
            F+  E A   I   N  +L  R +R++ A+
Sbjct: 55  EFELAEDAAAAIDNMNESELFGRTIRVNLAK 85

>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 = 43.7 bits (104), Expect = 6e-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

>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 = 48.0 bits (115), Expect = 2e-07
 Identities = 20/87 (22%), Positives = 35/87 (40%), Gaps = 9/87 (10%)

Query: 334 DIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
           D   T+ V NL  D ++ ++ +LF   G      S+  + + +       KG A++ F  
Sbjct: 13  DDNATIRVTNLSEDTRETDLQELFRPFG------SISRIYLAKDKTTGQSKGFAFISFHR 66

Query: 392 REAANLVIKRRN-LKLRDRELRLSHAQ 417
           RE A   I   +        L +  A+
Sbjct: 67  REDAARAIAGVSGFGYDHLILNVEWAK 93

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 15/85 (17%), Positives = 32/85 (37%), Gaps = 12/85 (14%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
              + V NLP D   +E++ L           +    +++ ++   K  A+V     E A
Sbjct: 5   SSGILVKNLPQDSNCQEVHDLL-------KDYD----LKYCYVDRNKRTAFVTLLNGEQA 53

Query: 396 NLVIKRRN-LKLRDRELRLSHAQQN 419
              I+  +    R ++L +     +
Sbjct: 54  QNAIQMFHQYSFRGKDLIVQLQPTD 78

>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 = 47.5 bits (114), Expect = 3e-07
 Identities = 16/84 (19%), Positives = 39/84 (46%), Gaps = 9/84 (10%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
             ++VG+L F++ ++ +  +F   G       ++ + +++       KG  ++ F   E 
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFG------KIDNIVLMKDSDTGRSKGYGFITFSDSEC 59

Query: 395 ANLVIKRRN-LKLRDRELRLSHAQ 417
           A   +++ N  +L  R +R+ H  
Sbjct: 60  ARRALEQLNGFELAGRPMRVGHVT 83

>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

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 48.1 bits (115), Expect = 4e-07
 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 9/82 (10%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           +F+ +LP +  D ++   F   G      +V + +V       + K   +V F   ++A 
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFG------NVISAKVFIDKQTSLSKCFGFVSFDNPDSAQ 96

Query: 397 LVIKRRN-LKLRDRELRLSHAQ 417
           + IK  N  ++  + L++   +
Sbjct: 97  VAIKAMNGFQVGTKRLKVQLKK 118

>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 = 48.0 bits (114), Expect = 4e-07
 Identities = 20/102 (19%), Positives = 36/102 (35%), Gaps = 13/102 (12%)

Query: 320 PPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMR 379
            PR    G+        + + +  LP DV + E+  L                + +  M 
Sbjct: 15  VPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLG----------LPFGKVTNLLML 64

Query: 380 VGKGIAYVLFKTREAANLVIKRRNLK---LRDRELRLSHAQQ 418
            GK  A++   T EAAN ++         LR + + +  +  
Sbjct: 65  KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 106

>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 = 39.5 bits (92), Expect = 4e-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

>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 = 47.2 bits (113), Expect = 4e-07
 Identities = 18/87 (20%), Positives = 36/87 (41%), Gaps = 9/87 (10%)

Query: 334 DIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
           D    + V  L     + ++ ++F   G       +  V ++     R  +G A+V F+ 
Sbjct: 13  DPNCCLGVFGLSLYTTERDLREVFSKYG------PIADVSIVYDQQSRRSRGFAFVYFEN 66

Query: 392 REAANLVIKRRN-LKLRDRELRLSHAQ 417
            + A    +R N ++L  R +R+S   
Sbjct: 67  VDDAKEAKERANGMELDGRRIRVSGPS 93

>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

>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 = 47.7 bits (114), Expect = 4e-07
 Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 12/83 (14%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
            ++VGNLP D++ ++I  +F   G         A+R I   + R G   A+V F+    A
Sbjct: 24  RIYVGNLPPDIRTKDIEDVFYKYG---------AIRDIDLKNRRGGPPFAFVEFEDPRDA 74

Query: 396 NLVIKRRN-LKLRDRELRLSHAQ 417
              +  R+        LR+   +
Sbjct: 75  EDAVYGRDGYDYDGYRLRVEFPR 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 = 43.5 bits (103), Expect = 1e-05
 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

>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 = 47.3 bits (113), Expect = 4e-07
 Identities = 17/82 (20%), Positives = 31/82 (37%), Gaps = 8/82 (9%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           KT+FV  L  D  +E + + F             R++        KG  +V F + E A 
Sbjct: 16  KTLFVKGLSEDTTEETLKESF-------DGSVRARIVTDRETGSSKGFGFVDFNSEEDAK 68

Query: 397 LVIKRRN-LKLRDRELRLSHAQ 417
              +     ++   ++ L  A+
Sbjct: 69  AAKEAMEDGEIDGNKVTLDWAK 90

>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 = 47.7 bits (114), Expect = 5e-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

>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 = 46.5 bits (111), Expect = 1e-06
 Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 5/82 (6%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           K +++ NL   V + ++  LF          +   +         +G A++ F  +E A 
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARF----QEKKGPPIQFRMMTGRMRGQAFITFPNKEIAW 81

Query: 397 LVIKRRN-LKLRDRELRLSHAQ 417
             +   N  KL  + L +   +
Sbjct: 82  QALHLVNGYKLYGKILVIEFGK 103

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 47.1 bits (112), Expect = 5e-07
 Identities = 10/85 (11%), Positives = 31/85 (36%), Gaps = 8/85 (9%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
            + + + N+P  ++ E +  L             V      +      +  V + +++ A
Sbjct: 15  IRKLQIRNIPPHLQWEVLDSLL-------VQYGVVESCEQVNTDSETAVVNVTYSSKDQA 67

Query: 396 NLVIKRRN-LKLRDRELRLSHAQQN 419
              + + N  +L +  L++++    
Sbjct: 68  RQALDKLNGFQLENFTLKVAYIPDE 92

>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 = 46.9 bits (112), Expect = 6e-07
 Identities = 18/84 (21%), Positives = 40/84 (47%), Gaps = 14/84 (16%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVG--KGIAYVLFKTREA 394
           +T+   NL F++ ++E+ ++F            +R++     + G  KGIAY+ FK+   
Sbjct: 17  RTLLAKNLSFNITEDELKEVF-------EDALEIRLVS----QDGKSKGIAYIEFKSEAD 65

Query: 395 ANLVIKRRN-LKLRDRELRLSHAQ 417
           A   ++ +   ++  R + L +  
Sbjct: 66  AEKNLEEKQGAEIDGRSVSLYYTG 89

>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 = 43.8 bits (104), Expect = 7e-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

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 46.9 bits (112), Expect = 6e-07
 Identities = 13/83 (15%), Positives = 31/83 (37%), Gaps = 9/83 (10%)

Query: 338 TVFVGNLPFDVKDEEIYQLFC--GLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
            +FV  +  +  +E+I+  F   G       ++ + +         KG   V ++T + A
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYG------EIKNIHLNLDRRTGYLKGYTLVEYETYKEA 78

Query: 396 NLVIKRRN-LKLRDRELRLSHAQ 417
              ++  N   L  + + +    
Sbjct: 79  QAAMEGLNGQDLMGQPISVDWCF 101

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 40.3 bits (95), 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

>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 = 46.0 bits (110), Expect = 8e-07
 Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 9/83 (10%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           +FVG+L  +V DE +   F          S  +  V+        +G  +V F +++ A 
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFP------SYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQ 57

Query: 397 LVIKRRNLK-LRDRELRLSHAQQ 418
             +     + L  R LR++ A +
Sbjct: 58  NAMDSMQGQDLNGRPLRINWAAK 80

>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 = 39.8 bits (94), 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

>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 = 8e-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

>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 = 45.7 bits (109), Expect = 2e-06
 Identities = 23/98 (23%), Positives = 44/98 (44%), Gaps = 13/98 (13%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRE 393
           K+ ++VG L  +V D+ ++  F   G       +  +++         +G A+V F+  E
Sbjct: 12  KRVLYVGGLAEEVDDKVLHAAFIPFG------DITDIQIPLDYETEKHRGFAFVEFELAE 65

Query: 394 AANLVIKRRN-LKLRDRELRLSHAQQNCTPSKRKDVAP 430
            A   I   N  +L  R +R++ A+    P + K+  P
Sbjct: 66  DAAAAIDNMNESELFGRTIRVNLAK----PMRIKESGP 99

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 46.5 bits (111), Expect = 9e-07
 Identities = 21/83 (25%), Positives = 33/83 (39%), Gaps = 10/83 (12%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
            + V NL F V D +I +LF   G      +++   V      R   G A V F+ +  A
Sbjct: 31  KLLVSNLDFGVSDADIQELFAEFG------TLKKAAVHYDRSGR-SLGTADVHFERKADA 83

Query: 396 NLVIKRRNLK-LRDRELRLSHAQ 417
              +K+ N   L  R + +    
Sbjct: 84  LKAMKQYNGVPLDGRPMNIQLVT 106

>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 = 46.0 bits (110), Expect = 1e-06
 Identities = 13/82 (15%), Positives = 35/82 (42%), Gaps = 7/82 (8%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           +++GNL +   DE++ +     G+ND+      ++   +      KG A V   +  ++ 
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILE----IKFFENRANGQSKGFALVGVGSEASSK 59

Query: 397 LVIKRRNLK-LRDRELRLSHAQ 417
            ++     + L  +   ++ + 
Sbjct: 60  KLMDLLPKRELHGQNPVVTPSN 81

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 45.6 bits (109), Expect = 1e-06
 Identities = 24/90 (26%), Positives = 35/90 (38%), Gaps = 11/90 (12%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
             +FV NLPFD   + +   F  CG       V    +         KG   V F++ E 
Sbjct: 9   CQIFVRNLPFDFTWKMLKDKFNECG------HVLYADIKMENG--KSKGCGVVKFESPEV 60

Query: 395 ANLVIKRRN-LKLRDRELRLSHAQQNCTPS 423
           A    +  N +KL  RE+ +   +    PS
Sbjct: 61  AERACRMMNGMKLSGREIDVRIDRNASGPS 90

>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 = 47.5 bits (113), Expect = 1e-06
 Identities = 14/103 (13%), Positives = 39/103 (37%), Gaps = 5/103 (4%)

Query: 316 DRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRH 375
           +R                     +FV ++  + +++EI + FC   ++++    + +   
Sbjct: 52  ERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKN----IHLNLD 107

Query: 376 PHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQ 417
                 KG A V ++T + A    +  N  ++  + +++    
Sbjct: 108 RRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF 150

>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 = 6e-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

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 46.6 bits (111), Expect = 1e-06
 Identities = 21/85 (24%), Positives = 33/85 (38%), Gaps = 10/85 (11%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
            + V NL F V D +I +LF   G      +++   V      R   G A V F+ R  A
Sbjct: 37  KLLVSNLDFGVSDADIQELFAEFG------TLKKAAVDYDRSGR-SLGTADVHFERRADA 89

Query: 396 NLVIKRRN-LKLRDRELRLSHAQQN 419
              +K+   + L  R + +      
Sbjct: 90  LKAMKQYKGVPLDGRPMDIQLVASQ 114

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 47.2 bits (112), Expect = 1e-06
 Identities = 14/88 (15%), Positives = 39/88 (44%), Gaps = 7/88 (7%)

Query: 334 DIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
           + +  V+VG+  +   D+++ Q+    G+ D+      ++   +      KG A V+  +
Sbjct: 53  NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVE----LKFAENRANGQSKGYAEVVVAS 108

Query: 392 REAANLVIKRRNLK-LRDRELRLSHAQQ 418
             + + +++    K L   ++ +  A +
Sbjct: 109 ENSVHKLLELLPGKVLNGEKVDVRPATR 136

>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 = 21/134 (15%), Positives = 43/134 (32%), Gaps = 13/134 (9%)

Query: 291 FKSEQSTEAALAFNMAVIGGNHIRLDRACP----PRKKLKGEDAPLYDIKKTVFVGNLPF 346
             +  + +    +            D A                   +   ++ V NL +
Sbjct: 21  VDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTY 80

Query: 347 DVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN- 403
               + + ++F   G       V  V + R  + +  +G A+V F  +  A   +   + 
Sbjct: 81  RTSPDTLRRVFEKYG------RVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134

Query: 404 LKLRDRELRLSHAQ 417
             L  RELR+  A+
Sbjct: 135 AVLDGRELRVQMAR 148

>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 = 46.4 bits (110), Expect = 3e-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

>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 = 45.7 bits (109), Expect = 2e-06
 Identities = 14/84 (16%), Positives = 36/84 (42%), Gaps = 9/84 (10%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFC--GLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
             +FV ++  + +++EI + FC  G       ++ + +         KG A V ++T + 
Sbjct: 27  WILFVTSIHEEAQEDEIQEKFCDYG------EIKNIHLNLDRRTGFSKGYALVEYETHKQ 80

Query: 395 ANLVIKRRN-LKLRDRELRLSHAQ 417
           A    +  N  ++  + +++    
Sbjct: 81  ALAAKEALNGAEIMGQTIQVDWCF 104

>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

>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 = 45.7 bits (109), Expect = 2e-06
 Identities = 21/92 (22%), Positives = 38/92 (41%), Gaps = 16/92 (17%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           K +FV NL   V +E + + F     LE     V+ +        K  A++ F  R+ A 
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQFGKLER----VKKL--------KDYAFIHFDERDGAV 59

Query: 397 LVIKRRNLK-LRDRELRLSHAQQNCTPSKRKD 427
             ++  N K L    + +  A+    P +++ 
Sbjct: 60  KAMEEMNGKDLEGENIEIVFAK---PPDQKRK 88

>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 = 40.7 bits (96), Expect = 1e-04
 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

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 46.3 bits (110), Expect = 2e-06
 Identities = 20/114 (17%), Positives = 47/114 (41%), Gaps = 13/114 (11%)

Query: 330 APLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYV 387
            P  D+ + + V  +P  V + ++ QLF   G       +E+V+++     R  +G  +V
Sbjct: 36  NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYG------PIESVKIVCDRETRQSRGYGFV 89

Query: 388 LFKTREAANLVIKRRN-LKLRDRELRLSHAQQNCTPSKRKDVAPAVNSPPKKFV 440
            F++  +A   I   N   + ++ L+++ A        ++            ++
Sbjct: 90  KFQSGSSAQQAIAGLNGFNILNKRLKVALAA----SGHQRPGIAGAVGDGNGYL 139

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 17/87 (19%), Positives = 34/87 (39%), Gaps = 17/87 (19%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFC--GLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
           + + +  LP DV + E+  L    G       V  + +++       K  A++   T EA
Sbjct: 17  RVIHIRKLPIDVTEGEVISLGLPFG------KVTNLLMLKG------KNQAFIEMNTEEA 64

Query: 395 ANLVIKRRNLK---LRDRELRLSHAQQ 418
           AN ++         LR + + +  +  
Sbjct: 65  ANTMVNYYTSVTPVLRGQPIYIQFSNH 91

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 39.8 bits (93), Expect = 2e-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: 17  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLM---------LKGKN-------------- 53

Query: 286 HAYIVFKSEQSTEAALAF---NMAVIGGNHIRLDRACPPRKKLKGEDAP 331
            A+I   +E++    + +      V+ G  I +  +    K+LK + +P
Sbjct: 54  QAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFS--NHKELKTDSSP 100

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 18/98 (18%), Positives = 39/98 (39%), Gaps = 20/98 (20%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFC--GLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
             +++GNL   V  +++ QLF    L        A +V+         G A+V +  +  
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKL------PLAGQVLLK------SGYAFVDYPDQNW 56

Query: 395 ANLVIKRRN--LKLRDRELRLSHAQQNCTPSKRKDVAP 430
           A   I+  +  ++L  + + + ++       K +   P
Sbjct: 57  AIRAIETLSGKVELHGKIMEVDYS----VSKKLRSSGP 90

>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 = 45.2 bits (107), Expect = 3e-06
 Identities = 15/84 (17%), Positives = 34/84 (40%), Gaps = 13/84 (15%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           + + +  LP +V + E+  L                + +  M  GK  A++   T EAA 
Sbjct: 16  RVLHIRKLPGEVTETEVIALG----------LPFGKVTNILMLKGKNQAFLELATEEAAI 65

Query: 397 LVIKRRNLK---LRDRELRLSHAQ 417
            ++   +     LR++ + + ++ 
Sbjct: 66  TMVNYYSAVTPHLRNQPIYIQYSN 89

>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 = 39.4 bits (92), Expect = 3e-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

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 14/82 (17%), Positives = 34/82 (41%), Gaps = 10/82 (12%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           +++ NLP  + ++E+  +    G       V + R++R       +G+ +   ++ E   
Sbjct: 28  LYISNLPLSMDEQELENMLKPFG------QVISTRILRDSSGT-SRGVGFARMESTEKCE 80

Query: 397 LVIKRRNLK-LRDRELRLSHAQ 417
            VI   N K ++      +  +
Sbjct: 81  AVIGHFNGKFIKTPPGVSAPTE 102

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 45.4 bits (108), Expect = 3e-06
 Identities = 15/82 (18%), Positives = 37/82 (45%), Gaps = 9/82 (10%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           +F+ +LP +  D+++ Q+F   G      +V + +V       + K   +V +    +A 
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFG------NVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQ 81

Query: 397 LVIKRRN-LKLRDRELRLSHAQ 417
             I+  N  ++  + L++   +
Sbjct: 82  AAIQSMNGFQIGMKRLKVQLKR 103

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 45.0 bits (107), Expect = 3e-06
 Identities = 22/107 (20%), Positives = 45/107 (42%), Gaps = 16/107 (14%)

Query: 321 PRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV 380
           PR                +FV   P DV++ E+ ++F     ++     V+++       
Sbjct: 16  PRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKE----VKIL------- 64

Query: 381 GKGIAYVLFKTREAANLVIKRRNLK-LRDRELRLSHAQQNCTPSKRK 426
             G A+V F+  E+A   I+  + K   ++ L + +++    P+KR 
Sbjct: 65  -NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKL---PAKRY 107

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 43.4 bits (103), Expect = 1e-05
 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

>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 = 44.9 bits (106), Expect = 4e-06
 Identities = 19/85 (22%), Positives = 29/85 (34%), Gaps = 5/85 (5%)

Query: 336 KKTVFVGNLPFDVKDEEI---YQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           K  VFV  L   + D E+    + F     +   V       +   +     AYV +   
Sbjct: 15  KNLVFVVGLSQRLADPEVLKRPEYFGKFGKI-HKVVINNSTSYAGSQGPSASAYVTYIRS 73

Query: 393 EAANLVIKRRNLK-LRDRELRLSHA 416
           E A   I+  N   +  R L+ S  
Sbjct: 74  EDALRAIQCVNNVVVDGRTLKASLG 98

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 44.5 bits (106), Expect = 4e-06
 Identities = 20/91 (21%), Positives = 41/91 (45%), Gaps = 16/91 (17%)

Query: 336 KKTVFVGNLPFDVKDEE----IYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLF 389
             T+++ NL   +K +E    ++ +F   G       +  + V R   MR   G A+V+F
Sbjct: 8   NHTIYINNLNEKIKKDELKKSLHAIFSRFG------QILDILVSRSLKMR---GQAFVIF 58

Query: 390 KTREAANLVIKRRNLK-LRDRELRLSHAQQN 419
           K   +A   ++        D+ +R+ +A+ +
Sbjct: 59  KEVSSATNALRSMQGFPFYDKPMRIQYAKTD 89

>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 = 41.4 bits (98), Expect = 5e-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

>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 = 44.5 bits (106), Expect = 4e-06
 Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 9/84 (10%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
             +FVG L FD  ++ + Q+F   G       +  V V++    +  +G  +V F+  + 
Sbjct: 13  GKLFVGGLSFDTNEQSLEQVFSKYG------QISEVVVVKDRETQRSRGFGFVTFENIDD 66

Query: 395 ANLVIKRRN-LKLRDRELRLSHAQ 417
           A   +   N   +  R++R+  A 
Sbjct: 67  AKDAMMAMNGKSVDGRQIRVDQAG 90

>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 = 4e-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

>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 = 44.6 bits (106), Expect = 4e-06
 Identities = 20/86 (23%), Positives = 33/86 (38%), Gaps = 13/86 (15%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           +FVG L     +E++ +LF   G       ++   V+R P     KG A+V F +   A 
Sbjct: 18  LFVGMLNKQQSEEDVLRLFQPFG------VIDECTVLRGPDGS-SKGCAFVKFSSHTEAQ 70

Query: 397 LVIKRRN----LKLRDRELRLSHAQQ 418
             I   +    +      L +  A  
Sbjct: 71  AAIHALHGSQTMPGASSSLVVKFADT 96

>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 = 44.6 bits (106), Expect = 4e-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 = 44.2 bits (105), Expect = 7e-06
 Identities = 22/88 (25%), Positives = 34/88 (38%), Gaps = 13/88 (14%)

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 REAANLVIK--RRNLKLRDRELRLSHAQ 417
           ++ A         +  L  R L L  A 
Sbjct: 68  KQDAKKAFNALCHSTHLYGRRLVLEWAD 95

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 44.6 bits (106), Expect = 4e-06
 Identities = 23/118 (19%), Positives = 40/118 (33%), Gaps = 22/118 (18%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           V+VGNL       E+ + F   G       +  V + R+P      G A+V F+    A 
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYG------PLRTVWIARNP-----PGFAFVEFEDPRDAE 51

Query: 397 LVIKRRN-LKLRDRELRLSHAQQNCTPSKRKDVAPAVNSPPKKFVLDSRTLGSGNRSN 453
             ++  +   +    +R+  +        R D  PA              L +G   +
Sbjct: 52  DAVRGLDGKVICGSRVRVELS-TGMPRRSRFDRPPARRKL-------LEVLFNGPLEH 101

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 41.1 bits (97), Expect = 7e-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

>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 = 4e-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

>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 = 43.0 bits (102), Expect = 1e-05
 Identities = 13/97 (13%), Positives = 36/97 (37%), Gaps = 17/97 (17%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
             T++V     D+    +   F    ++      + +         +  A+V ++  E+A
Sbjct: 15  GNTLYVYGE--DMTPTLLRGAFSPFGNIID----LSMDPP------RNCAFVTYEKMESA 62

Query: 396 NLVIKRRN-LKLRDRELRLSHAQQNCTPSKRKDVAPA 431
           +  +   N  ++   +L+++ A+         D  P+
Sbjct: 63  DQAVAELNGTQVESVQLKVNIAR----KQPMLDSGPS 95

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 44.4 bits (105), Expect = 5e-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

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 43.6 bits (103), Expect = 1e-05
 Identities = 11/104 (10%), Positives = 27/104 (25%), Gaps = 13/104 (12%)

Query: 320 PPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMR 379
                   +D         V +  L   V + ++ +           +  V V+      
Sbjct: 5   HHHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEF----GPISYVVVMPK---- 56

Query: 380 VGKGIAYVLFKTREAANLVIKR---RNLKLRDRELRLSHAQQNC 420
             K  A V F+    A   +       + +      ++++    
Sbjct: 57  --KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQK 98

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 45.1 bits (107), Expect = 5e-06
 Identities = 21/101 (20%), Positives = 39/101 (38%), Gaps = 9/101 (8%)

Query: 320 PPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPH 377
                  G   P  +   ++ V NL +    + + ++F   G       V  V + R  +
Sbjct: 31  GRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYG------RVGDVYIPRDRY 84

Query: 378 MRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQ 417
            +  +G A+V F  +  A   +   +   L  RELR+  A+
Sbjct: 85  TKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR 125

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 40.9 bits (96), Expect = 2e-04
 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

>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 = 44.5 bits (105), Expect = 1e-05
 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

>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 = 43.7 bits (103), Expect = 2e-05
 Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 10/83 (12%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            V+VGNL  +    E+ + F     L S    V V R+P      G A+V F+    A  
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRS----VWVARNP-----PGFAFVEFEDPRDAAD 125

Query: 398 VIKRRN-LKLRDRELRLSHAQQN 419
            ++  +   L    +R+  +   
Sbjct: 126 AVRELDGRTLCGCRVRVELSNGE 148

>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 = 43.9 bits (104), Expect = 1e-05
 Identities = 17/87 (19%), Positives = 37/87 (42%), Gaps = 10/87 (11%)

Query: 334 DIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
           D    +F+G L  +  ++ +  +F   G       +  V +I+    +  +G A++ F+ 
Sbjct: 5   DHPGKLFIGGLNRETNEKMLKAVFGKHG------PISEVLLIKDRTSK-SRGFAFITFEN 57

Query: 392 REAANLVIKRRNLK-LRDRELRLSHAQ 417
              A    K  N K L  + +++  A+
Sbjct: 58  PADAKNAAKDMNGKSLHGKAIKVEQAK 84

>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 = 43.9 bits (104), Expect = 1e-05
 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

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 44.1 bits (104), Expect = 1e-05
 Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 4/83 (4%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           + V + N+  +V  E+   L   L  L SS   +  I         G AY++F T+E+A 
Sbjct: 30  QVVLITNINPEVPKEK---LQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQ 86

Query: 397 LVIKRRN-LKLRDRELRLSHAQQ 418
             ++       +   L ++ ++ 
Sbjct: 87  AFVEAFQGYPFQGNPLVITFSET 109

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 38.7 bits (90), Expect = 8e-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

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 45.2 bits (107), Expect = 1e-05
 Identities = 21/85 (24%), Positives = 33/85 (38%), Gaps = 10/85 (11%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
            + V NL F V D +I +LF   G      +++   V      R   G A V F+ R  A
Sbjct: 90  KLLVSNLDFGVSDADIQELFAEFG------TLKKAAVDYDRSGR-SLGTADVHFERRADA 142

Query: 396 NLVIKRRN-LKLRDRELRLSHAQQN 419
              +K+   + L  R + +      
Sbjct: 143 LKAMKQYKGVPLDGRPMDIQLVASQ 167

>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 = 43.5 bits (103), Expect = 1e-05
 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

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 20/103 (19%), Positives = 34/103 (33%), Gaps = 20/103 (19%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
           ++VFV   P  V   ++ + F   G       V +V + +          A V      A
Sbjct: 9   RSVFVSGFPRGVDSAQLSEYFLAFG------PVASVVMDKDK-----GVFAIVEMGDVGA 57

Query: 395 ANLVIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAPAVNSPPK 437
              V+ +    L    LR         P ++K+     +  PK
Sbjct: 58  REAVLSQSQHSLGGHRLR-------VRPREQKEFQSPASKSPK 93

>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 = 43.0 bits (102), Expect = 2e-05
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 11/84 (13%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
           K + V N+PF  +D ++ Q+F   G       +  V +I +   R  KG  +V F+    
Sbjct: 16  KRLHVSNIPFRFRDPDLRQMFGQFG------KILDVEIIFNE--RGSKGFGFVTFENSAD 67

Query: 395 ANLVIKRRN-LKLRDRELRLSHAQ 417
           A+   ++ +   +  R++ +++A 
Sbjct: 68  ADRAREKLHGTVVEGRKIEVNNAT 91

>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 = 42.9 bits (101), Expect = 2e-05
 Identities = 12/86 (13%), Positives = 27/86 (31%), Gaps = 13/86 (15%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
             V V  L   V + ++ +            E    I +  M   K  A V F+  ++A 
Sbjct: 16  PVVHVRGLCESVVEADLVEAL----------EKFGTICYVMMMPFKRQALVEFENIDSAK 65

Query: 397 LVIKRRNLK---LRDRELRLSHAQQN 419
             +         +  ++   +++   
Sbjct: 66  ECVTFAADVPVYIAGQQAFFNYSTSK 91

>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 = 42.1 bits (99), Expect = 3e-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

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 44.4 bits (104), Expect = 3e-05
 Identities = 14/84 (16%), Positives = 35/84 (41%), Gaps = 5/84 (5%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           ++V++   P D   ++I +           V  ++ +R    +  KG  +V+F + E+A 
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKG----QVLNIQ-MRRTLHKAFKGSIFVVFDSIESAK 164

Query: 397 LVIKRRNLKLRDRELRLSHAQQNC 420
             ++    K ++ +L +       
Sbjct: 165 KFVETPGQKYKETDLLILFKDDYF 188

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 41.9 bits (99), Expect = 4e-05
 Identities = 16/83 (19%), Positives = 40/83 (48%), Gaps = 9/83 (10%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
            ++VG+L F++ ++ +  +F   G       +E+++++        KG  ++ F   E A
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFG------RIESIQLMMDSETGRSKGYGFITFSDSECA 81

Query: 396 NLVIKRRN-LKLRDRELRLSHAQ 417
              +++ N  +L  R +++ H  
Sbjct: 82  KKALEQLNGFELAGRPMKVGHVT 104

>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 = 42.9 bits (101), Expect = 4e-05
 Identities = 20/94 (21%), Positives = 41/94 (43%), Gaps = 7/94 (7%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVG--KGIAYVLFKTREA 394
             ++V NL   V+++++  +F    D  SS     +     M+ G  KG A++     +A
Sbjct: 46  CRIYVKNLAKHVQEKDLKYIFGRYVDF-SSETQRIMFDIRLMKEGRMKGQAFIGLPNEKA 104

Query: 395 ANLVIKRRNLK-LRDRELRLSHAQQNCTPSKRKD 427
           A   +K  N   L  + + +  A+   +   ++D
Sbjct: 105 AAKALKEANGYVLFGKPMVVQFAR---SARPKQD 135

>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 = 40.2 bits (94), Expect = 3e-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

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 41.0 bits (97), Expect = 5e-05
 Identities = 12/83 (14%), Positives = 29/83 (34%), Gaps = 9/83 (10%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           +++  L     D+++ +L    G       + + + I        KG  +V F +  AA 
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYG------KIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61

Query: 397 LVIKRRNLK-LRDRELRLSHAQQ 418
             +       ++ +  + S    
Sbjct: 62  KAVTALKASGVQAQMAKQSGPSS 84

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 41.5 bits (98), Expect = 5e-05
 Identities = 21/113 (18%), Positives = 47/113 (41%), Gaps = 11/113 (9%)

Query: 308 IGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLES 365
           +G +H     +     +    +       K + V N+PF  +D ++ Q+F   G      
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFG------ 54

Query: 366 SVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLK-LRDRELRLSHAQ 417
            +  V +I +   R  KG  +V F+    A+   ++ +   +  R++ +++A 
Sbjct: 55  KILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT 105

>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 = 1e-04
 Identities = 14/63 (22%), Positives = 26/63 (41%), Gaps = 2/63 (3%)

Query: 195 VGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDS 254
           +G       + +   LV R      +     + + V N+P + +   L + F +FG+I  
Sbjct: 1   MGSSHHHHHHSSG--LVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILD 58

Query: 255 VRI 257
           V I
Sbjct: 59  VEI 61

>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 = 41.0 bits (97), Expect = 6e-05
 Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 17/84 (20%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
             +F+GNLP +  ++EI  LF   G       V    +I        K   +V  + + A
Sbjct: 9   VKLFIGNLPREATEQEIRSLFEQYG------KVLECDII--------KNYGFVHIEDKTA 54

Query: 395 ANLVIKRRNLK-LRDRELRLSHAQ 417
           A   I+  +   L    + +  ++
Sbjct: 55  AEDAIRNLHHYKLHGVNINVEASK 78

>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 = 38.7 bits (91), Expect = 4e-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

>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 = 40.7 bits (96), Expect = 7e-05
 Identities = 10/82 (12%), Positives = 28/82 (34%), Gaps = 13/82 (15%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
             + VGN+     ++E+   F     +        +++          A+V  +  E A 
Sbjct: 11  TKLHVGNISPTCTNQELRAKFEEYGPVIE----CDIVK--------DYAFVHMERAEDAV 58

Query: 397 LVIKRRNLK-LRDRELRLSHAQ 417
             I+  +    + + + +  + 
Sbjct: 59  EAIRGLDNTEFQGKRMHVQLST 80

>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 = 5e-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

>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 = 41.0 bits (97), Expect = 8e-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

>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 = 38.3 bits (90), Expect = 7e-04
 Identities = 14/86 (16%), Positives = 36/86 (41%), Gaps = 9/86 (10%)

Query: 334 DIKKTVFVGNLPFDVKDEEIYQLFC--GLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
              K +FVG +P +  + E+ + F   G       V  V +I     +  +G  ++ F+ 
Sbjct: 9   KSNK-IFVGGIPHNCGETELREYFKKFG------VVTEVVMIYDAEKQRPRGFGFITFED 61

Query: 392 REAANLVIKRRNLKLRDRELRLSHAQ 417
            ++ +  +      +  +++ +  A+
Sbjct: 62  EQSVDQAVNMHFHDIMGKKVEVKRAE 87

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 25/110 (22%), Positives = 43/110 (39%), Gaps = 21/110 (19%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVG--KGIAYVLFKTR 392
            TVFVG +   + + EI   F   G      SV+ V++I     R G  KG  +V F   
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYG------SVKEVKIITD---RTGVSKGYGFVSFYND 60

Query: 393 EAANLVIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAPAVNSPPKKFVLD 442
                +++ +      ++L+L  A        RK      +  P+  + +
Sbjct: 61  VDVQKIVESQIN-FHGKKLKLGPAI-------RKQNLSTYHVQPRPLIFN 102

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 22/96 (22%), Positives = 37/96 (38%), Gaps = 6/96 (6%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
           ++FVG+L  DV D  +Y+ F     +  S    +V+        KG  +V F        
Sbjct: 11  SLFVGDLTPDVDDGMLYEFF---VKVYPSCRGGKVVLDQTGV-SKGYGFVKFTDELEQKR 66

Query: 398 VIKRRNLK--LRDRELRLSHAQQNCTPSKRKDVAPA 431
            +        L  + +RLS A    +  K  +  P+
Sbjct: 67  ALTECQGAVGLGSKPVRLSVAIPKASRVKPVESGPS 102

>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 = 40.3 bits (95), Expect = 1e-04
 Identities = 17/84 (20%), Positives = 31/84 (36%), Gaps = 17/84 (20%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
             +FVGN+      +E+  LF   G       V    V+        K  A+V  +    
Sbjct: 10  WKIFVGNVSAACTSQELRSLFERRG------RVIECDVV--------KDYAFVHMEKEAD 55

Query: 395 ANLVIKRRNLK-LRDRELRLSHAQ 417
           A   I + N K ++ + + +  + 
Sbjct: 56  AKAAIAQLNGKEVKGKRINVELST 79

>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

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 11/83 (13%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           ++V NL   + DE + + F   G      ++ + +V+        KG  +V F + E A 
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFG------TITSAKVMMEG--GRSKGFGFVCFSSPEEAT 69

Query: 397 LVIKRRNLK-LRDRELRLSHAQQ 418
             +   N + +  + L ++ AQ+
Sbjct: 70  KAVTEMNGRIVATKPLYVALAQR 92

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 13/81 (16%), Positives = 26/81 (32%), Gaps = 8/81 (9%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
           + + NLP     ++       L DL             + R   G   + F + E     
Sbjct: 31  ITMKNLPEGCSWQD-------LKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEA 83

Query: 399 IKRRN-LKLRDRELRLSHAQQ 418
           ++R N ++ R   + +     
Sbjct: 84  LERLNNIEFRGSVITVERDDN 104

>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 = 2e-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

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 15/81 (18%), Positives = 26/81 (32%), Gaps = 12/81 (14%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            V V  LP     +++        D    V    V R        G   V F  +E    
Sbjct: 17  RVVVSGLPPSGSWQDLKDHMREAGD----VCYADVYR-------DGTGVVEFVRKEDMTY 65

Query: 398 VIKRRN-LKLRDRELRLSHAQ 417
            +++ +  K R  E   ++ +
Sbjct: 66  AVRKLDNTKFRSHEGETAYIR 86

>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 = 39.5 bits (93), Expect = 2e-04
 Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 8/83 (9%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
           + ++VGNL +    E++ +LF   G       V  V++I     +  KG  +V  +    
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFG------KVFNVKLIYDRETKKPKGFGFVEMQEESV 55

Query: 395 ANLVIKRRNLKLRDRELRLSHAQ 417
           +  + K  N     R +R++ A 
Sbjct: 56  SEAIAKLDNTDFMGRTIRVTEAN 78

>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 = 5e-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

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 39.5 bits (93), 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 = 39.1 bits (92), Expect = 3e-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

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 39.9 bits (93), Expect = 3e-04
 Identities = 13/67 (19%), Positives = 23/67 (34%), Gaps = 14/67 (20%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           V  G L   V   ++  +   CG       V+A+       M   K  ++  ++T E + 
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCG------LVDALL------MPPNKPYSFARYRTTEESK 77

Query: 397 LVIKRRN 403
                 N
Sbjct: 78  RAYVTLN 84

>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 = 39.6 bits (93), Expect = 3e-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

>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 = 39.6 bits (93), Expect = 4e-04
 Identities = 23/84 (27%), Positives = 35/84 (41%), Gaps = 4/84 (4%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
           +FVG LP+   D  + + F G  D+E +V    VI        +G  +V    R AA   
Sbjct: 20  IFVGGLPYHTTDASLRKYFEGFGDIEEAV----VITDRQTGKSRGYGFVTMADRAAAERA 75

Query: 399 IKRRNLKLRDRELRLSHAQQNCTP 422
            K  N  +  R+  ++ A     P
Sbjct: 76  CKDPNPIIDGRKANVNLAYLGAKP 99

>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 = 4e-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

>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 = 4e-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

>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 = 6e-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

>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 = 38.0 bits (89), 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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	548
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.98
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.97
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.97
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.97
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.97
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.97
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.97
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.97
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.96
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.96
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.96
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.95
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.95
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.95
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.95
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.95
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.95
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.94
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.94
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.85
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.8
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.79
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.74
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.73
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.7
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.7
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.69
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.68
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.67
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.67
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.67
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.67
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.67
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.67
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.67
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.66
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.66
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.66
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.66
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.66
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.66
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.66
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.66
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.66
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.66
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.65
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.65
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.65
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.65
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.65
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.65
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	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
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.65
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.65
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.65
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.65
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.64
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.64
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.64
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.64
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.64
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.63
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.63
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.63
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.63
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.63
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.63
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.63
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.63
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.63
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.62
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.62
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.62
2div_A	99	TRNA selenocysteine associated protein; structural	99.62
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.62
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.62
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.62
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.62
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.62
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.62
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.61
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.61
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.61
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.61
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.61
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.61
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.61
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.61
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.61
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.61
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.61
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.61
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.61
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.61
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.61
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.61
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.6
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.6
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.6
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.6
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.6
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.6
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.6
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.6
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.6
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.6
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.6
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.6
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.6
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.6
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.6
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.59
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.59
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.59
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.59
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.59
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.59
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.59
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.59
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.59
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.59
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.59
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.59
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.59
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.59
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.59
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.59
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.59
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.59
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.59
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.58
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.58
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.58
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.58
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.58
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.58
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.58
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.58
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.58
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.58
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.58
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.58
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.58
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.58
2div_A	99	TRNA selenocysteine associated protein; structural	99.58
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.58
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.58
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.57
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.57
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.57
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.57
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.57
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.57
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.57
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.57
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.57
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.57
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.57
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.57
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.57
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.57
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.57
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.57
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.57
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.57
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.56
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.56
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.56
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.56
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.56
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.56
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.56
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.56
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.56
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.56
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.56
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.56
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.56
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.56
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.56
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.56
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.56
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.56
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.56
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.55
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.55
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.55
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.55
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.55
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.55
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.55
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.55
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.55
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.55
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.55
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.55
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.55
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.55
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.55
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.55
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.55
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.54
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.54
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.54
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.54
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.54
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.54
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.54
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.54
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.54
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.54
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.54
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.54
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.54
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.54
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.54
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.53
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.53
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.53
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.53
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.53
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.53
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.53
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.53
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.53
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.53
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.53
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.53
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.53
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.53
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.52
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.52
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.52
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.52
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.52
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.52
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.52
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.52
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.52
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.52
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.52
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.52
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.52
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.52
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.52
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.52
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.51
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.51
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.51
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.51
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.51
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.51
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.51
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.51
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.51
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.51
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.51
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.51
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.51
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.51
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.51
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.51
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.51
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.51
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.5
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.5
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.5
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.5
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.5
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.5
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.5
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.5
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.5
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.5
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.5
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.5
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.24
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.49
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.49
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.49
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.49
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.49
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.49
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.49
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.49
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.48
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.48
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.48
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.48
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.48
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.48
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.47
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.47
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.47
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.47
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.47
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.47
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.47
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.46
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.46
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.46
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.46
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.46
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.46
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.46
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.46
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.18
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.45
1x5p_A	97	Negative elongation factor E; structure genomics,	99.45
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.44
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.44
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.44
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.44
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.44
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.43
1x5p_A	97	Negative elongation factor E; structure genomics,	99.43
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.43
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.42
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.41
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.41
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.4
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.4
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.4
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.4
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.39
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.39
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.38
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.38
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.38
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.38
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.38
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.37
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.37
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.36
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.36
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.36
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.35
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.35
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.35
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.35
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.34
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.33
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.33
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.33
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.33
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.33
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.32
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.3
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.3
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.3
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.29
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.28
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.24
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.21
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.21
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.19
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.19
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.19
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.14
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.13
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.11
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.1
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.1
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.08
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.97
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.96
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.92
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.89
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.87
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.68
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.62
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.56
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.54
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.35
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.35
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.3
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.24
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.98
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.75
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.36
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.27
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.77
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.63
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.45
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.41
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	95.79
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	95.69
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	95.67
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	95.12
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	94.75
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	94.37
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	93.98
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	93.89
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	93.85
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	92.96
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	87.42
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	87.14
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	80.73

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=100.00  E-value=5.6e-32  Score=256.62  Aligned_cols=177  Identities=15%  Similarity=0.316  Sum_probs=149.6

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++|+++|.++|+.||.|.+|.|+.++.                 +|.++|||||+|.+.++|..||
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-----------------TKRSRGFGFVTYATVEEVDAAM   72 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----------------TCCEEEEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCC-----------------CCCccceEEEEeCCHHHHHHHH
Confidence            34578999999999999999999999999999999966542                 3457899999999999999999


Q ss_pred             HhcceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCC
Q 008920          302 AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVG  381 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~s  381 (548)
                      .+++..|.|+.|.|.++........   .......++|||+|||+.+++++|+++|+.|    |.|..|.|+.+..+|.+
T Consensus        73 ~~~~~~~~g~~l~v~~~~~~~~~~~---~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~g~~  145 (196)
T 1l3k_A           73 NARPHKVDGRVVEPKRAVSREDSQR---PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY----GKIEVIEIMTDRGSGKK  145 (196)
T ss_dssp             HTCSCEETTEECEEEECCC--------------CCSEEEEECCTTTCCHHHHHHHHTTT----SCEEEEEEEECTTTCCE
T ss_pred             hcCCCEECCEEeeeecccCcccccc---cccCCCcceEEEeCCCCCCCHHHHHHHHhcC----CCeEEEEEeecCCCCCc
Confidence            8899999999999999875432211   1123356899999999999999999999999    89999999999889999


Q ss_pred             ceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEeeecCCCC
Q 008920          382 KGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQNCTP  422 (548)
Q Consensus       382 rG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~Ak~~~~~  422 (548)
                      +|||||+|.+.++|..||..++..|+|+.|.|.|+.++...
T Consensus       146 ~g~afV~F~~~~~A~~A~~~~~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          146 RGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             EEEEEEEESSHHHHHHHHHCSCCEETTEECEEEECC-----
T ss_pred             cceEEEEECCHHHHHHHHHhCCcEECCEEEEEEecCChhHh
Confidence            99999999999999999988779999999999999887444

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.98  E-value=1.9e-31  Score=245.42  Aligned_cols=164  Identities=23%  Similarity=0.367  Sum_probs=148.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~ln  304 (548)
                      ++|||+|||+++|+++|.++|+.||.|.+|.|+.++                  .+.++|||||+|.+.++|..|+ .||
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 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK------------------NNKNVNYAFVEYHQSHDANIALQTLN   62 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC------------------C-CCEEEEEEEESSHHHHHHHHHHHT
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC------------------CCCCCCEEEEEeCCHHHHHHHHHHcC
Confidence            589999999999999999999999999999996543                  2347799999999999999999 799


Q ss_pred             ceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceE
Q 008920          305 MAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGI  384 (548)
Q Consensus       305 g~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~  384 (548)
                      +..+.|+.|.|.++.+...       .......+|||+|||+.+++++|+++|+.|    |.|..|.|+.+..+|.++||
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       234567899999999999999999999999    99999999999999999999


Q ss_pred             EEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeec
Q 008920          385 AYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQ  418 (548)
Q Consensus       385 AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~  418 (548)
                      |||+|.+.++|..|+..++ ..|+|+.|.|.||.+
T Consensus       132 afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          132 GFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             EEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             EEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecCC
Confidence            9999999999999999777 999999999999863

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.97  E-value=6.9e-31  Score=255.18  Aligned_cols=166  Identities=25%  Similarity=0.391  Sum_probs=146.5

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..+||||+|||+++|+++|+++|+.||.|.+|+|+.+..                 ++.++|||||+|.+.++|..|| .
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~-----------------tg~~~G~afV~F~~~~~A~~Ai~~   76 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMI-----------------TRRSLGYAYVNFQQPADAERALDT   76 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----------------TCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccC-----------------CCCccccccceeCCHHHHHHHHHH
Confidence            358999999999999999999999999999999976542                 3457899999999999999999 5


Q ss_pred             hcceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGK  382 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~sr  382 (548)
                      +|+..+.|+.|.|.++......       ......+|||+|||+.+++++|+++|+.|    |.|..|+|++|.  +.++
T Consensus        77 ~~~~~~~g~~i~~~~~~~~~~~-------~~~~~~~l~v~nl~~~~t~~~l~~~F~~~----G~i~~~~i~~d~--~~~~  143 (213)
T 4f02_A           77 MNFDVIKGKPVRIMWSQRDPSL-------RKSGVGNIFIKNLDKSIDNKALYDTFSAF----GNILSCKVVCDE--NGSK  143 (213)
T ss_dssp             HTTCEETTEECEEEECCCCTHH-------HHHCTTEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEEET--TEEE
T ss_pred             hhhhhcCCcccccccccccccc-------cccccccceECCcccccHHHHHHHHHhhc----CCeEEEEeeccC--CCCc
Confidence            9999999999999998653211       12245789999999999999999999999    899999999984  4579


Q ss_pred             eEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          383 GIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       383 G~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      |||||+|.+.++|..||..|| ..|+|+.|.|.||.++
T Consensus       144 g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          144 GYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             EEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCH
T ss_pred             eEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            999999999999999998877 9999999999999864

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.97  E-value=3.6e-31  Score=244.78  Aligned_cols=165  Identities=19%  Similarity=0.401  Sum_probs=146.8

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      +.++|||+|||+++|+++|.++|+.||.|.+|.|+.++                 .+|.++|||||+|.+.++|..||..
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-----------------~~g~~~g~afV~f~~~~~a~~A~~~   64 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDP-----------------ATGRSRGFGFLSFEKPSSVDEVVKT   64 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCT-----------------TTSSCCSCEEEEESSTHHHHHHHHS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECC-----------------CCCCccceEEEEEccHHHHHHHHhc
Confidence            46899999999999999999999999999999985543                 2356889999999999999999973


Q ss_pred             cceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCce
Q 008920          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG  383 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG  383 (548)
                       +..|.|+.|.|.++.+...         .....+|||+|||+.+++++|+++|+.|    |.|..|.|+.+..+|.++|
T Consensus        65 -~~~~~g~~i~v~~~~~~~~---------~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~~~i~~~~~~g~~~g  130 (167)
T 2cjk_A           65 -QHILDGKVIDPKRAIPRDE---------QDKTGKIFVGGIGPDVRPKEFEEFFSQW----GTIIDAQLMLDKDTGQSRG  130 (167)
T ss_dssp             -CCEETTEECCCEECCCHHH---------HHHCEEEEEEEECTTCCHHHHHHHHHTT----SCCSEEECCCSSSSSTTSE
T ss_pred             -ccccCCeEcccccccchhh---------ccCCCeEEECCCCCCCCHHHHHHHHHhC----ccEEEEEEEEcCCCCccce
Confidence             6789999999999865321         2346799999999999999999999999    8999999999988999999


Q ss_pred             EEEEEECCHHHHHHHHHHcCCccCCeEEEEEeeecC
Q 008920          384 IAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQN  419 (548)
Q Consensus       384 ~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~Ak~~  419 (548)
                      ||||+|.+.++|.+|+.+.+..|.|+.|.|.||.++
T Consensus       131 ~afV~f~~~~~a~~A~~~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          131 FGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             EEEEEESSHHHHHHHHHCSEECSSSSCEEEEECCCC
T ss_pred             EEEEEECCHHHHHHHHhCCCEEeCCeEEEEeecCCC
Confidence            999999999999999984339999999999999874

>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=99.97  E-value=3e-30  Score=238.50  Aligned_cols=162  Identities=22%  Similarity=0.325  Sum_probs=146.8

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      .++|||+|||+++++++|.++|+.||.|.+|.|+.++                 .+|.++|||||+|.+.++|..|+ .|
T Consensus         3 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~-----------------~~~~~~g~afV~f~~~~~A~~a~~~l   65 (168)
T 1b7f_A            3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDY-----------------KTGYSYGYAFVDFTSEMDSQRAIKVL   65 (168)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEET-----------------TTTEECSEEEEEESSHHHHHHHHHHH
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeC-----------------CCCccceEEEEEECCHHHHHHHHHhc
Confidence            5899999999999999999999999999999986543                 13457799999999999999999 49


Q ss_pred             cceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCce
Q 008920          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG  383 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG  383 (548)
                      ++..|.|+.|.|.++.+..         ......+|||+|||..+++++|+++|+.|    |.|..|.|+.+..+|.++|
T Consensus        66 ~~~~~~g~~l~v~~~~~~~---------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~----G~i~~~~i~~~~~~~~~~g  132 (168)
T 1b7f_A           66 NGITVRNKRLKVSYARPGG---------ESIKDTNLYVTNLPRTITDDQLDTIFGKY----GSIVQKNILRDKLTGRPRG  132 (168)
T ss_dssp             TTCEETTEECEEEECCCCS---------STTTTCEEEEESCCTTCCHHHHHHHHTSS----SCEEEEEEEECTTTCCEEE
T ss_pred             CCCEeCCcEEEEEecCCCc---------ccCCCCCEEEeCCCCCCCHHHHHHhhhcC----CcEEEEEEEEcCCCCCcce
Confidence            9999999999999987532         23456899999999999999999999999    8999999999988999999


Q ss_pred             EEEEEECCHHHHHHHHHHcC-CccCC--eEEEEEee
Q 008920          384 IAYVLFKTREAANLVIKRRN-LKLRD--RELRLSHA  416 (548)
Q Consensus       384 ~AFV~F~~~e~A~~Al~~ln-~~l~G--r~I~V~~A  416 (548)
                      ||||+|.+.++|..|+..++ ..|.|  ++|+|.||
T Consensus       133 ~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          133 VAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             EEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             EEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            99999999999999999887 88877  99999986

>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=99.97  E-value=4.2e-30  Score=236.59  Aligned_cols=162  Identities=20%  Similarity=0.318  Sum_probs=146.0

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-h
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-F  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-l  303 (548)
                      .++|||+|||+++++++|.++|+.||.|..|.|+.++.                 +|.++|||||+|.+.++|..|+. |
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~-----------------~~~~~g~afV~f~~~~~A~~a~~~l   64 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKI-----------------TGQSLGYGFVNYIDPKDAEKAINTL   64 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTT-----------------TCCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCC-----------------CCcceeEEEEEECCHHHHHHHHHHc
Confidence            47999999999999999999999999999999966431                 34577999999999999999995 9


Q ss_pred             cceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCce
Q 008920          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG  383 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG  383 (548)
                      |+..+.|+.|.|.++.+..         ......+|||+|||..+++++|+++|+.|    |.|..|.|+.+..+|.++|
T Consensus        65 ~~~~~~g~~l~v~~~~~~~---------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~----G~i~~~~i~~~~~~g~~~g  131 (167)
T 1fxl_A           65 NGLRLQTKTIKVSYARPSS---------ASIRDANLYVSGLPKTMTQKELEQLFSQY----GRIITSRILVDQVTGVSRG  131 (167)
T ss_dssp             TTCEETTEECEEEECCCCC---------GGGTTCEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEE
T ss_pred             CCCccCCceEEEEecCCCc---------ccCCCCcEEECCCCCcCCHHHHHHHHHhc----CCEeEEEEEecCCCCCccc
Confidence            9999999999999987532         23356889999999999999999999999    8999999999988999999


Q ss_pred             EEEEEECCHHHHHHHHHHcC-CccCCeE--EEEEee
Q 008920          384 IAYVLFKTREAANLVIKRRN-LKLRDRE--LRLSHA  416 (548)
Q Consensus       384 ~AFV~F~~~e~A~~Al~~ln-~~l~Gr~--I~V~~A  416 (548)
                      ||||+|.+.++|..|+..++ ..|.|+.  |.|.||
T Consensus       132 ~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          132 VGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             EEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             eEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            99999999999999999877 8999964  999886

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.97  E-value=1.5e-30  Score=250.49  Aligned_cols=178  Identities=18%  Similarity=0.347  Sum_probs=150.9

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-h
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-F  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-l  303 (548)
                      .++|||+|||+++|+++|+++|+.||.|..|.|+.+.                 .++.++|||||+|.+.++|..||. |
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 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDS-----------------VTMKHKGFAFVEYEVPEAAQLALEQM   90 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC------------------CC-CCCSEEEEEESSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecC-----------------CCCccCceEEEEeCCHHHHHHHHHHc
Confidence            5799999999999999999999999999999995543                 134578999999999999999995 9


Q ss_pred             cceeecCceeEeecCCCcccccCC--CCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCC
Q 008920          304 NMAVIGGNHIRLDRACPPRKKLKG--EDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVG  381 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~k~~~~--~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~s  381 (548)
                      |+..|.|+.|.|.++.........  .........++|||+|||+.+++++|+++|+.|    |.|..|.|+.+..+|.+
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            999999999999987653211000  000112456899999999999999999999999    89999999999999999


Q ss_pred             ceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecCCCCC
Q 008920          382 KGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQNCTPS  423 (548)
Q Consensus       382 rG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~~~~~  423 (548)
                      +|||||+|.+.++|..||..|+ ..|+|+.|.|.|+.+...+.
T Consensus       167 ~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~~~~  209 (216)
T 2qfj_A          167 KGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPL  209 (216)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCSSTT
T ss_pred             CceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCCCCC
Confidence            9999999999999999999877 99999999999999874443

>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=99.97  E-value=1.6e-29  Score=234.79  Aligned_cols=157  Identities=22%  Similarity=0.454  Sum_probs=142.0

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhc----C-------CeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEec
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKF----G-------EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFK  292 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~f----G-------~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~  292 (548)
                      +.++|||+|||+++|+++|.++|+.|    |       .|.++.+.                       .++|||||+|.
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            46899999999999999999999999    6       66666652                       25799999999


Q ss_pred             CHHHHHHHHHhcceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEE
Q 008920          293 SEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRV  372 (548)
Q Consensus       293 s~e~A~~Al~lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI  372 (548)
                      +.++|..||.+|+..|.|+.|.|.++....         ......+|||+|||+.+++++|+++|+.|    |.|..|.|
T Consensus        60 ~~~~A~~A~~~~~~~~~g~~i~v~~~~~~~---------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~----G~v~~v~i  126 (172)
T 2g4b_A           60 SVDETTQAMAFDGIIFQGQSLKIRRPHDYQ---------PLPGAHKLFIGGLPNYLNDDQVKELLTSF----GPLKAFNL  126 (172)
T ss_dssp             SHHHHHHHGGGTTCEETTEECEEECCSSCC---------CCTTTTCEEEECCCTTCCHHHHHHHHHTT----SCEEEEEE
T ss_pred             CHHHHHHHHHhCCcEecCceeeecCCcccC---------CCCCCCEEEEEcCCCcCCHHHHHHHHHhc----CCceEEEE
Confidence            999999999999999999999999875421         12347899999999999999999999999    89999999


Q ss_pred             eecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEee
Q 008920          373 IRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHA  416 (548)
Q Consensus       373 ~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~A  416 (548)
                      +.++.+|.++|||||+|.+.++|..|+..++ ..|+|+.|.|.||
T Consensus       127 ~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          127 VKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             EECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             EecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            9998899999999999999999999999877 9999999999997

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.97  E-value=2.7e-29  Score=238.45  Aligned_cols=170  Identities=21%  Similarity=0.414  Sum_probs=145.6

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcC-----------CeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEec
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFG-----------EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFK  292 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG-----------~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~  292 (548)
                      ..++|||+|||+++|+++|.++|+.||           .|..+.+                       +.++|||||+|.
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            468999999999999999999999994           4555544                       236799999999


Q ss_pred             CHHHHHHHHHhcceeecCceeEeecCCCcccccCCC-----------CCCcCCCccEEEEeCCCCCCCHHHHHHHHhccC
Q 008920          293 SEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGE-----------DAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLN  361 (548)
Q Consensus       293 s~e~A~~Al~lng~~~~gr~I~V~~a~~~~k~~~~~-----------~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g  361 (548)
                      +.++|..||.||+..|.|+.|.|.++..........           ........++|||+|||+.+++++|+++|+.| 
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           01122467899999999999999999999999 


Q ss_pred             CCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecCC
Q 008920          362 DLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQNC  420 (548)
Q Consensus       362 ~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~~  420 (548)
                         |.|..|.|+.+..+|.++|||||+|.+.++|..|+..|+ ..|.|+.|.|.|+.+..
T Consensus       139 ---G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          139 ---GPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             ---SCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             ---CCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence               899999999998899999999999999999999999877 99999999999998753

>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=99.96  E-value=5.9e-29  Score=230.97  Aligned_cols=166  Identities=19%  Similarity=0.313  Sum_probs=141.8

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      +.++|||+|||+++|+++|.++|+.||.|.+|+|+.+..+.               .+.++|||||+|.+.++|..|+ .
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~---------------~~~~~g~afV~f~~~~~A~~A~~~   66 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQN---------------PPQSKGCCFVTFYTRKAALEAQNA   66 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSS---------------SCEEEEEEEEEESSHHHHHHHHHH
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCC---------------CCCcceEEEEEECCHHHHHHHHHH
Confidence            35899999999999999999999999999999997765321               1147799999999999999999 5


Q ss_pred             hcceeec---CceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCC
Q 008920          303 FNMAVIG---GNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMR  379 (548)
Q Consensus       303 lng~~~~---gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg  379 (548)
                      |++..+.   ++.|.|.++....        ......++|||+|||+.+++++|+++|+.|    |.|..|.|+.+. +|
T Consensus        67 l~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~----G~i~~v~~~~~~-~g  133 (175)
T 3nmr_A           67 LHNMKVLPGMHHPIQMKPADSEK--------NNAVEDRKLFIGMISKKCTENDIRVMFSSF----GQIEECRILRGP-DG  133 (175)
T ss_dssp             HTTTCCCTTCSSCCEEEECGGGC--------CSCGGGSEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECT-TS
T ss_pred             hcCcEEccCCccceEEccccccc--------cccCCCCeEEEcCCCCcCCHHHHHHHHHhC----CCEEEEEEEECC-CC
Confidence            8988775   5678887765432        123357899999999999999999999999    899999999995 69


Q ss_pred             CCceEEEEEECCHHHHHHHHHHcC-CccC---CeEEEEEeee
Q 008920          380 VGKGIAYVLFKTREAANLVIKRRN-LKLR---DRELRLSHAQ  417 (548)
Q Consensus       380 ~srG~AFV~F~~~e~A~~Al~~ln-~~l~---Gr~I~V~~Ak  417 (548)
                      .++|||||+|.+.++|..||..++ ..+.   |++|.|.||.
T Consensus       134 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          134 LSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             CEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             CEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            999999999999999999998887 5554   4999999983

>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=99.96  E-value=1.8e-29  Score=235.75  Aligned_cols=164  Identities=20%  Similarity=0.325  Sum_probs=141.8

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++|+++|+++|..||.|..+.++.                  ..++.++|||||+|.+.++|..||
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~------------------~~~~~~~g~afV~f~~~~~a~~A~   71 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVD------------------VRTGTNRKFGYVDFESAEDLEKAL   71 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCE------------------EEEETTTTEEEEEESSHHHHHHHH
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEE------------------CCCCccccEEEEEECCHHHHHHHH
Confidence            34568999999999999999999999999876633211                  124568899999999999999999


Q ss_pred             HhcceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCC
Q 008920          302 AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVG  381 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~s  381 (548)
                      +||+..|.|+.|.|.++.+...       ......++|||+|||+.+++++|+++|+.|    |.|..|     ..++.+
T Consensus        72 ~l~g~~~~g~~l~v~~~~~~~~-------~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~----g~v~~~-----~~~~~~  135 (175)
T 1fje_B           72 ELTGLKVFGNEIKLEKPKGRDS-------KKVRAARTLLAKNLSFNITEDELKEVFEDA----LEIRLV-----SQDGKS  135 (175)
T ss_dssp             HGGGEEETTEEEEEECCCCSSC-------STTGGGGEEEEESCCSSCCHHHHHHHCTTC----SEEEEE-----CSSSSC
T ss_pred             hcCCCEeCCeEEEEecCCCccc-------cccccCCEEEEeCCCCCCCHHHHHHHHHhc----CeEEEe-----cCCCCC
Confidence            9999999999999999875432       223467899999999999999999999999    877655     467899


Q ss_pred             ceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          382 KGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       382 rG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      +|||||+|.+.++|..||..|+ ..|.|+.|.|.||.++
T Consensus       136 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          136 KGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             CSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             ceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            9999999999999999999887 9999999999999875

>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=99.96  E-value=3.4e-28  Score=245.92  Aligned_cols=160  Identities=21%  Similarity=0.278  Sum_probs=137.1

Q ss_pred             CCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       221 ~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      .+...++|||+|||+++|+++|.++|+.||.|.+|.|+.++.                   .++|||||+|.+.++|..|
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-------------------~~~g~afV~f~~~~~A~~A   97 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK-------------------KNFRFARIEFARYDGALAA   97 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT-------------------SSSEEEEEEESSHHHHHHH
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC-------------------CCcEEEEEEECCHHHHHHH
Confidence            345578999999999999999999999999999999966441                   1469999999999999999


Q ss_pred             HHhcceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCC-CeEEEEEeecCCCC
Q 008920          301 LAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLES-SVEAVRVIRHPHMR  379 (548)
Q Consensus       301 l~lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G-~I~~VrI~~d~~tg  379 (548)
                      |++++..|.|+.|.|.++                ..++|||+|||+.+++++|+++|..|    | .|..|.|+.+.. |
T Consensus        98 ~~~~~~~~~g~~i~v~~~----------------~~~~l~v~nlp~~~t~~~l~~~f~~~----G~~i~~v~i~~~~~-~  156 (292)
T 2ghp_A           98 ITKTHKVVGQNEIIVSHL----------------TECTLWMTNFPPSYTQRNIRDLLQDI----NVVALSIRLPSLRF-N  156 (292)
T ss_dssp             HTTTTCEETTEECEEEEC----------------CSCEEEEECCCTTCCHHHHHHHHHHT----TCCCCEEECC------
T ss_pred             HHhCCcEeCCcEEEEEEC----------------CCCEEEEECCCCCCCHHHHHHHHHHh----CCCeEEEEEEeCCC-C
Confidence            999999999999999986                25899999999999999999999999    9 999999999865 8


Q ss_pred             CCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecCC
Q 008920          380 VGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQNC  420 (548)
Q Consensus       380 ~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~~  420 (548)
                      .++|||||+|.+.++|..|+..++ ..|.|+.|.|.|+.+..
T Consensus       157 ~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  198 (292)
T 2ghp_A          157 TSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLE  198 (292)
T ss_dssp             --CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC-
T ss_pred             CcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCc
Confidence            899999999999999999999776 99999999999998653

>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=99.95  E-value=1.1e-27  Score=242.23  Aligned_cols=171  Identities=18%  Similarity=0.277  Sum_probs=143.8

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcC-CeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFG-EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG-~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ..++|||+|||+.+++++|.++|+.|| .|..|.|+.+.                  .|.++|||||+|.+.++|..|+.
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~------------------~~~~~g~afV~f~~~~~a~~A~~  177 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR------------------FNTSRRFAYIDVTSKEDARYCVE  177 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------------------------CCEEEEECSSHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCC------------------CCCcceEEEEEECCHHHHHHHHH
Confidence            468999999999999999999999999 99999985543                  23477999999999999999995


Q ss_pred             -hcceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCC-CCHHHHHHHHhccCCCCCCeEEEEEeecCC-CC
Q 008920          303 -FNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFD-VKDEEIYQLFCGLNDLESSVEAVRVIRHPH-MR  379 (548)
Q Consensus       303 -lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~-~teedL~~~F~~~g~~~G~I~~VrI~~d~~-tg  379 (548)
                       ||+..|.|+.|.|.++.+.......  ........+|||+|||+. +++++|+++|+.|    |.|..|.|+.+.. ||
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             9999999999999998765432211  123456789999999999 9999999999999    8999999999876 59


Q ss_pred             CCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          380 VGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       380 ~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      .++|||||+|.+.++|..|| .++ ..|.|+.|.|.|+.++
T Consensus       252 ~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          252 FNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             CCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            99999999999999999999 877 9999999999999875

>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=99.95  E-value=2.7e-27  Score=238.46  Aligned_cols=168  Identities=15%  Similarity=0.162  Sum_probs=149.9

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      .++|||+|||+.+|+++|.++|+.||.|..|.|+.+..                 +|.++|||||+|.+.++|..|+ .|
T Consensus        95 ~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~-----------------~g~~~g~afV~f~~~~~a~~A~~~l  157 (284)
T 3smz_A           95 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER-----------------TGQSKGYGFAEYMKKDSAARAKSDL  157 (284)
T ss_dssp             SCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----------------TCCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCC-----------------CCccceEEEEEECCHHHHHHHHHHh
Confidence            47999999999999999999999999999999865432                 3457899999999999999999 79


Q ss_pred             cceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCC-CHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCc
Q 008920          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDV-KDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGK  382 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~-teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~sr  382 (548)
                      ++..|.|+.|.|.++.+...      .......++|||+|||+.+ ++++|+++|+.|    |.|..|.|+.+. +|.++
T Consensus       158 ~~~~~~g~~i~v~~a~~~~~------~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~----G~i~~v~i~~~~-~g~~~  226 (284)
T 3smz_A          158 LGKPLGPRTLYVHWTDAGQL------TPALLHSRCLCVDRLPPGFNDVDALCRALSAV----HSPTFCQLACGQ-DGQLK  226 (284)
T ss_dssp             TTCEETTEECEEEECCGGGC------CTTTTSCSEEEEECCCTTCCCHHHHHHHTCSS----SCCSEEEEEECS-SCCEE
T ss_pred             CCCEeCCcEEEEEECCCCCC------CcccCCccEEEEecCCcccCCHHHHHHHhhCC----CCeEEEEEEECC-CCCcc
Confidence            99999999999999976432      1223467899999999995 999999999999    899999999996 79999


Q ss_pred             eEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecCC
Q 008920          383 GIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQNC  420 (548)
Q Consensus       383 G~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~~  420 (548)
                      |||||+|.+.++|..|+..++ ..|.|+.|.|.|+.+..
T Consensus       227 g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  265 (284)
T 3smz_A          227 GFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGP  265 (284)
T ss_dssp             EEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSS
T ss_pred             cEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCC
Confidence            999999999999999999887 99999999999998753

>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=99.95  E-value=2.8e-27  Score=229.60  Aligned_cols=165  Identities=13%  Similarity=0.190  Sum_probs=137.4

Q ss_pred             cccEEEEcCCC-CCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          224 LLRTIFVGNLP-LKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       224 ~~rtVfVgNLP-~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ..++|||+||| +.+|+++|.++|+.||.|.+|+|+.+                      .+|||||+|.+.++|+.|| 
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            35899999999 89999999999999999999998421                      3589999999999999999 


Q ss_pred             HhcceeecCceeEeecCCCcccccCC-----CC-----------------------CCcCCCccEEEEeCCCCCCCHHHH
Q 008920          302 AFNMAVIGGNHIRLDRACPPRKKLKG-----ED-----------------------APLYDIKKTVFVGNLPFDVKDEEI  353 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~~k~~~~-----~~-----------------------~~~~~~~~tLfV~NLp~~~teedL  353 (548)
                      .|||..|.|+.|.|.++.........     ..                       .....+..+|||+|||+.+++++|
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            59999999999999998643210000     00                       001235678999999999999999


Q ss_pred             HHHHhccCCCCCCe--EEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCe----EEEEEee
Q 008920          354 YQLFCGLNDLESSV--EAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDR----ELRLSHA  416 (548)
Q Consensus       354 ~~~F~~~g~~~G~I--~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr----~I~V~~A  416 (548)
                      +++|+.|    |.|  ..|+|+.+.  +..+|||||+|.+.++|..||..|| ..|.|+    ++.|.||
T Consensus       141 ~~~F~~~----G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          141 FEICDEL----GVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             HHHHHHH----TCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             HHHHHhc----CCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            9999999    888  889988874  5567999999999999999999888 888885    6888776

>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=99.95  E-value=7.2e-27  Score=235.07  Aligned_cols=167  Identities=22%  Similarity=0.329  Sum_probs=141.2

Q ss_pred             CCcccEEEEcCCCCCCcHHHHH----HHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLI----KEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQST  297 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~----~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A  297 (548)
                      ....++|||+|||+++|+++|+    ++|+.||.|..|+|+.                    ++.++|||||+|.+.++|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~--------------------~~~~~g~afV~f~~~~~a   65 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--------------------SLKMRGQAFVIFKEVSSA   65 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC--------------------CCCcceEEEEEECCHHHH
Confidence            3457899999999999999966    8999999999998842                    344779999999999999


Q ss_pred             HHHH-HhcceeecCceeEeecCCCcccccC---C----------------------------------------------
Q 008920          298 EAAL-AFNMAVIGGNHIRLDRACPPRKKLK---G----------------------------------------------  327 (548)
Q Consensus       298 ~~Al-~lng~~~~gr~I~V~~a~~~~k~~~---~----------------------------------------------  327 (548)
                      ..|| .|||..|.|+.|.|.++........   +                                              
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 6999999999999999864321000   0                                              


Q ss_pred             -----------------------------------------------------CCCCcCCCccEEEEeCCCCCCCHHHHH
Q 008920          328 -----------------------------------------------------EDAPLYDIKKTVFVGNLPFDVKDEEIY  354 (548)
Q Consensus       328 -----------------------------------------------------~~~~~~~~~~tLfV~NLp~~~teedL~  354 (548)
                                                                           .........++|||+|||+.+++++|+
T Consensus       146 ~~~~~~~~~~~~~g~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~  225 (282)
T 3pgw_A          146 PMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLS  225 (282)
T ss_pred             cccccccccccCCCCCCCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHH
Confidence                                                                 000122356889999999999999999


Q ss_pred             HHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccC-CeEEEEEeee
Q 008920          355 QLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLR-DRELRLSHAQ  417 (548)
Q Consensus       355 ~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~-Gr~I~V~~Ak  417 (548)
                      ++|+.|    |.|..|.|+.+.     +|||||+|.+.++|..||..|+ ..|. |+.|+|.|++
T Consensus       226 ~~F~~~----G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          226 MLFNQF----PGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             HHHHhc----CCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            999999    899999999763     5899999999999999999888 8888 9999999986

>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=99.95  E-value=4.3e-27  Score=235.48  Aligned_cols=155  Identities=24%  Similarity=0.305  Sum_probs=141.0

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++|+++|.++|+.||.|..|.|..                       ++|||||+|.+.++|..|+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~-----------------------~kg~afV~f~~~~~A~~A~   75 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR-----------------------DRGFGFIRLESRTLAEIAK   75 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET-----------------------TTTEEEEECSSHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC-----------------------CCcEEEEEECCHHHHHHHH
Confidence            34568999999999999999999999999999999832                       4699999999999999999


Q ss_pred             H-hcceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCC
Q 008920          302 A-FNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV  380 (548)
Q Consensus       302 ~-lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~  380 (548)
                      . +|+..|.|+.|.|.++.+               ..+|||+|||+.+++++|+++|+.|    |.|..|.|+.+ .+|.
T Consensus        76 ~~l~g~~i~g~~l~v~~a~~---------------~~~l~v~nl~~~~t~~~l~~~F~~~----G~i~~v~i~~~-~~g~  135 (261)
T 3sde_A           76 AELDGTILKSRPLRIRFATH---------------GAALTVKNLSPVVSNELLEQAFSQF----GPVEKAVVVVD-DRGR  135 (261)
T ss_dssp             HHHTTCEETTEECEEEECCC---------------SSEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEEE-TTSC
T ss_pred             HHcCCcEECCceeEeeeccc---------------CCcccccCCCCCCCHHHHHHHHHhc----CCeEEEEeeeC-CCCC
Confidence            4 999999999999999852               4789999999999999999999999    89999999999 6899


Q ss_pred             CceEEEEEECCHHHHHHHHHHcC--CccC---CeEEEEEeeecC
Q 008920          381 GKGIAYVLFKTREAANLVIKRRN--LKLR---DRELRLSHAQQN  419 (548)
Q Consensus       381 srG~AFV~F~~~e~A~~Al~~ln--~~l~---Gr~I~V~~Ak~~  419 (548)
                      ++|||||+|.+.++|..||..++  ..+.   |++|.|.++.+.
T Consensus       136 ~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~  179 (261)
T 3sde_A          136 ATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQF  179 (261)
T ss_dssp             EEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCE
T ss_pred             cCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeecccc
Confidence            99999999999999999999884  4444   899999999864

>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=99.95  E-value=7.5e-27  Score=235.19  Aligned_cols=153  Identities=16%  Similarity=0.236  Sum_probs=141.6

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      .++|||+|||+++|+++|.++|+.|| |.+|.+                       +.++|||||+|.+.++|..|+ .|
T Consensus        22 ~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~-----------------------~~~~g~afV~f~~~~~A~~A~~~l   77 (284)
T 3smz_A           22 RRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-----------------------DKYKGTAFVTLLNGEQAEAAINAF   77 (284)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE-----------------------ETTTTEEEEEESSHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE-----------------------ecCCCEEEEEeCCHHHHHHHHHHc
Confidence            58999999999999999999999999 988887                       126799999999999999999 58


Q ss_pred             cceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCce
Q 008920          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG  383 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG  383 (548)
                      |+..|.|+.|.|.++.               ...+|||+|||+.+++++|+++|+.|    |.|..|.|+.+..+|.++|
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            9999999999999853               34789999999999999999999999    8999999999999999999


Q ss_pred             EEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecCC
Q 008920          384 IAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQNC  420 (548)
Q Consensus       384 ~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~~  420 (548)
                      ||||+|.+.++|..|+..++ ..|.|+.|.|.|+.+..
T Consensus       139 ~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~  176 (284)
T 3smz_A          139 YGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQ  176 (284)
T ss_dssp             EEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGG
T ss_pred             EEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCC
Confidence            99999999999999997777 99999999999998753

>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=99.94  E-value=2.5e-26  Score=225.48  Aligned_cols=166  Identities=19%  Similarity=0.295  Sum_probs=140.4

Q ss_pred             CcccEEEEcCCCC-CCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          223 KLLRTIFVGNLPL-KVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~-~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ...++|||+|||+ ++++++|.++|+.||.|..|.|+.+                      .+|||||+|.+.++|..||
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~----------------------~~g~afV~F~~~~~A~~Ai   89 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----------------------KKENALVQMADGNQAQLAM   89 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCT----------------------TSCCEEEEESCHHHHHHHH
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEEC----------------------CCCEEEEEECCHHHHHHHH
Confidence            3468999999999 9999999999999999999999432                      2489999999999999999


Q ss_pred             H-hcceeecCceeEeecCCCcccccCCC--------------------------CCCcCCCccEEEEeCCCCCCCHHHHH
Q 008920          302 A-FNMAVIGGNHIRLDRACPPRKKLKGE--------------------------DAPLYDIKKTVFVGNLPFDVKDEEIY  354 (548)
Q Consensus       302 ~-lng~~~~gr~I~V~~a~~~~k~~~~~--------------------------~~~~~~~~~tLfV~NLp~~~teedL~  354 (548)
                      . ||+..|.|+.|.|.++..........                          ......+.++|||+|||+.+++++|+
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            4 99999999999999987531110000                          00113447899999999999999999


Q ss_pred             HHHhccCCCCC-CeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccC-CeEEEEEeeecC
Q 008920          355 QLFCGLNDLES-SVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLR-DRELRLSHAQQN  419 (548)
Q Consensus       355 ~~F~~~g~~~G-~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~-Gr~I~V~~Ak~~  419 (548)
                      ++|..|    | .|..|.|+.+     .+|||||+|.+.++|..||..|+ ..|. |+.|.|.|+.+.
T Consensus       170 ~~f~~~----G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          170 VLFSSN----GGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             HHHHTT----SCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             HHHHHc----CCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            999999    8 9999999764     37899999999999999999777 8888 999999999864

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.94  E-value=1.1e-26  Score=221.53  Aligned_cols=164  Identities=20%  Similarity=0.306  Sum_probs=139.6

Q ss_pred             ccEEEEcCCCC-CCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-
Q 008920          225 LRTIFVGNLPL-KVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-  302 (548)
Q Consensus       225 ~rtVfVgNLP~-~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-  302 (548)
                      .++|||+|||+ ++++++|.++|+.||.|..|.|+.+                      .+|||||+|.+.++|..||. 
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~----------------------~~g~afV~f~~~~~a~~A~~~   60 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----------------------KKENALVQMADGNQAQLAMSH   60 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTT----------------------CSSCCEEECTTTHHHHHHHHH
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeC----------------------CCCEEEEEECCHHHHHHHHHH
Confidence            57999999999 9999999999999999999998432                      24899999999999999995 


Q ss_pred             hcceeecCceeEeecCCCcccccCCC--------------------------CCCcCCCccEEEEeCCCCCCCHHHHHHH
Q 008920          303 FNMAVIGGNHIRLDRACPPRKKLKGE--------------------------DAPLYDIKKTVFVGNLPFDVKDEEIYQL  356 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~~k~~~~~--------------------------~~~~~~~~~tLfV~NLp~~~teedL~~~  356 (548)
                      ||+..|.|+.|.|.++..........                          ......+.++|||+|||..+++++|+++
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            99999999999999987532110000                          0111345789999999999999999999


Q ss_pred             HhccCCCCC-CeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccC-CeEEEEEeeecC
Q 008920          357 FCGLNDLES-SVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLR-DRELRLSHAQQN  419 (548)
Q Consensus       357 F~~~g~~~G-~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~-Gr~I~V~~Ak~~  419 (548)
                      |+.|    | .|..|.|+.+.     +|||||+|.+.++|..|+..++ ..|. |+.|.|.|+.+.
T Consensus       141 f~~~----G~~v~~v~i~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          141 FSSN----GGVVKGFKFFQKD-----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             HHHT----TSCCCEEEESSTT-----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             HHHc----CCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            9999    8 99999997652     7899999999999999999887 8888 999999999864

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.85  E-value=1.4e-20  Score=173.76  Aligned_cols=135  Identities=16%  Similarity=0.140  Sum_probs=105.8

Q ss_pred             CCcceEEEEecCHHHHHHHH-HhcceeecCceeEeecCCCcccc----cCCCCCCcCCCccEEEEeCCCCCCCHHHHHHH
Q 008920          282 ADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK----LKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQL  356 (548)
Q Consensus       282 ~skG~AFV~F~s~e~A~~Al-~lng~~~~gr~I~V~~a~~~~k~----~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~  356 (548)
                      .++|||||+|.+.++|++|+ .+++....+..+.+.........    .............+|||+|||+.+++++|+++
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            47899999999999999999 46543332322333222111000    00011222345789999999999999999999


Q ss_pred             HhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecCC
Q 008920          357 FCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQNC  420 (548)
Q Consensus       357 F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~~  420 (548)
                      |+.|    |.|..|.|+.|+.+|.++|||||+|.+.++|..||..|+ ..|.|+.|.|.|+.+..
T Consensus        91 F~~~----G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  151 (158)
T 2kn4_A           91 FEKY----GRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  151 (158)
T ss_dssp             HHHH----SCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSS
T ss_pred             HHhc----CCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            9999    899999999999899999999999999999999999887 89999999999998753

>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=99.80  E-value=1.2e-19  Score=159.50  Aligned_cols=108  Identities=18%  Similarity=0.271  Sum_probs=71.2

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      .++|||+|||+++|+++|+++|+.||.|.+|+|+.+.                   +.++|||||+|.+.++|+.|| .|
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-------------------NGSKGYGFVHFETQEAAERAIEKM   65 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-------------------TEEEEEEEEEESCHHHHHHHHHHH
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC-------------------CCCCceEEEEECCHHHHHHHHHHc
Confidence            4689999999999999999999999999999996643                   126799999999999999999 69


Q ss_pred             cceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHH
Q 008920          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEE  352 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teed  352 (548)
                      |+..|.|+.|.|.++.+........ ........+|||+|||+++|++-
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            9999999999999987643222111 12233456799999999998763

>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=99.79  E-value=2.7e-19  Score=164.14  Aligned_cols=128  Identities=17%  Similarity=0.184  Sum_probs=109.5

Q ss_pred             CCcceEEEEecCHHHHHHHH-Hh-cceeecCceeEeecCCCccccc-------CCCCCCcCCCccEEEEeCCCCCCCHHH
Q 008920          282 ADSVHAYIVFKSEQSTEAAL-AF-NMAVIGGNHIRLDRACPPRKKL-------KGEDAPLYDIKKTVFVGNLPFDVKDEE  352 (548)
Q Consensus       282 ~skG~AFV~F~s~e~A~~Al-~l-ng~~~~gr~I~V~~a~~~~k~~-------~~~~~~~~~~~~tLfV~NLp~~~teed  352 (548)
                      ..+|+++|+|.+.++|++|+ ++ |+..+.| .|.|+++.......       ...........++|||+|||+.+++++
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            46799999999999999999 68 9999999 99999986532110       011133345679999999999999999


Q ss_pred             HHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          353 IYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       353 L~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      |+++|+.|    |.|..|+|+.+     ++|||||+|.+.++|..||..++ ..|.|+.|+|.|+.++
T Consensus        90 l~~~F~~~----G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           90 LERAFGYY----GPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             HHHHHHHH----SCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             HHHHHHhh----CCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            99999999    89999999887     58999999999999999999777 9999999999999874

>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=99.74  E-value=1e-17  Score=143.69  Aligned_cols=82  Identities=26%  Similarity=0.440  Sum_probs=77.3

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      .-..++|||+|||+++|+++|+++|+.|    |.|..|.|++|+.+|.++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~----G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l   91 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSI----GEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI   91 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTT----SCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            3346789999999999999999999999    999999999999999999999999999999999998877 99999999


Q ss_pred             EEEeeec
Q 008920          412 RLSHAQQ  418 (548)
Q Consensus       412 ~V~~Ak~  418 (548)
                      +|.||+|
T Consensus        92 ~V~~AkP   98 (99)
T 4fxv_A           92 KVSYARP   98 (99)
T ss_dssp             EEEECCB
T ss_pred             EEEEeeC
Confidence            9999986

>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=99.73  E-value=1.2e-17  Score=179.36  Aligned_cols=85  Identities=14%  Similarity=0.280  Sum_probs=79.4

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ..+.++|||+|||+.+|+++|..+|..|    |.|..|.|+.+..+|.++|||||+|.+.++|..||..|| ..|.|+.|
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~----G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i  174 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVY----GPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRV  174 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHc----CCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEE
Confidence            3456899999999999999999999999    999999999999999999999999999999999998888 99999999


Q ss_pred             EEEeeecCCC
Q 008920          412 RLSHAQQNCT  421 (548)
Q Consensus       412 ~V~~Ak~~~~  421 (548)
                      .|.|+.+...
T Consensus       175 ~V~~a~~~~~  184 (437)
T 3pgw_S          175 LVDVERGRTV  184 (437)
T ss_pred             EEEEeCCCCC
Confidence            9999987643

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.70  E-value=1.2e-17  Score=140.84  Aligned_cols=82  Identities=16%  Similarity=0.289  Sum_probs=75.9

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCC-CeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHc-C-CccCCeEEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLES-SVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR-N-LKLRDRELR  412 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G-~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~l-n-~~l~Gr~I~  412 (548)
                      +++|||+|||+++|+++|+++|+.|    | .|.+|+|++|+.+|.++|||||+|.+.++|..||+.+ + ..|+|+.|+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~----G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~   76 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSH----GVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVS   76 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHH----TCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHh----CCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEE
Confidence            4689999999999999999999999    7 8999999999999999999999999999999999876 4 679999999


Q ss_pred             EEeeecCCC
Q 008920          413 LSHAQQNCT  421 (548)
Q Consensus       413 V~~Ak~~~~  421 (548)
                      |.||.++..
T Consensus        77 V~~a~~~~~   85 (91)
T 2lxi_A           77 MHYSDPKPK   85 (91)
T ss_dssp             EECCCSCCC
T ss_pred             EEEcCCCCC
Confidence            999987543

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.70  E-value=5e-17  Score=139.39  Aligned_cols=79  Identities=18%  Similarity=0.316  Sum_probs=71.7

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      .++|||+|||+++|+++|+++|+.||.|.+|.|+.++.                 +|.++|||||+|.+.++|..|| .|
T Consensus        19 gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~-----------------tg~~kG~afV~f~~~~~A~~Ai~~l   81 (99)
T 4fxv_A           19 GTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKV-----------------AGHSLGYGFVNYVTAKDAERAINTL   81 (99)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSS-----------------SCCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCC-----------------CCcccccEEEEECCHHHHHHHHHHh
Confidence            47899999999999999999999999999999976542                 3557899999999999999999 59


Q ss_pred             cceeecCceeEeecCCC
Q 008920          304 NMAVIGGNHIRLDRACP  320 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~  320 (548)
                      ||..|.|+.|.|.++.|
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

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.69  E-value=1.8e-17  Score=150.08  Aligned_cols=126  Identities=19%  Similarity=0.245  Sum_probs=82.7

Q ss_pred             cceEEEEecCHHHHHHHH-HhcceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCC
Q 008920          284 SVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLND  362 (548)
Q Consensus       284 kG~AFV~F~s~e~A~~Al-~lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~  362 (548)
                      +-|+|++|.+...+..|| .+++....|+. .+.+..+         .+.....++|||+|||+.+++++|+++|+.|  
T Consensus         4 ~~~~~~~~~~~~~~~~a~~~~~g~~~~g~~-~~~~~~~---------~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~--   71 (135)
T 2lea_A            4 SHHHHHHSSGLVPRGSHMASMTGGQQMGRG-SMSYGRP---------PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKY--   71 (135)
T ss_dssp             --------------------------------CCSCCS---------CSSGGGCCCEEEECCCSSCHHHHHHHHHGGG--
T ss_pred             cccccccccCCCchhhhhhhccCCCCCCCC-CCCcCCC---------CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhc--
Confidence            357889999999999999 47776655543 1222222         2334567899999999999999999999999  


Q ss_pred             CCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecCCCCC
Q 008920          363 LESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQNCTPS  423 (548)
Q Consensus       363 ~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~~~~~  423 (548)
                        |.|..|.|+.+..++.++|||||+|.+.++|..||..|+ ..|.|+.|.|.|+.+...+.
T Consensus        72 --G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~~~  131 (135)
T 2lea_A           72 --GRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD  131 (135)
T ss_dssp             --SCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCCCT
T ss_pred             --CCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCCc
Confidence              899999999998899999999999999999999999877 99999999999998765443

>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=99.68  E-value=1.6e-16  Score=148.28  Aligned_cols=129  Identities=12%  Similarity=0.178  Sum_probs=79.2

Q ss_pred             EEecCHHHHHHHH-Hhcceeec--CceeEeecCCCcccc----c-------CCCCCCcCCCccEEEEeCCCCCCCHHHHH
Q 008920          289 IVFKSEQSTEAAL-AFNMAVIG--GNHIRLDRACPPRKK----L-------KGEDAPLYDIKKTVFVGNLPFDVKDEEIY  354 (548)
Q Consensus       289 V~F~s~e~A~~Al-~lng~~~~--gr~I~V~~a~~~~k~----~-------~~~~~~~~~~~~tLfV~NLp~~~teedL~  354 (548)
                      .+|.+.++|..|+ .+++....  |+.+.+.+.......    .       ...........++|||+|||+.+++++|+
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            7899999999998 57766554  666666553221100    0       01112234456899999999999999999


Q ss_pred             HHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecCCC
Q 008920          355 QLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQNCT  421 (548)
Q Consensus       355 ~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~~~  421 (548)
                      .+|+.|    |.|..|.|+.+..+|.++|||||+|.+.++|..||..|+ ..|.|+.|.|.|+.+...
T Consensus        91 ~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  154 (165)
T 1rk8_A           91 EKFCDY----GEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP  154 (165)
T ss_dssp             HHHGGG----SCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC-
T ss_pred             HHhhcC----CCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCC
Confidence            999999    899999999999999999999999999999999999877 999999999999988643

>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=4e-16  Score=132.63  Aligned_cols=85  Identities=14%  Similarity=0.330  Sum_probs=78.4

Q ss_pred             cCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEE
Q 008920          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDREL  411 (548)
Q Consensus       332 ~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I  411 (548)
                      .....++|||+|||+.+++++|+++|..|    |.|..|.|+.++.++.++|||||+|.+.++|..||.+.+..|.|+.|
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l   81 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKF----GVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKV   81 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSS----SCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEE
Confidence            34567999999999999999999999999    89999999999999999999999999999999999944499999999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      .|.|+.+..
T Consensus        82 ~V~~a~~~~   90 (99)
T 2dgs_A           82 EVKRAEPRD   90 (99)
T ss_dssp             EEEECCCCC
T ss_pred             EEEECCCCc
Confidence            999998753

>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=7.7e-16  Score=134.46  Aligned_cols=87  Identities=23%  Similarity=0.313  Sum_probs=80.6

Q ss_pred             cCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeE
Q 008920          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE  410 (548)
Q Consensus       332 ~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~  410 (548)
                      .....++|||+|||+.+++++|+++|..|    |.|..|.|+.+..++.++|||||+|.+.++|..||..|+ ..|.|+.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   86 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPF----GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQ   86 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            34567999999999999999999999999    899999999998899999999999999999999999887 9999999


Q ss_pred             EEEEeeecCCCC
Q 008920          411 LRLSHAQQNCTP  422 (548)
Q Consensus       411 I~V~~Ak~~~~~  422 (548)
                      |.|.|+.+...+
T Consensus        87 l~V~~a~~~~~~   98 (115)
T 2dgo_A           87 IRTNWATRKPPA   98 (115)
T ss_dssp             CEEEESSCCCCC
T ss_pred             EEEEEccCCCCC
Confidence            999999876443

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.67  E-value=4e-16  Score=137.40  Aligned_cols=84  Identities=18%  Similarity=0.353  Sum_probs=78.1

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      +..++|||+|||+.+++++|+++|+.|    |.|..|.|+.+. +|.++|||||+|.+.++|..||..++ ..|.|+.|.
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~   79 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKH----GPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIK   79 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTS----SCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            456899999999999999999999999    899999999997 89999999999999999999999887 999999999


Q ss_pred             EEeeecCCCC
Q 008920          413 LSHAQQNCTP  422 (548)
Q Consensus       413 V~~Ak~~~~~  422 (548)
                      |.|+.+...+
T Consensus        80 V~~a~~~~~~   89 (116)
T 2fy1_A           80 VEQAKKPSFQ   89 (116)
T ss_dssp             EEECCCSSCS
T ss_pred             EEECCCCCCC
Confidence            9999876443

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.67  E-value=2.4e-16  Score=137.88  Aligned_cols=82  Identities=21%  Similarity=0.247  Sum_probs=77.3

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      .+.++|||+|||+.+++++|+++|+.|    |.|..|.|++|+.++.++|||||+|.+.++|..||..|| ..|.|+.|.
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~----G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~   79 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKY----GEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIH   79 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTT----SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhc----CCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            356899999999999999999999999    999999999999999999999999999999999999887 999999999


Q ss_pred             EEeeecC
Q 008920          413 LSHAQQN  419 (548)
Q Consensus       413 V~~Ak~~  419 (548)
                      |.++...
T Consensus        80 V~~a~~~   86 (110)
T 3s8s_A           80 AQLDIKG   86 (110)
T ss_dssp             EEECSTT
T ss_pred             EEECCCC
Confidence            9998643

>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=99.67  E-value=4.7e-16  Score=132.09  Aligned_cols=85  Identities=19%  Similarity=0.246  Sum_probs=79.3

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|..|.|+.+..++.++|||||+|.+.++|..||..++ ..|.|+.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   80 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAY----GPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRML   80 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTT----SCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            3467899999999999999999999999    899999999998899999999999999999999998887 99999999


Q ss_pred             EEEeeecCCC
Q 008920          412 RLSHAQQNCT  421 (548)
Q Consensus       412 ~V~~Ak~~~~  421 (548)
                      .|.|+.+...
T Consensus        81 ~V~~a~~~~~   90 (99)
T 1whw_A           81 HVLPSTIKKE   90 (99)
T ss_dssp             EEEECCCCST
T ss_pred             EEEEcCCCcc
Confidence            9999988643

>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=99.67  E-value=4.4e-16  Score=167.27  Aligned_cols=81  Identities=19%  Similarity=0.295  Sum_probs=72.4

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||+.||+++|..+|+.||.|..|.|+.+..                 ++.++|||||+|.+.++|..|| .
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~-----------------tg~~kG~aFV~F~~~e~A~~Ai~~  163 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKR-----------------SGKPRGYAFIEYEHERDMHSAYKH  163 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCC-----------------CCCccceEEEeeccHHHHHHHHHH
Confidence            457999999999999999999999999999999965432                 3457899999999999999999 6


Q ss_pred             hcceeecCceeEeecCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~  321 (548)
                      |||..|.|+.|.|.++.+.
T Consensus       164 lng~~i~gr~i~V~~a~~~  182 (437)
T 3pgw_S          164 ADGKKIDGRRVLVDVERGR  182 (437)
T ss_pred             cCCCEECCEEEEEEEeCCC
Confidence            9999999999999998753

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=4.7e-16  Score=130.93  Aligned_cols=83  Identities=18%  Similarity=0.454  Sum_probs=78.1

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      +.++|||+|||+.+++++|+++|+.|    |.|..|.|+.+..++.++|||||+|.+.++|..||..++ ..|.|+.|+|
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~----G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   79 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPF----GKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRV   79 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTT----SCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhc----CCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEE
Confidence            56899999999999999999999999    899999999999999999999999999999999999777 9999999999


Q ss_pred             EeeecCCC
Q 008920          414 SHAQQNCT  421 (548)
Q Consensus       414 ~~Ak~~~~  421 (548)
                      .|+.++..
T Consensus        80 ~~a~~~~~   87 (95)
T 2dnz_A           80 GHVTERLD   87 (95)
T ss_dssp             EESSCCCC
T ss_pred             EEcccccC
Confidence            99987543

>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=2.5e-16  Score=134.91  Aligned_cols=86  Identities=28%  Similarity=0.383  Sum_probs=79.9

Q ss_pred             CcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCe
Q 008920          331 PLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDR  409 (548)
Q Consensus       331 ~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr  409 (548)
                      +.....++|||+|||+.+++++|+++|..|    |.|..|.|+.+..++.++|||||+|.+.++|..||..|+ ..|.|+
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   83 (103)
T 2dnm_A            8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKY----GRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGR   83 (103)
T ss_dssp             SCCSCCCEEEEESCCTTCCHHHHHHHHTTT----SCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTB
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCc
Confidence            345567999999999999999999999999    899999999999999999999999999999999999777 999999


Q ss_pred             EEEEEeeecCC
Q 008920          410 ELRLSHAQQNC  420 (548)
Q Consensus       410 ~I~V~~Ak~~~  420 (548)
                      .|.|.|+.+..
T Consensus        84 ~l~V~~a~~~~   94 (103)
T 2dnm_A           84 ELRVQVARYGR   94 (103)
T ss_dssp             CCEEEECSSCC
T ss_pred             EEEEEECCcCC
Confidence            99999998753

>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=99.66  E-value=4.5e-16  Score=127.62  Aligned_cols=80  Identities=24%  Similarity=0.380  Sum_probs=76.0

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLS  414 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~  414 (548)
                      +.+|||+|||+.+++++|+++|+.|    |.|..|.|+.++.+|.++|||||+|.+.++|..|+..++ ..|.|+.|+|.
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~----G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   76 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDF----PSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN   76 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTS----TTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhc----CCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEE
Confidence            3689999999999999999999999    899999999999999999999999999999999999877 99999999999


Q ss_pred             eeecC
Q 008920          415 HAQQN  419 (548)
Q Consensus       415 ~Ak~~  419 (548)
                      |+.++
T Consensus        77 ~a~~~   81 (83)
T 3md1_A           77 WAAKL   81 (83)
T ss_dssp             ECCCC
T ss_pred             ecCcC
Confidence            99875

>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=99.66  E-value=3.8e-16  Score=129.24  Aligned_cols=82  Identities=23%  Similarity=0.343  Sum_probs=75.4

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      .+.++|||+|||+.+++++|+++|+.|    |.|..|.|+.++.++.++|||||+|.+.++|..||..++ ..|.|+.|.
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   79 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPF----GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIR   79 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhc----CCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            356899999999999999999999999    899999999998899999999999999999999999877 999999999


Q ss_pred             EEeeecC
Q 008920          413 LSHAQQN  419 (548)
Q Consensus       413 V~~Ak~~  419 (548)
                      |.|+.++
T Consensus        80 v~~a~~k   86 (87)
T 3bs9_A           80 TNWATRK   86 (87)
T ss_dssp             EEEEC--
T ss_pred             EEecCCC
Confidence            9999864

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=4.2e-16  Score=133.14  Aligned_cols=86  Identities=21%  Similarity=0.435  Sum_probs=79.9

Q ss_pred             cCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeE
Q 008920          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE  410 (548)
Q Consensus       332 ~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~  410 (548)
                      .....++|||+|||+.+++++|+++|..|    |.|..|.|+.++.++.++|||||+|.+.++|..||..|+ ..|.|+.
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   83 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKY----GQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQ   83 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHH----SCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhc----CCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            34567999999999999999999999999    899999999999999999999999999999999998877 9999999


Q ss_pred             EEEEeeecCCC
Q 008920          411 LRLSHAQQNCT  421 (548)
Q Consensus       411 I~V~~Ak~~~~  421 (548)
                      |+|.|+.+...
T Consensus        84 l~v~~a~~~~~   94 (102)
T 1x5s_A           84 IRVDQAGKSSD   94 (102)
T ss_dssp             CEEEEEECCCC
T ss_pred             EEEEECCCCCC
Confidence            99999997643

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=2.8e-16  Score=134.19  Aligned_cols=86  Identities=22%  Similarity=0.343  Sum_probs=79.7

Q ss_pred             cCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeE
Q 008920          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE  410 (548)
Q Consensus       332 ~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~  410 (548)
                      ...+.++|||+|||+.+++++|+++|..|    |.|..|.|+.+..++.++|||||+|.+.++|..||..|+ ..|.|+.
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   83 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPF----GDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRT   83 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTT----SCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhcc----CCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            34567999999999999999999999999    899999999999999999999999999999999998877 9999999


Q ss_pred             EEEEeeecCCC
Q 008920          411 LRLSHAQQNCT  421 (548)
Q Consensus       411 I~V~~Ak~~~~  421 (548)
                      |.|.|+.+...
T Consensus        84 l~V~~a~~~~~   94 (102)
T 2cqb_A           84 IRVNLAKPMRI   94 (102)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEeCCCCCC
Confidence            99999987643

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=2.7e-16  Score=132.67  Aligned_cols=83  Identities=23%  Similarity=0.432  Sum_probs=78.0

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEE-EEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAV-RVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~V-rI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      +.++|||+|||+.+++++|+++|+.|    |.|..| .|+.++.++.++|||||+|.+.++|..||..|+ ..|.|+.|.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   79 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAF----GVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPIT   79 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTT----SCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc----CCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            56899999999999999999999999    899999 999998999999999999999999999999877 999999999


Q ss_pred             EEeeecCCC
Q 008920          413 LSHAQQNCT  421 (548)
Q Consensus       413 V~~Ak~~~~  421 (548)
                      |.|+.+...
T Consensus        80 v~~a~~~~~   88 (96)
T 1x5t_A           80 VSYAFKKDS   88 (96)
T ss_dssp             EEESCCCCC
T ss_pred             EEEecccCC
Confidence            999987643

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.66  E-value=1e-16  Score=136.80  Aligned_cols=82  Identities=16%  Similarity=0.308  Sum_probs=74.6

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCC--CeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-C----c
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLES--SVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-L----K  405 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G--~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~----~  405 (548)
                      ...-.+|||+|||+.+|+++|+++|++|    |  .|.+|+|++|+.+|.++|||||+|.+.++|..||+.++ .    .
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~----G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~   81 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPY----ASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLK   81 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTT----CCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEE
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhh----CCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCce
Confidence            3456799999999999999999999999    6  46799999999999999999999999999999998876 3    5


Q ss_pred             cCCeEEEEEeeec
Q 008920          406 LRDRELRLSHAQQ  418 (548)
Q Consensus       406 l~Gr~I~V~~Ak~  418 (548)
                      |+|++|.|.||+.
T Consensus        82 i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           82 IDGKTIGVDFAKS   94 (95)
T ss_dssp             ETTEEEEEEECCC
T ss_pred             ECCEEEEEEEccC
Confidence            8999999999975

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=7.4e-16  Score=134.91  Aligned_cols=87  Identities=24%  Similarity=0.399  Sum_probs=80.7

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELR  412 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~  412 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|..|.|+.+..++.++|||||+|.+.++|..||..++..|.|+.|.
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~   89 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGF----GDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKAN   89 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTT----SCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhC----CCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCCcCCCEEEE
Confidence            4567999999999999999999999999    899999999999999999999999999999999999998889999999


Q ss_pred             EEeeecCCCCC
Q 008920          413 LSHAQQNCTPS  423 (548)
Q Consensus       413 V~~Ak~~~~~~  423 (548)
                      |.|+.+...+.
T Consensus        90 V~~a~~~~~~~  100 (116)
T 2cqd_A           90 VNLAYLGAKPR  100 (116)
T ss_dssp             EEESTTTCCCC
T ss_pred             EEEcccCCCcc
Confidence            99998765443

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.66  E-value=3e-16  Score=139.28  Aligned_cols=86  Identities=15%  Similarity=0.182  Sum_probs=79.9

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+.+|..|    |.|..|.|+.+..++.++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   94 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEY----GEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPI   94 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTT----SCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEE
Confidence            4457899999999999999999999999    899999999998899999999999999999999998777 99999999


Q ss_pred             EEEeeecCCCC
Q 008920          412 RLSHAQQNCTP  422 (548)
Q Consensus       412 ~V~~Ak~~~~~  422 (548)
                      .|.|+.+...+
T Consensus        95 ~v~~a~~~~~~  105 (126)
T 3ex7_B           95 SVDWCFVRGPP  105 (126)
T ss_dssp             EEEESEESSSC
T ss_pred             EEEEecCCCCC
Confidence            99999986544

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=5.7e-16  Score=132.65  Aligned_cols=84  Identities=23%  Similarity=0.326  Sum_probs=79.3

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|+.|    |.|..|.|+.++.++.++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   87 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPF----GSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLIL   87 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTT----CCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhC----CCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEE
Confidence            4567999999999999999999999999    899999999999899999999999999999999999887 99999999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      .|.|+.+..
T Consensus        88 ~v~~a~~~~   96 (103)
T 2cq0_A           88 NVEWAKPST   96 (103)
T ss_dssp             EEEESSCCC
T ss_pred             EEEECCCCC
Confidence            999998764

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.65  E-value=8e-16  Score=138.84  Aligned_cols=86  Identities=21%  Similarity=0.409  Sum_probs=79.8

Q ss_pred             cCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeE
Q 008920          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE  410 (548)
Q Consensus       332 ~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~  410 (548)
                      .....++|||+|||+.+++++|+++|+.|    |.|..|.|+.+..++.++|||||+|.+.++|..||..++ ..|.|+.
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~  113 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERY----GPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKR  113 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHH----SCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            34567899999999999999999999999    899999999999999999999999999999999999887 8999999


Q ss_pred             EEEEeeecCCC
Q 008920          411 LRLSHAQQNCT  421 (548)
Q Consensus       411 I~V~~Ak~~~~  421 (548)
                      |.|.|+.+...
T Consensus       114 l~v~~a~~~~~  124 (139)
T 1u6f_A          114 LKVALAASGHQ  124 (139)
T ss_dssp             EEEEESSCCCC
T ss_pred             EEEEECCCCCC
Confidence            99999987643

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.65  E-value=5.5e-16  Score=135.54  Aligned_cols=85  Identities=16%  Similarity=0.324  Sum_probs=79.0

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+++++++|+++|..|    |.|..|.|+.+..++.++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   97 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPF----GNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRL   97 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGG----SCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            3456899999999999999999999999    899999999999899999999999999999999998877 99999999


Q ss_pred             EEEeeecCCC
Q 008920          412 RLSHAQQNCT  421 (548)
Q Consensus       412 ~V~~Ak~~~~  421 (548)
                      +|.|+.+...
T Consensus        98 ~V~~a~~~~~  107 (115)
T 2cpz_A           98 KVQLKRSKND  107 (115)
T ss_dssp             EEECCCCSCC
T ss_pred             EEEEcCCCCc
Confidence            9999987643

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=5.5e-16  Score=131.41  Aligned_cols=83  Identities=16%  Similarity=0.356  Sum_probs=77.1

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCC---CCCCceEEEEEECCHHHHHHHHHHcC-CccCCeE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPH---MRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE  410 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~---tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~  410 (548)
                      +.++|||+|||+.+++++|+++|+.|    |.|..|.|+.+..   ++.++|||||+|.+.++|..||..|+ ..|.|+.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   79 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKV----GAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHK   79 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTT----SCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeE
Confidence            56899999999999999999999999    8999999999876   66899999999999999999999887 9999999


Q ss_pred             EEEEeeecCCC
Q 008920          411 LRLSHAQQNCT  421 (548)
Q Consensus       411 I~V~~Ak~~~~  421 (548)
                      |.|.|+.+...
T Consensus        80 l~V~~a~~~~~   90 (98)
T 2cpf_A           80 LEVRISERATK   90 (98)
T ss_dssp             CEEECSSCSSC
T ss_pred             EEEEEccCCCC
Confidence            99999987643

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.65  E-value=1.7e-16  Score=133.75  Aligned_cols=81  Identities=14%  Similarity=0.206  Sum_probs=70.5

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcC-CeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFG-EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-  302 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG-~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-  302 (548)
                      +++|||+|||+++|+++|+++|+.|| .|.+|+|+.++                 .+|.++|||||+|.+.++|..||+ 
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-----------------SSGQSRGFAFVEFSHLQDATRWMEA   63 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCS-----------------SSCCCSSEEEEECSSHHHHHHHHHT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecC-----------------CCCCcCceEEEEecCHHHHHHHHHh
Confidence            36899999999999999999999999 89999885543                 235688999999999999999995 


Q ss_pred             h-cceeecCceeEeecCCCcc
Q 008920          303 F-NMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       303 l-ng~~~~gr~I~V~~a~~~~  322 (548)
                      + ++..|.|+.|.|.++.+..
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 5778999999999997654

>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=99.65  E-value=1.1e-16  Score=134.09  Aligned_cols=81  Identities=14%  Similarity=0.229  Sum_probs=71.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCC--CeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLES--SVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G--~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      .+|||+|||+++++++|+++|+.|    |  .|..|.|+.++.+|.++|||||+|.+.++|..||+.++ ..|.|+.|.|
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~----G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V   77 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSL----GVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVV   77 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTT----TCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHh----CCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEE
Confidence            579999999999999999999999    8  99999999999999999999999999999999998887 9999999999


Q ss_pred             EeeecCCC
Q 008920          414 SHAQQNCT  421 (548)
Q Consensus       414 ~~Ak~~~~  421 (548)
                      .++.+...
T Consensus        78 ~~~~~~~~   85 (90)
T 3p5t_L           78 TPSNKLEH   85 (90)
T ss_dssp             CCC-----
T ss_pred             EECCCCcc
Confidence            99987643

>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=99.65  E-value=6.3e-16  Score=128.19  Aligned_cols=80  Identities=20%  Similarity=0.426  Sum_probs=75.6

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELR  412 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~  412 (548)
                      ....++|||+|||+.+++++|+++|+.|    |.|..|.|+.++.+|.++|||||+|.+.++|..||..++..|.|+.|.
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~   83 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKF----GEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVID   83 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTT----SCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhC----CCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEE
Confidence            4567899999999999999999999999    899999999999999999999999999999999998877889999999


Q ss_pred             EEee
Q 008920          413 LSHA  416 (548)
Q Consensus       413 V~~A  416 (548)
                      |.+|
T Consensus        84 v~~A   87 (87)
T 3s7r_A           84 PKKA   87 (87)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9986

>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=99.65  E-value=4.7e-16  Score=128.12  Aligned_cols=81  Identities=23%  Similarity=0.374  Sum_probs=76.2

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|.|+.+..++.++|||||+|.+.++|..|+..++ ..|.|+.|
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   79 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPF----GDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI   79 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGG----SCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcc----CCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            3467899999999999999999999999    899999999999999999999999999999999998777 99999999


Q ss_pred             EEEeee
Q 008920          412 RLSHAQ  417 (548)
Q Consensus       412 ~V~~Ak  417 (548)
                      +|.||+
T Consensus        80 ~v~~ak   85 (85)
T 3mdf_A           80 RVNLAK   85 (85)
T ss_dssp             EEEECC
T ss_pred             EEEEcC
Confidence            999985

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=7.7e-16  Score=132.40  Aligned_cols=84  Identities=14%  Similarity=0.156  Sum_probs=78.7

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|+.|    |.|..|.|+.+..+|.++|||||+|.+.++|..||..++ ..|.|+.|
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   95 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEY----GEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPI   95 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcc----CCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEE
Confidence            3457899999999999999999999999    899999999999999999999999999999999999777 99999999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      .|.|+.+..
T Consensus        96 ~V~~a~~~~  104 (106)
T 1p27_B           96 SVDWCFVRG  104 (106)
T ss_dssp             EEEESEESS
T ss_pred             EEEeecCCC
Confidence            999998753

>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=7.9e-16  Score=132.10  Aligned_cols=84  Identities=24%  Similarity=0.370  Sum_probs=79.1

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|+.|    |.|..|.|+.+..++.++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   87 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQA----GPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPI   87 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTT----SCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            4567899999999999999999999999    899999999998899999999999999999999999888 99999999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      .|.|+.+..
T Consensus        88 ~v~~a~~~~   96 (105)
T 1x5u_A           88 RVNKASAHN   96 (105)
T ss_dssp             EEEETTTTS
T ss_pred             EEEECCCCC
Confidence            999998753

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.65  E-value=3.2e-16  Score=133.72  Aligned_cols=98  Identities=21%  Similarity=0.365  Sum_probs=81.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-hc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-FN  304 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-ln  304 (548)
                      ++|||+|||+++|+++|+++|+.||.|..|.|+.+                      ++|||||+|.+.++|..|+. ||
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            48999999999999999999999999999998432                      35899999999999999995 99


Q ss_pred             ceeecCceeEeecCCCcccccCCCC-CCcCCCccEEEEeCCC
Q 008920          305 MAVIGGNHIRLDRACPPRKKLKGED-APLYDIKKTVFVGNLP  345 (548)
Q Consensus       305 g~~~~gr~I~V~~a~~~~k~~~~~~-~~~~~~~~tLfV~NLp  345 (548)
                      +..|.|+.|.|.++.+......... ........+|||+||+
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            9999999999999987553322221 1222346789999997

>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=8.7e-16  Score=133.02  Aligned_cols=86  Identities=33%  Similarity=0.467  Sum_probs=79.1

Q ss_pred             cCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHc-------CC
Q 008920          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR-------NL  404 (548)
Q Consensus       332 ~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~l-------n~  404 (548)
                      .....++|||+|||+.+++++|+++|..|    |.|..|.|+.+..++.++|||||+|.+.++|..||..+       +.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~   86 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQF----GDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGL   86 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTT----SCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCE
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhc----CCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCc
Confidence            34567899999999999999999999999    89999999999999999999999999999999999876       57


Q ss_pred             ccCCeEEEEEeeecCCC
Q 008920          405 KLRDRELRLSHAQQNCT  421 (548)
Q Consensus       405 ~l~Gr~I~V~~Ak~~~~  421 (548)
                      .|.|+.|.|.|+.+...
T Consensus        87 ~~~g~~l~v~~a~~~~~  103 (111)
T 1x4h_A           87 KLDGRQLKVDLAVTRDE  103 (111)
T ss_dssp             ESSSCEEEEECCCCCCC
T ss_pred             EEcCEEEEEEECCCCcc
Confidence            89999999999987643

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=8.6e-16  Score=132.17  Aligned_cols=86  Identities=24%  Similarity=0.410  Sum_probs=79.6

Q ss_pred             cCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeec-CCCCCCceEEEEEECCHHHHHHHHHHc-C-CccCC
Q 008920          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRH-PHMRVGKGIAYVLFKTREAANLVIKRR-N-LKLRD  408 (548)
Q Consensus       332 ~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d-~~tg~srG~AFV~F~~~e~A~~Al~~l-n-~~l~G  408 (548)
                      .....++|||+|||+.+++++|+++|..|    |.|..|.|+.+ ..++.++|||||+|.+.++|..||..| + ..|.|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g   86 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTF----GELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYG   86 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTT----SCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSS
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHcc----CCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECC
Confidence            34567999999999999999999999999    89999999999 789999999999999999999999988 6 99999


Q ss_pred             eEEEEEeeecCCC
Q 008920          409 RELRLSHAQQNCT  421 (548)
Q Consensus       409 r~I~V~~Ak~~~~  421 (548)
                      +.|.|.|+.+...
T Consensus        87 ~~l~v~~a~~~~~   99 (107)
T 2cph_A           87 RRLVLEWADSEVT   99 (107)
T ss_dssp             CBCEEEECCCCCC
T ss_pred             CEEEEEeCCCCCC
Confidence            9999999987643

>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=99.65  E-value=2.1e-16  Score=138.14  Aligned_cols=101  Identities=18%  Similarity=0.273  Sum_probs=88.2

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-  302 (548)
                      ..++|||+|||+++++++|..+|+.||.|.+|.|+.+                    +.++|||||+|.+.++|..|+. 
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~--------------------~~~~g~afV~f~~~~~A~~A~~~   66 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--------------------PETRGTAYVVYEDIFDAKNAVDH   66 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--------------------TTTTTCEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--------------------CCCCcEEEEEECCHHHHHHHHHH
Confidence            4589999999999999999999999999999998532                    2357999999999999999995 


Q ss_pred             hcceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccC
Q 008920          303 FNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLN  361 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g  361 (548)
                      |||..|.|+.|.|.++.+....                 .+++...++++|.++|..||
T Consensus        67 l~g~~~~g~~l~v~~a~~~~~~-----------------~~~~~~~~~~~l~~~~~~~g  108 (115)
T 3lqv_A           67 LSGFNVSNRYLVVLYYNANRAF-----------------QKMDTKKKEEQLKLLKEKYG  108 (115)
T ss_dssp             HTTCBSSSCBCEEEECCHHHHT-----------------TTSCHHHHHHHHHHHHHHHC
T ss_pred             cCCCEECCeEEEEEEecCChhh-----------------hhhhHhHhHHHHHHHHHHhC
Confidence            9999999999999999754321                 56778889999999999994

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.64  E-value=1.3e-15  Score=130.58  Aligned_cols=82  Identities=30%  Similarity=0.470  Sum_probs=76.6

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ..+.++|||+|||+.+++++|+++|..|    | |..|.|+.+..++.++|||||+|.+.++|..|| .|+ ..|.|+.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l   85 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDL----S-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSL   85 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTS----C-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhC----C-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEE
Confidence            4567999999999999999999999999    7 999999999999999999999999999999999 666 99999999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      .|.|+.+..
T Consensus        86 ~V~~a~~~~   94 (103)
T 2dng_A           86 RVDIAEGRK   94 (103)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEecCCC
Confidence            999998753

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=8e-16  Score=131.82  Aligned_cols=83  Identities=25%  Similarity=0.378  Sum_probs=77.5

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhc-cCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-Cc-cCCe
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCG-LNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LK-LRDR  409 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~-~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~-l~Gr  409 (548)
                      ..+.++|||+|||+.+++++|+++|.. |    |.|..|.|+.+. +|.++|||||+|.+.++|..||..++ .. |.|+
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~----G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~   80 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVY----PSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSK   80 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHC----TTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhC----CCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCE
Confidence            456789999999999999999999999 9    899999999998 99999999999999999999999888 77 9999


Q ss_pred             EEEEEeeecCC
Q 008920          410 ELRLSHAQQNC  420 (548)
Q Consensus       410 ~I~V~~Ak~~~  420 (548)
                      .|.|.|+.+..
T Consensus        81 ~l~v~~a~~~~   91 (104)
T 2dhg_A           81 PVRLSVAIPKA   91 (104)
T ss_dssp             CCCCCBCCCCC
T ss_pred             eEEEEEccCCC
Confidence            99999998754

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1e-15  Score=128.76  Aligned_cols=82  Identities=21%  Similarity=0.357  Sum_probs=77.5

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|.|+.++.++.++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~----G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   87 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKY----GPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI   87 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTT----SCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhc----CCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            4567899999999999999999999999    899999999999999999999999999999999999877 99999999


Q ss_pred             EEEeeec
Q 008920          412 RLSHAQQ  418 (548)
Q Consensus       412 ~V~~Ak~  418 (548)
                      .|.|+.+
T Consensus        88 ~v~~a~~   94 (95)
T 2cqc_A           88 RVSGPSS   94 (95)
T ss_dssp             EEECCSC
T ss_pred             EEEecCC
Confidence            9999874

>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=1.3e-15  Score=130.31  Aligned_cols=83  Identities=20%  Similarity=0.297  Sum_probs=77.1

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|..|.|+.+  ++.++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   85 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPF----GTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPL   85 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTT----SCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEE
Confidence            4467899999999999999999999999    89999999998  89999999999999999999999877 99999999


Q ss_pred             EEEeeecCCC
Q 008920          412 RLSHAQQNCT  421 (548)
Q Consensus       412 ~V~~Ak~~~~  421 (548)
                      .|.|+.+...
T Consensus        86 ~V~~a~~~~~   95 (103)
T 2d9p_A           86 YVALAQRKEE   95 (103)
T ss_dssp             EEEECSSCCC
T ss_pred             EEEEeccccc
Confidence            9999987643

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=1.5e-15  Score=129.34  Aligned_cols=83  Identities=18%  Similarity=0.398  Sum_probs=77.3

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|..|.|+.+. +|.++|||||+|.+.++|..||..++ ..|.|+.|
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   88 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAH----GTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENII   88 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTT----SCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhC----CCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            4457899999999999999999999999    899999999997 89999999999999999999998877 99999999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      .|.|+.+..
T Consensus        89 ~v~~a~~~~   97 (100)
T 2do4_A           89 KVAISNSGP   97 (100)
T ss_dssp             EEEECCCCS
T ss_pred             EEEECCCCC
Confidence            999998753

>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=99.63  E-value=8.3e-16  Score=130.06  Aligned_cols=81  Identities=22%  Similarity=0.476  Sum_probs=76.9

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      +.++|||+|||+.+++++|+++|+.|    |.|..|.|+.+..+|.++|||||+|.+.++|..|+..++ ..|.|+.|.|
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   76 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNV----GPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKC   76 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTT----SCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhc----CCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            35799999999999999999999999    899999999999999999999999999999999998777 9999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      .|+.+.
T Consensus        77 ~~a~~~   82 (96)
T 2x1f_A           77 GYSSNS   82 (96)
T ss_dssp             EECSCS
T ss_pred             EEcCCC
Confidence            999875

>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=8.9e-16  Score=133.61  Aligned_cols=84  Identities=18%  Similarity=0.345  Sum_probs=77.1

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELR  412 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~  412 (548)
                      ....++|||+|||+.+++++|+++|+.|    |.|..|.|+.+..+|.++|||||+|.+.++|..||..++..|.|+.|.
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~----G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~   97 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQF----GEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTID   97 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTT----SCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcc----CCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEE
Confidence            3457899999999999999999999999    899999999999999999999999999999999999999999999999


Q ss_pred             EEeeecCC
Q 008920          413 LSHAQQNC  420 (548)
Q Consensus       413 V~~Ak~~~  420 (548)
                      |.++.+..
T Consensus        98 V~~a~~~~  105 (109)
T 2rs2_A           98 PKVAFPRR  105 (109)
T ss_dssp             EEECCCCC
T ss_pred             EEEccCCC
Confidence            99998754

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=1e-15  Score=128.62  Aligned_cols=81  Identities=30%  Similarity=0.539  Sum_probs=76.6

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|.|+.++.++.++|||||+|.+.++|..||..++ ..|.|+.|
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~----G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   88 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKY----GKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVI   88 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTT----SCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhc----CCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEE
Confidence            4567899999999999999999999999    899999999999999999999999999999999998887 99999999


Q ss_pred             EEEeee
Q 008920          412 RLSHAQ  417 (548)
Q Consensus       412 ~V~~Ak  417 (548)
                      +|.||+
T Consensus        89 ~v~~ak   94 (94)
T 2e5h_A           89 KASIAI   94 (94)
T ss_dssp             EEEECC
T ss_pred             EEEecC
Confidence            999985

>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=99.63  E-value=2.3e-15  Score=128.85  Aligned_cols=85  Identities=16%  Similarity=0.253  Sum_probs=78.2

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELR  412 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~  412 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|..|.|+.++.++.++|||||+|.+.++|..||.. +..|.|+.|.
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~g~~l~   86 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTF----GEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ-RHMIDGRWCD   86 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGG----SCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS-CEEETTEEEE
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhc----CCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc-CCeeCCeEEE
Confidence            4467899999999999999999999999    8999999999999999999999999999999999984 5789999999


Q ss_pred             EEeeecCCCC
Q 008920          413 LSHAQQNCTP  422 (548)
Q Consensus       413 V~~Ak~~~~~  422 (548)
                      |.|+.+...+
T Consensus        87 v~~a~~~~~~   96 (103)
T 2cqg_A           87 CKLPNSKQSQ   96 (103)
T ss_dssp             EECCCTTCCC
T ss_pred             EEecCCCCcC
Confidence            9999886443

>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=99.63  E-value=1.1e-15  Score=126.62  Aligned_cols=80  Identities=29%  Similarity=0.397  Sum_probs=71.2

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      +...++|||+|||+++++++|.++|+.||.|..|.|+.++.                 +|.++|||||+|.+.++|..||
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-----------------TGRSRGFGFILFKDAASVEKVL   70 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTT-----------------TCCEEEEEEEEESSTHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCC-----------------CCccccEEEEEECCHHHHHHHH
Confidence            34568999999999999999999999999999999966542                 3457899999999999999999


Q ss_pred             HhcceeecCceeEeecC
Q 008920          302 AFNMAVIGGNHIRLDRA  318 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a  318 (548)
                      .+++..|.|+.|.|.++
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            98999999999999875

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=1.4e-15  Score=130.50  Aligned_cols=82  Identities=33%  Similarity=0.515  Sum_probs=76.2

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCC-CCCceEEEEEECCHHHHHHHHHHcC-CccCCeE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM-RVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE  410 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~t-g~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~  410 (548)
                      ..+.++|||+|||+.+++++|+++|..|    | |..|.|+.+..+ +.++|||||+|.+.++|..|| .++ ..|.|+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~   85 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGL----N-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKR   85 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTS----C-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHC----C-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcE
Confidence            3457999999999999999999999999    9 999999999887 999999999999999999999 666 9999999


Q ss_pred             EEEEeeecCC
Q 008920          411 LRLSHAQQNC  420 (548)
Q Consensus       411 I~V~~Ak~~~  420 (548)
                      |.|.|+.+..
T Consensus        86 l~V~~a~~~~   95 (104)
T 1wi8_A           86 IRVDVADQAQ   95 (104)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEEccCCC
Confidence            9999998753

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.63  E-value=1.1e-15  Score=133.63  Aligned_cols=80  Identities=20%  Similarity=0.279  Sum_probs=72.6

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||+++++++|.++|+.||.|.+|.|+.++.                 ++.++|||||+|.+.++|..|| .
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~-----------------tg~~rG~aFV~f~~~~~A~~Ai~~   67 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPR-----------------TRKHLGLARVLFTSTRGAKETVKN   67 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTT-----------------TCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCC-----------------CCceeeEEEEEECCHHHHHHHHHH
Confidence            458999999999999999999999999999999976552                 3558899999999999999999 5


Q ss_pred             hcceeecCceeEeecCCC
Q 008920          303 FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~  320 (548)
                      |||..|.|+.|.|.++..
T Consensus        68 lng~~~~gr~i~V~~a~~   85 (110)
T 3s8s_A           68 LHLTSVMGNIIHAQLDIK   85 (110)
T ss_dssp             HTTCEETTEECEEEECST
T ss_pred             hCCCEECCeEEEEEECCC
Confidence            999999999999999864

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=6.5e-16  Score=133.57  Aligned_cols=80  Identities=11%  Similarity=0.123  Sum_probs=71.7

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++|+++|.++|+.||.|.+|+|+.++                  .|.++|||||+|.+.++|..||.
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 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL------------------HKAFKGSIFVVFDSIESAKKFVE   70 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCC------------------TTSCCCEEEEEESSHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECC------------------CCCCccEEEEEECCHHHHHHHHH
Confidence            345899999999999999999999999999999996644                  14578999999999999999999


Q ss_pred             hcceeecCceeEeecCCC
Q 008920          303 FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~  320 (548)
                      +++..|.|+.|.|.++..
T Consensus        71 ~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A           71 TPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             SSCCCCTTTTCEEEEHHH
T ss_pred             cCCCEECCEEEEEEEchH
Confidence            999999999999998653

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=2.2e-15  Score=128.07  Aligned_cols=83  Identities=27%  Similarity=0.404  Sum_probs=74.0

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++++++|+++|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|..||.
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----------------~~~~~g~afV~f~~~~~a~~A~~   70 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAE-----------------KQRPRGFGFITFEDEQSVDQAVN   70 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTT-----------------TCSCCSEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCC-----------------CCCCCceEEEEECCHHHHHHHHH
Confidence            4568999999999999999999999999999999965431                 34578999999999999999999


Q ss_pred             hcceeecCceeEeecCCCcc
Q 008920          303 FNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~~  322 (548)
                      ||+..|.|+.|.|.++.+..
T Consensus        71 ~~~~~~~g~~l~V~~a~~~~   90 (99)
T 2dgs_A           71 MHFHDIMGKKVEVKRAEPRD   90 (99)
T ss_dssp             HCCCBSSSCBCEEEECCCCC
T ss_pred             hCCCEECCeEEEEEECCCCc
Confidence            99999999999999998654

>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=99.62  E-value=1.4e-15  Score=131.72  Aligned_cols=84  Identities=15%  Similarity=0.238  Sum_probs=78.6

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+.+|+.|    |.|..|.|+.+..+|.++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   98 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDY----GEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTI   98 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGG----SCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEE
Confidence            4467899999999999999999999999    899999999999999999999999999999999999777 99999999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      .|.|+.+..
T Consensus        99 ~V~~a~~~~  107 (110)
T 1oo0_B           99 QVDWCFVKG  107 (110)
T ss_dssp             EEEESEESS
T ss_pred             EEEEcccCC
Confidence            999998753

>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=1.6e-15  Score=130.34  Aligned_cols=84  Identities=18%  Similarity=0.338  Sum_probs=77.7

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-Ccc---CC
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKL---RD  408 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l---~G  408 (548)
                      ....++|||+|||+.+++++|+++|+.|    |.|..|.|+.++.++.++|||||+|.+.++|..||..|+ ..+   .|
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g   85 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEF----GKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMN   85 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHH----SCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCC
Confidence            4467899999999999999999999999    899999999999999999999999999999999999887 666   88


Q ss_pred             eEEEEEeeecCC
Q 008920          409 RELRLSHAQQNC  420 (548)
Q Consensus       409 r~I~V~~Ak~~~  420 (548)
                      +.|.|.|+.+..
T Consensus        86 ~~l~v~~a~~~~   97 (106)
T 2dgp_A           86 RPIQVKPADSES   97 (106)
T ss_dssp             SCCEEEECCCCS
T ss_pred             ceEEEEECCccc
Confidence            999999998753

>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=99.62  E-value=2.3e-15  Score=138.78  Aligned_cols=83  Identities=24%  Similarity=0.386  Sum_probs=78.6

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|+.|    |.|..|.|+.+..++.++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l  111 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKS----GDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRII  111 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            3467899999999999999999999999    899999999999999999999999999999999999887 99999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      .|.|+.+.
T Consensus       112 ~V~~a~~~  119 (156)
T 1h2v_Z          112 RTDWDAGF  119 (156)
T ss_dssp             EEEEESCC
T ss_pred             EEEECCCC
Confidence            99999875

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=1.1e-15  Score=129.72  Aligned_cols=84  Identities=18%  Similarity=0.302  Sum_probs=78.5

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeE-EEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVE-AVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE  410 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~-~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~  410 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|. .|.|+.++.++.++|||||+|.+.++|..||..|+ ..|.|+.
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATM----GETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGAT   81 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHT----TCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCS
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHh----CCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCC
Confidence            4467999999999999999999999999    8999 99999999999999999999999999999999887 9999999


Q ss_pred             ----EEEEeeecCC
Q 008920          411 ----LRLSHAQQNC  420 (548)
Q Consensus       411 ----I~V~~Ak~~~  420 (548)
                          |+|.||.+..
T Consensus        82 ~~~~l~v~~a~~~~   95 (99)
T 2div_A           82 PAKRFKLNYATYSG   95 (99)
T ss_dssp             SCEECCEEETTCCS
T ss_pred             cceeEEEeecCCCC
Confidence                9999998753

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.62  E-value=2.5e-15  Score=128.92  Aligned_cols=84  Identities=23%  Similarity=0.345  Sum_probs=77.0

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCC---
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRD---  408 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~G---  408 (548)
                      ....++|||+|||+.+++++|+++|+.|    |.|..|.|+.+. +|.++|||||+|.+.++|..||..|+ ..|.|   
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~   86 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPF----GVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGAS   86 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTT----SCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCC
Confidence            3457999999999999999999999999    899999999997 79999999999999999999999887 77887   


Q ss_pred             eEEEEEeeecCCC
Q 008920          409 RELRLSHAQQNCT  421 (548)
Q Consensus       409 r~I~V~~Ak~~~~  421 (548)
                      +.|.|.|+.+...
T Consensus        87 ~~l~V~~a~~~~~   99 (105)
T 2dnh_A           87 SSLVVKFADTDKE   99 (105)
T ss_dssp             SCCEEEESCSSCC
T ss_pred             ccEEEEECccCcc
Confidence            9999999987643

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.62  E-value=3.3e-16  Score=134.15  Aligned_cols=81  Identities=19%  Similarity=0.184  Sum_probs=76.5

Q ss_pred             CccEEEEeCCCC------CCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccC
Q 008920          335 IKKTVFVGNLPF------DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLR  407 (548)
Q Consensus       335 ~~~tLfV~NLp~------~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~  407 (548)
                      ..++|||+|||+      .+++++|+++|+.|    |.|..|.|++++.||.++|||||+|.+.++|..||..|+ ..|.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~----G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~   80 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKA----GKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD   80 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTT----SCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSS
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhc----CCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccC
Confidence            368999999999      99999999999999    999999999999999999999999999999999998877 9999


Q ss_pred             C-eEEEEEeeecC
Q 008920          408 D-RELRLSHAQQN  419 (548)
Q Consensus       408 G-r~I~V~~Ak~~  419 (548)
                      | +.|.|.++.+.
T Consensus        81 g~r~l~V~~a~~~   93 (100)
T 3ns6_A           81 LKHRLFLYTMKDV   93 (100)
T ss_dssp             SSCBCEEEESHHH
T ss_pred             CCeEEEEEECchh
Confidence            9 99999999763

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=1.1e-15  Score=131.24  Aligned_cols=85  Identities=19%  Similarity=0.325  Sum_probs=78.8

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELR  412 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~  412 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|..|.|+.++.++.++|||||+|.+.++|..||...+..|.|+.|.
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~   88 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQY----GEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNID   88 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTT----SCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEE
Confidence            4567999999999999999999999999    899999999999999999999999999999999999844999999999


Q ss_pred             EEeeecCCC
Q 008920          413 LSHAQQNCT  421 (548)
Q Consensus       413 V~~Ak~~~~  421 (548)
                      |.|+.+...
T Consensus        89 V~~a~~~~~   97 (105)
T 2dh8_A           89 PKPCTPRGM   97 (105)
T ss_dssp             CCCSCCSSC
T ss_pred             EEEccCCCC
Confidence            999987643

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.62  E-value=2e-15  Score=123.78  Aligned_cols=79  Identities=20%  Similarity=0.301  Sum_probs=71.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-hc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-FN  304 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-ln  304 (548)
                      .+|||+|||+++++++|.++|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|..|+. ||
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-----------------TGSSRGYGFVSFTSQDDAQNAMDSMQ   64 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTT-----------------TCCEEEEEEEEESCHHHHHHHHHHHT
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCC-----------------CCCccceEEEEECCHHHHHHHHHHhc
Confidence            5899999999999999999999999999999966442                 34578999999999999999995 99


Q ss_pred             ceeecCceeEeecCCCc
Q 008920          305 MAVIGGNHIRLDRACPP  321 (548)
Q Consensus       305 g~~~~gr~I~V~~a~~~  321 (548)
                      |..|.|+.|.|.++.+.
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            99999999999998753

>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=1.6e-15  Score=128.97  Aligned_cols=82  Identities=20%  Similarity=0.222  Sum_probs=76.7

Q ss_pred             cCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEE--------EEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC
Q 008920          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEA--------VRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN  403 (548)
Q Consensus       332 ~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~--------VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln  403 (548)
                      ...+.++|||+|||+++++++|+++|+.|    |.|..        |.|+.++.+|.++|||||+|.+.++|..||..|+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~   84 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQI----GIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFD   84 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTT----SCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHh----CCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhC
Confidence            34567999999999999999999999999    89999        9999999999999999999999999999998777


Q ss_pred             -CccCCeEEEEEeee
Q 008920          404 -LKLRDRELRLSHAQ  417 (548)
Q Consensus       404 -~~l~Gr~I~V~~Ak  417 (548)
                       ..|.|+.|+|.||+
T Consensus        85 g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           85 GKEFSGNPIKVSFAT   99 (99)
T ss_dssp             TCBSSSSBCEEEECC
T ss_pred             CCEeCCcEEEEEecC
Confidence             99999999999984

>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=1.5e-15  Score=132.17  Aligned_cols=84  Identities=15%  Similarity=0.201  Sum_probs=78.1

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeE--------EEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVE--------AVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-  403 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~--------~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-  403 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|.        .|.|+.++.++.++|||||+|.+.++|..||..|+ 
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g   87 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQC----GVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDG   87 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTT----SCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTT
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhc----CCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCC
Confidence            4467899999999999999999999999    8998        69999999999999999999999999999999877 


Q ss_pred             CccCCeEEEEEeeecCC
Q 008920          404 LKLRDRELRLSHAQQNC  420 (548)
Q Consensus       404 ~~l~Gr~I~V~~Ak~~~  420 (548)
                      ..|.|+.|+|.|+.+..
T Consensus        88 ~~~~g~~l~V~~a~~~~  104 (113)
T 2cpe_A           88 KDFQGSKLKVSLARKKP  104 (113)
T ss_dssp             CEETTEECEEECSSCCC
T ss_pred             CccCCCEEEEEECCCCC
Confidence            99999999999998754

>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=99.61  E-value=1.8e-15  Score=132.81  Aligned_cols=78  Identities=24%  Similarity=0.480  Sum_probs=72.4

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLS  414 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~  414 (548)
                      ..+|||+|||+++++++|+++|+.|    |.|.+|+|+++.  +.++|||||+|.+.++|..||..|+ ..|.|+.|.|.
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~----G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~   78 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAF----GNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVG   78 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhcc----CCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            4689999999999999999999999    999999999985  4579999999999999999998877 99999999999


Q ss_pred             eeecC
Q 008920          415 HAQQN  419 (548)
Q Consensus       415 ~Ak~~  419 (548)
                      ++.+.
T Consensus        79 ~a~~~   83 (115)
T 4f25_A           79 RFKSR   83 (115)
T ss_dssp             ESSCC
T ss_pred             ECCCc
Confidence            99864

>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=99.61  E-value=4.4e-15  Score=127.10  Aligned_cols=82  Identities=23%  Similarity=0.358  Sum_probs=74.9

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|+.|    |.|..|.|+.+..+  ++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   85 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQI----GPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEV   85 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHH----SCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhc----CCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeE
Confidence            4567999999999999999999999999    89999999998543  68999999999999999999777 89999999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      .|.|+.+..
T Consensus        86 ~V~~a~~~~   94 (103)
T 2cqi_A           86 KVNWATTPS   94 (103)
T ss_dssp             EEEECCCTT
T ss_pred             EEEECCCCc
Confidence            999998754

>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=99.61  E-value=1.9e-15  Score=133.11  Aligned_cols=83  Identities=23%  Similarity=0.328  Sum_probs=73.7

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||+++++++|.++|+.||.|..|.|+.+.                  +|.++|||||+|.+.++|+.|| .
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------------------TSKSRGFAFITFENPADAKNAAKD   67 (116)
T ss_dssp             SCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST------------------TTTCCCEEEEECSSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC------------------CCCcccEEEEEECCHHHHHHHHHH
Confidence            45899999999999999999999999999999996543                  3457799999999999999999 5


Q ss_pred             hcceeecCceeEeecCCCcccc
Q 008920          303 FNMAVIGGNHIRLDRACPPRKK  324 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~~k~  324 (548)
                      ||+..|.|+.|.|.++.++...
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            9999999999999999866443

>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=99.61  E-value=5.6e-15  Score=126.45  Aligned_cols=84  Identities=20%  Similarity=0.396  Sum_probs=76.2

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|..|.|+.+..  .++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~----G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   85 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQF----GKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKI   85 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGT----SCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            4567999999999999999999999999    8999999999854  389999999999999999999877 99999999


Q ss_pred             EEEeeecCCCC
Q 008920          412 RLSHAQQNCTP  422 (548)
Q Consensus       412 ~V~~Ak~~~~~  422 (548)
                      .|.|+.+....
T Consensus        86 ~v~~a~~~~~~   96 (103)
T 2cq3_A           86 EVNNATARVMT   96 (103)
T ss_dssp             EEEECCSSCCC
T ss_pred             EEEEcccCCCC
Confidence            99999886443

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=6.6e-15  Score=128.18  Aligned_cols=82  Identities=23%  Similarity=0.276  Sum_probs=76.3

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|..|.|+.+. ++.++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~----G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   86 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMA----GVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPM   86 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTT----SCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEE
Confidence            4457899999999999999999999999    899999999996 69999999999999999999999777 99999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      .|.|+...
T Consensus        87 ~v~~a~~~   94 (114)
T 2do0_A           87 HVKMDERA   94 (114)
T ss_dssp             EEEECSCC
T ss_pred             EEEEcccC
Confidence            99999754

>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=99.61  E-value=2.2e-15  Score=125.07  Aligned_cols=79  Identities=24%  Similarity=0.462  Sum_probs=74.9

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLS  414 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~  414 (548)
                      .++|||+|||+.+++++|+++|+.|    |.|..|.|+.+..++.++|||||+|.+.++|..|+ .++ ..|.|+.|.|.
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~   80 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGC----GSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVI   80 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGG----CCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhC----CCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEE
Confidence            5799999999999999999999999    89999999999989999999999999999999999 666 99999999999


Q ss_pred             eeecC
Q 008920          415 HAQQN  419 (548)
Q Consensus       415 ~Ak~~  419 (548)
                      ++.+.
T Consensus        81 ~a~~~   85 (89)
T 3ucg_A           81 PKRTN   85 (89)
T ss_dssp             ETTTT
T ss_pred             EccCC
Confidence            99764

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=3e-15  Score=127.46  Aligned_cols=82  Identities=17%  Similarity=0.274  Sum_probs=73.2

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++|+++|.++|+.||.|..|.|+.+.                  ++.++|||||+|.+.++|..||
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------------------AGKPKGLAYVEYENESQASQAV   75 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT------------------TSCEEEEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC------------------CCCEEeEEEEEECCHHHHHHHH
Confidence            3456899999999999999999999999999999996643                  2447799999999999999999


Q ss_pred             -HhcceeecCceeEeecCCCc
Q 008920          302 -AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 -~lng~~~~gr~I~V~~a~~~  321 (548)
                       .||+..|.|+.|.|.++.++
T Consensus        76 ~~l~g~~~~g~~l~v~~a~~~   96 (100)
T 2do4_A           76 MKMDGMTIKENIIKVAISNSG   96 (100)
T ss_dssp             HHHTTEESSSCEEEEEECCCC
T ss_pred             HHhCCCEECCEEEEEEECCCC
Confidence             69999999999999999764

>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=99.61  E-value=3.2e-15  Score=126.89  Aligned_cols=83  Identities=16%  Similarity=0.197  Sum_probs=73.6

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...++|||+|||+++++++|+++|+.||.|..|.|+.+.                 .++.++|||||+|.+.++|..|| 
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-----------------LTKKPKGFAFVTFMFPEHAVKAYA   68 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCT-----------------TTCCCCSEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecC-----------------CCCCcCeEEEEEECCHHHHHHHHH
Confidence            346899999999999999999999999999999985433                 13457899999999999999999 


Q ss_pred             HhcceeecCceeEeecCCCcc
Q 008920          302 AFNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~~  322 (548)
                      .||+..|.|+.|.|.++.+..
T Consensus        69 ~l~g~~~~g~~l~V~~a~~~~   89 (99)
T 1whw_A           69 EVDGQVFQGRMLHVLPSTIKK   89 (99)
T ss_dssp             HTTTEESSSCEEEEEECCCCS
T ss_pred             HhCCCEECCcEEEEEEcCCCc
Confidence            799999999999999998654

>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=99.61  E-value=5.1e-15  Score=128.24  Aligned_cols=77  Identities=18%  Similarity=0.224  Sum_probs=71.4

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCC---
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRD---  408 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~G---  408 (548)
                      ....++|||+|||+++++++|+++|..|    |.|..|.|+.+       |||||+|.+.++|..||..|+ ..|.|   
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~   80 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREA----GDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEG   80 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGG----SCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcC
Confidence            4557899999999999999999999999    89999999877       799999999999999999888 88999   


Q ss_pred             --eEEEEEeeecCC
Q 008920          409 --RELRLSHAQQNC  420 (548)
Q Consensus       409 --r~I~V~~Ak~~~  420 (548)
                        +.|.|.++.++.
T Consensus        81 ~~~~i~V~~a~~~~   94 (108)
T 1x4c_A           81 ETAYIRVKVDGPRS   94 (108)
T ss_dssp             CEEEEEEEESSCCS
T ss_pred             cceEEEEEeCCCCC
Confidence              999999998854

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=2.8e-15  Score=128.33  Aligned_cols=84  Identities=20%  Similarity=0.218  Sum_probs=74.2

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++++++|.++|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|..||
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-----------------TGQSKGFAFISFHRREDAARAI   74 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSS-----------------SCSEEEEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCC-----------------CCceeeEEEEEECCHHHHHHHH
Confidence            34568999999999999999999999999999999966432                 3457799999999999999999


Q ss_pred             H-hcceeecCceeEeecCCCcc
Q 008920          302 A-FNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 ~-lng~~~~gr~I~V~~a~~~~  322 (548)
                      . ||+..|.|+.|.|.++.+..
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            5 99999999999999997653

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=2.1e-15  Score=132.00  Aligned_cols=83  Identities=17%  Similarity=0.375  Sum_probs=77.5

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRL  413 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V  413 (548)
                      ...++|||+|||+.+++++|+++|..|    |.|..|.|+.++.++.++|||||+|.+.++|..||...+..|.|+.|.|
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V  100 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQW----GKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEP  100 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSS----CCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEE
Confidence            346899999999999999999999999    8999999999999999999999999999999999988449999999999


Q ss_pred             EeeecCC
Q 008920          414 SHAQQNC  420 (548)
Q Consensus       414 ~~Ak~~~  420 (548)
                      .|+.+..
T Consensus       101 ~~a~~~~  107 (116)
T 1x4b_A          101 KRAVARE  107 (116)
T ss_dssp             ECCSSCC
T ss_pred             EECCCCc
Confidence            9998764

>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=99.61  E-value=2.1e-15  Score=125.26  Aligned_cols=81  Identities=23%  Similarity=0.357  Sum_probs=72.5

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      ..++|||+|||+++++++|.++|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|..|+.|
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----------------~~~~~g~afV~f~~~~~a~~a~~~   67 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKF-----------------SGHPKGFAYIEFSDKESVRTSLAL   67 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCS-----------------SSSCCEEEEEEESSTHHHHHHGGG
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCC-----------------CCCcceEEEEEECCHHHHHHHHhc
Confidence            358999999999999999999999999999999965431                 345789999999999999999999


Q ss_pred             cceeecCceeEeecCCCc
Q 008920          304 NMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~  321 (548)
                      |+..|.|+.|.|.++.++
T Consensus        68 ~g~~~~g~~l~V~~a~~~   85 (89)
T 3ucg_A           68 DESLFRGRQIKVIPKRTN   85 (89)
T ss_dssp             TTCEETTEECEEEETTTT
T ss_pred             CCCEECCcEEEEEEccCC
Confidence            999999999999998653

>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=99.61  E-value=2.1e-15  Score=124.73  Aligned_cols=80  Identities=21%  Similarity=0.356  Sum_probs=70.7

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-  302 (548)
                      ..++|||+|||+++++++|+++|+.||.|.+|.|+.++.                 ++.++|||||+|.+.++|..|+. 
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-----------------TGKSKGYGFVSFFNKWDAENAIQQ   67 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----------------TCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCC-----------------CCccceEEEEEECCHHHHHHHHHH
Confidence            357999999999999999999999999999999966431                 34578999999999999999995 


Q ss_pred             hcceeecCceeEeecCCC
Q 008920          303 FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~  320 (548)
                      ||+..|.|+.|.|.++.+
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

>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=99.61  E-value=2.5e-15  Score=130.56  Aligned_cols=83  Identities=18%  Similarity=0.445  Sum_probs=78.2

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|+.|    |.|..|.|+.++.+|.++|||||+|.+.++|..||..++ ..|.|+.|
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l   98 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPF----GRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM   98 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTT----SCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            4567899999999999999999999999    899999999999999999999999999999999998777 99999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      .|.|+.++
T Consensus        99 ~V~~a~~k  106 (108)
T 2jrs_A           99 KVGHVTER  106 (108)
T ss_dssp             EEECSCSS
T ss_pred             EEEEcccC
Confidence            99999875

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.61  E-value=2e-15  Score=140.16  Aligned_cols=81  Identities=15%  Similarity=0.271  Sum_probs=76.2

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCC--CeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLES--SVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G--~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ..++|||+|||+++++++|+++|+.|    |  .|..|.|+.|+.+|.++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~----G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l  129 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSI----GVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKV  129 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHT----TCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHH----CCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEe
Confidence            45899999999999999999999999    8  99999999999999999999999999999999999988 99999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      .|.+|.+.
T Consensus       130 ~V~~a~~~  137 (156)
T 3n9u_C          130 DVRPATRQ  137 (156)
T ss_dssp             EEEECCHH
T ss_pred             EEEEcCCC
Confidence            99999764

>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=99.61  E-value=5.3e-15  Score=126.60  Aligned_cols=82  Identities=24%  Similarity=0.409  Sum_probs=72.6

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+.+++++|+++|+.||.|..|.|+.+.                   +.++|||||+|.+.++|..||
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-------------------~~~~g~afV~f~~~~~a~~A~   72 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH-------------------TSNDPYCFVEFYEHRDAAAAL   72 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCC-------------------CSSCCEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecC-------------------CCCCCEEEEEECCHHHHHHHH
Confidence            3456899999999999999999999999999999996542                   125699999999999999999


Q ss_pred             H-hcceeecCceeEeecCCCcc
Q 008920          302 A-FNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 ~-lng~~~~gr~I~V~~a~~~~  322 (548)
                      . ||+..|.|+.|.|.++.++.
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            5 99999999999999998654

>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=99.60  E-value=2.4e-15  Score=124.52  Aligned_cols=81  Identities=19%  Similarity=0.317  Sum_probs=75.3

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCC-CceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV-GKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~-srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      ..++|||+|||+++++++|+++|+.|    |.|..|.|+.+..++. ++|||||+|.+.++|..|+..++ ..|.|+.|.
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   78 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTY----GKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEIT   78 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTT----SCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhC----CCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEE
Confidence            35789999999999999999999999    8999999999987766 89999999999999999999777 999999999


Q ss_pred             EEeeecC
Q 008920          413 LSHAQQN  419 (548)
Q Consensus       413 V~~Ak~~  419 (548)
                      |.++.+.
T Consensus        79 v~~a~~~   85 (88)
T 4a8x_A           79 ATAVLAP   85 (88)
T ss_dssp             EEEECCC
T ss_pred             EEECCCC
Confidence            9999764

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=4e-15  Score=125.08  Aligned_cols=82  Identities=21%  Similarity=0.223  Sum_probs=72.6

Q ss_pred             CCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       221 ~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      .....++|||+|||+++++++|+++|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|..|
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~-----------------~~~~~g~afV~f~~~~~A~~A   73 (95)
T 2cqc_A           11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQ-----------------SRRSRGFAFVYFENVDDAKEA   73 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSS-----------------SSSEEEEEEEEESSHHHHHHH
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCC-----------------CCCcccEEEEEECCHHHHHHH
Confidence            344568999999999999999999999999999999966542                 244779999999999999999


Q ss_pred             HH-hcceeecCceeEeecCC
Q 008920          301 LA-FNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       301 l~-lng~~~~gr~I~V~~a~  319 (548)
                      |. ||+..|.|+.|.|.++.
T Consensus        74 ~~~l~g~~~~g~~l~v~~a~   93 (95)
T 2cqc_A           74 KERANGMELDGRRIRVSGPS   93 (95)
T ss_dssp             HHHHTTEEETTEEEEEECCS
T ss_pred             HHHhCCCEECCEEEEEEecC
Confidence            95 99999999999999985

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.60  E-value=1.2e-15  Score=130.00  Aligned_cols=80  Identities=15%  Similarity=0.275  Sum_probs=68.8

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCC--eeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGE--IDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~--I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      .-.||||+|||+.+|+++|+++|++||.  |.+|+|+.++                 .+|.++|||||+|.+.++|+.||
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~-----------------~tg~srG~aFV~f~~~~~A~~Ai   70 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDK-----------------QTQQNRGFAFVQLSSAMDASQLL   70 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCS-----------------SSSSCSSEEEEECSSSHHHHHHH
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecC-----------------CCCCCceEeEEEECCHHHHHHHH
Confidence            4579999999999999999999999995  5688885544                 24568899999999999999999


Q ss_pred             -Hhcce----eecCceeEeecCCC
Q 008920          302 -AFNMA----VIGGNHIRLDRACP  320 (548)
Q Consensus       302 -~lng~----~~~gr~I~V~~a~~  320 (548)
                       .||+.    .|.|+.|.|.++..
T Consensus        71 ~~lng~~~~~~i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           71 QILQSLHPPLKIDGKTIGVDFAKS   94 (95)
T ss_dssp             HHHHSSSSCEEETTEEEEEEECCC
T ss_pred             HHhcCCCCCceECCEEEEEEEccC
Confidence             58876    58999999999853

>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=99.60  E-value=3.5e-15  Score=128.00  Aligned_cols=85  Identities=22%  Similarity=0.362  Sum_probs=74.4

Q ss_pred             CCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       221 ~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      +....++|||+|||+++++++|.++|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|..|
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-----------------TGQHQGYGFVEFLSEEDADYA   73 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSS-----------------SCSBCSCEEEEESSHHHHHHH
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC-----------------CCcCCcEEEEEECCHHHHHHH
Confidence            344568999999999999999999999999999999855431                 345789999999999999999


Q ss_pred             HH-hcceeecCceeEeecCCCcc
Q 008920          301 LA-FNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       301 l~-lng~~~~gr~I~V~~a~~~~  322 (548)
                      |. ||+..|.|+.|.|.++.+..
T Consensus        74 ~~~l~g~~~~g~~l~v~~a~~~~   96 (105)
T 1x5u_A           74 IKIMDMIKLYGKPIRVNKASAHN   96 (105)
T ss_dssp             HHHSSSCBCSSCBCEEEETTTTS
T ss_pred             HHHhCCCeECCeEEEEEECCCCC
Confidence            95 89999999999999997654

>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=99.60  E-value=4.3e-15  Score=125.98  Aligned_cols=82  Identities=17%  Similarity=0.197  Sum_probs=74.9

Q ss_pred             CCCccEEEEeCCCCCCCHHHHH----HHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccC
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIY----QLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLR  407 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~----~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~  407 (548)
                      .....+|||+|||+.+++++|+    ++|+.|    |.|..|.|+.+..+   +|||||+|.+.++|..||..++ ..|.
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~----G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~   78 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARH----GKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIG   78 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHH----SCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccc----CcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            4456899999999999999999    999999    89999999999765   8899999999999999999887 9999


Q ss_pred             CeEEEEEeeecCCC
Q 008920          408 DRELRLSHAQQNCT  421 (548)
Q Consensus       408 Gr~I~V~~Ak~~~~  421 (548)
                      |+.|+|.||.+...
T Consensus        79 gr~l~V~~a~~~~~   92 (96)
T 2dgx_A           79 SKKILVSLATGASG   92 (96)
T ss_dssp             TEEEEEEECCCSSC
T ss_pred             CeEEEEEEcCCCCC
Confidence            99999999987643

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.60  E-value=1.1e-15  Score=130.96  Aligned_cols=81  Identities=16%  Similarity=0.138  Sum_probs=72.7

Q ss_pred             CcccEEEEcCCCC------CCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHH
Q 008920          223 KLLRTIFVGNLPL------KVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQS  296 (548)
Q Consensus       223 ~~~rtVfVgNLP~------~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~  296 (548)
                      ...++|||+|||+      ++++++|.++|+.||.|.+|.|+.++.                 +|.++|||||+|.+.++
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~-----------------tg~~kG~afV~f~~~~~   66 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEA-----------------TGKTKGFLFVECGSMND   66 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETT-----------------TTEECSEEEEEESSHHH
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCC-----------------CCccceEEEEEECCHHH
Confidence            3468999999999      999999999999999999999966542                 34578999999999999


Q ss_pred             HHHHH-HhcceeecC-ceeEeecCCC
Q 008920          297 TEAAL-AFNMAVIGG-NHIRLDRACP  320 (548)
Q Consensus       297 A~~Al-~lng~~~~g-r~I~V~~a~~  320 (548)
                      |..|| .|||..|.| +.|.|.++.+
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 599999999 9999999864

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=1.4e-15  Score=131.43  Aligned_cols=80  Identities=19%  Similarity=0.342  Sum_probs=74.4

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRL  413 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V  413 (548)
                      ...++|||+|||+++|+++|+++|+.|    |.|..|+|+++.. |.++|||||+|.+.++|..||.+.+..|.|+.|.|
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~----G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V   83 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDK----GQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLI   83 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTS----SCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhc----CCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEE
Confidence            356899999999999999999999999    9999999999987 99999999999999999999994449999999999


Q ss_pred             Eeeec
Q 008920          414 SHAQQ  418 (548)
Q Consensus       414 ~~Ak~  418 (548)
                      .++.+
T Consensus        84 ~~~~~   88 (103)
T 1s79_A           84 LFKDD   88 (103)
T ss_dssp             EEHHH
T ss_pred             EEchH
Confidence            99875

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.60  E-value=4.9e-15  Score=129.34  Aligned_cols=84  Identities=20%  Similarity=0.324  Sum_probs=74.2

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+.+++++|+++|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|+.||
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-----------------TGKSKGYGFVSFFNKWDAENAI   74 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----------------TCCEEEEEEEEESSHHHHHHHH
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCC-----------------CCCcceEEEEEECCHHHHHHHH
Confidence            34568999999999999999999999999999999965431                 3457799999999999999999


Q ss_pred             -HhcceeecCceeEeecCCCcc
Q 008920          302 -AFNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 -~lng~~~~gr~I~V~~a~~~~  322 (548)
                       .||+..|.|+.|.|.++.+..
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             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=99.60  E-value=2.6e-15  Score=123.60  Aligned_cols=78  Identities=28%  Similarity=0.434  Sum_probs=70.4

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||+++++++|.++|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|..|+ .
T Consensus         6 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~-----------------~~~~~g~afV~f~~~~~a~~A~~~   68 (85)
T 3mdf_A            6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-----------------TEKHRGFAFVEFELAEDAAAAIDN   68 (85)
T ss_dssp             CSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETT-----------------TTEECSEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCC-----------------CCccccEEEEEECCHHHHHHHHHH
Confidence            468999999999999999999999999999999865532                 3447799999999999999999 6


Q ss_pred             hcceeecCceeEeecC
Q 008920          303 FNMAVIGGNHIRLDRA  318 (548)
Q Consensus       303 lng~~~~gr~I~V~~a  318 (548)
                      ||+..|.|+.|.|.++
T Consensus        69 l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A           69 MNESELFGRTIRVNLA   84 (85)
T ss_dssp             HTTCEETTEECEEEEC
T ss_pred             hCCCEECCcEEEEEEc
Confidence            9999999999999986

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.60  E-value=4.5e-15  Score=127.79  Aligned_cols=81  Identities=23%  Similarity=0.324  Sum_probs=76.2

Q ss_pred             cCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeE
Q 008920          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE  410 (548)
Q Consensus       332 ~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~  410 (548)
                      ...+.++|||+|||+.+++++|+++|..|    |.|..|.|+.+. +|.++|||||+|.+.++|..||..|+ ..|.|+.
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   99 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEF----GTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRP   99 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTT----SCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcE
Confidence            34567999999999999999999999999    899999999997 99999999999999999999999877 9999999


Q ss_pred             EEEEeee
Q 008920          411 LRLSHAQ  417 (548)
Q Consensus       411 I~V~~Ak  417 (548)
                      |.|.|+.
T Consensus       100 l~V~~a~  106 (107)
T 3ulh_A          100 MNIQLVT  106 (107)
T ss_dssp             CEEEEEC
T ss_pred             EEEEEeC
Confidence            9999985

>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=99.60  E-value=3.2e-15  Score=125.77  Aligned_cols=81  Identities=28%  Similarity=0.467  Sum_probs=75.4

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|..|.|+.+.. +.++|||||+|.+.++|..||..++ ..|.|+.|
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~----G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   87 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQA----GPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPI   87 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGG----SCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhc----CCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEE
Confidence            4467899999999999999999999999    8999999999975 9999999999999999999999777 99999999


Q ss_pred             EEEeeec
Q 008920          412 RLSHAQQ  418 (548)
Q Consensus       412 ~V~~Ak~  418 (548)
                      .|.|+..
T Consensus        88 ~V~~a~~   94 (95)
T 2ywk_A           88 NVSGPSS   94 (95)
T ss_dssp             EEECCCC
T ss_pred             EEEEcCC
Confidence            9999864

>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=99.60  E-value=3.6e-15  Score=125.48  Aligned_cols=79  Identities=28%  Similarity=0.426  Sum_probs=71.1

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+.+++++|+++|+.||.|..|.|+.++                  ++.++|||||+|.+.++|..||.
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~------------------~g~~~g~afV~f~~~~~a~~A~~   75 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR------------------EGKPKSFGFVCFKHPESVSYAIA   75 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT------------------TSCEEEEEEEEESSTHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC------------------CCCCceEEEEEECCHHHHHHHHH
Confidence            346899999999999999999999999999999996643                  23477999999999999999995


Q ss_pred             -hcceeecCceeEeecCC
Q 008920          303 -FNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       303 -lng~~~~gr~I~V~~a~  319 (548)
                       ||+..|.|+.|.|.++.
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             99999999999999975

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.60  E-value=8.7e-16  Score=128.66  Aligned_cols=79  Identities=14%  Similarity=0.192  Sum_probs=67.4

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcC--CeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFG--EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG--~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      .+|||+|||+++|+++|.++|+.||  .|.+|+|+.++.                 +|.++|||||+|.+.++|..|| .
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-----------------NGQSKGFALVGVGSEASSKKLMDL   64 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTT-----------------TCCEEEEEEECC-CHHHHHHHHHH
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCC-----------------CCccCcEEEEEECCHHHHHHHHHH
Confidence            5899999999999999999999999  999999966542                 3557899999999999999999 6


Q ss_pred             hcceeecCceeEeecCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~  321 (548)
                      |||..|.|+.|.|.++.++
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

>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=99.60  E-value=5.4e-15  Score=126.84  Aligned_cols=82  Identities=22%  Similarity=0.326  Sum_probs=72.8

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...++|||+|||+++++++|..+|+.||.|..|.|+.++                  ++.++|||||+|.+.++|..|| 
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------------------DGSSKGCAFVKFSSHTEAQAAIH   74 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS------------------SSCEEEEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC------------------CCCcCcEEEEEeCCHHHHHHHHH
Confidence            346899999999999999999999999999999996654                  2346799999999999999999 


Q ss_pred             HhcceeecC---ceeEeecCCCcc
Q 008920          302 AFNMAVIGG---NHIRLDRACPPR  322 (548)
Q Consensus       302 ~lng~~~~g---r~I~V~~a~~~~  322 (548)
                      .||+..|.|   +.|.|.++.+..
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            599999988   999999997653

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=3.4e-15  Score=127.78  Aligned_cols=83  Identities=25%  Similarity=0.359  Sum_probs=73.3

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++++++|.++|+.||.|..|.|+.+..                 ++.++|||||+|.+.++|..||.
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~-----------------~~~~~g~afV~f~~~~~A~~A~~   73 (103)
T 2dnm_A           11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPH-----------------TKAPRGFAFVRFHDRRDAQDAEA   73 (103)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSS-----------------SCSBCSCEEEEESSSSHHHHHHH
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCC-----------------CCCCCeEEEEEECCHHHHHHHHH
Confidence            4468999999999999999999999999999999855431                 34578999999999999999995


Q ss_pred             -hcceeecCceeEeecCCCcc
Q 008920          303 -FNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       303 -lng~~~~gr~I~V~~a~~~~  322 (548)
                       ||+..|.|+.|.|.++.+..
T Consensus        74 ~l~g~~~~g~~l~V~~a~~~~   94 (103)
T 2dnm_A           74 AMDGAELDGRELRVQVARYGR   94 (103)
T ss_dssp             HHSSCCBTTBCCEEEECSSCC
T ss_pred             HcCCCEECCcEEEEEECCcCC
Confidence             99999999999999997543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=3.3e-15  Score=127.48  Aligned_cols=84  Identities=29%  Similarity=0.423  Sum_probs=73.9

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...++|||+|||+++++++|.++|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|..|| 
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~-----------------~~~~~g~afV~f~~~~~A~~A~~   72 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-----------------TEKHRGFAFVEFELAEDAAAAID   72 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSS-----------------SCCCSSEEEECCSSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCC-----------------CCCcceEEEEEECCHHHHHHHHH
Confidence            4568999999999999999999999999999999855431                 3457899999999999999999 


Q ss_pred             HhcceeecCceeEeecCCCccc
Q 008920          302 AFNMAVIGGNHIRLDRACPPRK  323 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~~k  323 (548)
                      .||+..|.|+.|.|.++.+...
T Consensus        73 ~l~g~~~~g~~l~V~~a~~~~~   94 (102)
T 2cqb_A           73 NMNESELFGRTIRVNLAKPMRI   94 (102)
T ss_dssp             HHTTEEETTEEEEEEECCCCCC
T ss_pred             HhCCCEECCcEEEEEeCCCCCC
Confidence            5999999999999999976543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=5.8e-15  Score=124.22  Aligned_cols=82  Identities=20%  Similarity=0.313  Sum_probs=73.0

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-  302 (548)
                      ..++|||+|||+++++++|+++|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|..||. 
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-----------------TGRSKGYGFITFSDSECARRALEQ   66 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSS-----------------SCCCCSEEEEEESCHHHHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCC-----------------CCceeeEEEEEECCHHHHHHHHHH
Confidence            458999999999999999999999999999999965432                 34578999999999999999995 


Q ss_pred             hcceeecCceeEeecCCCcc
Q 008920          303 FNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~~  322 (548)
                      ||+..|.|+.|.|.++.+..
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

>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=99.59  E-value=5e-15  Score=127.94  Aligned_cols=85  Identities=20%  Similarity=0.312  Sum_probs=77.6

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCC-eEEEEEe-ecCCCCCCceEEEEEECCHHHHHHHHHHcC---CccCC
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESS-VEAVRVI-RHPHMRVGKGIAYVLFKTREAANLVIKRRN---LKLRD  408 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~-I~~VrI~-~d~~tg~srG~AFV~F~~~e~A~~Al~~ln---~~l~G  408 (548)
                      .+.++|||+|||+.+++++|+++|..|    |. |..|.|+ .+..+|.++|||||+|.+.++|..||..++   ..|.|
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~----G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g   81 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKV----TEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWG   81 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHH----STTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTT
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHh----cCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecC
Confidence            356899999999999999999999999    87 9999998 788889999999999999999999999773   78999


Q ss_pred             eEEEEEeeecCCCC
Q 008920          409 RELRLSHAQQNCTP  422 (548)
Q Consensus       409 r~I~V~~Ak~~~~~  422 (548)
                      +.|.|.|+.+...+
T Consensus        82 ~~l~V~~a~~~~~~   95 (109)
T 2dis_A           82 HQIAVDWAEPEIDV   95 (109)
T ss_dssp             BCCEEEESCSSCST
T ss_pred             CeEEEEEcCCCCCc
Confidence            99999999876443

>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=99.59  E-value=6.2e-15  Score=127.62  Aligned_cols=84  Identities=20%  Similarity=0.334  Sum_probs=73.7

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++++++|+.+|..||.|..|.|+.++.                 ++.++|||||+|.+.++|..||
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-----------------TEHSKGCAFAQFMTQEAAQKCL   74 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSS-----------------SCCBCSEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCC-----------------CCCCccEEEEEECCHHHHHHHH
Confidence            34568999999999999999999999999999999965432                 3457899999999999999999


Q ss_pred             -Hhc------ceeecCceeEeecCCCcc
Q 008920          302 -AFN------MAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 -~ln------g~~~~gr~I~V~~a~~~~  322 (548)
                       .||      +..|.|+.|.|.++.+..
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             588      999999999999997653

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.59  E-value=4.8e-15  Score=123.95  Aligned_cols=84  Identities=25%  Similarity=0.296  Sum_probs=76.7

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|..|.|+.+  ++.++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~----G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l   78 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNEC----GHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREI   78 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTT----SCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            3467899999999999999999999999    89999999985  78999999999999999999999877 99999999


Q ss_pred             EEEeeecCCCC
Q 008920          412 RLSHAQQNCTP  422 (548)
Q Consensus       412 ~V~~Ak~~~~~  422 (548)
                      .|.|+.+...+
T Consensus        79 ~v~~a~~~~~~   89 (92)
T 2dgv_A           79 DVRIDRNASGP   89 (92)
T ss_dssp             CCEECSCCSSC
T ss_pred             EEEEcCCCCCC
Confidence            99999876443

>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=99.59  E-value=8.3e-15  Score=125.36  Aligned_cols=83  Identities=19%  Similarity=0.350  Sum_probs=73.0

Q ss_pred             CCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       221 ~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      .....++|||+|||+++++++|+++|+.||.|..|.|+.+.                   +.++|||||+|.+.++|..|
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-------------------RGSKGFGFVTFENSADADRA   71 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT-------------------TTTCCEEEEEESCHHHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC-------------------CCCcEEEEEEECCHHHHHHH
Confidence            34556899999999999999999999999999999996543                   12679999999999999999


Q ss_pred             H-HhcceeecCceeEeecCCCcc
Q 008920          301 L-AFNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       301 l-~lng~~~~gr~I~V~~a~~~~  322 (548)
                      | .||+..|.|+.|.|.++.+..
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 599999999999999997653

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.59  E-value=2.5e-15  Score=131.79  Aligned_cols=81  Identities=19%  Similarity=0.340  Sum_probs=76.2

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+++++++|+++|+.|    |.|..|.|+.+..+|.++|||||+|.+.++|..||..++ ..|.|+.|
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l  112 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPF----GNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRL  112 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTS----CEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            4467899999999999999999999999    999999999999999999999999999999999999887 99999999


Q ss_pred             EEEeee
Q 008920          412 RLSHAQ  417 (548)
Q Consensus       412 ~V~~Ak  417 (548)
                      +|.|++
T Consensus       113 ~V~~ak  118 (118)
T 2khc_A          113 KVQLKK  118 (118)
T ss_dssp             CEEEC-
T ss_pred             EEEecC
Confidence            999974

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.59  E-value=5.8e-15  Score=126.49  Aligned_cols=82  Identities=26%  Similarity=0.357  Sum_probs=73.0

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++++++|.++|+.|| |..|.|+.+..                 ++.++|||||+|.+.++|..||.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~-----------------~g~~~g~afV~f~~~~~a~~A~~   74 (103)
T 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKD-----------------TDKFKGFCYVEFDEVDSLKEALT   74 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSS-----------------SCSEEEEEEEEESSHHHHHHHGG
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCC-----------------CCccceEEEEEECCHHHHHHHHh
Confidence            4468999999999999999999999997 99999966542                 34578999999999999999999


Q ss_pred             hcceeecCceeEeecCCCcc
Q 008920          303 FNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~~  322 (548)
                      ||+..|.|+.|.|.++.+..
T Consensus        75 l~g~~~~g~~l~V~~a~~~~   94 (103)
T 2dng_A           75 YDGALLGDRSLRVDIAEGRK   94 (103)
T ss_dssp             GTTCEETTEECEEEECCCCC
T ss_pred             hCCCeECCeEEEEEEecCCC
Confidence            99999999999999997643

>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=99.59  E-value=5.5e-15  Score=126.86  Aligned_cols=84  Identities=27%  Similarity=0.377  Sum_probs=73.2

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++++++|.++|+.|| |..|.|+.++.+                .+.++|||||+|.+.++|..||.
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-ISAVRLPREPSN----------------PERLKGFGYAEFEDLDSLLSALS   75 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSC----------------TTSBCSCEEEEESSHHHHHHHHG
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCC----------------CCCcCeEEEEEECCHHHHHHHHh
Confidence            3458999999999999999999999999 999998554311                14578999999999999999999


Q ss_pred             hcceeecCceeEeecCCCccc
Q 008920          303 FNMAVIGGNHIRLDRACPPRK  323 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~~k  323 (548)
                      ||+..|.|+.|.|.++.+...
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            999999999999999986543

>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=99.59  E-value=2.1e-15  Score=132.10  Aligned_cols=82  Identities=11%  Similarity=0.136  Sum_probs=72.8

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCe-eEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEI-DSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I-~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      ....++|||+|||+++|+++|+++|+.||.| ..|.|+.+.                  +|.++|||||+|.+.++|..|
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------------------NGQGLGQALVQFKNEDDARKS   73 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT------------------TSSCSSCEEEECSSHHHHHHH
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC------------------CCCcceEEEEEECCHHHHHHH
Confidence            3456899999999999999999999999999 889985543                  345789999999999999999


Q ss_pred             HHhcceeecCceeEeecCCCc
Q 008920          301 LAFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       301 l~lng~~~~gr~I~V~~a~~~  321 (548)
                      |.+|+..|.|+.|.|.++.+.
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            988999999999999998643

>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=99.59  E-value=5.8e-15  Score=129.00  Aligned_cols=83  Identities=18%  Similarity=0.325  Sum_probs=73.8

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...++|||+|||+++++++|+++|+.||.|..|.|+.+..                 ++.++|||||+|.+.++|..|| 
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-----------------TNLSKCFGFVSYDNPVSAQAAIQ   85 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSS-----------------SCSEEEEEEEECSSHHHHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC-----------------CCCcCccEEEEECCHHHHHHHHH
Confidence            3468999999999999999999999999999999966442                 3457799999999999999999 


Q ss_pred             HhcceeecCceeEeecCCCcc
Q 008920          302 AFNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~~  322 (548)
                      .||+..|.|+.|.|.++.+..
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            699999999999999997653

>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=99.59  E-value=4.1e-15  Score=125.79  Aligned_cols=80  Identities=15%  Similarity=0.341  Sum_probs=71.8

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      .++|||+|||+++++++|.++|+.||.|..|.|+.++                 .+|.++|||||+|.+.++|..|+ .|
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 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDP-----------------QTGRSKGYAFIEFRDLESSASAVRNL   64 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCT-----------------TTCCBCSEEEEEESSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCC-----------------CCCccceEEEEEECCHHHHHHHHHHh
Confidence            5799999999999999999999999999999985543                 13457899999999999999999 69


Q ss_pred             cceeecCceeEeecCCCc
Q 008920          304 NMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~  321 (548)
                      ||..|.|+.|.|.++.+.
T Consensus        65 ~g~~~~g~~l~V~~a~~~   82 (96)
T 2x1f_A           65 NGYQLGSRFLKCGYSSNS   82 (96)
T ss_dssp             TTCEETTEECEEEECSCS
T ss_pred             CCCeECCeEEEEEEcCCC
Confidence            999999999999999764

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.59  E-value=1.1e-15  Score=123.59  Aligned_cols=76  Identities=20%  Similarity=0.429  Sum_probs=73.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEee
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHA  416 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~A  416 (548)
                      ++|||+|||+.+++++|+++|+.|    |.|..|.|+.++.+|.++|||||+|.+.++|..|+..++..|.|+.|.|.+|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~----G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQF----GEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTT----SCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCCCccCCEEEEEEec
Confidence            479999999999999999999999    8999999999998999999999999999999999999999999999999987

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=4.4e-15  Score=127.55  Aligned_cols=84  Identities=21%  Similarity=0.331  Sum_probs=74.2

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++++++|+++|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|..||
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-----------------TNQSRGFGFVKFKDPNCVGTVL   75 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSS-----------------SCCEEEEEEEEESSTTHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCC-----------------CCCcceEEEEEECCHHHHHHHH
Confidence            34568999999999999999999999999999999966542                 3457899999999999999999


Q ss_pred             HhcceeecCceeEeecCCCcc
Q 008920          302 AFNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~~  322 (548)
                      .+++..|.|+.|.|.++.+..
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            779999999999999997654

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=3.8e-15  Score=125.60  Aligned_cols=82  Identities=27%  Similarity=0.352  Sum_probs=72.8

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEE-EEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSV-RIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sV-ri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ..++|||+|||+++++++|..+|+.||.|..| .|+.++                 .++.++|||||+|.+.++|..||.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~-----------------~~g~~~g~afV~f~~~~~A~~A~~   66 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDP-----------------DTGNSKGYAFINFASFDASDAAIE   66 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCT-----------------TTCSCCSEEEEEBSSHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcC-----------------CCCCcCeEEEEEECCHHHHHHHHH
Confidence            46899999999999999999999999999999 885543                 134578999999999999999996


Q ss_pred             -hcceeecCceeEeecCCCcc
Q 008920          303 -FNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       303 -lng~~~~gr~I~V~~a~~~~  322 (548)
                       ||+..|.|+.|.|.++.+..
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

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.59  E-value=1.6e-15  Score=122.19  Aligned_cols=75  Identities=21%  Similarity=0.378  Sum_probs=67.6

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhcce
Q 008920          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMA  306 (548)
Q Consensus       227 tVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~lng~  306 (548)
                      +|||+|||+++++++|.++|+.||.|..|.|+.++                 .++.++|||||+|.+.++|+.|+++|+.
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-----------------~~~~~~g~afV~f~~~~~a~~a~~~~~~   63 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDK-----------------TTNRHRGFGFVTFESEDIVEKVCEIHFH   63 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCS-----------------SSTTSCBEEEEECSCHHHHHHHHSSSCC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecC-----------------CCCCcCcEEEEEECCHHHHHHHHHCCCC
Confidence            49999999999999999999999999999985543                 1345789999999999999999999999


Q ss_pred             eecCceeEeecC
Q 008920          307 VIGGNHIRLDRA  318 (548)
Q Consensus       307 ~~~gr~I~V~~a  318 (548)
                      .|.|+.|.|.++
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

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.59  E-value=5.3e-15  Score=125.33  Aligned_cols=85  Identities=18%  Similarity=0.233  Sum_probs=73.2

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-  302 (548)
                      ..++|||+|||+++++++|+++|+.||.|..|.|+.++...              .++.++|||||+|.+.++|..||. 
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~--------------gt~~~~g~afV~f~~~~~a~~A~~~   69 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKA--------------GVLLSMGFGFVEYKKPEQAQKALKQ   69 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTT--------------CCEEEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCC--------------CCcCcccEEEEEECCHHHHHHHHHH
Confidence            45899999999999999999999999999999997654210              022477999999999999999995 


Q ss_pred             hcceeecCceeEeecCCCcc
Q 008920          303 FNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~~  322 (548)
                      ||+..|.|+.|.|.++.+..
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            89999999999999997653

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.59  E-value=6.1e-15  Score=130.46  Aligned_cols=80  Identities=20%  Similarity=0.418  Sum_probs=75.4

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      ..++|||+|||+.+++++|+++|+.|    |.|..|.|+.++.+|.++|||||+|.+.++|..|| .++ ..|.|+.|.|
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V  109 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSC----GSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKV  109 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTT----SCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEE
Confidence            46899999999999999999999999    89999999999889999999999999999999999 566 9999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      .|+.+.
T Consensus       110 ~~a~~~  115 (124)
T 2jwn_A          110 LPKRTN  115 (124)
T ss_dssp             EESSCC
T ss_pred             EECCCC
Confidence            999864

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=4e-15  Score=126.98  Aligned_cols=83  Identities=23%  Similarity=0.399  Sum_probs=73.3

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...++|||+|||+++++++|+++|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|..|| 
T Consensus        10 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~-----------------~~~~~g~afV~f~~~~~A~~A~~   72 (102)
T 1x5s_A           10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRE-----------------TQRSRGFGFVTFENIDDAKDAMM   72 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSS-----------------SCSCCSEEEEECSSHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCC-----------------CCCcccEEEEEECCHHHHHHHHH
Confidence            4568999999999999999999999999999999955431                 3457799999999999999999 


Q ss_pred             HhcceeecCceeEeecCCCcc
Q 008920          302 AFNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~~  322 (548)
                      .||+..|.|+.|.|.++.+..
T Consensus        73 ~l~g~~~~g~~l~v~~a~~~~   93 (102)
T 1x5s_A           73 AMNGKSVDGRQIRVDQAGKSS   93 (102)
T ss_dssp             HHTTCCTTSCCCEEEEEECCC
T ss_pred             HhCCCEECCeEEEEEECCCCC
Confidence            699999999999999987543

>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=99.58  E-value=3.4e-15  Score=123.53  Aligned_cols=81  Identities=21%  Similarity=0.377  Sum_probs=71.2

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-h
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-F  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-l  303 (548)
                      .++|||+|||+++|+++|.++|+.||.|..|.|+.+..+                .+.++|||||+|.+.++|..|+. |
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~----------------~~~~~g~afV~f~~~~~a~~A~~~l   67 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMH----------------PHLSKGYAYVEFENPDEAEKALKHM   67 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTE----------------EEEECSEEEEEESSHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCC----------------CCCCCcEEEEEEecHHHHHHHHHHc
Confidence            579999999999999999999999999999998664421                12267999999999999999995 9


Q ss_pred             cceeecCceeEeecCCCc
Q 008920          304 NMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~  321 (548)
                      ||..|.|+.|.|.++.++
T Consensus        68 ~g~~~~g~~l~v~~a~~~   85 (88)
T 4a8x_A           68 DGGQIDGQEITATAVLAP   85 (88)
T ss_dssp             TTCEETTEECEEEEECCC
T ss_pred             CCCeECCeEEEEEECCCC
Confidence            999999999999998754

>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=99.58  E-value=2.5e-15  Score=128.61  Aligned_cols=83  Identities=23%  Similarity=0.468  Sum_probs=77.8

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      ...++|||+|||+.+++++|+++|+.|    |.|..|.|+.++.+|.++|||||+|.+.++|..||..++ ..|.|+.|.
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~----G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   81 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEV----GPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALR   81 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTT----SCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBE
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhc----CCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Confidence            346899999999999999999999999    899999999999899999999999999999999999887 999999999


Q ss_pred             EEeeecCC
Q 008920          413 LSHAQQNC  420 (548)
Q Consensus       413 V~~Ak~~~  420 (548)
                      |.|+.+..
T Consensus        82 v~~a~~~~   89 (104)
T 1p1t_A           82 VDNAASEK   89 (104)
T ss_dssp             EEETTCTT
T ss_pred             EEeCCCcc
Confidence            99998753

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=5.9e-15  Score=123.90  Aligned_cols=79  Identities=25%  Similarity=0.358  Sum_probs=70.6

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...++|||+|||+++++++|+++|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|..|| 
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~-----------------~~~~~g~afV~f~~~~~A~~A~~   76 (94)
T 2e5h_A           14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKD-----------------TRKSKGVAFILFLDKDSAQNCTR   76 (94)
T ss_dssp             CCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSS-----------------SCCCTTCEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCC-----------------CCCcccEEEEEECCHHHHHHHHH
Confidence            4568999999999999999999999999999999955431                 2457799999999999999999 


Q ss_pred             HhcceeecCceeEeecC
Q 008920          302 AFNMAVIGGNHIRLDRA  318 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a  318 (548)
                      .||+..|.|+.|.|.++
T Consensus        77 ~l~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           77 AINNKQLFGRVIKASIA   93 (94)
T ss_dssp             HTTTEEETTEEEEEEEC
T ss_pred             HcCCCeeCCcEEEEEec
Confidence            59999999999999986

>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=99.58  E-value=3e-15  Score=130.63  Aligned_cols=82  Identities=23%  Similarity=0.256  Sum_probs=72.9

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++++++|.++|+.||.|..|.|+.+..                 ++.++|||||+|.+.++|..||.
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-----------------SRRSKGIAYVEFCEIQSVPLAIG   85 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCC-----------------SSSCCCCEEEEESCGGGHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCC-----------------CCccCcEEEEEeCcHHHHHHHHH
Confidence            4468999999999999999999999999999999965431                 34578999999999999999999


Q ss_pred             hcceeecCceeEeecCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~  321 (548)
                      ||+..|.|+.|.|.++.+.
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

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.58  E-value=6.8e-15  Score=126.51  Aligned_cols=85  Identities=21%  Similarity=0.373  Sum_probs=73.4

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+.+++++|+++|+.||.|..|.|+.+.                ..++.++|||||+|.+.++|..||
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~----------------~~~~~~~g~afV~f~~~~~a~~A~   75 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKM----------------TGTGAHRGFGFVDFITKQDAKKAF   75 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCC----------------SSSCSSCSEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCC----------------CCCCCcCceEEEEECCHHHHHHHH
Confidence            3456899999999999999999999999999999985431                013457899999999999999999


Q ss_pred             -Hh-cceeecCceeEeecCCCcc
Q 008920          302 -AF-NMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 -~l-ng~~~~gr~I~V~~a~~~~  322 (548)
                       .| |+..|.|+.|.|.++.+..
T Consensus        76 ~~l~~~~~~~g~~l~v~~a~~~~   98 (107)
T 2cph_A           76 NALCHSTHLYGRRLVLEWADSEV   98 (107)
T ss_dssp             HHHHTCCBSSSCBCEEEECCCCC
T ss_pred             HHhccCCeECCCEEEEEeCCCCC
Confidence             58 8999999999999997653

>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=99.58  E-value=1e-14  Score=126.25  Aligned_cols=81  Identities=21%  Similarity=0.384  Sum_probs=73.4

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|..|.|+.+   +.++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   91 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKY----GAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRL   91 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            4467899999999999999999999999    89999999655   5589999999999999999998877 99999999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      .|.|+.+..
T Consensus        92 ~V~~a~~~~  100 (109)
T 1x4a_A           92 RVEFPRSGR  100 (109)
T ss_dssp             EEECCCCCC
T ss_pred             EEEEcccCC
Confidence            999998753

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=5.3e-15  Score=127.11  Aligned_cols=81  Identities=15%  Similarity=0.210  Sum_probs=72.3

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++++++|..+|+.||.|..|.|+.+..                 +|.++|||||+|.+.++|..||.
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-----------------TGYLKGYTLVEYETYKEAQAAME   83 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----------------TSSEEEEEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCC-----------------CCceeeEEEEEECCHHHHHHHHH
Confidence            3468999999999999999999999999999999966442                 34578999999999999999994


Q ss_pred             -hcceeecCceeEeecCCC
Q 008920          303 -FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 -lng~~~~gr~I~V~~a~~  320 (548)
                       ||+..|.|+.|.|.++.+
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             999999999999999864

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.58  E-value=2.7e-15  Score=127.14  Aligned_cols=83  Identities=22%  Similarity=0.323  Sum_probs=77.0

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|..+.++.+..+|.++|||||+|.+.++|..||..++ ..|.|+.|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~----G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l   87 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGY----QVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKV   87 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTS----CCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHc----CCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEE
Confidence            3456899999999999999999999999    899888889988999999999999999999999998888 99999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      .|.|+..+
T Consensus        88 ~V~~a~~~   95 (98)
T 2cqp_A           88 KLVLGSGP   95 (98)
T ss_dssp             EEEESSCS
T ss_pred             EEEEcCCC
Confidence            99998754

>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=99.58  E-value=9.1e-15  Score=123.97  Aligned_cols=79  Identities=19%  Similarity=0.254  Sum_probs=70.2

Q ss_pred             CcccEEEEcCCCCCCcHHHHH----HHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLI----KEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~----~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~  298 (548)
                      ...++|||+|||+++++++|+    ++|+.||.|.+|.|+.+..                    .+|||||+|.+.++|+
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            345799999999999999999    9999999999999954331                    1589999999999999


Q ss_pred             HHHH-hcceeecCceeEeecCCCc
Q 008920          299 AALA-FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       299 ~Al~-lng~~~~gr~I~V~~a~~~  321 (548)
                      .||. ||+..|.|+.|.|.++.+.
T Consensus        67 ~Ai~~l~g~~~~gr~l~V~~a~~~   90 (96)
T 2dgx_A           67 GAVNSLHRYKIGSKKILVSLATGA   90 (96)
T ss_dssp             HHHHHHTTEEETTEEEEEEECCCS
T ss_pred             HHHHHhCCCEECCeEEEEEEcCCC
Confidence            9995 9999999999999999754

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.58  E-value=6.3e-15  Score=128.20  Aligned_cols=84  Identities=19%  Similarity=0.306  Sum_probs=70.8

Q ss_pred             CCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       221 ~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      +....++|||+|||+++|+++|..+|+.||.|..|.|+.+.                 .+|.++|||||+|.+.++|..|
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~-----------------~tg~~kg~afV~f~~~~~A~~A   83 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP-----------------LTKRSRGFGFVTFMDQAGVDKV   83 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCT-----------------TTCCCTTCEEEEESSHHHHHHH
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECC-----------------CCCCcCcEEEEEECCHHHHHHH
Confidence            34456899999999999999999999999999999995543                 2355789999999999999999


Q ss_pred             HHhcceeecCceeEeecCCCc
Q 008920          301 LAFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       301 l~lng~~~~gr~I~V~~a~~~  321 (548)
                      |...+..|.|+.|.|.++.+.
T Consensus        84 i~~~~~~l~g~~l~V~~a~~~  104 (109)
T 2rs2_A           84 LAQSRHELDSKTIDPKVAFPR  104 (109)
T ss_dssp             HHSSCEEETTEEEEEEECCCC
T ss_pred             HHHCCCcCCCEEEEEEEccCC
Confidence            976679999999999998754

>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=99.58  E-value=1.2e-15  Score=133.05  Aligned_cols=81  Identities=26%  Similarity=0.381  Sum_probs=76.1

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      ...++|||+|||+.+++++|+++|..|    |.|..|.|+.+..++.++|||||+|.+.++|..|| .++ ..|.|+.|.
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~   97 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAV----GKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPII   97 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTT----SCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhC----CCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEE
Confidence            346899999999999999999999999    89999999999999999999999999999999999 666 999999999


Q ss_pred             EEeeecC
Q 008920          413 LSHAQQN  419 (548)
Q Consensus       413 V~~Ak~~  419 (548)
                      |.|+.+.
T Consensus        98 V~~a~~~  104 (114)
T 2cq4_A           98 VQASQAE  104 (114)
T ss_dssp             EEEHHHH
T ss_pred             EEecCCC
Confidence            9999875

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.58  E-value=1.4e-14  Score=128.45  Aligned_cols=86  Identities=22%  Similarity=0.292  Sum_probs=79.1

Q ss_pred             CcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCe
Q 008920          331 PLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDR  409 (548)
Q Consensus       331 ~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr  409 (548)
                      ......++|||+|||+.+++++|+++|+.|    |.|..|.|+.+. +|.++|||||+|.+.++|..||..++ ..|.|+
T Consensus        30 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~  104 (124)
T 2kt5_A           30 EGVETGAKLLVSNLDFGVSDADIQELFAEF----GTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGR  104 (124)
T ss_dssp             CCCSSCEEEEEESCCSSCCHHHHHHHHHTT----SCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCc
Confidence            345667899999999999999999999999    899999999997 89999999999999999999999777 999999


Q ss_pred             EEEEEeeecCCC
Q 008920          410 ELRLSHAQQNCT  421 (548)
Q Consensus       410 ~I~V~~Ak~~~~  421 (548)
                      .|.|.||.+...
T Consensus       105 ~l~V~~a~~~~~  116 (124)
T 2kt5_A          105 PMDIQLVASQID  116 (124)
T ss_dssp             EEEEEEECCTTC
T ss_pred             EEEEEEeCCCCC
Confidence            999999987643

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=1.2e-14  Score=121.57  Aligned_cols=80  Identities=20%  Similarity=0.322  Sum_probs=74.4

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|..|     .|..|.|+++ .+|.++|||||+|.+.++|..||. ++ ..|.|+.|
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-----~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i   79 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-----KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYI   79 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-----CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-----CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEE
Confidence            3457899999999999999999999998     5889999999 789999999999999999999999 77 99999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      .|.++.+.
T Consensus        80 ~v~~a~~~   87 (91)
T 2dgw_A           80 EVFREKSG   87 (91)
T ss_dssp             EEEEESSC
T ss_pred             EEEECCcC
Confidence            99999875

>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=99.58  E-value=8.7e-15  Score=126.02  Aligned_cols=83  Identities=24%  Similarity=0.344  Sum_probs=75.8

Q ss_pred             cCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEE-EEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeE
Q 008920          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEA-VRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRE  410 (548)
Q Consensus       332 ~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~-VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~  410 (548)
                      ......+|||+|||+.+++++|+++|..|    |.|.. |.|+.+ .+|.++|||||+|.+.++|..||...+..|+|+.
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~----G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~   85 (104)
T 1wg5_A           11 DTANDGFVRLRGLPFGCSKEEIVQFFSGL----EIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRY   85 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTC----CEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHhCcchhCCcE
Confidence            34567899999999999999999999999    89987 889998 7899999999999999999999998559999999


Q ss_pred             EEEEeeecC
Q 008920          411 LRLSHAQQN  419 (548)
Q Consensus       411 I~V~~Ak~~  419 (548)
                      |.|.++.+.
T Consensus        86 i~v~~~~~~   94 (104)
T 1wg5_A           86 IEIFKSSRA   94 (104)
T ss_dssp             CEEEEECTT
T ss_pred             EEEEECCHH
Confidence            999998764

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=5.3e-15  Score=125.56  Aligned_cols=82  Identities=18%  Similarity=0.306  Sum_probs=72.9

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCee-EEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEID-SVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~-sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ...++|||+|||+++++++|+++|+.||.|. +|.|+.++.                 ++.++|||||+|.+.++|+.||
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~-----------------~g~~~g~afV~f~~~~~a~~A~   69 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRL-----------------TGIPAGYCFVEFADLATAEKCL   69 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSS-----------------SCCEEEEEEEECSCHHHHHHHH
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCC-----------------CCCcCCEEEEEeCCHHHHHHHH
Confidence            3468999999999999999999999999999 999966542                 3457799999999999999999


Q ss_pred             H-hcceeecCce----eEeecCCCc
Q 008920          302 A-FNMAVIGGNH----IRLDRACPP  321 (548)
Q Consensus       302 ~-lng~~~~gr~----I~V~~a~~~  321 (548)
                      . ||+..|.|+.    |.|.++.+.
T Consensus        70 ~~l~g~~~~g~~~~~~l~v~~a~~~   94 (99)
T 2div_A           70 HKINGKPLPGATPAKRFKLNYATYS   94 (99)
T ss_dssp             HTTTTSEESSCSSCEECCEEETTCC
T ss_pred             HHHcCCccCCCCcceeEEEeecCCC
Confidence            5 9999999999    999998754

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.58  E-value=1.8e-15  Score=121.88  Aligned_cols=75  Identities=16%  Similarity=0.340  Sum_probs=70.7

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEee
Q 008920          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHA  416 (548)
Q Consensus       338 tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~A  416 (548)
                      +|||+|||+++++++|+++|+.|    |.|..|.|+.++.+|.++|||||+|.+.++|..|+.+.+..|.|+.|.|.||
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQF----GKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTT----SCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhc----CCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEeC
Confidence            48999999999999999999999    8999999999988999999999999999999999984449999999999986

>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=99.58  E-value=1.2e-14  Score=125.82  Aligned_cols=81  Identities=23%  Similarity=0.439  Sum_probs=71.8

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++|+++|+++|+.||.|..|.|+.                    ++.++|||||+|.+.++|+.||
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~--------------------~~~~~g~afV~f~~~~~A~~A~   78 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN--------------------RRGGPPFAFVEFEDPRDAEDAV   78 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC--------------------SSSSSCCEEEEESCHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE--------------------CCCCCcEEEEEECCHHHHHHHH
Confidence            34568999999999999999999999999999999832                    1236799999999999999999


Q ss_pred             -HhcceeecCceeEeecCCCcc
Q 008920          302 -AFNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 -~lng~~~~gr~I~V~~a~~~~  322 (548)
                       .||+..|.|+.|.|.++.+..
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             699999999999999997654

>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=99.57  E-value=4e-15  Score=133.62  Aligned_cols=83  Identities=19%  Similarity=0.348  Sum_probs=78.3

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|.|+.++.++.++|||||+|.+.++|..||..++ ..|.|+.|
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~----G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l  118 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKY----GPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI  118 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTT----SCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            4567899999999999999999999999    899999999999999999999999999999999999877 99999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      .|.|+.+.
T Consensus       119 ~V~~a~~~  126 (129)
T 2kxn_B          119 RVDFSITK  126 (129)
T ss_dssp             EESCCSSS
T ss_pred             EEEEecCC
Confidence            99999864

>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=99.57  E-value=3.2e-15  Score=130.94  Aligned_cols=82  Identities=24%  Similarity=0.327  Sum_probs=76.0

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCe-EEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSV-EAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I-~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|..|    |.| ..|.|+.|. +|.++|||||+|.+.++|..||...+..|.|+.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i   86 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGI----PVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERLHRKKLNGREA   86 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTS----CCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhC----CCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHhCCCccCCeEE
Confidence            3457899999999999999999999999    889 889999997 9999999999999999999999884499999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      .|.++.+.
T Consensus        87 ~v~~a~~~   94 (114)
T 2cpy_A           87 FVHVVTLE   94 (114)
T ss_dssp             EEEEECHH
T ss_pred             EEEECCHH
Confidence            99999865

>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=99.57  E-value=2.4e-15  Score=126.54  Aligned_cols=81  Identities=23%  Similarity=0.365  Sum_probs=74.2

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      ...++|||+|||+.+++++|+++|..|    |.|..|.++.+..++.++|||||+|.+.++|..||..|+ ..|.|+.|+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~   88 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGY----QVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVK   88 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTS----CBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc----CCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEE
Confidence            346899999999999999999999999    899989999998999999999999999999999999777 999999999


Q ss_pred             EEeeec
Q 008920          413 LSHAQQ  418 (548)
Q Consensus       413 V~~Ak~  418 (548)
                      |.++.+
T Consensus        89 v~~a~s   94 (95)
T 2ek1_A           89 LSGPSS   94 (95)
T ss_dssp             EECCC-
T ss_pred             EEeccC
Confidence            999764

>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=99.57  E-value=6.8e-15  Score=126.41  Aligned_cols=84  Identities=18%  Similarity=0.251  Sum_probs=73.3

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      +...++|||+|||+++++++|+++|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|..||
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-----------------TGMHKGCAFLTYCERESALKAQ   72 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSS-----------------SCSCCSEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC-----------------CCCcceEEEEEECCHHHHHHHH
Confidence            44568999999999999999999999999999999855431                 3457899999999999999999


Q ss_pred             -Hhcceee---cCceeEeecCCCcc
Q 008920          302 -AFNMAVI---GGNHIRLDRACPPR  322 (548)
Q Consensus       302 -~lng~~~---~gr~I~V~~a~~~~  322 (548)
                       .||+..+   .|+.|.|.++.+..
T Consensus        73 ~~l~g~~~~~~~g~~l~v~~a~~~~   97 (106)
T 2dgp_A           73 SALHEQKTLPGMNRPIQVKPADSES   97 (106)
T ss_dssp             HHHTTTCCCTTCSSCCEEEECCCCS
T ss_pred             HHhcCCcccCCCCceEEEEECCccc
Confidence             5999887   88999999997654

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=8.3e-15  Score=125.44  Aligned_cols=82  Identities=23%  Similarity=0.335  Sum_probs=73.0

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhh-cCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIK-FGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~-fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ...++|||+|||+++|+++|.++|+. ||.|..|.|+.+.                  ++.++|||||+|.+.++|..||
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~------------------~g~~~g~afV~f~~~~~a~~A~   68 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ------------------TGVSKGYGFVKFTDELEQKRAL   68 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT------------------TCCEEEEEEEEESCHHHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC------------------CCCccceEEEEECCHHHHHHHH
Confidence            44689999999999999999999999 9999999996653                  2347799999999999999999


Q ss_pred             H-hccee-ecCceeEeecCCCcc
Q 008920          302 A-FNMAV-IGGNHIRLDRACPPR  322 (548)
Q Consensus       302 ~-lng~~-~~gr~I~V~~a~~~~  322 (548)
                      . ||+.. |.|+.|.|.++.+..
T Consensus        69 ~~l~g~~~~~g~~l~v~~a~~~~   91 (104)
T 2dhg_A           69 TECQGAVGLGSKPVRLSVAIPKA   91 (104)
T ss_dssp             HHTTTCCSSSSSCCCCCBCCCCC
T ss_pred             HHccCCcccCCEeEEEEEccCCC
Confidence            5 99999 999999999997643

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=6.3e-15  Score=128.96  Aligned_cols=82  Identities=20%  Similarity=0.389  Sum_probs=73.1

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      ..++|||+|||+++|+++|+++|..||.|..|.|+.++.                 ++.++|||||+|.+.++|..||.+
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 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPA-----------------SKRSRGFGFVTFSSMAEVDAAMAA   88 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTT-----------------TSSCCSEEEEECSSHHHHHHHHTS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-----------------CCCcCceEEEEeCCHHHHHHHHHh
Confidence            458999999999999999999999999999999965431                 345789999999999999999977


Q ss_pred             cceeecCceeEeecCCCcc
Q 008920          304 NMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~  322 (548)
                      ++..|.|+.|.|.++.+..
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            9999999999999997653

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=1.1e-14  Score=126.69  Aligned_cols=82  Identities=22%  Similarity=0.245  Sum_probs=72.7

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++++++|+++|..||.|..|.|+.+.                  ++.++|||||+|.+.++|..||
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~------------------~g~~~g~afV~f~~~~~a~~A~   73 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK------------------DGKSRGIGTVTFEQSIEAVQAI   73 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT------------------TCSEEEEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC------------------CCCeeeEEEEEECCHHHHHHHH
Confidence            3446899999999999999999999999999999996643                  2347799999999999999999


Q ss_pred             H-hcceeecCceeEeecCCCc
Q 008920          302 A-FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 ~-lng~~~~gr~I~V~~a~~~  321 (548)
                      . ||+..|.|+.|.|.++...
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            5 9999999999999998643

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=6.7e-15  Score=127.83  Aligned_cols=78  Identities=19%  Similarity=0.380  Sum_probs=68.8

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++|+++|+++|++||.|.+|+|+.                       .+|||||+|.+.++|..|+
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~-----------------------~kGfaFVeF~~~~~A~~Ai   69 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-----------------------GKNQAFIEMNTEEAANTMV   69 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEET-----------------------TTTEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEc-----------------------CCCEEEEEECCHHHHHHHH
Confidence            34568999999999999999999999999999999843                       3589999999999999999


Q ss_pred             H-hc--ceeecCceeEeecCCCcc
Q 008920          302 A-FN--MAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 ~-ln--g~~~~gr~I~V~~a~~~~  322 (548)
                      . |+  +..|.|+.|.|.++.+..
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            5 65  578999999999997643

>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=99.57  E-value=7.4e-15  Score=126.48  Aligned_cols=81  Identities=16%  Similarity=0.211  Sum_probs=70.7

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeE-EEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDS-VRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~s-Vri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ...++|||+|||+++|+++|+++|..||.|.. |.|+.+                  .+|.++|||||+|.+.++|..||
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 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD------------------FQGRSTGEAFVQFASQEIAEKAL   74 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC------------------SSSCBCSEEEEEESSHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC------------------CCCCcceEEEEEECCHHHHHHHH
Confidence            44689999999999999999999999999987 777432                  14557899999999999999999


Q ss_pred             HhcceeecCceeEeecCCCc
Q 008920          302 AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~  321 (548)
                      .+|+..|.|+.|.|.++...
T Consensus        75 ~~~~~~~~gr~i~v~~~~~~   94 (104)
T 1wg5_A           75 KKHKERIGHRYIEIFKSSRA   94 (104)
T ss_dssp             TTTTCCSSSSCCEEEEECTT
T ss_pred             HhCcchhCCcEEEEEECCHH
Confidence            77999999999999988643

>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=99.57  E-value=6.7e-15  Score=126.75  Aligned_cols=81  Identities=22%  Similarity=0.298  Sum_probs=73.1

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELR  412 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~  412 (548)
                      ....++|||+|||+++++++|+++|..|    | +..|.|+.+. ++.++|||||+|.+.++|..||.+.+..|.|+.|.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~----G-~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~   85 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPL----N-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVE   85 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSC----C-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHc----C-ceEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEE
Confidence            3456899999999999999999999999    8 4499999997 89999999999999999999996544999999999


Q ss_pred             EEeeecC
Q 008920          413 LSHAQQN  419 (548)
Q Consensus       413 V~~Ak~~  419 (548)
                      |.++.+.
T Consensus        86 V~~~~~~   92 (102)
T 1wez_A           86 LFLNSTA   92 (102)
T ss_dssp             EEEECCC
T ss_pred             EEECCCC
Confidence            9998764

>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=99.57  E-value=3.6e-15  Score=128.48  Aligned_cols=81  Identities=16%  Similarity=0.205  Sum_probs=71.1

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++|+++|+++|+.||.| .|.|+.++                  ++.++|||||+|.+.++|+.||
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------------------DGRVTGEADVEFATHEDAVAAM   72 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS------------------SSCEEEEEEEECSSSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC------------------CCCEeeEEEEEECCHHHHHHHH
Confidence            3446899999999999999999999999954 99986643                  3457899999999999999999


Q ss_pred             HhcceeecCceeEeecCCCc
Q 008920          302 AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~  321 (548)
                      .+|+..|.|+.|.|.++.+.
T Consensus        73 ~~~~~~~~gr~i~V~~~~~~   92 (102)
T 1wez_A           73 AKDKANMQHRYVELFLNSTA   92 (102)
T ss_dssp             TTSSCCSSSSCCEEEEECCC
T ss_pred             HhCCCeECCcEEEEEECCCC
Confidence            99999999999999988654

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=8.7e-15  Score=127.35  Aligned_cols=85  Identities=18%  Similarity=0.209  Sum_probs=73.4

Q ss_pred             CCCcccEEEEcCCCCCCcHHHHHHHhhhcCCee--------EEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEec
Q 008920          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEID--------SVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFK  292 (548)
Q Consensus       221 ~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~--------sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~  292 (548)
                      +....++|||+|||+++|+++|+++|+.||.|.        .|.|+.+.                 .++.++|||||+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~-----------------~~g~~~g~afV~f~   73 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDK-----------------ETGKPKGDATVSYE   73 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCT-----------------TTCSBCSEEEEEBS
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeC-----------------CCCCeeeEEEEEEC
Confidence            344578999999999999999999999999998        58775432                 23557899999999


Q ss_pred             CHHHHHHHHH-hcceeecCceeEeecCCCcc
Q 008920          293 SEQSTEAALA-FNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       293 s~e~A~~Al~-lng~~~~gr~I~V~~a~~~~  322 (548)
                      +.++|..||. ||+..|.|+.|.|.++.+..
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            9999999995 99999999999999997653

>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=99.57  E-value=3.1e-15  Score=127.95  Aligned_cols=81  Identities=22%  Similarity=0.391  Sum_probs=72.7

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||+.+++++|+++|+.||.|..|.|+.++.                 +|.++|||||+|.+.++|..|| .
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~-----------------~g~~~g~afV~f~~~~~a~~A~~~   69 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRE-----------------TGKPKGYGFCEYQDQETALSAMRN   69 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETT-----------------TTEEEEEEEEECSCHHHHHHHHHH
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCC-----------------CCccceEEEEEECCHHHHHHHHHH
Confidence            458999999999999999999999999999999966542                 3457899999999999999999 5


Q ss_pred             hcceeecCceeEeecCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~  321 (548)
                      ||+..|.|+.|.|.++.+.
T Consensus        70 l~g~~~~g~~l~v~~a~~~   88 (104)
T 1p1t_A           70 LNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             SSSBSCSSSCBEEEETTCT
T ss_pred             hCCCeeCCcEEEEEeCCCc
Confidence            9999999999999999764

>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=99.57  E-value=8.2e-15  Score=126.88  Aligned_cols=81  Identities=19%  Similarity=0.259  Sum_probs=71.9

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+.+++++|..+|+.||.|..|.|+.+.                 .+|.++|||||+|.+.++|..||.
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-----------------RTGFSKGYALVEYETHKQALAAKE   86 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCT-----------------TTSSBCSEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC-----------------CCCCcceEEEEEECCHHHHHHHHH
Confidence            346899999999999999999999999999999985433                 234578999999999999999995


Q ss_pred             -hcceeecCceeEeecCCC
Q 008920          303 -FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 -lng~~~~gr~I~V~~a~~  320 (548)
                       |||..|.|+.|.|.++.+
T Consensus        87 ~l~g~~~~g~~l~V~~a~~  105 (110)
T 1oo0_B           87 ALNGAEIMGQTIQVDWCFV  105 (110)
T ss_dssp             HHTTCEETTEECEEEESEE
T ss_pred             HcCCCEECCcEEEEEEccc
Confidence             999999999999999864

>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=99.57  E-value=7.4e-15  Score=127.95  Aligned_cols=83  Identities=23%  Similarity=0.251  Sum_probs=75.5

Q ss_pred             CCccEEEEeCCCCCCCHHHHH---HHHhccCCCCCCeEEEEEeecCCCC---CCceEEEEEECCHHHHHHHHHHcC-Ccc
Q 008920          334 DIKKTVFVGNLPFDVKDEEIY---QLFCGLNDLESSVEAVRVIRHPHMR---VGKGIAYVLFKTREAANLVIKRRN-LKL  406 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~---~~F~~~g~~~G~I~~VrI~~d~~tg---~srG~AFV~F~~~e~A~~Al~~ln-~~l  406 (548)
                      ...++|||+|||+.+++++|+   ++|..|    |.|..|.|+.+..++   .++|||||+|.+.++|..||..|+ ..|
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~----G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~   88 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKF----GKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVV   88 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTT----SCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhcc----CCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEE
Confidence            356899999999999999999   999999    999999999987644   566999999999999999999877 999


Q ss_pred             CCeEEEEEeeecCC
Q 008920          407 RDRELRLSHAQQNC  420 (548)
Q Consensus       407 ~Gr~I~V~~Ak~~~  420 (548)
                      .|+.|.|.||.++.
T Consensus        89 ~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           89 DGRTLKASLGTTKY  102 (111)
T ss_dssp             TTEEEEEESCCCCS
T ss_pred             CCEEEEEEeccccc
Confidence            99999999998764

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.57  E-value=4.5e-15  Score=131.01  Aligned_cols=80  Identities=15%  Similarity=0.131  Sum_probs=71.8

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCC---eeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGE---IDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~---I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~  299 (548)
                      ...++|||+|||+++|+++|+++|+.||.   |..|+|+.+.                  .|.++|||||+|.+.++|.+
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~------------------~g~~~G~afV~F~~~~~a~~   76 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR------------------EGRQSGEAFVELESEDDVKL   76 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECS------------------SSCEEEEEEEEBSSHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECC------------------CCCCCeEEEEEECCHHHHHH
Confidence            34689999999999999999999999999   8999996643                  24578999999999999999


Q ss_pred             HHHhcceeecCceeEeecCCC
Q 008920          300 ALAFNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       300 Al~lng~~~~gr~I~V~~a~~  320 (548)
                      ||.+|+..|.|+.|.|.++..
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            999999999999999999853

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=1.2e-14  Score=121.54  Aligned_cols=80  Identities=19%  Similarity=0.277  Sum_probs=71.7

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++++++|+++|+.| .|..|.|+.+.                  +|.++|||||+|.+.++|..||.
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------------------HGNKTGYIFVDFSNEEEVKQALK   68 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECT------------------TSCEEEEEEEECSSHHHHHHHHH
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECC------------------CCCCceEEEEEECCHHHHHHHHH
Confidence            346899999999999999999999999 89999996542                  34578999999999999999999


Q ss_pred             hcceeecCceeEeecCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~  321 (548)
                      ||+..|.|+.|.|.++.+.
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            9999999999999998654

>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=99.57  E-value=9.6e-15  Score=125.71  Aligned_cols=79  Identities=15%  Similarity=0.252  Sum_probs=71.1

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+.+++++|.++|+.||.|..|.|+.+.                  +|.++|||||+|.+.++|..||.
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------------------SGRSLGTADVHFERKADALKAMK   88 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT------------------TSCEEEEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC------------------CCCcceEEEEEECCHHHHHHHHH
Confidence            446899999999999999999999999999999996644                  34477999999999999999995


Q ss_pred             -hcceeecCceeEeecCC
Q 008920          303 -FNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       303 -lng~~~~gr~I~V~~a~  319 (548)
                       ||+..|.|+.|.|.++.
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             99999999999999874

>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=99.56  E-value=9.3e-15  Score=126.98  Aligned_cols=83  Identities=18%  Similarity=0.316  Sum_probs=73.4

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+.+++++|.++|+.||.|..|.|+.++.                 +|.++|||||+|.+.++|..||
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-----------------TGRSKGYGFITFSDSECAKKAL   85 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETT-----------------TTEEEEEEEEEESCHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCC-----------------CCccceEEEEEECCHHHHHHHH
Confidence            34568999999999999999999999999999999976542                 3447799999999999999999


Q ss_pred             -HhcceeecCceeEeecCCCc
Q 008920          302 -AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 -~lng~~~~gr~I~V~~a~~~  321 (548)
                       .|||..|.|+.|.|.++.+.
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             59999999999999998653

>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=99.56  E-value=4.7e-15  Score=134.67  Aligned_cols=81  Identities=14%  Similarity=0.235  Sum_probs=74.7

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCC---eEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCC
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESS---VEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRD  408 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~---I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~G  408 (548)
                      ....++|||+|||+++|+++|+++|..|    |.   |..|+|++|.. |.++|||||+|.+.++|..||. ++ ..|.|
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~----G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~g  114 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDC----TIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGH  114 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTC----CCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHh----CCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECC
Confidence            4457899999999999999999999999    77   88999999976 9999999999999999999999 76 99999


Q ss_pred             eEEEEEeeecC
Q 008920          409 RELRLSHAQQN  419 (548)
Q Consensus       409 r~I~V~~Ak~~  419 (548)
                      +.|.|.++.+.
T Consensus       115 r~i~V~~a~~~  125 (136)
T 2hgl_A          115 RYIEVFKSHRT  125 (136)
T ss_dssp             SEEEEEECCHH
T ss_pred             EEEEEEECChH
Confidence            99999998653

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=1.4e-14  Score=126.66  Aligned_cols=83  Identities=22%  Similarity=0.333  Sum_probs=72.2

Q ss_pred             CCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       221 ~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      .+...++|||+|||+++|+++|+++|+.||.|..|+|+.++.                 ++.++|||||+|.+.++|+.|
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-----------------TGKSRGYGFVTMADRAAAERA   75 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSS-----------------SCCCCSEEEEEESSHHHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCC-----------------CCccceEEEEEECCHHHHHHH
Confidence            345578999999999999999999999999999999955431                 345789999999999999999


Q ss_pred             HH-hcceeecCceeEeecCCCc
Q 008920          301 LA-FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       301 l~-lng~~~~gr~I~V~~a~~~  321 (548)
                      |. +++ .|.|+.|.|.++...
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            95 777 899999999999654

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.56  E-value=1.1e-14  Score=121.71  Aligned_cols=80  Identities=23%  Similarity=0.253  Sum_probs=71.3

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++++++|+++|+.||.|..|.|+.+                   ++.++|||||+|.+.++|..||.
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-------------------NGKSKGCGVVKFESPEVAERACR   66 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-------------------SSCEEEEEEEEESSHHHHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-------------------CCCcceEEEEEECCHHHHHHHHH
Confidence            34689999999999999999999999999999998541                   23467999999999999999995


Q ss_pred             -hcceeecCceeEeecCCCc
Q 008920          303 -FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 -lng~~~~gr~I~V~~a~~~  321 (548)
                       ||+..|.|+.|.|.++.+.
T Consensus        67 ~l~g~~~~g~~l~v~~a~~~   86 (92)
T 2dgv_A           67 MMNGMKLSGREIDVRIDRNA   86 (92)
T ss_dssp             HHTTCCBTTBCCCCEECSCC
T ss_pred             HhCCCEECCcEEEEEEcCCC
Confidence             9999999999999998764

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1.4e-14  Score=123.61  Aligned_cols=82  Identities=22%  Similarity=0.310  Sum_probs=74.2

Q ss_pred             cCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeE
Q 008920          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE  410 (548)
Q Consensus       332 ~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~  410 (548)
                      .....++|||+|||+.+++++|+++|..|    +   .|.++.+..++.++|||||+|.+.++|..||..|+ ..|.|+.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~----~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   83 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGS----V---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNK   83 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTC----S---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCC----e---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeE
Confidence            34567999999999999999999999987    3   57788898899999999999999999999999877 9999999


Q ss_pred             EEEEeeecCC
Q 008920          411 LRLSHAQQNC  420 (548)
Q Consensus       411 I~V~~Ak~~~  420 (548)
                      |.|.|+.+..
T Consensus        84 l~V~~a~~~~   93 (102)
T 2fc8_A           84 VTLDWAKPKG   93 (102)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEEecCCC
Confidence            9999998754

>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=99.56  E-value=2.2e-14  Score=122.97  Aligned_cols=78  Identities=23%  Similarity=0.353  Sum_probs=70.6

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|.|+        +|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~----G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l   75 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQF----GKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENI   75 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHH----SCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEE
Confidence            4467899999999999999999999999    899999887        4599999999999999999877 99999999


Q ss_pred             EEEeeecCCCC
Q 008920          412 RLSHAQQNCTP  422 (548)
Q Consensus       412 ~V~~Ak~~~~~  422 (548)
                      .|.|+.+....
T Consensus        76 ~v~~a~~~~~~   86 (103)
T 2dgu_A           76 EIVFAKPPDQK   86 (103)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEcCCCccc
Confidence            99999886443

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=2.1e-14  Score=122.78  Aligned_cols=83  Identities=16%  Similarity=0.230  Sum_probs=72.4

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++++++|.++|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|..||
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-----------------TGHSKGFGFVRFTEYETQVKVM   74 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSS-----------------SCSEEEEEEEEESSHHHHHHHH
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCC-----------------CCCccceEEEEECCHHHHHHHH
Confidence            34468999999999999999999999999999999966542                 3457899999999999999999


Q ss_pred             HhcceeecCceeEeecCCCcc
Q 008920          302 AFNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~~  322 (548)
                      . ++..|.|+.|.|.++.+..
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

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.56  E-value=3.5e-15  Score=133.87  Aligned_cols=82  Identities=17%  Similarity=0.328  Sum_probs=76.4

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEE--EEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-C----c
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEA--VRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-L----K  405 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~--VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~----~  405 (548)
                      ....++|||+|||+++++++|+++|..|    |.|..  |+|++|+.+|.++|||||+|.+. +|..||..|+ .    .
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~----G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~   94 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPY----AVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLT   94 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGG----CCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHh----CCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCcc
Confidence            3457899999999999999999999999    89976  99999999999999999999999 9999999888 7    9


Q ss_pred             cCCeEEEEEeeecC
Q 008920          406 LRDRELRLSHAQQN  419 (548)
Q Consensus       406 l~Gr~I~V~~Ak~~  419 (548)
                      |.|+.|.|.|+.+.
T Consensus        95 ~~gr~l~V~~a~~~  108 (131)
T 2m2b_A           95 IDGKTINVEFAKGS  108 (131)
T ss_dssp             GGGCCCCCEECCCS
T ss_pred             CCCEEEEEEECCCC
Confidence            99999999999864

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1.4e-14  Score=123.57  Aligned_cols=80  Identities=21%  Similarity=0.338  Sum_probs=72.5

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|   .|+.+ .++.++|||||+|.+.++|..||..++ ..|.|+.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   83 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKA----TFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAI   83 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSC----SEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhC----CEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEE
Confidence            4567999999999999999999999999    766   56777 689999999999999999999999887 99999999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      .|.|+.+..
T Consensus        84 ~v~~a~~~~   92 (101)
T 2fc9_A           84 RLELQGPRG   92 (101)
T ss_dssp             EEEECSSCC
T ss_pred             EEEEcCCCC
Confidence            999998763

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=2e-15  Score=124.60  Aligned_cols=80  Identities=14%  Similarity=0.196  Sum_probs=74.3

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      .+.++|||+|||+.+++++|+++|+.|    |.|..|.|+.++.++.++|||||+|.+.++|..||..|+ ..|.|+.|+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~----G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~   78 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPY----GKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   78 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTT----SCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEe
Confidence            356899999999999999999999999    899999999999999999999999999999999999887 899999998


Q ss_pred             EEeee
Q 008920          413 LSHAQ  417 (548)
Q Consensus       413 V~~Ak  417 (548)
                      |.|+.
T Consensus        79 ~~~~~   83 (85)
T 1x4e_A           79 QSGPS   83 (85)
T ss_dssp             SSCCC
T ss_pred             ecCCC
Confidence            87653

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.56  E-value=1.1e-14  Score=125.51  Aligned_cols=81  Identities=17%  Similarity=0.182  Sum_probs=70.9

Q ss_pred             CCcccEEEEcCCCCCC------cHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHH
Q 008920          222 GKLLRTIFVGNLPLKV------KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQ  295 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~------tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e  295 (548)
                      ....++|||+|||+.+      |+++|..+|+.||.|..|.|+.    .               +|.++|||||+|.+.+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~----~---------------~g~~~G~afV~f~~~~   72 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE----E---------------DGKTKGYIFLEYASPA   72 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC----B---------------TTBSCCEEEEEECSSS
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC----C---------------CCCeeeEEEEEECCHH
Confidence            3446899999999999      8899999999999999998841    1               3457899999999999


Q ss_pred             HHHHHHH-hcceeecCc-eeEeecCCCc
Q 008920          296 STEAALA-FNMAVIGGN-HIRLDRACPP  321 (548)
Q Consensus       296 ~A~~Al~-lng~~~~gr-~I~V~~a~~~  321 (548)
                      +|..||. |||..|.|+ .|.|.++...
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            9999995 999999998 9999998643

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.56  E-value=1.3e-14  Score=123.42  Aligned_cols=80  Identities=24%  Similarity=0.258  Sum_probs=71.1

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeE--------EEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecC
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDS--------VRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKS  293 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~s--------Vri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s  293 (548)
                      ....++|||+|||+++++++|+++|+.||.|..        |.|+.++.                 +|.++|||||+|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~-----------------~g~~~G~afV~f~~   72 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRE-----------------TGKLKGEATVSFDD   72 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTT-----------------TCSEEEEEEEEBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCC-----------------CCCeeeEEEEEECC
Confidence            345689999999999999999999999999999        88865431                 34578999999999


Q ss_pred             HHHHHHHH-HhcceeecCceeEeecC
Q 008920          294 EQSTEAAL-AFNMAVIGGNHIRLDRA  318 (548)
Q Consensus       294 ~e~A~~Al-~lng~~~~gr~I~V~~a  318 (548)
                      .++|..|| .|||..|.|+.|.|.++
T Consensus        73 ~~~a~~Ai~~l~g~~~~g~~l~V~~A   98 (99)
T 2la6_A           73 PPSAKAAIDWFDGKEFSGNPIKVSFA   98 (99)
T ss_dssp             HHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             HHHHHHHHHHhCCCEeCCcEEEEEec
Confidence            99999999 59999999999999987

>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=99.56  E-value=7.2e-15  Score=127.03  Aligned_cols=77  Identities=12%  Similarity=0.164  Sum_probs=70.1

Q ss_pred             CCCccEEEEeCCCC-CCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC---CccCC
Q 008920          333 YDIKKTVFVGNLPF-DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN---LKLRD  408 (548)
Q Consensus       333 ~~~~~tLfV~NLp~-~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln---~~l~G  408 (548)
                      .++.++|||+|||+ .+++++|+++|.+|    |.|..|.|+++      +|||||+|.+.++|..||..|+   ..|.|
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~f----G~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~G   81 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPF----GVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFG   81 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGG----SCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETT
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhc----CCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECC
Confidence            44678999999999 99999999999999    99999999876      5899999999999999998776   45999


Q ss_pred             eEEEEEeeecC
Q 008920          409 RELRLSHAQQN  419 (548)
Q Consensus       409 r~I~V~~Ak~~  419 (548)
                      ++|.|.||...
T Consensus        82 r~l~V~~a~~~   92 (102)
T 1x4d_A           82 KPVRVHLSQKY   92 (102)
T ss_dssp             EECEEEEECCC
T ss_pred             cEEEEEECCCC
Confidence            99999999864

>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=99.56  E-value=2.9e-15  Score=128.04  Aligned_cols=81  Identities=35%  Similarity=0.544  Sum_probs=73.2

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecC-CCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP-HMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE  410 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~-~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~  410 (548)
                      ....++|||+|||+++++++|+++|+.|    | |..|.|+.+. .+|.++|||||+|.+.++|..|| .++ ..|.|+.
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~   89 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGL----N-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRR   89 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSS----C-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhc----C-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeE
Confidence            4567999999999999999999999999    9 9999999998 68999999999999999999999 666 9999999


Q ss_pred             EEEEeeecC
Q 008920          411 LRLSHAQQN  419 (548)
Q Consensus       411 I~V~~Ak~~  419 (548)
                      |.|.|+.+.
T Consensus        90 l~V~~a~~~   98 (100)
T 2j76_E           90 IRVDVADQA   98 (100)
T ss_dssp             CCCEECCCS
T ss_pred             EEEEeccCC
Confidence            999999864

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1.7e-14  Score=120.51  Aligned_cols=76  Identities=21%  Similarity=0.305  Sum_probs=69.1

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++|+++|+.+|+.||.|..|.|+                         ++||||+|.+.++|..||
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            3456899999999999999999999999999999982                         369999999999999999


Q ss_pred             H-hcceeecCceeEeecCCCcc
Q 008920          302 A-FNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 ~-lng~~~~gr~I~V~~a~~~~  322 (548)
                      . ||+..|.|+.|.|.++.+..
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            4 99999999999999997653

>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=99.56  E-value=1.8e-15  Score=126.18  Aligned_cols=79  Identities=22%  Similarity=0.439  Sum_probs=72.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEe
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSH  415 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~  415 (548)
                      ++|||+|||+.+++++|+++|+.|    |.|..|.|+.+..+|.++|||||+|.+.+ |..|+..++ ..|.|+.|.|.+
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~   76 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQF----GKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTE   76 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHH----TCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEE
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhc----CCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEE
Confidence            589999999999999999999999    89999999999999999999999999999 999999888 999999999999


Q ss_pred             eecCC
Q 008920          416 AQQNC  420 (548)
Q Consensus       416 Ak~~~  420 (548)
                      |.+..
T Consensus        77 a~~~~   81 (90)
T 2ki2_A           77 ANPKK   81 (90)
T ss_dssp             C----
T ss_pred             cCCCC
Confidence            98764

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1.4e-14  Score=123.90  Aligned_cols=82  Identities=18%  Similarity=0.283  Sum_probs=72.8

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++|+++|.++|+.||.|..|.|+.+                   ++.++|||||+|.+.++|..||
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-------------------GGRSKGFGFVCFSSPEEATKAV   72 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-------------------SSSEEEEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-------------------CCCcCEEEEEEECCHHHHHHHH
Confidence            345689999999999999999999999999999999553                   2346799999999999999999


Q ss_pred             H-hcceeecCceeEeecCCCcc
Q 008920          302 A-FNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 ~-lng~~~~gr~I~V~~a~~~~  322 (548)
                      . ||+..|.|+.|.|.++.+..
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            5 99999999999999997654

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=3.4e-14  Score=120.78  Aligned_cols=76  Identities=24%  Similarity=0.381  Sum_probs=69.2

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhc--CCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKF--GEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~f--G~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~  299 (548)
                      ....++|||+|||+++|+++|+.+|+.|  |.|..|.+                         .+|||||+|.+.++|..
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            3456899999999999999999999999  99998887                         45899999999999999


Q ss_pred             HHH-hcceeecCceeEeecCCCcc
Q 008920          300 ALA-FNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       300 Al~-lng~~~~gr~I~V~~a~~~~  322 (548)
                      ||. ||+..|.|+.|.|.++.+..
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            995 99999999999999997654

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.56  E-value=8.9e-15  Score=128.26  Aligned_cols=81  Identities=20%  Similarity=0.379  Sum_probs=71.5

Q ss_pred             CCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       221 ~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      +....++|||+|||+++++++|+++|+.||.|..|.|+.++                 .++.++|||||+|.+.++|..|
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-----------------~~g~~~g~afV~f~~~~~A~~A   98 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDK-----------------QTSLSKCFGFVSFDNPDSAQVA   98 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCS-----------------SSSCCCCEEEEEEESSHHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCC-----------------CCCCcCcEEEEEECCHHHHHHH
Confidence            34456899999999999999999999999999999995543                 1345789999999999999999


Q ss_pred             H-HhcceeecCceeEeecC
Q 008920          301 L-AFNMAVIGGNHIRLDRA  318 (548)
Q Consensus       301 l-~lng~~~~gr~I~V~~a  318 (548)
                      | .||+..|.|+.|.|.++
T Consensus        99 ~~~l~g~~~~g~~l~V~~a  117 (118)
T 2khc_A           99 IKAMNGFQVGTKRLKVQLK  117 (118)
T ss_dssp             HHHCCCCEETTEECCEEEC
T ss_pred             HHHcCCCEECCEEEEEEec
Confidence            9 59999999999999986

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=6.8e-15  Score=127.79  Aligned_cols=77  Identities=21%  Similarity=0.336  Sum_probs=70.2

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC---CccCCeE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN---LKLRDRE  410 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln---~~l~Gr~  410 (548)
                      .+.++|||+|||+.+++++|+++|++|    |.|..|.|+++      +|||||+|.+.++|..||..++   ..|.|++
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~f----G~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~   83 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPF----GKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQP   83 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHH----CCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEE
Confidence            357899999999999999999999999    99999999976      7899999999999999998653   6899999


Q ss_pred             EEEEeeecCC
Q 008920          411 LRLSHAQQNC  420 (548)
Q Consensus       411 I~V~~Ak~~~  420 (548)
                      |.|.||.++.
T Consensus        84 l~V~~A~~~~   93 (105)
T 1sjq_A           84 IYIQFSNHKE   93 (105)
T ss_dssp             CCBCCCSSSS
T ss_pred             EEEEEcCCCC
Confidence            9999998753

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=2.7e-14  Score=119.72  Aligned_cols=76  Identities=16%  Similarity=0.302  Sum_probs=69.3

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++++++|+++|+.||.|..|.|                         .++||||+|.+.++|..|+
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~-------------------------~~~~afV~f~~~~~a~~A~   61 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDI-------------------------VKDYAFVHMERAEDAVEAI   61 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEE-------------------------CSSEEEEEESCHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEE-------------------------ECCEEEEEECCHHHHHHHH
Confidence            345689999999999999999999999999999998                         2369999999999999999


Q ss_pred             -HhcceeecCceeEeecCCCcc
Q 008920          302 -AFNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 -~lng~~~~gr~I~V~~a~~~~  322 (548)
                       .||+..|.|+.|.|.++.+..
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             599999999999999997653

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.55  E-value=1.3e-14  Score=128.29  Aligned_cols=80  Identities=25%  Similarity=0.366  Sum_probs=72.6

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhc
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~ln  304 (548)
                      .++|||+|||+++|+++|.++|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|..||.||
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-----------------SGHPKGYAYIEFAERNSVDAAVAMD   98 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECT-----------------TSSCEEEEEEEESSHHHHHHHHTTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC-----------------CCCcccEEEEEECCHHHHHHHHhcC
Confidence            58999999999999999999999999999999976542                 3457899999999999999999999


Q ss_pred             ceeecCceeEeecCCCc
Q 008920          305 MAVIGGNHIRLDRACPP  321 (548)
Q Consensus       305 g~~~~gr~I~V~~a~~~  321 (548)
                      +..|.|+.|.|.++.+.
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

>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=99.55  E-value=1.8e-15  Score=121.70  Aligned_cols=75  Identities=21%  Similarity=0.435  Sum_probs=71.6

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEee
Q 008920          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHA  416 (548)
Q Consensus       338 tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~A  416 (548)
                      +|||+|||+.+++++|+++|+.|    |.|..|.|+.++.+|.++|||||+|.+.++|..||..++..|.|+.|.|.+|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGF----GEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHH----SCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEC
Confidence            59999999999999999999999    8999999999999999999999999999999999998669999999999885

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.55  E-value=2e-14  Score=129.28  Aligned_cols=81  Identities=23%  Similarity=0.359  Sum_probs=75.9

Q ss_pred             cCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeE
Q 008920          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE  410 (548)
Q Consensus       332 ~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~  410 (548)
                      .....++|||+|||+.+++++|+++|..|    |.|..|.|+.++.++.++|||||+|.+.++|..||..++ ..|.|+.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~  134 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPF----GDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRT  134 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGG----SCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhc----CCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            34567999999999999999999999999    899999999999999999999999999999999999888 9999999


Q ss_pred             EEEEee
Q 008920          411 LRLSHA  416 (548)
Q Consensus       411 I~V~~A  416 (548)
                      |+|.||
T Consensus       135 l~v~~A  140 (140)
T 2ku7_A          135 IRVNLA  140 (140)
T ss_dssp             EEEEC-
T ss_pred             EEEEeC
Confidence            999986

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.55  E-value=1.7e-15  Score=138.21  Aligned_cols=122  Identities=17%  Similarity=0.197  Sum_probs=72.3

Q ss_pred             ceEEEEecCHHHHHHHHHhcceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCC
Q 008920          285 VHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLE  364 (548)
Q Consensus       285 G~AFV~F~s~e~A~~Al~lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~  364 (548)
                      |+||.+|..++.+..++..-..++.|...--.....       .........++|||+|||+++++++|+++|..|    
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            678888888887766663222223333221111100       001123456899999999999999999999999    


Q ss_pred             CCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeecCC
Q 008920          365 SSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQNC  420 (548)
Q Consensus       365 G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~~  420 (548)
                      | |..|.|+.|.. |.++|||||+|.+.++|..|| .++ ..|.|+.|.|.++.+..
T Consensus        71 G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~  124 (139)
T 2hgn_A           71 N-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTG  124 (139)
T ss_dssp             C-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSC
T ss_pred             C-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCC
Confidence            8 67999999975 999999999999999999999 555 99999999999987653

>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=99.55  E-value=3e-14  Score=124.13  Aligned_cols=82  Identities=16%  Similarity=0.330  Sum_probs=75.4

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-Ccc-----
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKL-----  406 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l-----  406 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|..|.|+.+. ++.++|||||+|.+.++|..||..|+ ..|     
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~   96 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPF----GQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPG   96 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTT----SCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCcc
Confidence            3457899999999999999999999999    899999999997 89999999999999999999999777 777     


Q ss_pred             ---CCeEEEEEeeecC
Q 008920          407 ---RDRELRLSHAQQN  419 (548)
Q Consensus       407 ---~Gr~I~V~~Ak~~  419 (548)
                         .+++|.|.|+.+.
T Consensus        97 ~~~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           97 VSAPTEPLLCKFSGPS  112 (114)
T ss_dssp             SCCCSSCBEEEECCCS
T ss_pred             ccCCCCceeEEccCCC
Confidence               6888999999864

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.55  E-value=1.7e-14  Score=124.14  Aligned_cols=77  Identities=13%  Similarity=0.086  Sum_probs=69.8

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-C--ccCCe
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-L--KLRDR  409 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~--~l~Gr  409 (548)
                      ..++++|||+|||+.+++++|+++|++|    |.|.+|.|+++      +|||||+|.+.++|..|+..++ .  .|.|+
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~f----G~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr   87 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEF----GPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGH   87 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcc----CCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCc
Confidence            4578999999999999999999999999    89999999854      7899999999999999998876 4  48999


Q ss_pred             EEEEEeeecC
Q 008920          410 ELRLSHAQQN  419 (548)
Q Consensus       410 ~I~V~~Ak~~  419 (548)
                      +|.|.|++.+
T Consensus        88 ~i~V~~S~~k   97 (100)
T 3r27_A           88 PAFVNYSTSQ   97 (100)
T ss_dssp             EEEEEECSCS
T ss_pred             EEEEEecccc
Confidence            9999999764

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=2.2e-14  Score=119.76  Aligned_cols=75  Identities=16%  Similarity=0.340  Sum_probs=69.0

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...++|||+|||+++++++|+++|+.||.|..|.|+                         +|||||+|.+.++|..|| 
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-------------------------~g~afV~f~~~~~A~~A~~   60 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------------------------KNYGFVHIEDKTAAEDAIR   60 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-------------------------TTEEEEEESSHHHHHHHHH
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-------------------------CCEEEEEECCHHHHHHHHH
Confidence            456899999999999999999999999999999982                         389999999999999999 


Q ss_pred             HhcceeecCceeEeecCCCcc
Q 008920          302 AFNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~~  322 (548)
                      .||+..|.|+.|.|.++.+..
T Consensus        61 ~l~g~~~~g~~l~v~~a~~~~   81 (90)
T 2dnq_A           61 NLHHYKLHGVNINVEASKNKS   81 (90)
T ss_dssp             HHTTCBCSSCBCEEECSSCCC
T ss_pred             HhcCCccCCcEEEEEECCCCC
Confidence            699999999999999997654

>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=99.55  E-value=5.7e-15  Score=128.76  Aligned_cols=85  Identities=18%  Similarity=0.243  Sum_probs=72.2

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|.+..+..++.++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~----G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l   97 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARF----QEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKIL   97 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHH----HHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHh----CCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEE
Confidence            3467899999999999999999999999    788443333332378899999999999999999999887 99999999


Q ss_pred             EEEeeecCCC
Q 008920          412 RLSHAQQNCT  421 (548)
Q Consensus       412 ~V~~Ak~~~~  421 (548)
                      .|.|+.+...
T Consensus        98 ~v~~a~~~~~  107 (115)
T 2cpx_A           98 VIEFGKNKKQ  107 (115)
T ss_dssp             EEEECCCCSC
T ss_pred             EEEEccCCCC
Confidence            9999987643

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=3.1e-14  Score=118.94  Aligned_cols=77  Identities=23%  Similarity=0.382  Sum_probs=70.5

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ..+.++|||+|||+++++++|+++|+.|    |.|..|.|+        +|||||+|.+.++|..||..++ ..|.|+.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   72 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQY----GKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNI   72 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTS----SCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhC----CCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEE
Confidence            4467999999999999999999999999    899999987        5799999999999999998887 89999999


Q ss_pred             EEEeeecCCC
Q 008920          412 RLSHAQQNCT  421 (548)
Q Consensus       412 ~V~~Ak~~~~  421 (548)
                      .|.|+.+...
T Consensus        73 ~v~~a~~~~~   82 (90)
T 2dnq_A           73 NVEASKNKSK   82 (90)
T ss_dssp             EEECSSCCCC
T ss_pred             EEEECCCCCC
Confidence            9999987643

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.55  E-value=1.7e-14  Score=124.21  Aligned_cols=76  Identities=16%  Similarity=0.173  Sum_probs=67.5

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ..+++|||+|||+++|+++|.++|++||.|.+|.|+.                       .+|||||+|.+.++|..|+ 
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            4568999999999999999999999999999999842                       4589999999999999999 


Q ss_pred             Hhccee--ecCceeEeecCCCc
Q 008920          302 AFNMAV--IGGNHIRLDRACPP  321 (548)
Q Consensus       302 ~lng~~--~~gr~I~V~~a~~~  321 (548)
                      .|++..  |.|+.|.|.++...
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            588764  78999999998653

>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=99.55  E-value=1.9e-14  Score=124.03  Aligned_cols=78  Identities=18%  Similarity=0.266  Sum_probs=70.5

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC---CccCCe
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN---LKLRDR  409 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln---~~l~Gr  409 (548)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|.|+.+      +|||||+|.+.++|..|+..++   ..|.|+
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~f----G~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr   81 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPF----GKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQ   81 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTT----SCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCc
Confidence            4567899999999999999999999999    89999998865      7899999999999999998653   779999


Q ss_pred             EEEEEeeecCC
Q 008920          410 ELRLSHAQQNC  420 (548)
Q Consensus       410 ~I~V~~Ak~~~  420 (548)
                      +|.|.|+.+..
T Consensus        82 ~l~V~~a~~~~   92 (101)
T 2cq1_A           82 PIYIQYSNHKE   92 (101)
T ss_dssp             ECEEEECSCSS
T ss_pred             EEEEEEcCccc
Confidence            99999998653

>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=99.55  E-value=1.1e-14  Score=125.74  Aligned_cols=75  Identities=19%  Similarity=0.256  Sum_probs=66.8

Q ss_pred             cccEEEEcCCCC-CCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          224 LLRTIFVGNLPL-KVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       224 ~~rtVfVgNLP~-~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ..++|||+|||+ ++|+++|..+|++||.|.+|+|+.                       .+|||||+|.+.++|..|| 
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            468999999999 999999999999999999999843                       3489999999999999999 


Q ss_pred             Hhcc--eeecCceeEeecCCCc
Q 008920          302 AFNM--AVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 ~lng--~~~~gr~I~V~~a~~~  321 (548)
                      .||+  ..|.|++|.|.++...
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  4599999999999754

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.55  E-value=2.1e-14  Score=129.48  Aligned_cols=86  Identities=24%  Similarity=0.356  Sum_probs=75.4

Q ss_pred             cCCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHH
Q 008920          220 DEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (548)
Q Consensus       220 ~~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~  299 (548)
                      .+....++|||+|||+++++++|..+|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|..
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-----------------~~~~~g~afV~f~~~~~a~~   99 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRE-----------------TRQSRGYGFVKFQSGSSAQQ   99 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETT-----------------TTEEEEEEEEEESSHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCC-----------------CCCcceEEEEEECCHHHHHH
Confidence            3445578999999999999999999999999999999976542                 24477999999999999999


Q ss_pred             HHH-hcceeecCceeEeecCCCcc
Q 008920          300 ALA-FNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       300 Al~-lng~~~~gr~I~V~~a~~~~  322 (548)
                      ||. ||+..|.|+.|.|.++.+..
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            995 99999999999999997653

>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=99.55  E-value=3.7e-15  Score=119.91  Aligned_cols=75  Identities=23%  Similarity=0.377  Sum_probs=67.0

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhcce
Q 008920          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMA  306 (548)
Q Consensus       227 tVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~lng~  306 (548)
                      +|||+|||+++++++|.++|+.||.|..|.|+.++                 .++.++|||||+|.+.++|..||.+++.
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-----------------~~~~~~g~afV~f~~~~~a~~Ai~~~~~   63 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDN-----------------KTNKRRGFCFITFKEEEPVKKIMEKKYH   63 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSC-----------------CCSSSCCCEEEECSSSHHHHHHHTTSSC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC-----------------CCCCcCCEEEEEECCHHHHHHHHHhCCC
Confidence            59999999999999999999999999999885433                 1345789999999999999999988999


Q ss_pred             eecCceeEeecC
Q 008920          307 VIGGNHIRLDRA  318 (548)
Q Consensus       307 ~~~gr~I~V~~a  318 (548)
                      .|.|+.|.|.++
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            999999999864

>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=99.55  E-value=1.3e-14  Score=130.25  Aligned_cols=84  Identities=21%  Similarity=0.222  Sum_probs=73.8

Q ss_pred             CCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       221 ~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      .....++|||+|||+++++++|+++|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|+.|
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~-----------------tg~~~G~afV~F~~~~~A~~A  104 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQ-----------------SRRSRGFAFVYFENVDDAKEA  104 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSS-----------------SSCCCCEEEEEESCHHHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC-----------------CCccceEEEEEECCHHHHHHH
Confidence            344568999999999999999999999999999999965442                 345779999999999999999


Q ss_pred             HH-hcceeecCceeEeecCCCc
Q 008920          301 LA-FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       301 l~-lng~~~~gr~I~V~~a~~~  321 (548)
                      |. ||+..|.|+.|.|.++.+.
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            95 9999999999999998754

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=5.9e-15  Score=121.72  Aligned_cols=79  Identities=13%  Similarity=0.165  Sum_probs=70.1

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-  302 (548)
                      ..++|||+|||+++++++|+++|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|..|+. 
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~-----------------~~~~~g~afV~f~~~~~a~~A~~~   66 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKT-----------------TNKCKGYGFVDFDSPSAAQKAVTA   66 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSS-----------------SCSCCSEEEEEESCHHHHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC-----------------CCCcCcEEEEEECCHHHHHHHHHH
Confidence            458999999999999999999999999999999965431                 34578999999999999999995 


Q ss_pred             hcceeecCceeEeecCC
Q 008920          303 FNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~  319 (548)
                      ||+..|.|+.|.|.++.
T Consensus        67 l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A           67 LKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             HHHHTCCEESCCSSCCC
T ss_pred             hcCCeEeeEEEeecCCC
Confidence            99999999999988763

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=1.4e-14  Score=126.65  Aligned_cols=77  Identities=17%  Similarity=0.158  Sum_probs=69.3

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhc
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~ln  304 (548)
                      .++|||+|||+++|+++|+++|+.| .|..|.|+.+.                  .|+++|||||+|.+.++|++||.+|
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------------------VGRNNGNGLVKFLSPQDTFEALKRN   76 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT------------------TCCCCSEEEEECSSHHHHHHHHHTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC------------------CCCCCeEEEEEECCHHHHHHHHhcC
Confidence            4799999999999999999999999 79999995543                  2457899999999999999999999


Q ss_pred             ceeecCceeEeecCCC
Q 008920          305 MAVIGGNHIRLDRACP  320 (548)
Q Consensus       305 g~~~~gr~I~V~~a~~  320 (548)
                      +..|.|+.|.|..+..
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            9999999999988753

>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=99.54  E-value=4.6e-15  Score=128.43  Aligned_cols=81  Identities=15%  Similarity=0.105  Sum_probs=71.8

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCC---eeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGE---IDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~---I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~  298 (548)
                      ....++|||+|||+++|+++|+++|+.||.   |..|.|+.+.                  .|.++|||||+|.+.++|.
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------------------DGKRRGDALIEMESEQDVQ   69 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCT------------------TSTTCSEEEEEBSSHHHHH
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECC------------------CCCEeeEEEEEECCHHHHH
Confidence            345689999999999999999999999998   8899985433                  2457899999999999999


Q ss_pred             HHHHhcceeecCceeEeecCCC
Q 008920          299 AALAFNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       299 ~Al~lng~~~~gr~I~V~~a~~  320 (548)
                      .||.+|+..|.|+.|.|.++.+
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

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=1.6e-14  Score=125.56  Aligned_cols=80  Identities=20%  Similarity=0.375  Sum_probs=71.2

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||.++++++|.++|+.||.|..|.|+.+.                   +.++|||||+|.+.++|..|+
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-------------------RGSKGFGFVTFENSADADRAR   86 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT-------------------TBCTTEEEEECCCSHHHHHHH
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC-------------------CCCceEEEEEECCHHHHHHHH
Confidence            3456899999999999999999999999999999995432                   126799999999999999999


Q ss_pred             H-hcceeecCceeEeecCCC
Q 008920          302 A-FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       302 ~-lng~~~~gr~I~V~~a~~  320 (548)
                      . |||..|.|+.|.|.++.+
T Consensus        87 ~~l~g~~~~g~~l~V~~a~~  106 (109)
T 2err_A           87 EKLHGTVVEGRKIEVNNATA  106 (109)
T ss_dssp             HHHTTCEETTEECEEEECCC
T ss_pred             HHcCCCEECCEEEEEEECCC
Confidence            5 999999999999999864

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.54  E-value=1.3e-14  Score=134.55  Aligned_cols=80  Identities=18%  Similarity=0.260  Sum_probs=71.1

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcC--CeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFG--EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG--~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ..++|||+|||+++|+++|.++|+.||  .|.+|.|+.+..                 +|.++|||||+|.+.++|..||
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~-----------------tg~skGfaFV~f~~~~~A~~Ai  116 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRA-----------------NGQSKGYAEVVVASENSVHKLL  116 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTT-----------------TCCEEEEEEEEESCHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCC-----------------CCccceEEEEEECCHHHHHHHH
Confidence            458999999999999999999999999  999999976542                 3567899999999999999999


Q ss_pred             -HhcceeecCceeEeecCCC
Q 008920          302 -AFNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       302 -~lng~~~~gr~I~V~~a~~  320 (548)
                       .|||..|.|+.|.|.++.+
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             5899999999999999864

>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=99.54  E-value=9.3e-15  Score=132.73  Aligned_cols=80  Identities=15%  Similarity=0.103  Sum_probs=71.9

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCC---eeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGE---IDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~---I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~  299 (548)
                      ...++|||+|||+++|+++|+++|+.||.   |..|+|+.+.                  .|.++|||||+|.+.++|+.
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~------------------~g~srG~aFV~F~~~e~a~~  103 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR------------------EGRQSGEAFVELGSEDDVKM  103 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECS------------------SSCEEEEEEEECSSHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECC------------------CCCCCeEEEEEECCHHHHHH
Confidence            44689999999999999999999999999   8899996654                  24578999999999999999


Q ss_pred             HHHhcceeecCceeEeecCCC
Q 008920          300 ALAFNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       300 Al~lng~~~~gr~I~V~~a~~  320 (548)
                      ||.+|+..|.|+.|.|.++.+
T Consensus       104 Al~~~g~~l~gr~i~V~~a~~  124 (136)
T 2hgl_A          104 ALKKDRESMGHRYIEVFKSHR  124 (136)
T ss_dssp             HHTTTEEESSSSEEEEEECCH
T ss_pred             HHhcCCCEECCEEEEEEECCh
Confidence            999999999999999999753

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.54  E-value=9.1e-15  Score=129.07  Aligned_cols=82  Identities=16%  Similarity=0.252  Sum_probs=74.5

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCC---eEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCe
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESS---VEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDR  409 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~---I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr  409 (548)
                      ....++|||+|||+++++++|+++|..|    |.   |..|+|+.+.. |.++|||||+|.+.++|..||.+.+..|.|+
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~----G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr   88 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDC----TIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALKKDRESMGHR   88 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTS----CBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGGGTTEEETTE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHc----CCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCe
Confidence            3457899999999999999999999999    77   89999999976 9999999999999999999999434999999


Q ss_pred             EEEEEeeecC
Q 008920          410 ELRLSHAQQN  419 (548)
Q Consensus       410 ~I~V~~Ak~~  419 (548)
                      .|.|.++...
T Consensus        89 ~i~V~~a~~~   98 (118)
T 2db1_A           89 YIEVFKSHRT   98 (118)
T ss_dssp             EEEEEEECHH
T ss_pred             EEEEEECCHH
Confidence            9999999754

>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=99.54  E-value=6e-15  Score=126.03  Aligned_cols=82  Identities=29%  Similarity=0.402  Sum_probs=70.4

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++++++|.++|+.|| |.+|.|+.+..                .+|.++|||||+|.+.++|..||.
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----------------NPERLKGFGYAEFEDLDSLLSALS   79 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTT----------------TTCCCCSCEEEEECCHHHHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCC----------------cCCccCeEEEEEECCHHHHHHHHh
Confidence            4468999999999999999999999999 99999854321                135578999999999999999999


Q ss_pred             hcceeecCceeEeecCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~  321 (548)
                      ||+..|.|+.|.|.++.+.
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

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=1.9e-14  Score=122.00  Aligned_cols=78  Identities=18%  Similarity=0.379  Sum_probs=68.7

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++++++|+.+|+.||.|. +.+++.                     .++|||||+|.+.++|..||
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~---------------------~~~g~afV~f~~~~~a~~A~   73 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ---------------------GPRRRAFLHYPDSAAAQQAV   73 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE---------------------TTTTEEEEECSSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC---------------------CCCcEEEEEECCHHHHHHHH
Confidence            34468999999999999999999999999996 666432                     26799999999999999999


Q ss_pred             -HhcceeecCceeEeecCCCc
Q 008920          302 -AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 -~lng~~~~gr~I~V~~a~~~  321 (548)
                       .||+..|.|+.|.|.++.+.
T Consensus        74 ~~l~g~~~~g~~l~V~~a~~~   94 (97)
T 2e5j_A           74 SCLQGLRLGTDTLRVALARQQ   94 (97)
T ss_dssp             HHHTTCCSSSSCCEEEECCCC
T ss_pred             HHhCCCEECCcEEEEEEcCCC
Confidence             69999999999999998754

>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=99.54  E-value=1.6e-14  Score=128.14  Aligned_cols=83  Identities=14%  Similarity=0.216  Sum_probs=72.8

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++|+++|..+|+.||.|..|.|+.+.                 .++.++|||||+|.+.++|..||
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-----------------~~~~~~g~afV~f~~~~~a~~A~   81 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR-----------------RTGYLKGYTLVEYETYKEAQAAM   81 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCT-----------------TTSSBCSCEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC-----------------CCCccceEEEEEECCHHHHHHHH
Confidence            3446899999999999999999999999999999985543                 13457899999999999999999


Q ss_pred             -HhcceeecCceeEeecCCCc
Q 008920          302 -AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 -~lng~~~~gr~I~V~~a~~~  321 (548)
                       .||+..|.|+.|.|.++.+.
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             59999999999999998643

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.54  E-value=2.3e-14  Score=122.19  Aligned_cols=75  Identities=20%  Similarity=0.287  Sum_probs=70.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEe
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSH  415 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~  415 (548)
                      ++|||+|||+.+++++|+++|+.|    |.|..|.|+.+     ++|||||+|.+.++|..|+..|+ ..|.|+.|.|.|
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   71 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYY----GPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVEL   71 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHH----CCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEE
Confidence            479999999999999999999999    89999999987     68999999999999999999877 999999999999


Q ss_pred             eecCC
Q 008920          416 AQQNC  420 (548)
Q Consensus       416 Ak~~~  420 (548)
                      +.+..
T Consensus        72 a~~~~   76 (101)
T 2hvz_A           72 STGMP   76 (101)
T ss_dssp             SSSCC
T ss_pred             ccCCC
Confidence            98764

>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=99.54  E-value=1.1e-14  Score=123.36  Aligned_cols=81  Identities=21%  Similarity=0.274  Sum_probs=71.0

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||+++++++|+++|..||.|..+.++.+.                 .++.++|||||+|.+.++|+.|| .
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~-----------------~~g~~~g~afV~f~~~~~a~~Ai~~   76 (98)
T 2cqp_A           14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-----------------EKGMPTGEAMVAFESRDEATAAVID   76 (98)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC-----------------SSSCEEEEEEEEESCHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEEC-----------------CCCCeeeEEEEEECCHHHHHHHHHH
Confidence            45899999999999999999999999999877775543                 13457799999999999999999 6


Q ss_pred             hcceeecCceeEeecCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~  321 (548)
                      ||+..|.|+.|.|.++..+
T Consensus        77 l~g~~~~g~~l~V~~a~~~   95 (98)
T 2cqp_A           77 LNDRPIGSRKVKLVLGSGP   95 (98)
T ss_dssp             TTTCEETTEECEEEESSCS
T ss_pred             hCCCeeCCeEEEEEEcCCC
Confidence            9999999999999998643

>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=99.54  E-value=2.8e-14  Score=123.65  Aligned_cols=77  Identities=19%  Similarity=0.235  Sum_probs=67.6

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.                       .+|||||+|.+.++|..|+.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~-----------------------~kg~aFVef~~~~~A~~Ai~   69 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-----------------------FKRQALVEFENIDSAKECVT   69 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET-----------------------TTTEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEC-----------------------CCCEEEEEECCHHHHHHHHH
Confidence            4568999999999999999999999999999998832                       35899999999999999995


Q ss_pred             -hcc--eeecCceeEeecCCCcc
Q 008920          303 -FNM--AVIGGNHIRLDRACPPR  322 (548)
Q Consensus       303 -lng--~~~~gr~I~V~~a~~~~  322 (548)
                       |++  ..|.|+.|.|.++....
T Consensus        70 ~l~~~~~~i~Gr~l~V~~a~~~~   92 (104)
T 1wex_A           70 FAADVPVYIAGQQAFFNYSTSKR   92 (104)
T ss_dssp             HHHHSCCBSSSSBCEEEECSSSS
T ss_pred             HhccCCceECCEEEEEEEccCcc
Confidence             765  45999999999997654

>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=99.54  E-value=2e-14  Score=118.44  Aligned_cols=74  Identities=26%  Similarity=0.484  Sum_probs=67.4

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      +...++|||+|||.++++++|.++|+.||.|..|.|+.                       ++|||||+|.+.++|..|+
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            34568999999999999999999999999999999843                       3589999999999999999


Q ss_pred             H-h-cceeecCceeEeecC
Q 008920          302 A-F-NMAVIGGNHIRLDRA  318 (548)
Q Consensus       302 ~-l-ng~~~~gr~I~V~~a  318 (548)
                      . | ++..|.|+.|.|.++
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 7 999999999999986

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.54  E-value=8.9e-15  Score=123.06  Aligned_cols=78  Identities=21%  Similarity=0.297  Sum_probs=69.5

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-h
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-F  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-l  303 (548)
                      .++|||+|||+++++++|+++|..||.|..+.++.+.                 .++.++|||||+|.+.++|..||. |
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~-----------------~~g~~~g~afV~f~~~~~a~~Ai~~l   77 (95)
T 2ek1_A           15 PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-----------------EKGMPTGEAMVAFESRDEATAAVIDL   77 (95)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEEC-----------------TTSCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeC-----------------CCCCEeeEEEEEECCHHHHHHHHHHh
Confidence            4899999999999999999999999999888776543                 134577999999999999999994 9


Q ss_pred             cceeecCceeEeecCC
Q 008920          304 NMAVIGGNHIRLDRAC  319 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~  319 (548)
                      |+..|.|+.|.|.++.
T Consensus        78 ~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           78 NDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             TTCEETTEECEEECCC
T ss_pred             CCCeECCcEEEEEecc
Confidence            9999999999999875

>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=99.53  E-value=4.7e-14  Score=122.16  Aligned_cols=77  Identities=13%  Similarity=0.157  Sum_probs=69.8

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC---CccCCe
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN---LKLRDR  409 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln---~~l~Gr  409 (548)
                      ..+.++|||+|||+.+++++|+++|++|    |.|..|.|+.+      +|||||+|.+.++|..|+..++   ..|.|+
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~f----G~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr   81 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKF----GTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQ   81 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTT----SCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhC----CCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCE
Confidence            4567899999999999999999999999    89999998864      7899999999999999998764   569999


Q ss_pred             EEEEEeeecC
Q 008920          410 ELRLSHAQQN  419 (548)
Q Consensus       410 ~I~V~~Ak~~  419 (548)
                      +|.|.|+.+.
T Consensus        82 ~l~V~~a~~~   91 (104)
T 1wex_A           82 QAFFNYSTSK   91 (104)
T ss_dssp             BCEEEECSSS
T ss_pred             EEEEEEccCc
Confidence            9999999865

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.53  E-value=1.6e-14  Score=121.03  Aligned_cols=71  Identities=17%  Similarity=0.191  Sum_probs=66.1

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      +.-|||+||++.+|+++|+++|.+||+|.++.|..                       ++|||||+|.+.++|.+|+ .|
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~-----------------------~kGfaFVey~~~~eA~~Ai~~L   63 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-----------------------NQGIALCKYTTREEANKAQMAL   63 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET-----------------------TTTEEEEEESSHHHHHHHHHHH
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC-----------------------CCcEEEEEECCHHHHHHHHHHh
Confidence            46799999999999999999999999999999832                       5699999999999999999 69


Q ss_pred             cceeecCceeEeecC
Q 008920          304 NMAVIGGNHIRLDRA  318 (548)
Q Consensus       304 ng~~~~gr~I~V~~a  318 (548)
                      |+..|.|+.|+|..+
T Consensus        64 n~~~l~gr~I~V~~A   78 (89)
T 2wbr_A           64 NNCVLANTTIFAESP   78 (89)
T ss_dssp             TTEEETTEEEEEECC
T ss_pred             cCCEECCcEEEEEEC
Confidence            999999999999997

>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=99.53  E-value=4e-14  Score=121.99  Aligned_cols=77  Identities=13%  Similarity=0.258  Sum_probs=68.0

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++++++|+.+|+.||.|..|.|+.                       .+|||||+|.+.++|..|+.
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            3568999999999999999999999999999998842                       35899999999999999994


Q ss_pred             -h--cceeecCceeEeecCCCcc
Q 008920          303 -F--NMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       303 -l--ng~~~~gr~I~V~~a~~~~  322 (548)
                       |  ++..|.|+.|.|.++.+..
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             5  5678999999999997643

>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=99.53  E-value=3e-14  Score=121.13  Aligned_cols=77  Identities=26%  Similarity=0.433  Sum_probs=69.9

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+.+++++|+.+|+.||.|..|.|+.                       ++|||||+|.+.++|..||
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            34568999999999999999999999999999999832                       4589999999999999999


Q ss_pred             -HhcceeecCceeEeecCCCc
Q 008920          302 -AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 -~lng~~~~gr~I~V~~a~~~  321 (548)
                       .||+..|.|+.|.|.++.+.
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             69999999999999999764

>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=99.53  E-value=2.4e-14  Score=124.19  Aligned_cols=93  Identities=25%  Similarity=0.374  Sum_probs=77.1

Q ss_pred             cCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCC-CCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEE
Q 008920          309 GGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFD-VKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYV  387 (548)
Q Consensus       309 ~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~-~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV  387 (548)
                      .|..|.|..+.....      .......++|||+|||+. +++++|+++|..|    |.|..|.|        ++|||||
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            466677766653221      112334689999999999 9999999999999    89999988        4789999


Q ss_pred             EECCHHHHHHHHHHcC-CccCCeEEEEEeeecC
Q 008920          388 LFKTREAANLVIKRRN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       388 ~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      +|.+.++|..||..|+ ..|.|+.|.|.|+.+.
T Consensus        68 ~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~  100 (110)
T 1wf1_A           68 QYSNERHARAAVLGENGRVLAGQTLDINMAGEP  100 (110)
T ss_dssp             ECSSSHHHHHHHHHHTTCEETTEECCEEESCCC
T ss_pred             EECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            9999999999998877 9999999999999864

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.53  E-value=2.1e-14  Score=122.41  Aligned_cols=74  Identities=19%  Similarity=0.331  Sum_probs=68.1

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||.++++++|+.+|+.||.|.+|.|..                       ++|||||+|.+.++|..|+ .
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            458999999999999999999999999999999841                       5699999999999999999 6


Q ss_pred             hcceeecCceeEeecCCC
Q 008920          303 FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~  320 (548)
                      ||+..|.|+.|.|.++.+
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

>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=99.53  E-value=3.7e-14  Score=122.82  Aligned_cols=78  Identities=22%  Similarity=0.345  Sum_probs=72.0

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      ...++|||+|||+.+++++|+.+|..|    |.|..|.|+.+      +|||||+|.+.++|..||..|+ ..|.|+.|.
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~----G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   92 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPF----GQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVK   92 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHH----SCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            356899999999999999999999999    89999999877      7899999999999999998877 999999999


Q ss_pred             EEeeecCCC
Q 008920          413 LSHAQQNCT  421 (548)
Q Consensus       413 V~~Ak~~~~  421 (548)
                      |.|+.+...
T Consensus        93 v~~a~~~~~  101 (109)
T 1x4g_A           93 CYWGKESPD  101 (109)
T ss_dssp             EECCCCCCS
T ss_pred             EEecCCCCC
Confidence            999987643

>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=99.53  E-value=3.4e-14  Score=120.94  Aligned_cols=74  Identities=27%  Similarity=0.501  Sum_probs=68.2

Q ss_pred             CCcccEEEEcCCCC-CCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          222 GKLLRTIFVGNLPL-KVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       222 ~~~~rtVfVgNLP~-~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      ....++|||+|||+ ++++++|..+|+.||.|..|.|                         .+|||||+|.+.++|..|
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            34568999999998 9999999999999999999998                         358999999999999999


Q ss_pred             HH-hcceeecCceeEeecCCC
Q 008920          301 LA-FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       301 l~-lng~~~~gr~I~V~~a~~  320 (548)
                      +. |||..|.|+.|.|.++..
T Consensus        74 i~~l~g~~~~g~~l~V~~a~~   94 (97)
T 2xnq_A           74 IEXESQEMNFGKKLILEVSSS   94 (97)
T ss_dssp             HHHHTTSEETTEECEEEECCC
T ss_pred             HHHcCCCEECCEEEEEEecCC
Confidence            95 999999999999999864

>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=99.53  E-value=1.5e-14  Score=126.08  Aligned_cols=85  Identities=20%  Similarity=0.307  Sum_probs=72.3

Q ss_pred             cccEEEEcCCCCCCcHHHHH---HHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          224 LLRTIFVGNLPLKVKKKTLI---KEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~---~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      ..++|||+|||+++++++|.   ++|+.||.|..|.|+.+..+  +.            .+.++|||||+|.+.++|+.|
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~--~~------------~~~~~G~afV~f~~~~~A~~A   79 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSY--AG------------SQGPSASAYVTYIRSEDALRA   79 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSC--CS------------SSCCCEEEEEEESSHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCc--Cc------------cCCCCeEEEEEECcHHHHHHH
Confidence            35799999999999999999   99999999999999654321  10            123679999999999999999


Q ss_pred             HH-hcceeecCceeEeecCCCcc
Q 008920          301 LA-FNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       301 l~-lng~~~~gr~I~V~~a~~~~  322 (548)
                      |. ||+..|.|+.|.|.++.+..
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            95 89999999999999997643

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.53  E-value=7.2e-15  Score=118.66  Aligned_cols=75  Identities=19%  Similarity=0.354  Sum_probs=66.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-hc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-FN  304 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-ln  304 (548)
                      ++|||+|||+++++++|.++|+.||.|..|.|+.++.                 +|.++|||||+|.+.++|..|+. ++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~-----------------~~~~~g~afV~f~~~~~a~~a~~~~~   63 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL-----------------TKRSRGFGFVTFMDQAGVDKVLAQSR   63 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCC-----------------SSSCSSEEEECCCCTTHHHHHHHTTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCC-----------------CCCcCceEEEEEcCHHHHHHHHHhCC
Confidence            4799999999999999999999999999999965431                 34578999999999999999996 66


Q ss_pred             ceeecCceeEeecC
Q 008920          305 MAVIGGNHIRLDRA  318 (548)
Q Consensus       305 g~~~~gr~I~V~~a  318 (548)
                       ..|.|+.|.|.++
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

>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=99.53  E-value=4.5e-14  Score=120.98  Aligned_cols=75  Identities=28%  Similarity=0.438  Sum_probs=68.7

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++|+++|+++|+.||.|..|.|                         .+|||||+|.+.++|..||.
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~-------------------------~~~~afV~f~~~~~a~~A~~   63 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKK-------------------------LKDYAFIHFDERDGAVKAME   63 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEE-------------------------CSSCEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE-------------------------ECCEEEEEeCCHHHHHHHHH
Confidence            34689999999999999999999999999999998                         23799999999999999995


Q ss_pred             -hcceeecCceeEeecCCCcc
Q 008920          303 -FNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       303 -lng~~~~gr~I~V~~a~~~~  322 (548)
                       ||+..|.|+.|.|.++.+..
T Consensus        64 ~l~g~~~~g~~l~v~~a~~~~   84 (103)
T 2dgu_A           64 EMNGKDLEGENIEIVFAKPPD   84 (103)
T ss_dssp             HHTTEEETTEEEEEEECCCCC
T ss_pred             HHCCCccCCCEEEEEEcCCCc
Confidence             99999999999999997654

>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=99.53  E-value=2e-14  Score=127.65  Aligned_cols=78  Identities=21%  Similarity=0.322  Sum_probs=71.2

Q ss_pred             cCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC---CccCC
Q 008920          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN---LKLRD  408 (548)
Q Consensus       332 ~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln---~~l~G  408 (548)
                      ...+.++|||+|||+++++++|+++|+.|    |.|..|.|+.+      +|||||+|.+.++|..|+..++   ..|.|
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~f----G~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~G   96 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPF----GKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRG   96 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTT----SCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTT
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            34567899999999999999999999999    89999999876      7999999999999999998775   57999


Q ss_pred             eEEEEEeeecC
Q 008920          409 RELRLSHAQQN  419 (548)
Q Consensus       409 r~I~V~~Ak~~  419 (548)
                      ++|.|.|+.+.
T Consensus        97 r~l~V~~a~~k  107 (119)
T 2ad9_A           97 QPIYIQFSNHK  107 (119)
T ss_dssp             BCCEEEECSSS
T ss_pred             eEEEEEEccCC
Confidence            99999999865

>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=99.53  E-value=8.6e-15  Score=129.96  Aligned_cols=82  Identities=17%  Similarity=0.284  Sum_probs=74.5

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|..|.++.+..+|.++|||||+|.+.++|..||. ++ ..|.|+.|
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~----G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i   96 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKL----DIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFI   96 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSS----CBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCB
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhc----CCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEE
Confidence            4456899999999999999999999999    899886677776899999999999999999999999 66 99999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      .|.++.+.
T Consensus        97 ~V~~a~~~  104 (124)
T 1wel_A           97 QVHPITKK  104 (124)
T ss_dssp             EEEEECHH
T ss_pred             EEEECCHH
Confidence            99999764

>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=99.53  E-value=3e-14  Score=131.20  Aligned_cols=82  Identities=21%  Similarity=0.300  Sum_probs=73.1

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++|+++|.++|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|..||.
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-----------------KKTACGFCFVEYYSRADAENAMR   99 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----------------TCCEEEEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC-----------------CCccceEEEEEECCHHHHHHHHH
Confidence            3468999999999999999999999999999999966542                 34577999999999999999995


Q ss_pred             -hcceeecCceeEeecCCCc
Q 008920          303 -FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 -lng~~~~gr~I~V~~a~~~  321 (548)
                       ||+..|.|+.|.|.++.+.
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             9999999999999999754

>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=99.52  E-value=3.7e-14  Score=123.53  Aligned_cols=80  Identities=21%  Similarity=0.322  Sum_probs=70.2

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++++++|+.+|+.||.|..|.|+.+.                  ++.++|||||+|.+.++|..||.
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------------------SGTSRGVGFARMESTEKCEAVIG   84 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS------------------SSCEEEEEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC------------------CCCcceEEEEEECCHHHHHHHHH
Confidence            456899999999999999999999999999999996654                  23477999999999999999994


Q ss_pred             -hcceee--------cCceeEeecCCC
Q 008920          303 -FNMAVI--------GGNHIRLDRACP  320 (548)
Q Consensus       303 -lng~~~--------~gr~I~V~~a~~  320 (548)
                       |||..|        .++.|.|.++.+
T Consensus        85 ~l~g~~~~~~~~~~~~~~~l~v~~a~p  111 (114)
T 1x5o_A           85 HFNGKFIKTPPGVSAPTEPLLCKFSGP  111 (114)
T ss_dssp             HHBTCCCCCCTTSCCCSSCBEEEECCC
T ss_pred             HhCCCEEcCCccccCCCCceeEEccCC
Confidence             999999        567888888864

>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=99.52  E-value=4.6e-14  Score=122.21  Aligned_cols=76  Identities=17%  Similarity=0.326  Sum_probs=69.4

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||..+++++|+.+|+.||.|..|.|+.                       .+|||||+|.+.++|..|| .
T Consensus        24 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~-----------------------~~g~afV~f~~~~~a~~A~~~   80 (109)
T 1x4g_A           24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP-----------------------EKGYSFVRFSTHESAAHAIVS   80 (109)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEET-----------------------TTTEEEEEESSHHHHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----------------------CCCEEEEEECCHHHHHHHHHH
Confidence            458999999999999999999999999999999843                       2589999999999999999 6


Q ss_pred             hcceeecCceeEeecCCCcc
Q 008920          303 FNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~~  322 (548)
                      ||+..|.|+.|.|.++.+..
T Consensus        81 l~g~~~~g~~l~v~~a~~~~  100 (109)
T 1x4g_A           81 VNGTTIEGHVVKCYWGKESP  100 (109)
T ss_dssp             HTTCEETTEECEEECCCCCC
T ss_pred             cCCCEECCcEEEEEecCCCC
Confidence            99999999999999997653

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.52  E-value=1e-14  Score=130.86  Aligned_cols=83  Identities=17%  Similarity=0.229  Sum_probs=72.5

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeE--EEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDS--VRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~s--Vri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~  299 (548)
                      ....++|||+|||+++|+++|+++|+.||.|..  |+|+.+..                 +|.++|||||+|.+. +|..
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~-----------------tg~~rG~aFV~f~~~-~a~~   81 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQ-----------------TQLNRGFAFIQLSTI-EAAQ   81 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSS-----------------SSSBCSCEEEECCHH-HHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCC-----------------CCCcceEEEEEECCH-HHHH
Confidence            345689999999999999999999999999977  88865442                 355789999999999 9999


Q ss_pred             HH-Hhcce----eecCceeEeecCCCcc
Q 008920          300 AL-AFNMA----VIGGNHIRLDRACPPR  322 (548)
Q Consensus       300 Al-~lng~----~~~gr~I~V~~a~~~~  322 (548)
                      || .||+.    .|.|+.|.|.++.+..
T Consensus        82 Ai~~l~g~~~~~~~~gr~l~V~~a~~~~  109 (131)
T 2m2b_A           82 LLQILQALHPPLTIDGKTINVEFAKGSK  109 (131)
T ss_dssp             HHHHHTTCCCSCCGGGCCCCCEECCCSC
T ss_pred             HHHHhcCCCCCccCCCEEEEEEECCCCC
Confidence            99 69999    9999999999997653

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.52  E-value=4.2e-14  Score=125.29  Aligned_cols=82  Identities=13%  Similarity=0.215  Sum_probs=73.1

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+.+++++|.++|+.||.|..|.|+.+.                  +|.++|||||+|.+.++|..|+
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------------------SGRSLGTADVHFERRADALKAM   93 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS------------------SSSCCSEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC------------------CCCEeeEEEEEECCHHHHHHHH
Confidence            3456899999999999999999999999999999996543                  2457799999999999999999


Q ss_pred             H-hcceeecCceeEeecCCCc
Q 008920          302 A-FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 ~-lng~~~~gr~I~V~~a~~~  321 (548)
                      . ||+..|.|+.|.|.++.+.
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            5 9999999999999998754

>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=99.52  E-value=3.7e-14  Score=125.87  Aligned_cols=77  Identities=18%  Similarity=0.357  Sum_probs=68.1

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++|+++|+++|+.||.|.+|.|+.                       .+|||||+|.+.++|..|+.
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~-----------------------~kG~AFVeF~~~e~A~~Ai~   85 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-----------------------GKNQAFIEMNTEEAANTMVN   85 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEG-----------------------GGTEEEEECSCHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-----------------------CCCEEEEEECCHHHHHHHHH
Confidence            3468999999999999999999999999999999843                       35899999999999999995


Q ss_pred             -hc--ceeecCceeEeecCCCcc
Q 008920          303 -FN--MAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       303 -ln--g~~~~gr~I~V~~a~~~~  322 (548)
                       |+  +..|.|+.|.|.++.+..
T Consensus        86 ~l~~~~~~l~Gr~l~V~~a~~k~  108 (119)
T 2ad9_A           86 YYTSVTPVLRGQPIYIQFSNHKE  108 (119)
T ss_dssp             HHHHHCCCBTTBCCEEEECSSSS
T ss_pred             HhccCCceECCeEEEEEEccCCC
Confidence             66  468999999999997643

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.52  E-value=2e-14  Score=126.03  Aligned_cols=79  Identities=20%  Similarity=0.118  Sum_probs=69.1

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcC-CeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFG-EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG-~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      ....++|||+|||+++++++|+++|+.|| .|..|.|...                     .++|||||+|.+.++|+.|
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            33457999999999999999999999999 8999887321                     2669999999999999999


Q ss_pred             H-HhcceeecCceeEeecCCCc
Q 008920          301 L-AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       301 l-~lng~~~~gr~I~V~~a~~~  321 (548)
                      | .|||..|.|+.|.|.++..+
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 59999999999999998643

>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=99.52  E-value=7.3e-15  Score=130.42  Aligned_cols=81  Identities=16%  Similarity=0.278  Sum_probs=70.0

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++|+++|.++|+.||.|..+.++.+.                 .+|.++|||||+|.+.++|..||.
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~-----------------~~g~~~G~afV~F~~~~~a~~Al~   85 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYG-----------------PNGKATGEGFVEFRNEADYKAALC   85 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEEC-----------------TTSSEEEEEEEEBSSSHHHHHHHT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEEC-----------------CCCCCCeEEEEEECCHHHHHHHHH
Confidence            345899999999999999999999999999875443322                 145578999999999999999999


Q ss_pred             hcceeecCceeEeecCCC
Q 008920          303 FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~  320 (548)
                      ||+..|.|+.|.|.++..
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

>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=99.52  E-value=1.4e-14  Score=142.72  Aligned_cols=81  Identities=14%  Similarity=0.256  Sum_probs=75.8

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCC--CeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLES--SVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G--~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ..++|||+|||+.+++++|+++|..|    |  .|..|.|++|..++.++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~----G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l  142 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSL----GVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNP  142 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTT----TCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHH----CCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEe
Confidence            45789999999999999999999999    8  99999999999999999999999999999999999888 99999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      .|.|+.+.
T Consensus       143 ~V~~a~~~  150 (229)
T 3q2s_C          143 VVTPVNKQ  150 (229)
T ss_dssp             EEEECCHH
T ss_pred             EEEECCCC
Confidence            99999754

>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=99.52  E-value=1.4e-14  Score=126.42  Aligned_cols=74  Identities=18%  Similarity=0.239  Sum_probs=67.6

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||+++++++|+.+|+.||.|..|.|+.                       ++|||||+|.+.++|..|| .
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~-----------------------~~g~afV~f~~~~~A~~Ai~~   65 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----------------------GGITAIVEFLEPLEARKAFRH   65 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----------------------SSSCEEEEESCHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-----------------------CCCEEEEEeCCHHHHHHHHHH
Confidence            468999999999999999999999999999998731                       5589999999999999999 5


Q ss_pred             hcceeecCceeEeecCCC
Q 008920          303 FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~  320 (548)
                      |||..|.|+.|.|.|+..
T Consensus        66 l~g~~~~g~~l~V~~a~~   83 (111)
T 1whx_A           66 LAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             HTTCBSSSSBCEEEEEET
T ss_pred             hCCCEECCeEEEEEECCC
Confidence            999999999999999853

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=9.1e-15  Score=130.55  Aligned_cols=85  Identities=21%  Similarity=0.271  Sum_probs=74.2

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRL  413 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V  413 (548)
                      ....+|||+|||+++|+++|+++|..|+.+.|.|..|.|+.+ .+|.++|||||+|.+.++|..||...+..|.||.|.|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~V   99 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIEL   99 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEE
Confidence            346899999999999999999999999432234579999999 5899999999999999999999998559999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      ..+.+.
T Consensus       100 ~~a~~~  105 (123)
T 2dha_A          100 FRSTAA  105 (123)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            998654

>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=99.52  E-value=3.9e-14  Score=130.33  Aligned_cols=82  Identities=24%  Similarity=0.372  Sum_probs=73.2

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...++|||+|||+++++++|.++|+.||.|..|.|+.++                 .+|.++|||||+|.+.++|..|| 
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~-----------------~~g~~~g~afV~f~~~~~a~~A~~  130 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDR-----------------YTKESRGFAFVRFHDKRDAEDAMD  130 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCS-----------------SCTTSCCEEEEEESBHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC-----------------CCCccceEEEEEECCHHHHHHHHH
Confidence            456899999999999999999999999999999985543                 13557899999999999999999 


Q ss_pred             HhcceeecCceeEeecCCCc
Q 008920          302 AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~  321 (548)
                      .|||..|.|+.|.|.++.+.
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            59999999999999999764

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=7.6e-14  Score=116.98  Aligned_cols=77  Identities=14%  Similarity=0.251  Sum_probs=70.1

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|+.|    |.|..|.|+++        ||||+|.+.++|..||..|+ ..|.|+.|
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~v~~v~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~l   74 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEY----GPVIECDIVKD--------YAFVHMERAEDAVEAIRGLDNTEFQGKRM   74 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTT----SCCCEEEECSS--------EEEEEESCHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCeeCCcEE
Confidence            4567999999999999999999999999    89999998743        99999999999999998877 99999999


Q ss_pred             EEEeeecCCC
Q 008920          412 RLSHAQQNCT  421 (548)
Q Consensus       412 ~V~~Ak~~~~  421 (548)
                      .|.|+.+...
T Consensus        75 ~V~~a~~~~~   84 (92)
T 2dgt_A           75 HVQLSTSRLR   84 (92)
T ss_dssp             EEEESSCCCS
T ss_pred             EEEEccCCCC
Confidence            9999987543

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.52  E-value=4e-14  Score=127.24  Aligned_cols=81  Identities=27%  Similarity=0.436  Sum_probs=71.0

Q ss_pred             CCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       221 ~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      .....++|||+|||+.+++++|+++|+.||.|..|.|+.++                 .++.++|||||+|.+.++|..|
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~-----------------~~~~~~g~afV~f~~~~~a~~A  121 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY-----------------ETEKHRGFAFVEFELAEDAAAA  121 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCT-----------------TTCCCCSEEEEEESCHHHHHHH
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecC-----------------CCCCcCcEEEEEECCHHHHHHH
Confidence            34567899999999999999999999999999999985543                 1345789999999999999999


Q ss_pred             H-HhcceeecCceeEeecC
Q 008920          301 L-AFNMAVIGGNHIRLDRA  318 (548)
Q Consensus       301 l-~lng~~~~gr~I~V~~a  318 (548)
                      | .||+..|.|+.|.|.++
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 59999999999999875

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=4.4e-14  Score=120.41  Aligned_cols=80  Identities=26%  Similarity=0.306  Sum_probs=68.5

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++|+++|+++|+.||.|   .|+.+                  .++.++|||||+|.+.++|+.||
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------------------QNGKSKGYAFIEFASFEDAKEAL   70 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC------------------SSSCBCSEEEEECSSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC------------------CCCCEeeEEEEEECCHHHHHHHH
Confidence            3456899999999999999999999999977   34221                  13457899999999999999999


Q ss_pred             H-hcceeecCceeEeecCCCcc
Q 008920          302 A-FNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 ~-lng~~~~gr~I~V~~a~~~~  322 (548)
                      . ||+..|.|+.|.|.++.+..
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            5 99999999999999997653

>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=99.52  E-value=3.6e-14  Score=120.15  Aligned_cols=76  Identities=26%  Similarity=0.385  Sum_probs=68.6

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++++++|.++|+.||.|..|.|+.                       .+|||||+|.+.++|+.|+.
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            3458999999999999999999999999999998832                       25899999999999999995


Q ss_pred             -hcceeec--CceeEeecCCCc
Q 008920          303 -FNMAVIG--GNHIRLDRACPP  321 (548)
Q Consensus       303 -lng~~~~--gr~I~V~~a~~~  321 (548)
                       ||+..|.  |+.|.|.++.+.
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             9999999  999999999764

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.52  E-value=2.6e-14  Score=123.25  Aligned_cols=80  Identities=16%  Similarity=0.198  Sum_probs=73.2

Q ss_pred             CCccEEEEeCCCCCC------CHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-Ccc
Q 008920          334 DIKKTVFVGNLPFDV------KDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKL  406 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~------teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l  406 (548)
                      ...++|||+|||+.+      ++++|+.+|+.|    |.|..|.|+  ..+|.++|||||+|.+.++|..||..|+ ..|
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~----G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~   86 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKF----GKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKL   86 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGG----SCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEEC
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcC----CCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCccc
Confidence            346899999999999      789999999999    899999988  3689999999999999999999999887 999


Q ss_pred             CCe-EEEEEeeecC
Q 008920          407 RDR-ELRLSHAQQN  419 (548)
Q Consensus       407 ~Gr-~I~V~~Ak~~  419 (548)
                      .|+ .|.|.|+.+.
T Consensus        87 ~g~~~l~V~~a~~~  100 (105)
T 2nlw_A           87 DKQHTFRVNLFTDF  100 (105)
T ss_dssp             STTCEEEEECSCCC
T ss_pred             CCCceEEEEEcchH
Confidence            998 9999999754

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.51  E-value=4.7e-15  Score=126.46  Aligned_cols=81  Identities=17%  Similarity=0.233  Sum_probs=73.7

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      ...++|||+|||+.+++++|+++|..|    |.|.. .++.+..+|.++|||||+|.+.++|..||. ++ ..|.|+.|.
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~   88 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISEL----FAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIK   88 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHH----HHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHh----CCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEE
Confidence            357899999999999999999999999    88877 677777889999999999999999999999 76 999999999


Q ss_pred             EEeeecCC
Q 008920          413 LSHAQQNC  420 (548)
Q Consensus       413 V~~Ak~~~  420 (548)
                      |.|+.++.
T Consensus        89 V~~a~~~~   96 (101)
T 1fj7_A           89 LEKPKGRD   96 (101)
T ss_dssp             EECCSCCC
T ss_pred             EEEcCCCC
Confidence            99998753

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=2.6e-14  Score=124.14  Aligned_cols=81  Identities=22%  Similarity=0.424  Sum_probs=74.4

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||..+++++|+++|+.|    |.|..|.|+.+.  +.++|||||+|.+.++|..|+..++ ..|.|+.|
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~----G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   99 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQF----GKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKI   99 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGT----CCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhc----CCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            4467899999999999999999999999    899999999985  3489999999999999999999877 99999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      .|.|+.++
T Consensus       100 ~V~~a~~~  107 (109)
T 2err_A          100 EVNNATAR  107 (109)
T ss_dssp             EEEECCCS
T ss_pred             EEEECCCC
Confidence            99999864

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=1.8e-14  Score=125.85  Aligned_cols=81  Identities=22%  Similarity=0.348  Sum_probs=72.4

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELR  412 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~  412 (548)
                      .....+|||+|||+++++++|+++|..|     .|..|.|+.|.. |.++|||||+|.+.++|..||.+.+..|+||.|.
T Consensus        13 ~~~~~~v~V~nLp~~~te~dl~~~F~~~-----~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~   86 (109)
T 2dnn_A           13 NPDDLYVSVHGMPFSAMENDVRDFFHGL-----RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVE   86 (109)
T ss_dssp             CHHHHEEEEECCCSSCCHHHHHHHTTTS-----CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhccC-----CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEE
Confidence            3446899999999999999999999999     588999999965 9999999999999999999995444999999999


Q ss_pred             EEeeecC
Q 008920          413 LSHAQQN  419 (548)
Q Consensus       413 V~~Ak~~  419 (548)
                      |..+.+.
T Consensus        87 V~~a~~~   93 (109)
T 2dnn_A           87 VSPATER   93 (109)
T ss_dssp             EEECCHH
T ss_pred             EEECCcc
Confidence            9988654

>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=99.51  E-value=5e-14  Score=119.27  Aligned_cols=77  Identities=19%  Similarity=0.355  Sum_probs=70.6

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccC--Ce
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLR--DR  409 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~--Gr  409 (548)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|.|+.+      +|||||+|.+.++|..||..|+ ..|.  |+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~   83 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRF----GSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDR   83 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTT----SCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCc
Confidence            3456899999999999999999999999    89999998754      7899999999999999999877 8899  99


Q ss_pred             EEEEEeeecC
Q 008920          410 ELRLSHAQQN  419 (548)
Q Consensus       410 ~I~V~~Ak~~  419 (548)
                      .|.|.|+.++
T Consensus        84 ~l~V~~a~~~   93 (97)
T 1why_A           84 RLRVDFAKSG   93 (97)
T ss_dssp             BCEEEECCCC
T ss_pred             EEEEEECCCC
Confidence            9999999875

>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=99.51  E-value=4.6e-14  Score=121.81  Aligned_cols=82  Identities=21%  Similarity=0.320  Sum_probs=70.5

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCC-eeEEEEe-eecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGE-IDSVRIR-SVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~-I~sVri~-~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ..++|||+|||+++++++|.++|..||. |..|.|+ .+.                 .+|.++|||||+|.+.++|..||
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-----------------DKMKNRGFAFVEYESHRAAAMAR   69 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSC-----------------TTTTTCCEEEEEESSHHHHHHHH
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCC-----------------CCCCcCcEEEEEecCHHHHHHHH
Confidence            4589999999999999999999999998 9999884 211                 23457899999999999999999


Q ss_pred             H-hc--ceeecCceeEeecCCCcc
Q 008920          302 A-FN--MAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 ~-ln--g~~~~gr~I~V~~a~~~~  322 (548)
                      . |+  +..|.|+.|.|.++.+..
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            5 85  589999999999997643

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=1.4e-13  Score=117.02  Aligned_cols=79  Identities=27%  Similarity=0.329  Sum_probs=70.0

Q ss_pred             cCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeE
Q 008920          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE  410 (548)
Q Consensus       332 ~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~  410 (548)
                      .....++|||+|||+.+++++|+++|..|+.  |.|..|.++        +|||||+|.+.++|..||..|+ ..|.|+.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~--g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKP--GAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSP   80 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTST--TCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEE
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCC--cceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            3456789999999999999999999999954  688888764        5699999999999999999777 9999999


Q ss_pred             EEEEeeecCC
Q 008920          411 LRLSHAQQNC  420 (548)
Q Consensus       411 I~V~~Ak~~~  420 (548)
                      |.|.|+.+..
T Consensus        81 l~v~~a~~~~   90 (99)
T 2cpd_A           81 IEVTLAKPVD   90 (99)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEECCCCC
Confidence            9999998754

>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=99.51  E-value=6.7e-15  Score=122.72  Aligned_cols=78  Identities=22%  Similarity=0.371  Sum_probs=68.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~ln  304 (548)
                      ++|||+|||+++++++|.++|+.||.|..|.|+.++.                 +|.++|||||+|.+.+ |..|+ .||
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-----------------TKKPKGFGFVEMQEES-VSEAIAKLD   63 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSS-----------------SCCCCEEEEEEECTTH-HHHHHHTSC
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCC-----------------CCCcceEEEEEECCHH-HHHHHHHhC
Confidence            6899999999999999999999999999999955431                 3457899999999999 99999 589


Q ss_pred             ceeecCceeEeecCCCc
Q 008920          305 MAVIGGNHIRLDRACPP  321 (548)
Q Consensus       305 g~~~~gr~I~V~~a~~~  321 (548)
                      +..|.|+.|.|.++.+.
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            99999999999998754

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.51  E-value=1.9e-14  Score=121.93  Aligned_cols=74  Identities=27%  Similarity=0.467  Sum_probs=67.6

Q ss_pred             CcccEEEEcCCCC-CCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          223 KLLRTIFVGNLPL-KVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~-~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ...++|||+|||+ .+++++|..+|+.||.|..|.|                         .+|||||+|.+.++|..||
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i-------------------------~~g~afV~f~~~~~A~~A~   62 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------------------------KNAFGFIQFDNPQSVRDAI   62 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEE-------------------------ETTEEEEEESCHHHHHHHH
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE-------------------------eCCEEEEEECCHHHHHHHH
Confidence            3468999999999 9999999999999999999998                         3489999999999999999


Q ss_pred             H-hcceeecCceeEeecCCCc
Q 008920          302 A-FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 ~-lng~~~~gr~I~V~~a~~~  321 (548)
                      . ||+..|.|+.|.|.++.+.
T Consensus        63 ~~l~g~~~~g~~l~V~~a~~~   83 (96)
T 2kvi_A           63 ECESQEMNFGKKLILEVSSSN   83 (96)
T ss_dssp             HHHTCSSCBTTTBCEEEEECC
T ss_pred             HHcCCCeeCCcEEEEEEcCcC
Confidence            5 9999999999999998654

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.51  E-value=1.2e-14  Score=124.01  Aligned_cols=81  Identities=19%  Similarity=0.203  Sum_probs=70.0

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++|+++|..+|+.||.|.. .++.+.                 .++.++|||||+|.+.++|..||+
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            34689999999999999999999999999877 332221                 245688999999999999999999


Q ss_pred             hcceeecCceeEeecCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~  321 (548)
                      ||+..|.|+.|.|.++.+.
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

>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=99.51  E-value=2.2e-14  Score=121.12  Aligned_cols=79  Identities=25%  Similarity=0.338  Sum_probs=70.1

Q ss_pred             CcccEEEEcCCCCCCcHHHHH----HHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLI----KEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~----~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~  298 (548)
                      ...++|||+|||+++++++|.    .+|+.||.|..|.|+.                    +|.++|||||+|.+.++|.
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~--------------------~~~~~g~afV~f~~~~~A~   65 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--------------------SLKMRGQAFVIFKEVSSAT   65 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--------------------HHHHTTCEEEEESSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc--------------------CCCcCcEEEEEeCCHHHHH
Confidence            346899999999999999999    9999999999998831                    2346799999999999999


Q ss_pred             HHH-HhcceeecCceeEeecCCCc
Q 008920          299 AAL-AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       299 ~Al-~lng~~~~gr~I~V~~a~~~  321 (548)
                      .|+ .|||..|.|+.|.|.++.+.
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 59999999999999998754

>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=99.51  E-value=8.1e-15  Score=126.87  Aligned_cols=81  Identities=10%  Similarity=0.219  Sum_probs=74.4

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCC---eEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCC
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESS---VEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRD  408 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~---I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~G  408 (548)
                      ....++|||+|||+++++++|+++|..|    |.   |..|.|+.+.. |.++|||||+|.+.++|..||. ++ ..|+|
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~----g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~g   81 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDC----RIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQ   81 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTS----CBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSS
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhc----CCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCC
Confidence            4567899999999999999999999998    66   89999999976 9999999999999999999999 55 99999


Q ss_pred             eEEEEEeeecC
Q 008920          409 RELRLSHAQQN  419 (548)
Q Consensus       409 r~I~V~~Ak~~  419 (548)
                      +.|.|.++.+.
T Consensus        82 r~i~V~~a~~~   92 (107)
T 2lmi_A           82 RYVEVYEINNE   92 (107)
T ss_dssp             SCCCCEECCHH
T ss_pred             eEEEEEECCHH
Confidence            99999998764

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.51  E-value=4.5e-14  Score=126.71  Aligned_cols=81  Identities=17%  Similarity=0.262  Sum_probs=72.3

Q ss_pred             CCCccEEEEeCCCCCCCHHHHH----HHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccC
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIY----QLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLR  407 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~----~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~  407 (548)
                      ..+.++|||+|||+.+++++|+    ++|+.|    |.|..|.+..   ++.++|||||+|.+.++|..||..|+ ..|.
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~----G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~   98 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQ----GDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQ   98 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHH----SCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccC----CCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeC
Confidence            4457899999999999999876    799999    8999988753   57889999999999999999999888 9999


Q ss_pred             CeEEEEEeeecCC
Q 008920          408 DRELRLSHAQQNC  420 (548)
Q Consensus       408 Gr~I~V~~Ak~~~  420 (548)
                      |+.|.|.||....
T Consensus        99 gr~l~V~~a~~~~  111 (127)
T 2a3j_A           99 GNPLVITFSETPQ  111 (127)
T ss_dssp             TSCCEEEECCCCC
T ss_pred             CCEEEEEEccCcc
Confidence            9999999998753

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=1.6e-14  Score=129.04  Aligned_cols=77  Identities=18%  Similarity=0.316  Sum_probs=68.5

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCe----eEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEI----DSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I----~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      .++|||+|||+++|+++|++||+.||.|    ..|.|+.+.                  +|+++|||||+|.+.++|++|
T Consensus        23 ~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~------------------~gr~~G~aFV~F~~~~~A~~A   84 (123)
T 2dha_A           23 QVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP------------------DGRPTGDAFVLFACEEYAQNA   84 (123)
T ss_dssp             CCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT------------------TSCEEEEEEECCSSHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC------------------CCCEeeEEEEEECCHHHHHHH
Confidence            4799999999999999999999999975    688886542                  355789999999999999999


Q ss_pred             HHhcceeecCceeEeecCC
Q 008920          301 LAFNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       301 l~lng~~~~gr~I~V~~a~  319 (548)
                      |.+|+..|.|+.|.|..+.
T Consensus        85 l~~~~~~l~gR~i~V~~a~  103 (123)
T 2dha_A           85 LRKHKDLLGKRYIELFRST  103 (123)
T ss_dssp             HTTTTEESSSCEECCEEEC
T ss_pred             HHhCCCeeCCeEEEEEECC
Confidence            9889999999999998875

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.51  E-value=4e-14  Score=127.03  Aligned_cols=79  Identities=24%  Similarity=0.333  Sum_probs=69.2

Q ss_pred             CcccEEEEcCCCCCCcHHHHH----HHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLI----KEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~----~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~  298 (548)
                      ...++|||+|||+.+++++|+    ++|+.||.|..|.+..                    ++.++|||||+|.+.++|.
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~--------------------~~~~rG~aFV~F~~~~~A~   86 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL--------------------SDDNSGKAYIVFATQESAQ   86 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC--------------------CCSSCCCEEEEESSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc--------------------CCCcCCEEEEEECCHHHHH
Confidence            346899999999999999866    7999999999988732                    2347799999999999999


Q ss_pred             HHH-HhcceeecCceeEeecCCCc
Q 008920          299 AAL-AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       299 ~Al-~lng~~~~gr~I~V~~a~~~  321 (548)
                      .|+ .|||..|.|+.|.|.++...
T Consensus        87 ~Ai~~lng~~l~gr~l~V~~a~~~  110 (127)
T 2a3j_A           87 AFVEAFQGYPFQGNPLVITFSETP  110 (127)
T ss_dssp             HHHHHSTTCCCTTSCCEEEECCCC
T ss_pred             HHHHHHCCCEeCCCEEEEEEccCc
Confidence            999 69999999999999999754

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.51  E-value=3.7e-14  Score=118.86  Aligned_cols=73  Identities=18%  Similarity=0.167  Sum_probs=68.5

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      .+..|||+||++.+|+++|+++|.+|    |+|.+|+|+.      ++|||||+|.+.++|..|++.|| ..|.|++|+|
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~----G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V   75 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQH----GPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFA   75 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHH----SCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhh----CCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEE
Confidence            46789999999999999999999999    9999999865      58999999999999999999998 9999999999


Q ss_pred             Eeee
Q 008920          414 SHAQ  417 (548)
Q Consensus       414 ~~Ak  417 (548)
                      .+|.
T Consensus        76 ~~A~   79 (89)
T 2wbr_A           76 ESPS   79 (89)
T ss_dssp             ECCC
T ss_pred             EECC
Confidence            9985

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.51  E-value=2.4e-14  Score=117.32  Aligned_cols=72  Identities=19%  Similarity=0.259  Sum_probs=63.9

Q ss_pred             cEEEEcCCCCCC------cHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHH
Q 008920          226 RTIFVGNLPLKV------KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (548)
Q Consensus       226 rtVfVgNLP~~~------tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~  299 (548)
                      ++|||+|||+.+      ++++|..+|+.||.|.+|.|+.    .               +|.++|||||+|.+.++|..
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~----~---------------~g~~~g~afV~f~~~~~A~~   62 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE----E---------------DGKTKGYIFLEYASPAHAVD   62 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC----B---------------TTBCCCEEEEEESSHHHHHH
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC----C---------------CCcEeEEEEEEECCHHHHHH
Confidence            789999999999      7899999999999999998831    1               34577999999999999999


Q ss_pred             HH-HhcceeecCc-eeEee
Q 008920          300 AL-AFNMAVIGGN-HIRLD  316 (548)
Q Consensus       300 Al-~lng~~~~gr-~I~V~  316 (548)
                      |+ .|||..|.|+ .|.|.
T Consensus        63 Ai~~lng~~~~g~~~l~V~   81 (81)
T 2krb_A           63 AVKNADGYKLDKQHTFRVN   81 (81)
T ss_dssp             HHTTSSSCCCSSSSCCCCC
T ss_pred             HHHHhcCcccCCceeEEeC
Confidence            99 5999999999 88773

>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=99.51  E-value=5.4e-14  Score=115.77  Aligned_cols=75  Identities=21%  Similarity=0.444  Sum_probs=69.3

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHc-C-CccCCeE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR-N-LKLRDRE  410 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~l-n-~~l~Gr~  410 (548)
                      ....++|||+|||+.+++++|+++|+.|    |.|..|.|+.+      +|||||+|.+.++|..|+..| + ..|.|+.
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~----G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~   78 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQF----GEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRR   78 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTT----SCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhC----CCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCE
Confidence            4567899999999999999999999999    89999999875      789999999999999999976 6 9999999


Q ss_pred             EEEEeee
Q 008920          411 LRLSHAQ  417 (548)
Q Consensus       411 I~V~~Ak  417 (548)
                      |.|.||+
T Consensus        79 l~v~~ak   85 (85)
T 2ytc_A           79 LNVKWGR   85 (85)
T ss_dssp             CCEEECC
T ss_pred             EEEEecC
Confidence            9999984

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.51  E-value=4.5e-14  Score=122.69  Aligned_cols=75  Identities=21%  Similarity=0.333  Sum_probs=69.0

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      +...++|||+|||+++++++|..+|+.||.|..|.|+                         +|||||+|.+.++|..|+
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            4456899999999999999999999999999999983                         389999999999999999


Q ss_pred             -HhcceeecCceeEeecCCCc
Q 008920          302 -AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 -~lng~~~~gr~I~V~~a~~~  321 (548)
                       .|||..|.|+.|.|.++.+.
T Consensus        83 ~~l~g~~~~g~~l~V~~a~~~  103 (108)
T 2jvo_A           83 EEVHGKSFANQPLEVVYSKLP  103 (108)
T ss_dssp             HHHTTCEETTEECEEESCSCC
T ss_pred             HHcCCCEECCeEEEEEEecCC
Confidence             59999999999999999764

>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=99.50  E-value=5.1e-14  Score=122.85  Aligned_cols=79  Identities=22%  Similarity=0.468  Sum_probs=72.5

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      ++.++|||+|||+.+++++|+.+|+.|    |.|..|.|+.+   +.++|||||+|.+.++|..|+..++ ..|.|+.|.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   78 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKY----GPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLV   78 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTT----SCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            456899999999999999999999999    89999999976   4458999999999999999999777 999999999


Q ss_pred             EEeeecC
Q 008920          413 LSHAQQN  419 (548)
Q Consensus       413 V~~Ak~~  419 (548)
                      |.|+.+.
T Consensus        79 v~~a~~~   85 (115)
T 3lqv_A           79 VLYYNAN   85 (115)
T ss_dssp             EEECCHH
T ss_pred             EEEecCC
Confidence            9999864

>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=99.50  E-value=5.1e-14  Score=119.67  Aligned_cols=78  Identities=28%  Similarity=0.533  Sum_probs=71.6

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|.|+.+      +|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l   81 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKY----GKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQL   81 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTT----CCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhc----CCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceE
Confidence            4567899999999999999999999999    89999999865      7899999999999999998887 89999999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      .|.|+.+..
T Consensus        82 ~v~~a~~~~   90 (99)
T 2cpj_A           82 RVRFACHSA   90 (99)
T ss_dssp             EEEESSCCS
T ss_pred             EEEEcCCCC
Confidence            999998753

>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=99.50  E-value=2.4e-14  Score=120.83  Aligned_cols=81  Identities=21%  Similarity=0.395  Sum_probs=73.3

Q ss_pred             CCCccEEEEeCCCCCCCHHHHH----HHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccC
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIY----QLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLR  407 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~----~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~  407 (548)
                      ..+.++|||+|||+.+++++|+    ++|+.|    |.|..|.|+.   +|.++|||||+|.+.++|..|+..++ ..|.
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~----G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~   77 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRF----GQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFY   77 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGG----SCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhC----CCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEEC
Confidence            4567899999999999999999    999999    8999998873   57789999999999999999998877 9999


Q ss_pred             CeEEEEEeeecCC
Q 008920          408 DRELRLSHAQQNC  420 (548)
Q Consensus       408 Gr~I~V~~Ak~~~  420 (548)
                      |+.|.|.|+.+..
T Consensus        78 g~~l~v~~a~~~~   90 (97)
T 1nu4_A           78 DKPMRIQYAKTDS   90 (97)
T ss_dssp             TEECEEEECSSCC
T ss_pred             CcEEEEEEccCCC
Confidence            9999999998753

>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=99.50  E-value=7.6e-14  Score=120.82  Aligned_cols=76  Identities=14%  Similarity=0.184  Sum_probs=68.7

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++|+++|.++|..||.|..|.|+.                       . |||||+|.+.++|+.||.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~-----------------------~-g~afV~f~~~~~a~~Ai~   68 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-----------------------D-GTGVVEFVRKEDMTYAVR   68 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEET-----------------------T-TEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEec-----------------------C-CEEEEEECCHHHHHHHHH
Confidence            3468999999999999999999999999999999832                       1 799999999999999995


Q ss_pred             -hcceeecC-----ceeEeecCCCcc
Q 008920          303 -FNMAVIGG-----NHIRLDRACPPR  322 (548)
Q Consensus       303 -lng~~~~g-----r~I~V~~a~~~~  322 (548)
                       ||+..|.|     +.|.|.++.+..
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             99999999     999999998653

>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=99.50  E-value=6.9e-14  Score=121.27  Aligned_cols=74  Identities=26%  Similarity=0.467  Sum_probs=68.3

Q ss_pred             CcccEEEEcCCCCC-CcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLK-VKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~-~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ...++|||+|||++ +++++|+++|+.||.|..|.|                         ++|||||+|.+.++|..||
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-------------------------~~g~afV~f~~~~~A~~A~   79 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------------------------HKGYAFVQYSNERHARAAV   79 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-------------------------ETTEEEEECSSSHHHHHHH
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-------------------------eCCEEEEEECCHHHHHHHH
Confidence            34589999999999 999999999999999999988                         3489999999999999999


Q ss_pred             -HhcceeecCceeEeecCCCc
Q 008920          302 -AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 -~lng~~~~gr~I~V~~a~~~  321 (548)
                       .||+..|.|+.|.|.++.++
T Consensus        80 ~~l~g~~~~g~~l~V~~a~~~  100 (110)
T 1wf1_A           80 LGENGRVLAGQTLDINMAGEP  100 (110)
T ss_dssp             HHHTTCEETTEECCEEESCCC
T ss_pred             HHcCCCEECCeEEEEEECCCC
Confidence             69999999999999999754

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.50  E-value=2.4e-14  Score=122.22  Aligned_cols=80  Identities=25%  Similarity=0.475  Sum_probs=75.2

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRL  413 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V  413 (548)
                      ...++|||+|||+.+++++|+++|+.|    |.|..|.|+.+. +|.++|||||+|.+.++|..||. .+..|.|+.|.|
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~-~~~~~~g~~l~v   80 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARY----GSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKLKL   80 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGG----SCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT-CCCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhC----CCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh-CCCeECCEEEEE
Confidence            356899999999999999999999999    899999999997 99999999999999999999999 559999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      .++.+.
T Consensus        81 ~~a~~~   86 (102)
T 2xs2_A           81 GPAIRK   86 (102)
T ss_dssp             EEEEEC
T ss_pred             EECCcC
Confidence            999875

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.50  E-value=4.4e-14  Score=119.60  Aligned_cols=78  Identities=19%  Similarity=0.434  Sum_probs=69.5

Q ss_pred             CCCccEEEEeCCCC-CCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeE
Q 008920          333 YDIKKTVFVGNLPF-DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE  410 (548)
Q Consensus       333 ~~~~~tLfV~NLp~-~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~  410 (548)
                      ..+.++|||+|||+ .+++++|+.+|+.|    |.|..|.|.        +|||||+|.+.++|..||..++ ..|.|+.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~----G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   74 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPY----GHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKK   74 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTT----CCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTT
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhc----CCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcE
Confidence            45679999999999 99999999999999    899999884        6899999999999999999877 9999999


Q ss_pred             EEEEeeecCCCC
Q 008920          411 LRLSHAQQNCTP  422 (548)
Q Consensus       411 I~V~~Ak~~~~~  422 (548)
                      |.|.|+.+...+
T Consensus        75 l~V~~a~~~~~~   86 (96)
T 2kvi_A           75 LILEVSSSNARP   86 (96)
T ss_dssp             BCEEEEECCCC-
T ss_pred             EEEEEcCcCCCC
Confidence            999999876443

>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=99.50  E-value=3.2e-14  Score=124.96  Aligned_cols=77  Identities=18%  Similarity=0.248  Sum_probs=67.6

Q ss_pred             CCcccEEEEcCCCCC-CcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLK-VKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~-~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      ....++|||+|||++ +++++|.++|++||.|.+|+|+.                       ++|||||+|.+.++|..|
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            345689999999998 99999999999999999999832                       469999999999999999


Q ss_pred             HH-hc--ceeecCceeEeecCCCc
Q 008920          301 LA-FN--MAVIGGNHIRLDRACPP  321 (548)
Q Consensus       301 l~-ln--g~~~~gr~I~V~~a~~~  321 (548)
                      +. |+  +..|.|+.|.|.++...
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            94 65  45699999999998754

>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=99.50  E-value=2.2e-14  Score=128.63  Aligned_cols=80  Identities=25%  Similarity=0.384  Sum_probs=72.9

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeE--EEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVE--AVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRE  410 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~--~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~  410 (548)
                      .....+|||+|||+++++++|+++|+.|    + |.  .|+|+.|+. |.++|||||+|.+.++|..||..++..|+||.
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~----~-i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~  112 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL----E-IVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGKHKERIGHRY  112 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS----C-EEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTTTTCCBTTBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC----C-ceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHCCCEECCEE
Confidence            3456889999999999999999999999    4 55  899999976 99999999999999999999998779999999


Q ss_pred             EEEEeeec
Q 008920          411 LRLSHAQQ  418 (548)
Q Consensus       411 I~V~~Ak~  418 (548)
                      |.|.++.+
T Consensus       113 I~V~~a~~  120 (126)
T 2hgm_A          113 IEVFKSSQ  120 (126)
T ss_dssp             CCCEEECH
T ss_pred             EEEEECCH
Confidence            99998864

>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=99.50  E-value=5.3e-14  Score=131.09  Aligned_cols=82  Identities=20%  Similarity=0.252  Sum_probs=72.3

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...++|||+|||+.+++++|..+|+.||.|..|.|+.+..                 +|.++|||||+|.+.++|..|| 
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            3467999999999999999999999999999999965431                 3457899999999999999999 


Q ss_pred             HhcceeecCceeEeecCCCc
Q 008920          302 AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~  321 (548)
                      .||+..|.|+.|.|.++.+.
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            59999999999999998653

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.50  E-value=2.2e-14  Score=122.51  Aligned_cols=79  Identities=15%  Similarity=0.359  Sum_probs=71.0

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++++++|..+|+.||.|..|.|+.+.                  +|.++|||||+|.+.++|..||.
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------------------TGVSKGYGFVSFYNDVDVQKIVE   68 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT------------------TSCEEEEEEEEESSCCCHHHHTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC------------------CCCccceEEEEECCHHHHHHHHh
Confidence            346899999999999999999999999999999996654                  24477999999999999999999


Q ss_pred             hcceeecCceeEeecCCC
Q 008920          303 FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~  320 (548)
                       ++..|.|+.|.|.++.+
T Consensus        69 -~~~~~~g~~l~v~~a~~   85 (102)
T 2xs2_A           69 -SQINFHGKKLKLGPAIR   85 (102)
T ss_dssp             -CCCEETTEECEEEEEEE
T ss_pred             -CCCeECCEEEEEEECCc
Confidence             99999999999999864

>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=99.50  E-value=3.2e-14  Score=124.96  Aligned_cols=78  Identities=18%  Similarity=0.317  Sum_probs=69.9

Q ss_pred             CCCccEEEEeCCCCC-CCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC---CccCC
Q 008920          333 YDIKKTVFVGNLPFD-VKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN---LKLRD  408 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~-~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln---~~l~G  408 (548)
                      ..+.++|||+|||++ +++++|+++|..|    |.|..|.|++.      +|||||+|.+.++|..||..++   ..|.|
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~f----G~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~G   91 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPY----GKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQG   91 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTT----SCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSS
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhc----CCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            456789999999998 9999999999999    89999999753      7899999999999999998764   56999


Q ss_pred             eEEEEEeeecCC
Q 008920          409 RELRLSHAQQNC  420 (548)
Q Consensus       409 r~I~V~~Ak~~~  420 (548)
                      +.|.|.|+....
T Consensus        92 r~l~V~~a~~~~  103 (112)
T 1x4f_A           92 RCVKVDLSEKYK  103 (112)
T ss_dssp             SCCEEEEECSCS
T ss_pred             EEEEEEECcccc
Confidence            999999998653

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.24  E-value=1.9e-15  Score=132.47  Aligned_cols=83  Identities=19%  Similarity=0.246  Sum_probs=77.6

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEE--------EEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-C
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEA--------VRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-L  404 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~--------VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~  404 (548)
                      .+.++|||+|||+.+++++|+++|+.|    |.|..        |.|+.++.++.++|||||+|.+.++|..||..|+ .
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   80 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQI----GIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   80 (116)
Confidence            456899999999999999999999999    89998        9999998899999999999999999999999877 9


Q ss_pred             ccCCeEEEEEeeecCC
Q 008920          405 KLRDRELRLSHAQQNC  420 (548)
Q Consensus       405 ~l~Gr~I~V~~Ak~~~  420 (548)
                      .|.|+.|.|.|+.+..
T Consensus        81 ~~~g~~l~V~~a~~~~   96 (116)
T 2lcw_A           81 EFSGNPIKVSFATRRA   96 (116)
Confidence            9999999999998753

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.49  E-value=5.8e-14  Score=118.41  Aligned_cols=78  Identities=28%  Similarity=0.299  Sum_probs=67.9

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+.+++++|..+|+.||.|..| .                     .++.++|||||+|.+.++|..||
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-~---------------------~~~~~~g~afV~f~~~~~a~~A~   70 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-S---------------------QDGKSKGIAYIEFKSEADAEKNL   70 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-E---------------------ETTEEEEEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-C---------------------CCCCcceEEEEEECCHHHHHHHH
Confidence            3456899999999999999999999999987665 1                     13447799999999999999999


Q ss_pred             H-hcceeecCceeEeecCCCc
Q 008920          302 A-FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 ~-lng~~~~gr~I~V~~a~~~  321 (548)
                      . ||+..|.|+.|.|.++.+.
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            5 9999999999999998654

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.49  E-value=2e-14  Score=117.79  Aligned_cols=71  Identities=17%  Similarity=0.227  Sum_probs=65.8

Q ss_pred             cEEEEeCCCCCC------CHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCe
Q 008920          337 KTVFVGNLPFDV------KDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDR  409 (548)
Q Consensus       337 ~tLfV~NLp~~~------teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr  409 (548)
                      ++|||+|||+.+      ++++|+++|+.|    |.|..|.|+  ..+|.++|||||+|.+.++|..||..|+ ..|.|+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~----G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~   75 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKF----GKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   75 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTT----CCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSS
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhc----CCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCc
Confidence            689999999999      679999999999    899999988  3689999999999999999999999887 999999


Q ss_pred             -EEEE
Q 008920          410 -ELRL  413 (548)
Q Consensus       410 -~I~V  413 (548)
                       .|+|
T Consensus        76 ~~l~V   80 (81)
T 2krb_A           76 HTFRV   80 (81)
T ss_dssp             SCCCC
T ss_pred             eeEEe
Confidence             8876

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.49  E-value=4e-14  Score=128.04  Aligned_cols=82  Identities=24%  Similarity=0.372  Sum_probs=72.7

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...++|||+|||+++|+++|.++|+.||.|..|.|+.+.                 .++.++|||||+|.+.++|+.|| 
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 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDR-----------------YTKESRGFAFVRFHDKRDAEDAMD  107 (135)
T ss_dssp             GGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCS-----------------SSSSCCSCCEEECSCHHHHHHHHT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC-----------------CCCccceEEEEEECCHHHHHHHHH
Confidence            346899999999999999999999999999999985433                 13457899999999999999999 


Q ss_pred             HhcceeecCceeEeecCCCc
Q 008920          302 AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~  321 (548)
                      .||+..|.|+.|.|.++.+.
T Consensus       108 ~l~g~~i~g~~l~V~~a~~~  127 (135)
T 2lea_A          108 AMDGAVLDGRELRVQMARYG  127 (135)
T ss_dssp             TTTTCCSSSSCCEEEECCCC
T ss_pred             HcCCCEECCEEEEEEECCCC
Confidence            59999999999999999764

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.49  E-value=5.1e-14  Score=118.74  Aligned_cols=79  Identities=22%  Similarity=0.399  Sum_probs=70.9

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|..|     ..++.++|||||+|.+.++|..||..++ ..|.|+.|
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~----g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   83 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDA----LEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV   83 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSE----EEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhC----CcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            4467899999999999999999999999    777655     3578899999999999999999999888 99999999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      .|.|+.+..
T Consensus        84 ~v~~a~~~~   92 (96)
T 1fjc_A           84 SLYYTGEKG   92 (96)
T ss_dssp             EEEECSSSC
T ss_pred             EEEEcCCCC
Confidence            999998753

>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=99.49  E-value=3.7e-14  Score=127.17  Aligned_cols=79  Identities=22%  Similarity=0.280  Sum_probs=68.5

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCee--EEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEID--SVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~--sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      ...++|||+|||+++|+++|+++|+.| .|.  .|+|+.++                  .|.++|||||+|.+.++|++|
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~------------------~GrsrGfaFV~F~~~e~A~~A  100 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDP------------------EGKITGEAFVQFASQELAEKA  100 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCS------------------SSSSCSEEEEEESSTTHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECC------------------CCCCceEEEEEECCHHHHHHH
Confidence            345799999999999999999999999 566  88885543                  245789999999999999999


Q ss_pred             HHhcceeecCceeEeecCCC
Q 008920          301 LAFNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       301 l~lng~~~~gr~I~V~~a~~  320 (548)
                      |.+++..|.|+.|.|.++.+
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

>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=99.49  E-value=5.4e-14  Score=123.40  Aligned_cols=75  Identities=20%  Similarity=0.271  Sum_probs=64.7

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeE--
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE--  410 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~--  410 (548)
                      ...++|||+|||+++++++|+++|..|    |.|..|.|+.+       |||||+|.+.++|..||..|+ ..|.|+.  
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~----G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~   82 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREA----GDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGE   82 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGG----SCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEee
Confidence            356899999999999999999999999    89999999876       899999999999999999887 9999998  


Q ss_pred             ---EEEEeeecC
Q 008920          411 ---LRLSHAQQN  419 (548)
Q Consensus       411 ---I~V~~Ak~~  419 (548)
                         |.|..+.+.
T Consensus        83 ~~~i~v~~~~~~   94 (115)
T 3beg_B           83 TAYIRVKVDGPR   94 (115)
T ss_dssp             CCBCEEEECC--
T ss_pred             eEEEEeccCCCC
Confidence               666666553

>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=134.21  Aligned_cols=82  Identities=24%  Similarity=0.391  Sum_probs=76.4

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      .+.++|||+|||+++++++|+++|+.|    |.|.+|+|++|..++.++|||||+|.+.++|..||..++ ..+.|+.|+
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~----G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~   88 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPA----GPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVR   88 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhh----CCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccc
Confidence            456899999999999999999999999    999999999999999999999999999999999999888 899999999


Q ss_pred             EEeeecC
Q 008920          413 LSHAQQN  419 (548)
Q Consensus       413 V~~Ak~~  419 (548)
                      |.++...
T Consensus        89 ~~~~~~~   95 (213)
T 4f02_A           89 IMWSQRD   95 (213)
T ss_dssp             EEECCCC
T ss_pred             ccccccc
Confidence            9998754

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.49  E-value=8.3e-14  Score=115.01  Aligned_cols=72  Identities=26%  Similarity=0.546  Sum_probs=65.8

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhc----C-------CeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEe
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKF----G-------EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVF  291 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~f----G-------~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F  291 (548)
                      ...++|||+|||+++++++|.++|+.|    |       .|.+|.+..                       ++|||||+|
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            456899999999999999999999999    8       899998832                       459999999


Q ss_pred             cCHHHHHHHHHhcceeecCceeEeec
Q 008920          292 KSEQSTEAALAFNMAVIGGNHIRLDR  317 (548)
Q Consensus       292 ~s~e~A~~Al~lng~~~~gr~I~V~~  317 (548)
                      .+.++|..|+.||+..|.|+.|.|.+
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

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=1.8e-13  Score=114.19  Aligned_cols=75  Identities=19%  Similarity=0.316  Sum_probs=69.1

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+.+|+.|    |.|..|.|+++        ||||+|.+.++|..||..|+ ..|.|+.|
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~v~~~~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~l   73 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERR----GRVIECDVVKD--------YAFVHMEKEADAKAAIAQLNGKEVKGKRI   73 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHH----SCEEEEEECSS--------CEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcC----CCEEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            3467899999999999999999999999    89999998743        99999999999999999877 99999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      .|.|+.+.
T Consensus        74 ~v~~a~~~   81 (90)
T 2dnp_A           74 NVELSTKG   81 (90)
T ss_dssp             EEEESCCC
T ss_pred             EEEECCCC
Confidence            99999875

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.48  E-value=6.5e-14  Score=122.80  Aligned_cols=77  Identities=16%  Similarity=0.145  Sum_probs=69.5

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCC-CeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLES-SVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G-~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      ...+|||+|||+++++++|+++|..|    | .|..|.|+.+    .++|||||+|.+.++|..||..|+ ..|.|+.|.
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~----G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~   98 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLAREN----SLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVIT   98 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHH----TCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHh----CCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            46899999999999999999999999    8 8999988643    478999999999999999999888 999999999


Q ss_pred             EEeeecC
Q 008920          413 LSHAQQN  419 (548)
Q Consensus       413 V~~Ak~~  419 (548)
                      |.++...
T Consensus        99 V~~a~~~  105 (111)
T 2jvr_A           99 VERDDNP  105 (111)
T ss_dssp             EEESCC-
T ss_pred             EEECCCC
Confidence            9998753

>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=99.48  E-value=8.6e-14  Score=121.24  Aligned_cols=83  Identities=18%  Similarity=0.247  Sum_probs=68.9

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...++|||+|||+++|+++|.++|+.||.|..|.+..+..                 ++.++|||||+|.+.++|..|| 
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~-----------------~g~~~g~afV~f~~~~~a~~Ai~   85 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM-----------------TGRMRGQAFITFPNKEIAWQALH   85 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE-----------------CSSSCSEEEEECSSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC-----------------CCccceEEEEEECCHHHHHHHHH
Confidence            3468999999999999999999999999984432211111                 3457899999999999999999 


Q ss_pred             HhcceeecCceeEeecCCCcc
Q 008920          302 AFNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~~  322 (548)
                      .||+..|.|+.|.|.++.+..
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            599999999999999997654

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=8.3e-14  Score=118.04  Aligned_cols=78  Identities=26%  Similarity=0.386  Sum_probs=69.6

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|. +.++.+    .++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~----G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   86 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALREL----GSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTL   86 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHT----TCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhc----CCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            3457899999999999999999999999    8886 666654    578999999999999999998877 99999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      .|.|+.++
T Consensus        87 ~V~~a~~~   94 (97)
T 2e5j_A           87 RVALARQQ   94 (97)
T ss_dssp             EEEECCCC
T ss_pred             EEEEcCCC
Confidence            99999875

>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=99.48  E-value=5.7e-14  Score=117.85  Aligned_cols=76  Identities=14%  Similarity=0.218  Sum_probs=67.0

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCC-eeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGE-IDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~-I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ...++|||+|||+++|+++|+++|+.||. |..+.++                        ++|||||+|.+.++|..||
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 6666551                        4589999999999999999


Q ss_pred             -Hhcc-eeecCceeEeecCCCcc
Q 008920          302 -AFNM-AVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 -~lng-~~~~gr~I~V~~a~~~~  322 (548)
                       .||+ ..|.|+.|.|.++.+..
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             5999 99999999999997653

>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=99.48  E-value=1.6e-13  Score=125.45  Aligned_cols=80  Identities=24%  Similarity=0.435  Sum_probs=75.9

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLS  414 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~  414 (548)
                      .++|||+|||+.+++++|+++|+.|    |.|..|.|+.+..+|.++|||||+|.+.++|..|+..++ ..|.|+.|.|.
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~----G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~   77 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSI----GEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVS   77 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTT----SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhc----CCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEE
Confidence            5799999999999999999999999    899999999998899999999999999999999998777 99999999999


Q ss_pred             eeecC
Q 008920          415 HAQQN  419 (548)
Q Consensus       415 ~Ak~~  419 (548)
                      |+.+.
T Consensus        78 ~~~~~   82 (167)
T 1fxl_A           78 YARPS   82 (167)
T ss_dssp             ECCCC
T ss_pred             ecCCC
Confidence            99764

>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=1.4e-13  Score=129.74  Aligned_cols=83  Identities=22%  Similarity=0.424  Sum_probs=77.7

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELR  412 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~  412 (548)
                      ....++|||+|||+++++++|+++|+.|    |.|..|.|+.++.+|.++|||||+|.+.++|..||..++..|.|+.|.
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~   85 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQW----GTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVE   85 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhC----CCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEee
Confidence            4567899999999999999999999999    899999999999999999999999999999999999877999999999


Q ss_pred             EEeeecC
Q 008920          413 LSHAQQN  419 (548)
Q Consensus       413 V~~Ak~~  419 (548)
                      |.++.+.
T Consensus        86 v~~~~~~   92 (196)
T 1l3k_A           86 PKRAVSR   92 (196)
T ss_dssp             EEECCC-
T ss_pred             eecccCc
Confidence            9998765

>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=99.47  E-value=1.5e-14  Score=131.78  Aligned_cols=80  Identities=18%  Similarity=0.172  Sum_probs=70.1

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++|+++|+++|+.|| |..|.|+.++                  ++.++|||||+|.+.++|..||.
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------------------DGRVTGEADVEFATHEEAVAAMS  104 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSS------------------SSCSSCCCEEECSHHHHHHHHTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECC------------------CCCCceEEEEEeCCHHHHHHHHh
Confidence            3457999999999999999999999999 6689885543                  24578999999999999999999


Q ss_pred             hcceeecCceeEeecCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~  321 (548)
                      +|+..|.|+.|.|.++.+.
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

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.47  E-value=6.8e-14  Score=119.20  Aligned_cols=75  Identities=20%  Similarity=0.399  Sum_probs=69.1

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      ..++|||+|||+.+++++|+.+|..|    |.|..|.|+.      ++|||||+|.+.++|..|+..++ ..|.|+.|+|
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~----G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   95 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNF----GFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRT   95 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTT----SCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhC----CCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            46899999999999999999999999    8999999873      47999999999999999998877 9999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      .|++++
T Consensus        96 ~~a~~~  101 (101)
T 2la4_A           96 GWGKER  101 (101)
T ss_dssp             CBCCCC
T ss_pred             EeccCC
Confidence            999763

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.47  E-value=2.1e-13  Score=114.86  Aligned_cols=76  Identities=22%  Similarity=0.328  Sum_probs=68.0

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      ...++|||+|||+.+++++|+.+|..|    |.|..|  +.+..++.   ||||+|.+.++|..||. ++ ..|.|+.|.
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~----G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~   75 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAF----GPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLR   75 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGT----SCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhc----CCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEE
Confidence            346799999999999999999999999    899987  66666665   99999999999999999 77 999999999


Q ss_pred             EEeeecC
Q 008920          413 LSHAQQN  419 (548)
Q Consensus       413 V~~Ak~~  419 (548)
                      |.++.+.
T Consensus        76 V~~a~~~   82 (94)
T 2e5g_A           76 VRPREQK   82 (94)
T ss_dssp             CBCSCCS
T ss_pred             EEECCcC
Confidence            9988764

>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=99.47  E-value=8.1e-14  Score=116.92  Aligned_cols=77  Identities=17%  Similarity=0.264  Sum_probs=66.6

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCC-eEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC--CccCCeE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESS-VEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN--LKLRDRE  410 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~-I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln--~~l~Gr~  410 (548)
                      ...++|||+|||+++++++|+++|..|    |. |..+.+.       ++|||||+|.+.++|..||..++  ..|.|+.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~   74 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDR----KLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKI   74 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHT----TCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHc----CCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEE
Confidence            456899999999999999999999999    77 5555552       47899999999999999998665  7899999


Q ss_pred             EEEEeeecCCC
Q 008920          411 LRLSHAQQNCT  421 (548)
Q Consensus       411 I~V~~Ak~~~~  421 (548)
                      |.|.|+.+...
T Consensus        75 l~v~~a~~~~~   85 (93)
T 2cqh_A           75 MEVDYSVSKKL   85 (93)
T ss_dssp             CEEEECCCCCC
T ss_pred             EEEEEccCccc
Confidence            99999987643

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.47  E-value=1.1e-13  Score=120.28  Aligned_cols=76  Identities=21%  Similarity=0.426  Sum_probs=70.1

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+.+|+.|    |.|..|.|+        +|||||+|.+.++|..|+..|+ ..|.|+.|
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~----G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   95 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPF----GPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPL   95 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTT----SCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhc----CCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            4467899999999999999999999999    899999987        6899999999999999998877 99999999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      .|.|+.+..
T Consensus        96 ~V~~a~~~~  104 (108)
T 2jvo_A           96 EVVYSKLPA  104 (108)
T ss_dssp             EEESCSCCC
T ss_pred             EEEEecCCC
Confidence            999998753

>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=99.47  E-value=1.6e-13  Score=125.93  Aligned_cols=81  Identities=27%  Similarity=0.489  Sum_probs=76.5

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      +.++|||+|||+++++++|+++|+.|    |.|..|.|+.++.+|.++|||||+|.+.++|..|+..++ ..|.|+.|.|
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v   77 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAI----GPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKV   77 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTT----SCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhc----CCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEE
Confidence            46899999999999999999999999    899999999998899999999999999999999998777 9999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      .|+.+.
T Consensus        78 ~~~~~~   83 (168)
T 1b7f_A           78 SYARPG   83 (168)
T ss_dssp             EECCCC
T ss_pred             EecCCC
Confidence            999865

>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=99.46  E-value=2.4e-13  Score=115.62  Aligned_cols=75  Identities=19%  Similarity=0.447  Sum_probs=69.0

Q ss_pred             CCCccEEEEeCCCC-CCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeE
Q 008920          333 YDIKKTVFVGNLPF-DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE  410 (548)
Q Consensus       333 ~~~~~tLfV~NLp~-~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~  410 (548)
                      ..+.++|||+|||+ .+++++|+++|+.|    |.|..|.|.        +|||||+|.+.++|..||..++ ..|.|+.
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~----G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~   86 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPY----GHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKK   86 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGG----SCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhc----CCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            45679999999998 99999999999999    899999883        7899999999999999999777 9999999


Q ss_pred             EEEEeeecC
Q 008920          411 LRLSHAQQN  419 (548)
Q Consensus       411 I~V~~Ak~~  419 (548)
                      |.|.|+.+.
T Consensus        87 l~V~~a~~~   95 (97)
T 2xnq_A           87 LILEVSSSN   95 (97)
T ss_dssp             CEEEECCCC
T ss_pred             EEEEecCCC
Confidence            999999764

>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=99.46  E-value=7.6e-14  Score=137.37  Aligned_cols=80  Identities=14%  Similarity=0.181  Sum_probs=71.1

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcC--CeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFG--EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG--~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ..++|||+|||+++|+++|+++|+.||  .|..|.|+.+..                 ++.++|||||+|.+.++|.+||
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~-----------------tg~skGfaFV~f~~~~~a~~Ai  129 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRA-----------------NGQSKGFALVGVGSEASSKKLM  129 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTT-----------------TCCEEEEEEEEESCTTHHHHHH
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCC-----------------CCccceEEEEEECCHHHHHHHH
Confidence            467999999999999999999999999  999999976542                 3568899999999999999999


Q ss_pred             H-hcceeecCceeEeecCCC
Q 008920          302 A-FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       302 ~-lng~~~~gr~I~V~~a~~  320 (548)
                      . ||+..|.|+.|.|.++.+
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            5 999999999999999863

>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=99.46  E-value=1.2e-13  Score=120.59  Aligned_cols=75  Identities=24%  Similarity=0.219  Sum_probs=69.3

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      ..++|||+|||+.+++++|+++|..|    |.|..|.|+.      ++|||||+|.+.++|..||..|| ..|.|+.|.|
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~----G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   78 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRF----GSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYL   78 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTT----SCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEE
Confidence            46799999999999999999999999    8999998874      47899999999999999999887 9999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      .|+...
T Consensus        79 ~~a~~~   84 (111)
T 1whx_A           79 EWAPIG   84 (111)
T ss_dssp             EEEETT
T ss_pred             EECCCC
Confidence            999875

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.46  E-value=1.4e-13  Score=115.99  Aligned_cols=77  Identities=13%  Similarity=0.279  Sum_probs=67.8

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEE-EeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVR-IRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVr-i~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ..++|||+|||+++++++|..+|+.||.|..|+ |+.++                     ..|.|||+|.+.++|..|| 
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            358999999999999999999999999999994 64432                     3355999999999999999 


Q ss_pred             HhcceeecCceeEeecCCCc
Q 008920          302 AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~  321 (548)
                      .||+..|.|+.|.|.++.+.
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            59999999999999999764

>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=99.46  E-value=1.3e-13  Score=126.04  Aligned_cols=79  Identities=20%  Similarity=0.311  Sum_probs=70.6

Q ss_pred             CCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       221 ~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      .....++|||+|||+++|+++|+++|+.||.|.+|+|+.+                      ++|||||+|.+.++|..|
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            3445689999999999999999999999999999999432                      458999999999999999


Q ss_pred             HH-hcceeecCceeEeecCCCc
Q 008920          301 LA-FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       301 l~-lng~~~~gr~I~V~~a~~~  321 (548)
                      |. |||..|.|+.|.|.++.++
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            94 9999999999999998754

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.46  E-value=3.2e-13  Score=113.68  Aligned_cols=76  Identities=25%  Similarity=0.374  Sum_probs=65.8

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      ..++|||+|||+++|+++|..+|+.||.|..|.+  +..                 +  .. ||||+|.+.++|..||.|
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~--~~~-----------------~--g~-~afV~f~~~~~a~~ai~l   64 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVM--DKD-----------------K--GV-FAIVEMGDVGAREAVLSQ   64 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEE--CSS-----------------S--CC-EEEEEESSHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEE--cCC-----------------C--Cc-EEEEEECCHHHHHHHHhc
Confidence            3579999999999999999999999999998722  210                 1  12 999999999999999999


Q ss_pred             cceeecCceeEeecCCCc
Q 008920          304 NMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~  321 (548)
                      |+..|.|+.|.|.++.+.
T Consensus        65 ~g~~~~g~~l~V~~a~~~   82 (94)
T 2e5g_A           65 SQHSLGGHRLRVRPREQK   82 (94)
T ss_dssp             SCCEETTEECCCBCSCCS
T ss_pred             CCeEECCEEEEEEECCcC
Confidence            999999999999988654

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.46  E-value=1.4e-13  Score=130.14  Aligned_cols=82  Identities=23%  Similarity=0.330  Sum_probs=77.1

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|+.|    |.|..|.|+.+. ++.++|||||+|.+.++|..||..++ ..|.|+.|
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~----G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l  159 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEF----GTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPM  159 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHT----SCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEE
Confidence            4457899999999999999999999999    899999999997 89999999999999999999999888 99999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      .|.||...
T Consensus       160 ~V~~a~~~  167 (177)
T 2f3j_A          160 DIQLVASQ  167 (177)
T ss_dssp             EEEEESSG
T ss_pred             EEEEecCC
Confidence            99999765

>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=99.46  E-value=1.4e-13  Score=131.99  Aligned_cols=122  Identities=15%  Similarity=0.203  Sum_probs=91.9

Q ss_pred             CHHHHHHHHH-h--cceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEE
Q 008920          293 SEQSTEAALA-F--NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEA  369 (548)
Q Consensus       293 s~e~A~~Al~-l--ng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~  369 (548)
                      +.+.+..|+. .  ....+.+..+.|.....................++|||+|||+.+++++|+++|+.|    |.|..
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 3  455666666666554211000000000011235899999999999999999999999    89999


Q ss_pred             EEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEeeecC
Q 008920          370 VRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQN  419 (548)
Q Consensus       370 VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~Ak~~  419 (548)
                      |+|+++. +|.++|||||+|.+.++|..||..++..|.|+.|.|.|+..-
T Consensus       139 v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          139 IQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDY  187 (193)
T ss_dssp             EEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTTC
T ss_pred             EEEEECC-CCCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHHH
Confidence            9999985 599999999999999999999998889999999999997653

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.18  E-value=6.1e-15  Score=129.15  Aligned_cols=85  Identities=22%  Similarity=0.268  Sum_probs=73.0

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeE--------EEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecC
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDS--------VRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKS  293 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~s--------Vri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s  293 (548)
                      ....++|||+|||+++++++|.++|+.||.|..        |.|+.++                 .++.++|||||+|.+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~-----------------~~g~~~g~afV~f~~   66 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDR-----------------ETGKLKGEATVSFDD   66 (116)
Confidence            345689999999999999999999999999988        6664432                 235578999999999


Q ss_pred             HHHHHHHHH-hcceeecCceeEeecCCCccc
Q 008920          294 EQSTEAALA-FNMAVIGGNHIRLDRACPPRK  323 (548)
Q Consensus       294 ~e~A~~Al~-lng~~~~gr~I~V~~a~~~~k  323 (548)
                      .++|..||. ||+..|.|+.|.|.++.+...
T Consensus        67 ~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           67 PPSAKAAIDWFDGKEFSGNPIKVSFATRRAD   97 (116)
Confidence            999999995 999999999999999976543

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.45  E-value=4.1e-14  Score=128.41  Aligned_cols=83  Identities=19%  Similarity=0.254  Sum_probs=70.6

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEE--E---eecCCCCCCceEEEEEECCHHHHHHHHHHcC-Ccc
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVR--V---IRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKL  406 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~Vr--I---~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l  406 (548)
                      ..+.++|||+|||+.+++++|+.+|+.|    |.|..|.  +   +....+|.++|||||+|.+.++|..||..|| ..|
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~----G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~  117 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRY----VDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVL  117 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGG----CCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHh----CCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEe
Confidence            3467899999999999999999999999    7776641  1   1112468899999999999999999999877 999


Q ss_pred             CCeEEEEEeeecC
Q 008920          407 RDRELRLSHAQQN  419 (548)
Q Consensus       407 ~Gr~I~V~~Ak~~  419 (548)
                      .|+.|.|.||.+.
T Consensus       118 ~g~~l~V~~a~~~  130 (143)
T 3egn_A          118 FGKPMVVQFARSA  130 (143)
T ss_dssp             TTEECEEEECCCS
T ss_pred             CCcEEEEEECCCC
Confidence            9999999999864

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=6.2e-13  Score=112.58  Aligned_cols=75  Identities=16%  Similarity=0.265  Sum_probs=67.4

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...++|||+||  ++|+++|+++|+.||.|..|.|.                       .++|||||+|.+.++|..|| 
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  99999999999999999999882                       16699999999999999999 


Q ss_pred             HhcceeecCceeEeecCCCcc
Q 008920          302 AFNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~~  322 (548)
                      .||+..|.|+.|.|.++.+..
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            699999999999999997643

>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=99.44  E-value=1.7e-13  Score=124.28  Aligned_cols=85  Identities=24%  Similarity=0.209  Sum_probs=69.1

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEE--EeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVR--IRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVr--i~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      ...++|||+|||+++|+++|..+|+.||.|..|.  ++.+-              ....+|.++|||||+|.+.++|..|
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di--------------~~~~~g~~~g~afV~f~~~~~A~~A  108 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDI--------------RLMKEGRMKGQAFIGLPNEKAAAKA  108 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEE--------------EEEEETTTEEEEEEECSSHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeE--------------EeccCCCcccEEEEEeCCHHHHHHH
Confidence            4568999999999999999999999999987641  10000              0012456889999999999999999


Q ss_pred             HH-hcceeecCceeEeecCCCc
Q 008920          301 LA-FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       301 l~-lng~~~~gr~I~V~~a~~~  321 (548)
                      |. |||..|.|+.|.|.++.+.
T Consensus       109 i~~lng~~~~g~~l~V~~a~~~  130 (143)
T 3egn_A          109 LKEANGYVLFGKPMVVQFARSA  130 (143)
T ss_dssp             HHHHTTBEETTEECEEEECCCS
T ss_pred             HHHhCCCEeCCcEEEEEECCCC
Confidence            95 9999999999999999754

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.44  E-value=2.6e-13  Score=114.40  Aligned_cols=79  Identities=15%  Similarity=0.265  Sum_probs=71.2

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEE-EeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVR-VIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE  410 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~Vr-I~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~  410 (548)
                      ....++|||+|||+.+++++|+.+|..|    |.|..|+ |+.++.++    .|||+|.+.++|..||..|+ ..|.|+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~   83 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQY----GVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFT   83 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHH----SCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCB
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhc----CCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            3456899999999999999999999999    8999994 88886644    49999999999999998777 9999999


Q ss_pred             EEEEeeecC
Q 008920          411 LRLSHAQQN  419 (548)
Q Consensus       411 I~V~~Ak~~  419 (548)
                      |.|.|+.+.
T Consensus        84 l~V~~a~~~   92 (96)
T 2e44_A           84 LKVAYIPDE   92 (96)
T ss_dssp             CEEEECCCC
T ss_pred             EEEEEcCcc
Confidence            999999876

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=3.4e-13  Score=114.89  Aligned_cols=81  Identities=26%  Similarity=0.332  Sum_probs=68.2

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++++++|+++|+.|+   .|.++.+.                 .++.++|||||+|.+.++|..||
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~-----------------~~~~~~g~afV~f~~~~~A~~A~   71 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDR-----------------ETGSSKGFGFVDFNSEEDAKAAK   71 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECS-----------------SSCSEEEEEEEECSSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecC-----------------CCCCcCcEEEEEECCHHHHHHHH
Confidence            34568999999999999999999999885   55554432                 13457799999999999999999


Q ss_pred             H-hcceeecCceeEeecCCCcc
Q 008920          302 A-FNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       302 ~-lng~~~~gr~I~V~~a~~~~  322 (548)
                      . ||+..|.|+.|.|.++.+..
T Consensus        72 ~~l~g~~~~g~~l~V~~a~~~~   93 (102)
T 2fc8_A           72 EAMEDGEIDGNKVTLDWAKPKG   93 (102)
T ss_dssp             HHHTTCEETTEECEEEECCCCC
T ss_pred             HHhCCCeECCeEEEEEEecCCC
Confidence            5 99999999999999997653

>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=99.44  E-value=1.9e-13  Score=114.55  Aligned_cols=77  Identities=25%  Similarity=0.388  Sum_probs=63.4

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELR  412 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~  412 (548)
                      ..+..+|||+|||+++++++|+++|+.|    |.|..|.|+++     ++|||||+|.+.++|..+. .....+.|+.|.
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~----G~i~~v~i~~~-----srGfaFV~F~~~~~A~~~~-~~~~~~~g~~v~   77 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQY----GEVVDVFIPKP-----FRAFAFVTFADDKVAQSLC-GEDLIIKGISVH   77 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTT----SCEEEEECCSS-----CCSEEEEEESCHHHHHHHT-TCEEEETTEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcc----CCEEEEEEeeC-----CCCEEEEEECCHHHHHHHc-CCCcccCCEEEE
Confidence            3457899999999999999999999999    99999999875     6899999999999998432 112567799999


Q ss_pred             EEeeecC
Q 008920          413 LSHAQQN  419 (548)
Q Consensus       413 V~~Ak~~  419 (548)
                      |.+|.++
T Consensus        78 v~~a~~k   84 (89)
T 3d2w_A           78 ISNAEPK   84 (89)
T ss_dssp             EEECC--
T ss_pred             EEEcCCC
Confidence            9999875

>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=99.44  E-value=2.2e-13  Score=113.38  Aligned_cols=73  Identities=12%  Similarity=0.228  Sum_probs=66.5

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-  302 (548)
                      ..++|||+|||+++++++|+++|+.| .|..|.|.                       .++|||||+|.+.++|..|+. 
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-----------------------~~~g~afV~f~~~~~a~~Ai~~   59 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-----------------------RNKRTAFVTLLNGEQAQNAIQM   59 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-----------------------GGGTEEEECCSCHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-----------------------CCCcEEEEEECCHHHHHHHHHH
Confidence            45899999999999999999999999 99999882                       156999999999999999995 


Q ss_pred             hcceeecCceeEeecCCC
Q 008920          303 FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~  320 (548)
                      ||+..|.|+.|.|.++..
T Consensus        60 l~g~~~~g~~l~V~~a~~   77 (88)
T 1wg1_A           60 FHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             HTTEEETTEEEEEEECCC
T ss_pred             hCCCeECCcEEEEEEcCC
Confidence            999999999999999853

>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=99.43  E-value=1.1e-13  Score=115.00  Aligned_cols=76  Identities=21%  Similarity=0.333  Sum_probs=66.4

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLS  414 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~  414 (548)
                      ..++|||+|||+.+++++|+++|..|    |.|..|.|+.+     ++|||||+|.+.++|+.|+.. ...+.|+.|.|.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~----G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~-~~~~~g~~l~v~   73 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQY----GDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE-DLIIKGISVHIS   73 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTT----SCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC-EEEETTEEEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHc----CCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC-CceeCCEEEEEE
Confidence            46899999999999999999999999    89999999865     689999999999999865332 366799999999


Q ss_pred             eeecCC
Q 008920          415 HAQQNC  420 (548)
Q Consensus       415 ~Ak~~~  420 (548)
                      ++.++.
T Consensus        74 ~a~~~~   79 (88)
T 1wf0_A           74 NAEPKH   79 (88)
T ss_dssp             CCCCCC
T ss_pred             ecCCCC
Confidence            998753

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.43  E-value=8.8e-13  Score=111.65  Aligned_cols=76  Identities=14%  Similarity=0.215  Sum_probs=68.4

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+||  .+++++|+++|..|    |.|..|.|.      .++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~----G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l   79 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPF----GNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQL   79 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTT----SCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEE
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhC----CCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            345789999996  89999999999999    899999884      458899999999999999998887 99999999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      .|.|+.+..
T Consensus        80 ~v~~a~~~~   88 (97)
T 1x5p_A           80 KVNIARKQP   88 (97)
T ss_dssp             EEECCSSCC
T ss_pred             EEEECCCCC
Confidence            999998753

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.43  E-value=3.1e-13  Score=127.87  Aligned_cols=81  Identities=14%  Similarity=0.231  Sum_probs=72.1

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+.+++++|.++|+.||.|..|.|+.+.                  ++.++|||||+|.+.++|..||.
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~------------------~g~~kG~afV~F~~~~~A~~Ai~  147 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR------------------SGRSLGTADVHFERRADALKAMK  147 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT------------------TSSCSCCEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC------------------CCCEeeEEEEEeCCHHHHHHHHH
Confidence            346899999999999999999999999999999995543                  34577999999999999999995


Q ss_pred             -hcceeecCceeEeecCCCc
Q 008920          303 -FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 -lng~~~~gr~I~V~~a~~~  321 (548)
                       ||+..|.|+.|.|.++...
T Consensus       148 ~lng~~l~Gr~l~V~~a~~~  167 (177)
T 2f3j_A          148 QYKGVPLDGRPMDIQLVASQ  167 (177)
T ss_dssp             HSTTCBCSSSBCEEEEESSG
T ss_pred             HhCCCEECCEEEEEEEecCC
Confidence             9999999999999998653

>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=99.42  E-value=3.1e-13  Score=113.29  Aligned_cols=76  Identities=20%  Similarity=0.311  Sum_probs=60.9

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ....+|||+|||+++|+++|+++|+.||.|.+|.|+.+                      ++|||||+|.+.++|..+..
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~----------------------srGfaFV~F~~~~~A~~~~~   66 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----------------------FRAFAFVTFADDKVAQSLCG   66 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS----------------------CCSEEEEEESCHHHHHHHTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC----------------------CCCEEEEEECCHHHHHHHcC
Confidence            34689999999999999999999999999999998431                      56999999999999984322


Q ss_pred             hcceeecCceeEeecCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~  321 (548)
                      . ...+.|+.|.|.++.+.
T Consensus        67 ~-~~~~~g~~v~v~~a~~k   84 (89)
T 3d2w_A           67 E-DLIIKGISVHISNAEPK   84 (89)
T ss_dssp             C-EEEETTEEEEEEECC--
T ss_pred             C-CcccCCEEEEEEEcCCC
Confidence            1 34456999999998754

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.41  E-value=8.1e-13  Score=111.90  Aligned_cols=75  Identities=19%  Similarity=0.185  Sum_probs=65.0

Q ss_pred             CCccE-EEEeCCCCCCCHHH----HHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccC
Q 008920          334 DIKKT-VFVGNLPFDVKDEE----IYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLR  407 (548)
Q Consensus       334 ~~~~t-LfV~NLp~~~teed----L~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~  407 (548)
                      .+..+ |||+|||+.+++++    |+++|++||   |.|.+|       ++   |||||.|.+.++|..|++.|+ ..|.
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yG---G~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~   72 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCG---GKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVF   72 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTT---CCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSS
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcC---CeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccC
Confidence            34455 99999999999988    558999994   499988       33   999999999999999998887 9999


Q ss_pred             CeEEEEEeeecCCC
Q 008920          408 DRELRLSHAQQNCT  421 (548)
Q Consensus       408 Gr~I~V~~Ak~~~~  421 (548)
                      ||+|+|.||+..+.
T Consensus        73 gr~i~v~~A~~~sd   86 (96)
T 2diu_A           73 GNRIIVSFTPKNRE   86 (96)
T ss_dssp             SSCCEEESSCCSCC
T ss_pred             CceEEEEecCCCcc
Confidence            99999999998643

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=4e-13  Score=111.61  Aligned_cols=76  Identities=20%  Similarity=0.293  Sum_probs=64.7

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      ..++|||+|||+++++++|.++|+.||.|..|.|+.+                      ++|||||+|.+.++|++|+..
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            3589999999999999999999999999999998321                      569999999999999866433


Q ss_pred             cceeecCceeEeecCCCcc
Q 008920          304 NMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~  322 (548)
                       ...+.|+.|.|.++.+..
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             456789999999987654

>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=99.40  E-value=6e-13  Score=127.55  Aligned_cols=79  Identities=11%  Similarity=0.132  Sum_probs=69.9

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      ..++|||+|||+++|+++|.++|+.||.|.+|+|+.+.                  ++.++|||||+|.+.++|..||.+
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~------------------~~~~kG~aFVeF~~~e~A~~A~~~  169 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL------------------HKAFKGSIFVVFDSIESAKKFVET  169 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT------------------TCCEEEEEEEEESSHHHHHHHHHC
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC------------------CCCcccEEEEEECCHHHHHHHHHh
Confidence            35899999999999999999999999999999996643                  244789999999999999999986


Q ss_pred             cceeecCceeEeecCCC
Q 008920          304 NMAVIGGNHIRLDRACP  320 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~  320 (548)
                      .+..|.|+.|.|.+...
T Consensus       170 ~~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          170 PGQKYKETDLLILFKDD  186 (193)
T ss_dssp             TTCEETTEECEEEETTT
T ss_pred             CCCeECCEEEEEEEhHH
Confidence            66799999999998753

>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=99.40  E-value=3.6e-13  Score=118.62  Aligned_cols=73  Identities=15%  Similarity=0.259  Sum_probs=64.7

Q ss_pred             cccEEEE--cCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          224 LLRTIFV--GNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       224 ~~rtVfV--gNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ..++|||  +|||+++++++|+++|++||.|..|.|+.                       .+|||||+|.+.++|+.|+
T Consensus        24 pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~-----------------------~rgfaFV~f~~~~~A~~Ai   80 (114)
T 2cq2_A           24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----------------------NKPYSFARYRTTEESKRAY   80 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT-----------------------TCSCEEEEESSHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----------------------CCCEEEEEECCHHHHHHHH
Confidence            4578999  77999999999999999999999988731                       3589999999999999999


Q ss_pred             -Hhcceee-----cCceeEeecCC
Q 008920          302 -AFNMAVI-----GGNHIRLDRAC  319 (548)
Q Consensus       302 -~lng~~~-----~gr~I~V~~a~  319 (548)
                       .|||..|     .|+.|.|.++.
T Consensus        81 ~~lnG~~~~~~lg~g~~l~v~~a~  104 (114)
T 2cq2_A           81 VTLNGKEVVDDLGQKITLYLNFVE  104 (114)
T ss_dssp             HHTTTCEEECTTSCEEECEEEEES
T ss_pred             HHhCCCEEccccCCCcEEEEEecc
Confidence             5999988     67889998875

>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=4e-13  Score=120.11  Aligned_cols=78  Identities=8%  Similarity=0.117  Sum_probs=69.4

Q ss_pred             cEEEEeCC----CCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECC----HHH----HHHHHH--Hc
Q 008920          337 KTVFVGNL----PFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT----REA----ANLVIK--RR  402 (548)
Q Consensus       337 ~tLfV~NL----p~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~----~e~----A~~Al~--~l  402 (548)
                      ..|||+||    |+.+++.+|+.+|+.|    |.|.+|.++.|+.||.++|||||+|.+    +++    |..|+.  .+
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~f----GeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~l   78 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKY----GEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHES   78 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTT----SCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTT
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhc----CCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhh
Confidence            67999999    9999999999999999    999999999999999999999999996    333    788887  55


Q ss_pred             C-CccCCeEEEEEeeec
Q 008920          403 N-LKLRDRELRLSHAQQ  418 (548)
Q Consensus       403 n-~~l~Gr~I~V~~Ak~  418 (548)
                      + ..|.|+.|+|.+-..
T Consensus        79 ng~~I~Gr~irV~ln~~   95 (136)
T 2j8a_A           79 SGCFIMGFKFEVILNKH   95 (136)
T ss_dssp             TCEEETTEEEEEEECCT
T ss_pred             cCCeecCcEEEEEECcc
Confidence            6 999999999998653

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.40  E-value=4.8e-13  Score=116.99  Aligned_cols=78  Identities=22%  Similarity=0.299  Sum_probs=69.2

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCC---CCCceEEEEEECCHHHHHHHHHHcCCccCCeE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM---RVGKGIAYVLFKTREAANLVIKRRNLKLRDRE  410 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~t---g~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~  410 (548)
                      ...++|||+|||+.+++++|+++|+.|    |.|. +.++.+..+   |.++|||||+|.+.++|..||..++ .|+|+.
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~----G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~-~~~G~~   79 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRF----GPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL-EEDGKL   79 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTT----CCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE-EETTEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhc----CCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh-hcCCcE
Confidence            456899999999999999999999999    8999 888888777   7999999999999999999999884 578888


Q ss_pred             EEEEeee
Q 008920          411 LRLSHAQ  417 (548)
Q Consensus       411 I~V~~Ak  417 (548)
                      |.|..+.
T Consensus        80 ~~~~~~~   86 (114)
T 2dnl_A           80 YLCVSSP   86 (114)
T ss_dssp             EEEECCS
T ss_pred             EEeccCC
Confidence            8777554

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.39  E-value=1.1e-12  Score=119.74  Aligned_cols=78  Identities=17%  Similarity=0.336  Sum_probs=72.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEe
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSH  415 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~  415 (548)
                      ++|||+|||+++++++|+++|+.|    |.|..|.|+.+. ++.++|||||+|.+.++|..|+..++ ..|.|+.|.|.|
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~----G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~   75 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVG----GPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINW   75 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGG----SCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhc----CCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEE
Confidence            589999999999999999999999    899999999996 57899999999999999999997777 999999999999


Q ss_pred             eecC
Q 008920          416 AQQN  419 (548)
Q Consensus       416 Ak~~  419 (548)
                      +.+.
T Consensus        76 ~~~~   79 (166)
T 3md3_A           76 AFQS   79 (166)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9764

>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=99.39  E-value=7.3e-13  Score=116.64  Aligned_cols=77  Identities=16%  Similarity=0.208  Sum_probs=68.3

Q ss_pred             CCCccEEEE--eCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-Ccc---
Q 008920          333 YDIKKTVFV--GNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKL---  406 (548)
Q Consensus       333 ~~~~~tLfV--~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l---  406 (548)
                      ..+.++|||  +||++.+++++|+++|++|    |.|..|.|+.+      +|||||+|.+.++|..|+..|| ..|   
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~f----G~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~   91 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKC----GLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDD   91 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHH----SCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECT
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhc----CCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccc
Confidence            346789999  7799999999999999999    89999987643      7899999999999999999888 766   


Q ss_pred             --CCeEEEEEeeecC
Q 008920          407 --RDRELRLSHAQQN  419 (548)
Q Consensus       407 --~Gr~I~V~~Ak~~  419 (548)
                        .|++|.|.|+...
T Consensus        92 lg~g~~l~v~~a~~~  106 (114)
T 2cq2_A           92 LGQKITLYLNFVEKV  106 (114)
T ss_dssp             TSCEEECEEEEESCC
T ss_pred             cCCCcEEEEEecccC
Confidence              6899999999864

>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=99.38  E-value=4.9e-13  Score=117.28  Aligned_cols=73  Identities=15%  Similarity=0.203  Sum_probs=63.1

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-  302 (548)
                      ..++|||+|||+++++++|.++|+.||.|..|.|+.                       . |||||+|.+.++|+.||. 
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~-----------------------~-g~afV~f~~~~~a~~Ai~~   70 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-----------------------D-GTGVVEFVRKEDMTYAVRK   70 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-----------------------T-SEEEEEESSHHHHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEec-----------------------C-CEEEEEECCHHHHHHHHHH
Confidence            357899999999999999999999999999999832                       1 799999999999999995 


Q ss_pred             hcceeecCce-----eEeecCCC
Q 008920          303 FNMAVIGGNH-----IRLDRACP  320 (548)
Q Consensus       303 lng~~~~gr~-----I~V~~a~~  320 (548)
                      ||+..|.|+.     |.|....+
T Consensus        71 l~g~~~~gr~~~~~~i~v~~~~~   93 (115)
T 3beg_B           71 LDNTKFRSHEGETAYIRVKVDGP   93 (115)
T ss_dssp             HTTCBCCCTTSCCCBCEEEECC-
T ss_pred             hCCCEECCcEeeeEEEEeccCCC
Confidence            9999999988     66666554

>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=99.38  E-value=8.9e-13  Score=121.55  Aligned_cols=77  Identities=17%  Similarity=0.332  Sum_probs=69.9

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      .++|||+|||+.+++++|.++|+.||.|..|.|+.++.                 +|.++|||||+|.+.++|..|+ .|
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 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSA-----------------TGLSKGYAFCEYVDINVTDQAIAGL  156 (172)
T ss_dssp             TTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTT-----------------TCSEEEEEEEEESSTTHHHHHHHHH
T ss_pred             CCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCC-----------------CCCcceEEEEEeCCHHHHHHHHHHc
Confidence            58999999999999999999999999999999966431                 3457799999999999999999 59


Q ss_pred             cceeecCceeEeecC
Q 008920          304 NMAVIGGNHIRLDRA  318 (548)
Q Consensus       304 ng~~~~gr~I~V~~a  318 (548)
                      ||..|.|+.|.|.++
T Consensus       157 ~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          157 NGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTCEETTEECEEEEC
T ss_pred             CCCEECCeEEEEEeC
Confidence            999999999999987

>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=99.38  E-value=5.4e-13  Score=122.45  Aligned_cols=80  Identities=16%  Similarity=0.400  Sum_probs=74.4

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLS  414 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~  414 (548)
                      +.++|||+|||+++++++|+++|+.|    |.|..|.|++++.+|.++|||||+|.+.++|..||.. ...|.|+.|.|.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~g~~i~v~   76 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKY----GTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT-QHILDGKVIDPK   76 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTT----CCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS-CCEETTEECCCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhC----CCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc-ccccCCeEcccc
Confidence            46899999999999999999999999    9999999999999999999999999999999999985 478999999999


Q ss_pred             eeecC
Q 008920          415 HAQQN  419 (548)
Q Consensus       415 ~Ak~~  419 (548)
                      ++.+.
T Consensus        77 ~~~~~   81 (167)
T 2cjk_A           77 RAIPR   81 (167)
T ss_dssp             ECCCH
T ss_pred             cccch
Confidence            98653

>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=99.38  E-value=7.5e-13  Score=110.15  Aligned_cols=74  Identities=22%  Similarity=0.253  Sum_probs=66.6

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      ..++|||+|||+.+++++|+++|..|     .|..|.|.      .++|||||+|.+.++|..|+..++ ..|.|+.|+|
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-----~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V   72 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-----DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIV   72 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-----CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-----CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEE
Confidence            45789999999999999999999998     47777774      468999999999999999999887 9999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      .|+...
T Consensus        73 ~~a~~~   78 (88)
T 1wg1_A           73 QLQPTD   78 (88)
T ss_dssp             EECCCC
T ss_pred             EEcCCC
Confidence            999764

>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=99.38  E-value=1.3e-12  Score=122.03  Aligned_cols=77  Identities=21%  Similarity=0.211  Sum_probs=67.8

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ...+|||+|||+.+|+++|.++|+.||.|..|.|...                     ..+|||||+|.+.++|..|+ .
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k---------------------~~rgfAFVeF~d~~~A~~Ai~~  103 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---------------------NNQFQALLQYADPVSAQHAKLS  103 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES---------------------SSCEEEEEEESCHHHHHHHHHH
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC---------------------CCCCEEEEEECCHHHHHHHHHH
Confidence            3467999999999999999999999999999998421                     14589999999999999999 5


Q ss_pred             hcceeecC--ceeEeecCCCc
Q 008920          303 FNMAVIGG--NHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~g--r~I~V~~a~~~  321 (548)
                      |||..|.|  +.|+|.++.+.
T Consensus       104 LnG~~i~g~g~~L~V~~Ak~~  124 (164)
T 1sjr_A          104 LDGQNIYNACCTLRIDFSKLT  124 (164)
T ss_dssp             STTBCSSSSCSCEEEEECSSS
T ss_pred             hCCCEecCCCcEEEEEEecCC
Confidence            99999966  99999999764

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.37  E-value=9.9e-13  Score=125.74  Aligned_cols=81  Identities=22%  Similarity=0.448  Sum_probs=72.7

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      ..++|||+|||+++++++|+++|..|    |.|..|.|+++..+|.++|||||+|.+.++|..||..++ ..|.|+.|.|
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v  102 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPF----GPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV  102 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGG----SCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEE
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhC----CCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEE
Confidence            45799999999999999999999999    899999999998899999999999999999999999776 9999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      .++...
T Consensus       103 ~~~~~~  108 (216)
T 2qfj_A          103 GRPSNI  108 (216)
T ss_dssp             ECCSCC
T ss_pred             ecCCCc
Confidence            887643

>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=99.37  E-value=6.7e-13  Score=109.51  Aligned_cols=74  Identities=20%  Similarity=0.489  Sum_probs=65.1

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCC-------CeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-Ccc
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLES-------SVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKL  406 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G-------~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l  406 (548)
                      ..++|||+|||+.+++++|+++|..|+...|       .|..|.++.+      +|||||+|.+.++|..|+ .++ ..|
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~~   77 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGIIF   77 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            5689999999999999999999999832224       7999988765      789999999999999999 777 999


Q ss_pred             CCeEEEEEe
Q 008920          407 RDRELRLSH  415 (548)
Q Consensus       407 ~Gr~I~V~~  415 (548)
                      .|+.|+|.+
T Consensus        78 ~g~~l~V~r   86 (87)
T 2hzc_A           78 QGQSLKIRR   86 (87)
T ss_dssp             TTEECEEEC
T ss_pred             CCeEEEEeC
Confidence            999999974

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.36  E-value=1.9e-12  Score=122.12  Aligned_cols=82  Identities=17%  Similarity=0.299  Sum_probs=73.0

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+.+++++|.++|+.||.|..|.|+.++.                 +|.++|||||+|.+.++|..|+.
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-----------------~~~~~g~afV~f~~~~~a~~A~~  174 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSA-----------------TGLSKGYAFCEYVDINVTDQAIA  174 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTT-----------------TCSEEEEEEEEESSSSHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCC-----------------CCCcceEEEEEECCHHHHHHHHH
Confidence            4568999999999999999999999999999999965431                 34577999999999999999995


Q ss_pred             -hcceeecCceeEeecCCCc
Q 008920          303 -FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 -lng~~~~gr~I~V~~a~~~  321 (548)
                       |||..|.|+.|.|.++.+.
T Consensus       175 ~l~g~~~~g~~l~v~~a~~~  194 (198)
T 2yh0_A          175 GLNGMQLGDKKLLVQRASVG  194 (198)
T ss_dssp             HHTTCEETTEECEEEESCCC
T ss_pred             HcCCCEECCEEEEEEECCCC
Confidence             9999999999999999764

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.36  E-value=2.9e-12  Score=111.04  Aligned_cols=81  Identities=14%  Similarity=0.040  Sum_probs=72.0

Q ss_pred             CCccEEEEeCCCC-----CCCHHHHHHHHhccCCCCCCeEEEEEeecCCC-CCCceEEEEEECCHHHHHHHHHHcC-Ccc
Q 008920          334 DIKKTVFVGNLPF-----DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM-RVGKGIAYVLFKTREAANLVIKRRN-LKL  406 (548)
Q Consensus       334 ~~~~tLfV~NLp~-----~~teedL~~~F~~~g~~~G~I~~VrI~~d~~t-g~srG~AFV~F~~~e~A~~Al~~ln-~~l  406 (548)
                      .++++|+|.||..     +.++++|+++|++|    |.|..|.|+.++.+ +.++|||||+|.+.++|..|+..|| ..|
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~----G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~   81 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKY----GKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYF   81 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGG----SCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhc----CCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEE
Confidence            4678999999963     23789999999999    99999999998754 6899999999999999999999888 999


Q ss_pred             CCeEEEEEeeec
Q 008920          407 RDRELRLSHAQQ  418 (548)
Q Consensus       407 ~Gr~I~V~~Ak~  418 (548)
                      .||.|.|.|+.+
T Consensus        82 ~Gr~i~v~~a~~   93 (105)
T 2pe8_A           82 GGRVVKACFYNL   93 (105)
T ss_dssp             TTEECEEEECCH
T ss_pred             CCcEEEEEEcCH
Confidence            999999999975

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.36  E-value=2.7e-12  Score=115.51  Aligned_cols=75  Identities=21%  Similarity=0.218  Sum_probs=66.7

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcce-EEEEecCHHHHHHHH-H
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH-AYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~-AFV~F~s~e~A~~Al-~  302 (548)
                      -..|||+||++.+|+++|.++|+.||.|.+|.|...                      .+|| |||+|.+.++|..|+ .
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            357889999999999999999999999999988431                      2467 999999999999999 6


Q ss_pred             hcceeecC--ceeEeecCCCc
Q 008920          303 FNMAVIGG--NHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~g--r~I~V~~a~~~  321 (548)
                      |||..|.|  +.|+|+++.+.
T Consensus        86 LnG~~i~g~~~~LrI~~ak~~  106 (130)
T 3zzy_A           86 LDGQNIYNACCTLRIDFSKLT  106 (130)
T ss_dssp             HTTCEEETTEEEEEEEECSCS
T ss_pred             cCCCeecCCCcEEEEEecCCC
Confidence            99999988  89999999764

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.35  E-value=2.7e-12  Score=114.66  Aligned_cols=74  Identities=20%  Similarity=0.192  Sum_probs=64.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcce-EEEEecCHHHHHHHH-Hh
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH-AYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~-AFV~F~s~e~A~~Al-~l  303 (548)
                      ..|||+|||+.+|+++|.++|+.||.|..|+|..                       ..|| |||+|.+.++|..|+ .|
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 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-----------------------RNGIQAMVEFESVLCAQKAKAAL   82 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-----------------------SSSEEEEEEESSHHHHHHHHHHH
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-----------------------CCCCEEEEEECCHHHHHHHHHHh
Confidence            3478999999999999999999999999999832                       1275 999999999999999 59


Q ss_pred             cceeecC--ceeEeecCCCcc
Q 008920          304 NMAVIGG--NHIRLDRACPPR  322 (548)
Q Consensus       304 ng~~~~g--r~I~V~~a~~~~  322 (548)
                      ||..|.|  +.|.|.++.+..
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            9999988  699999997653

>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=99.35  E-value=3.3e-12  Score=119.26  Aligned_cols=78  Identities=14%  Similarity=0.160  Sum_probs=69.7

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCC--eEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRD--REL  411 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~G--r~I  411 (548)
                      ...+|||+||++.+++++|+++|+.|    |.|..|.|+.+.    ++|||||+|.+.++|..|+..|+ ..|.|  +.|
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~f----G~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L  116 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKF----GTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTL  116 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHH----SCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCE
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhc----CCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEE
Confidence            34679999999999999999999999    999999987542    57899999999999999999988 88855  999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      +|.|+++..
T Consensus       117 ~V~~Ak~~~  125 (164)
T 1sjr_A          117 RIDFSKLTS  125 (164)
T ss_dssp             EEEECSSSS
T ss_pred             EEEEecCCc
Confidence            999999864

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.35  E-value=3.3e-12  Score=114.92  Aligned_cols=76  Identities=14%  Similarity=0.208  Sum_probs=68.7

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceE-EEEEECCHHHHHHHHHHcC-CccCC--eEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGI-AYVLFKTREAANLVIKRRN-LKLRD--REL  411 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~-AFV~F~~~e~A~~Al~~ln-~~l~G--r~I  411 (548)
                      --.|||+||++.+|+++|+++|+.|    |.|..|.|+.+     .+|| |||+|.+.++|..|+..|+ ..|.|  +.|
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~y----G~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~L   98 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKF----GTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTL   98 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTS----SCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEE
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCc----CCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEE
Confidence            4578899999999999999999999    99999988765     2677 9999999999999999888 88888  999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      +|.|+++..
T Consensus        99 rI~~ak~~~  107 (130)
T 3zzy_A           99 RIDFSKLTS  107 (130)
T ss_dssp             EEEECSCSS
T ss_pred             EEEecCCCc
Confidence            999999764

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.35  E-value=1.5e-12  Score=113.83  Aligned_cols=79  Identities=20%  Similarity=0.269  Sum_probs=62.5

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++|+++|+++|+.||.|. +.++.+..+.              ..|.++|||||+|.+.++|+.||.
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~--------------~~g~~~G~aFV~f~~~~~a~~Ai~   70 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESK--------------SYFPPKGYAFLLFQEESSVQALID   70 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSC--------------CCSCTTSEEEECCSSHHHHHHHHH
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCC--------------CCCCcccEEEEEECCHHHHHHHHH
Confidence            3468999999999999999999999999998 7664322110              115688999999999999999994


Q ss_pred             -hcceeecCceeEeecC
Q 008920          303 -FNMAVIGGNHIRLDRA  318 (548)
Q Consensus       303 -lng~~~~gr~I~V~~a  318 (548)
                       |+  .+.|+.|.|..+
T Consensus        71 ~~~--~~~G~~~~~~~~   85 (114)
T 2dnl_A           71 ACL--EEDGKLYLCVSS   85 (114)
T ss_dssp             HSE--EETTEEEEEECC
T ss_pred             hhh--hcCCcEEEeccC
Confidence             63  377887777654

>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=99.34  E-value=3.1e-12  Score=117.88  Aligned_cols=81  Identities=23%  Similarity=0.371  Sum_probs=72.5

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCC--CCceEEEEEECCHHHHHHHHHHcC-CccC---C
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMR--VGKGIAYVLFKTREAANLVIKRRN-LKLR---D  408 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg--~srG~AFV~F~~~e~A~~Al~~ln-~~l~---G  408 (548)
                      ..++|||+|||+++++++|+++|..|    |.|..|.|+++..++  .++|||||+|.+.++|..|+..++ ..+.   +
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~----G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~   77 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQY----GAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMH   77 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTT----SCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCS
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhC----CCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCc
Confidence            35899999999999999999999999    899999999998876  899999999999999999998877 5554   5


Q ss_pred             eEEEEEeeecC
Q 008920          409 RELRLSHAQQN  419 (548)
Q Consensus       409 r~I~V~~Ak~~  419 (548)
                      +.|.|.++.+.
T Consensus        78 ~~~~~~~~~~~   88 (175)
T 3nmr_A           78 HPIQMKPADSE   88 (175)
T ss_dssp             SCCEEEECGGG
T ss_pred             cceEEcccccc
Confidence            88888887754

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.33  E-value=2.3e-12  Score=109.09  Aligned_cols=70  Identities=24%  Similarity=0.263  Sum_probs=61.6

Q ss_pred             cEEEEcCCCCCCcHHH----HHHHhhhc-CCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          226 RTIFVGNLPLKVKKKT----LIKEFIKF-GEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       226 rtVfVgNLP~~~tee~----L~~~Fs~f-G~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      ++|||+|||+.+++++    |.++|+.| |.|.+|.                           .|+|||+|.+.++|..|
T Consensus        10 T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~Vt---------------------------gG~AfV~F~~~esA~~A   62 (96)
T 2diu_A           10 TLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSIT---------------------------GCSAILRFINQDSAERA   62 (96)
T ss_dssp             EEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEECC---------------------------TTCEEEEESSHHHHHHH
T ss_pred             eEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEEe---------------------------cCEEEEEECCHHHHHHH
Confidence            3499999999999988    55899999 5997761                           18999999999999999


Q ss_pred             H-HhcceeecCceeEeecCCCcc
Q 008920          301 L-AFNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       301 l-~lng~~~~gr~I~V~~a~~~~  322 (548)
                      + .|+|..|.|+.|+|.++....
T Consensus        63 ~~~l~G~~l~gr~i~v~~A~~~s   85 (96)
T 2diu_A           63 QKRMENEDVFGNRIIVSFTPKNR   85 (96)
T ss_dssp             HHHHTTCCSSSSCCEEESSCCSC
T ss_pred             HHHhcCCccCCceEEEEecCCCc
Confidence            9 699999999999999997643

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.33  E-value=4.4e-12  Score=113.29  Aligned_cols=75  Identities=16%  Similarity=0.228  Sum_probs=66.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceE-EEEEECCHHHHHHHHHHcC-CccCC--eEEE
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGI-AYVLFKTREAANLVIKRRN-LKLRD--RELR  412 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~-AFV~F~~~e~A~~Al~~ln-~~l~G--r~I~  412 (548)
                      ..|||+||++.+++++|+++|+.|    |.|..|.|+..      .|| |||+|.+.++|..|+..|+ ..|.|  +.|+
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~y----G~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~   95 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPV----GKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLK   95 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTT----SCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEE
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhc----CCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEE
Confidence            457899999999999999999999    99999998652      276 9999999999999999888 88877  6999


Q ss_pred             EEeeecCCC
Q 008920          413 LSHAQQNCT  421 (548)
Q Consensus       413 V~~Ak~~~~  421 (548)
                      |.||++...
T Consensus        96 V~~Ak~~~l  104 (124)
T 2e5i_A           96 IEYARPTRL  104 (124)
T ss_dssp             EECCSCSCC
T ss_pred             EEEecCCcc
Confidence            999998643

>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=99.33  E-value=2.8e-12  Score=123.96  Aligned_cols=76  Identities=18%  Similarity=0.277  Sum_probs=70.3

Q ss_pred             CccEEEEeCCC-CCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          335 IKKTVFVGNLP-FDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       335 ~~~tLfV~NLp-~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      +.++|||+||| +.+++++|+++|+.|    |.|..|.|+.+     .+|||||+|.+.++|..||..|| ..|.|+.|.
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~----G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   73 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLY----GNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMN   73 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTT----SCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhc----CCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEE
Confidence            46899999999 899999999999999    99999999876     37999999999999999999887 999999999


Q ss_pred             EEeeecC
Q 008920          413 LSHAQQN  419 (548)
Q Consensus       413 V~~Ak~~  419 (548)
                      |.|++..
T Consensus        74 v~~s~~~   80 (205)
T 3tyt_A           74 VCVSKQP   80 (205)
T ss_dssp             EEECSCS
T ss_pred             EEEccCC
Confidence            9999754

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.33  E-value=2.3e-12  Score=127.62  Aligned_cols=111  Identities=19%  Similarity=0.237  Sum_probs=78.7

Q ss_pred             HHHhcceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCC---------CHHHHHHHHhccCCCCCCeEEE
Q 008920          300 ALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDV---------KDEEIYQLFCGLNDLESSVEAV  370 (548)
Q Consensus       300 Al~lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~---------teedL~~~F~~~g~~~G~I~~V  370 (548)
                      +|..+...+.|+.....+.....     ...+.....++|||+||+..+         ++++|+.+|+.|    |.|..|
T Consensus       103 ~~~~~~~D~fGr~k~~~~~d~~~-----g~gs~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~f----G~I~~v  173 (240)
T 3u1l_A          103 ALRTEVLDCFGREKFADYREDMG-----GIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRL----GDIDRI  173 (240)
T ss_dssp             HHHCSSBCTTSSBCGGGTC--------------CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTT----SCEEEE
T ss_pred             cccccCcccccchhcccchhccc-----CcCccccCCceeecCCCChhhhcccccccCcHHHHHHHHHcc----CCEEEE
Confidence            33335555667765444432211     112234467899999999998         799999999999    999999


Q ss_pred             EEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-Ccc------------CCeEEEEEeeecCCCCCCC
Q 008920          371 RVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKL------------RDRELRLSHAQQNCTPSKR  425 (548)
Q Consensus       371 rI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l------------~Gr~I~V~~Ak~~~~~~~r  425 (548)
                      +|+.+      +|||||+|.+.++|+.|+..|+ ..|            .|+.|.|.||.+...|..+
T Consensus       174 ~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~~e~~~~~~gr~L~V~wA~~~pnp~~~  235 (240)
T 3u1l_A          174 RYVES------KNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANEDPDPAAQ  235 (240)
T ss_dssp             EEEGG------GTEEEEEESSHHHHHHHHHHHTTCCCCCTTSTTGGGGGGSCCCEEEECC--------
T ss_pred             EEECC------CCEEEEEeCCHHHHHHHHHHhCCCEEeccccccccccCCCCEEEEEEccCCCCHHHh
Confidence            99864      7999999999999999998887 777            8999999999987665443

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.32  E-value=2.2e-12  Score=115.29  Aligned_cols=77  Identities=17%  Similarity=0.096  Sum_probs=66.2

Q ss_pred             cEEEEcCC----CCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecC----HHH-
Q 008920          226 RTIFVGNL----PLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKS----EQS-  296 (548)
Q Consensus       226 rtVfVgNL----P~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s----~e~-  296 (548)
                      ..|||+||    |+.+++.+|+++|+.||+|.+|.++.|+.                 +|.++|||||+|.+    ++. 
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~-----------------Tg~slGfgfVef~d~~g~~d~a   65 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPN-----------------SALPLHVYLIKYASSDGKINDA   65 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTT-----------------TCCEEEEEEEECC------CCH
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC-----------------CCceeeEEEEEECCCCCCcchH
Confidence            57999999    99999999999999999999999988874                 45678999999996    433 


Q ss_pred             ---HHHHHH---hcceeecCceeEeecCC
Q 008920          297 ---TEAALA---FNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       297 ---A~~Al~---lng~~~~gr~I~V~~a~  319 (548)
                         |..|+.   ++|..|.|+.|+|.+-.
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               677764   69999999999999864

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.30  E-value=1e-11  Score=107.65  Aligned_cols=81  Identities=16%  Similarity=0.222  Sum_probs=68.3

Q ss_pred             cccEEEEcCCCC-----CCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHH
Q 008920          224 LLRTIFVGNLPL-----KVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (548)
Q Consensus       224 ~~rtVfVgNLP~-----~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~  298 (548)
                      .+++|+|.||..     +.++++|+++|++||.|.+|.|+.++..                ++.++|||||+|.+.++|.
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~----------------~~~~~G~~FV~f~~~~~A~   70 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGA----------------PDDEAVRIFLEFERVESAI   70 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSC----------------CTTTSEEEEEEESSHHHHH
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCC----------------CCCCcEEEEEEECCHHHHH
Confidence            468999999963     2478999999999999999999664311                1347799999999999999


Q ss_pred             HHH-HhcceeecCceeEeecCCC
Q 008920          299 AAL-AFNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       299 ~Al-~lng~~~~gr~I~V~~a~~  320 (548)
                      .|+ .|||..|.|+.|.|.++..
T Consensus        71 ~Ai~~lnG~~~~Gr~i~v~~a~~   93 (105)
T 2pe8_A           71 KAVVDLNGRYFGGRVVKACFYNL   93 (105)
T ss_dssp             HHHHHHTTCEETTEECEEEECCH
T ss_pred             HHHHHHCCCEECCcEEEEEEcCH
Confidence            999 6999999999999999864

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.30  E-value=3e-12  Score=126.69  Aligned_cols=76  Identities=21%  Similarity=0.333  Sum_probs=68.4

Q ss_pred             CCcccEEEEcCCCCCC---------cHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEec
Q 008920          222 GKLLRTIFVGNLPLKV---------KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFK  292 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~---------tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~  292 (548)
                      ....++|||+|||..+         ++++|..+|+.||.|.+|+|+.                       ++|||||+|.
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            3457899999999998         7999999999999999999842                       4699999999


Q ss_pred             CHHHHHHHH-Hhcceee------------cCceeEeecCCC
Q 008920          293 SEQSTEAAL-AFNMAVI------------GGNHIRLDRACP  320 (548)
Q Consensus       293 s~e~A~~Al-~lng~~~------------~gr~I~V~~a~~  320 (548)
                      +.++|+.|+ .|++..|            .|+.|.|.|+..
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 6999999            899999999974

>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=99.30  E-value=7.7e-12  Score=125.20  Aligned_cols=82  Identities=21%  Similarity=0.378  Sum_probs=74.0

Q ss_pred             cCCCccEEEEeCCCCCCCHHHHH----HHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-Ccc
Q 008920          332 LYDIKKTVFVGNLPFDVKDEEIY----QLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKL  406 (548)
Q Consensus       332 ~~~~~~tLfV~NLp~~~teedL~----~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l  406 (548)
                      ...+.++|||+|||+.+++++|+    ++|+.|    |.|..|.|+.   ++.++|||||+|.+.++|..||..++ ..|
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~----G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~   77 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQF----GQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPF   77 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhcc----CCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCee
Confidence            34568999999999999999966    899999    9999999886   57899999999999999999998887 999


Q ss_pred             CCeEEEEEeeecCC
Q 008920          407 RDRELRLSHAQQNC  420 (548)
Q Consensus       407 ~Gr~I~V~~Ak~~~  420 (548)
                      .|+.|.|.|+....
T Consensus        78 ~g~~l~v~~a~~~~   91 (282)
T 3pgw_A           78 YDKPMRIQYAKTDS   91 (282)
T ss_pred             CCcEEEEEEeccCc
Confidence            99999999997653

>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=99.28  E-value=1e-11  Score=115.03  Aligned_cols=76  Identities=29%  Similarity=0.323  Sum_probs=66.7

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+.+|+++|+++|+.||.|..+ .                     .++.++|||||+|.+.++|..||.
T Consensus        97 ~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-~---------------------~~~~~~g~afV~f~~~~~A~~A~~  154 (175)
T 1fje_B           97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-S---------------------QDGKSKGIAYIEFKSEADAEKNLE  154 (175)
T ss_dssp             GGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-C---------------------SSSSCCSEEEEECSSHHHHHHHHH
T ss_pred             ccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-c---------------------CCCCCceEEEEEECCHHHHHHHHH
Confidence            356899999999999999999999999987655 1                     134577999999999999999995


Q ss_pred             -hcceeecCceeEeecCCC
Q 008920          303 -FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 -lng~~~~gr~I~V~~a~~  320 (548)
                       |||..|.|+.|.|.++.+
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             999999999999999864

>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=99.24  E-value=1.7e-11  Score=119.64  Aligned_cols=79  Identities=22%  Similarity=0.302  Sum_probs=72.5

Q ss_pred             CCCccEEEEeCCCC-CCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeE
Q 008920          333 YDIKKTVFVGNLPF-DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRE  410 (548)
Q Consensus       333 ~~~~~tLfV~NLp~-~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~  410 (548)
                      ..+.++|||+|||+ .+++++|+++|+.|    |.|..|.|+.+.     +|||||+|.+.++|..||..++ ..|.|+.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~----G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~  101 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVY----GDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKP  101 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHH----TCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSB
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhC----CCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeE
Confidence            34678999999999 99999999999999    899999999885     7899999999999999998776 9999999


Q ss_pred             EEEEeeecCC
Q 008920          411 LRLSHAQQNC  420 (548)
Q Consensus       411 I~V~~Ak~~~  420 (548)
                      |.|.|+.+..
T Consensus       102 l~v~~a~~~~  111 (229)
T 2adc_A          102 IRITLSKHQN  111 (229)
T ss_dssp             CEEECCSCCC
T ss_pred             EEEEEecCcc
Confidence            9999998653

>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=99.21  E-value=5.8e-11  Score=103.40  Aligned_cols=79  Identities=16%  Similarity=0.207  Sum_probs=66.3

Q ss_pred             CCcccEEEEcCCCCCC-----------cHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEE
Q 008920          222 GKLLRTIFVGNLPLKV-----------KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIV  290 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~-----------tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~  290 (548)
                      ....++|+|.||....           ++++|+++|++||.|..|.| .+.                    .++|||||+
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~--------------------~~~G~afV~   70 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR--------------------HPDGVASVS   70 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT--------------------CTTCEEEEE
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC--------------------CCCEEEEEE
Confidence            3457899999994433           26899999999999999966 211                    156999999


Q ss_pred             ecCHHHHHHHH-HhcceeecCceeEeecCCCc
Q 008920          291 FKSEQSTEAAL-AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       291 F~s~e~A~~Al-~lng~~~~gr~I~V~~a~~~  321 (548)
                      |.+.++|..|+ .|||..|.|+.|.|.++.+.
T Consensus        71 f~~~~~A~~Ai~~lng~~~~gr~l~v~~a~~~  102 (112)
T 2dit_A           71 FRDPEEADYCIQTLDGRWFGGRQITAQAWDGT  102 (112)
T ss_dssp             CSCHHHHHHHHHHSTTCEETTEECEEEECCSC
T ss_pred             ECCHHHHHHHHHHcCCCEECCcEEEEEEeCCC
Confidence            99999999999 69999999999999998764

>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=99.21  E-value=7.4e-11  Score=102.71  Aligned_cols=79  Identities=14%  Similarity=0.196  Sum_probs=67.7

Q ss_pred             CCCccEEEEeCCCCCCC-----------HHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHH
Q 008920          333 YDIKKTVFVGNLPFDVK-----------DEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKR  401 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~t-----------eedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~  401 (548)
                      ..++++|+|.||.....           +++|+++|++|    |.|..|.| .+.   .++|||||+|.+.++|..||..
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~----G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~   83 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKF----GQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQT   83 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGT----SCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHH
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHcc----CCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHH
Confidence            34679999999944332           58999999999    89999955 553   3799999999999999999998


Q ss_pred             cC-CccCCeEEEEEeeecC
Q 008920          402 RN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       402 ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      |+ ..|.|+.|.|.|+.+.
T Consensus        84 lng~~~~gr~l~v~~a~~~  102 (112)
T 2dit_A           84 LDGRWFGGRQITAQAWDGT  102 (112)
T ss_dssp             STTCEETTEECEEEECCSC
T ss_pred             cCCCEECCcEEEEEEeCCC
Confidence            88 9999999999999875

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.19  E-value=1.8e-11  Score=115.94  Aligned_cols=76  Identities=22%  Similarity=0.352  Sum_probs=70.4

Q ss_pred             ccEEEEeCCCC-CCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          336 KKTVFVGNLPF-DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       336 ~~tLfV~NLp~-~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      .++|||+|||+ .+++++|+++|+.|    |.|..|.|+.+.     +|||||+|.+.++|..||..++ ..|.|+.|.|
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~----G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v   73 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVY----GDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI   73 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTT----CCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEE
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhc----CCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEE
Confidence            57999999999 99999999999999    899999999874     7899999999999999998776 9999999999


Q ss_pred             EeeecCC
Q 008920          414 SHAQQNC  420 (548)
Q Consensus       414 ~~Ak~~~  420 (548)
                      .|+.+..
T Consensus        74 ~~a~~~~   80 (198)
T 1qm9_A           74 TLSKHQN   80 (198)
T ss_dssp             EECCCCS
T ss_pred             EEecCCC
Confidence            9998763

>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=99.19  E-value=4e-11  Score=119.41  Aligned_cols=77  Identities=27%  Similarity=0.515  Sum_probs=70.3

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+++|+++|+.+|+.|    |.|..|.|.++      +|||||+|.+.++|..||..++ ..|.|+.|
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~----G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l   88 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERY----GEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPL   88 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGG----CCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhc----CCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCcee
Confidence            4567899999999999999999999999    89999998654      7899999999999999998776 99999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      .|.|+.+.
T Consensus        89 ~v~~a~~~   96 (261)
T 3sde_A           89 RIRFATHG   96 (261)
T ss_dssp             EEEECCCS
T ss_pred             EeeecccC
Confidence            99999753

>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=99.19  E-value=4.2e-11  Score=103.68  Aligned_cols=80  Identities=14%  Similarity=0.151  Sum_probs=69.9

Q ss_pred             CccEEEEeCC--CCCCC--------HHHHHHHHhccCCCCCCeEEEEEeecCCC--CCCceEEEEEECCHHHHHHHHHHc
Q 008920          335 IKKTVFVGNL--PFDVK--------DEEIYQLFCGLNDLESSVEAVRVIRHPHM--RVGKGIAYVLFKTREAANLVIKRR  402 (548)
Q Consensus       335 ~~~tLfV~NL--p~~~t--------eedL~~~F~~~g~~~G~I~~VrI~~d~~t--g~srG~AFV~F~~~e~A~~Al~~l  402 (548)
                      ++++|+|.||  |..+.        +++|++.|++|    |.|..|.|+++..+  +.++|||||+|.+.++|.+|+..|
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~----G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~l   79 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKY----GLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGL   79 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTT----SCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHcc----CCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHh
Confidence            5789999998  33443        37999999999    99999999998754  368999999999999999999888


Q ss_pred             C-CccCCeEEEEEeeec
Q 008920          403 N-LKLRDRELRLSHAQQ  418 (548)
Q Consensus       403 n-~~l~Gr~I~V~~Ak~  418 (548)
                      | ..|.||.|.|.|+.+
T Consensus        80 nG~~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           80 TGRKFANRVVVTKYCDP   96 (105)
T ss_dssp             TTCEETTEECEEEEECH
T ss_pred             CCCEeCCCEEEEEEeCH
Confidence            8 999999999999864

>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=99.14  E-value=1e-10  Score=103.43  Aligned_cols=80  Identities=14%  Similarity=0.088  Sum_probs=69.8

Q ss_pred             CccEEEEeCCCC--CC---CHHHHHHHHhccCCCCCCeEEEEEeecCC----CCCCceEEEEEECCHHHHHHHHHHcC-C
Q 008920          335 IKKTVFVGNLPF--DV---KDEEIYQLFCGLNDLESSVEAVRVIRHPH----MRVGKGIAYVLFKTREAANLVIKRRN-L  404 (548)
Q Consensus       335 ~~~tLfV~NLp~--~~---teedL~~~F~~~g~~~G~I~~VrI~~d~~----tg~srG~AFV~F~~~e~A~~Al~~ln-~  404 (548)
                      ++++|+|.||-.  ++   .++||++.|++|    |.|..|.|+++..    ++.++|||||+|.+.++|..|+..|| .
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~----G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr   94 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKF----GAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGR   94 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTT----SCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhcc----CCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCC
Confidence            578999999832  22   368999999999    9999999999864    45778999999999999999999888 9


Q ss_pred             ccCCeEEEEEeeec
Q 008920          405 KLRDRELRLSHAQQ  418 (548)
Q Consensus       405 ~l~Gr~I~V~~Ak~  418 (548)
                      .|.||.|.|.|+..
T Consensus        95 ~f~GR~i~v~~~~~  108 (118)
T 3ue2_A           95 WFAGRKVVAEVYDQ  108 (118)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EECCcEEEEEEcCh
Confidence            99999999999864

>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=99.13  E-value=2.5e-11  Score=104.90  Aligned_cols=71  Identities=20%  Similarity=0.188  Sum_probs=62.4

Q ss_pred             EeCCCCCCCHHHHHHHH------------hccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccC
Q 008920          341 VGNLPFDVKDEEIYQLF------------CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLR  407 (548)
Q Consensus       341 V~NLp~~~teedL~~~F------------~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~  407 (548)
                      +.|||+.+++++|+++|            ++|    |.|..|.|+++. ++.++|||||+|.+.++|..|+..|| ..|.
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~----G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~   94 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKY----GEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFN   94 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT----CCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEET
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccC----CceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            56777777877777666            999    999999999985 48899999999999999999998887 9999


Q ss_pred             CeEEEEEee
Q 008920          408 DRELRLSHA  416 (548)
Q Consensus       408 Gr~I~V~~A  416 (548)
                      ||.|.|.|+
T Consensus        95 Gr~i~v~~s  103 (104)
T 1jmt_A           95 GQPIHAELS  103 (104)
T ss_dssp             TEECCEEEC
T ss_pred             CEEEEEEEc
Confidence            999999986

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.11  E-value=3.4e-11  Score=103.98  Aligned_cols=71  Identities=18%  Similarity=0.332  Sum_probs=59.9

Q ss_pred             EcCCCCCCcHHHHHHHh------------hhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHH
Q 008920          230 VGNLPLKVKKKTLIKEF------------IKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQST  297 (548)
Q Consensus       230 VgNLP~~~tee~L~~~F------------s~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A  297 (548)
                      +.|||+.+++++|.++|            ++||.|.+|.|+.+.                  .+.++|||||+|.+.++|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~------------------~~~~~G~~fV~f~~~~~A   81 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL------------------GDHLVGNVYVKFRREEDA   81 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS------------------SSSSEEEEEEEESCHHHH
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC------------------CCCccEEEEEEECCHHHH
Confidence            56777888888877776            999999999995432                  234789999999999999


Q ss_pred             HHHH-HhcceeecCceeEeecC
Q 008920          298 EAAL-AFNMAVIGGNHIRLDRA  318 (548)
Q Consensus       298 ~~Al-~lng~~~~gr~I~V~~a  318 (548)
                      .+|+ .|||..|.|+.|.|.++
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 69999999999999886

>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=99.10  E-value=1.7e-10  Score=99.87  Aligned_cols=81  Identities=14%  Similarity=0.122  Sum_probs=66.6

Q ss_pred             cccEEEEcCC--CCCC--------cHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecC
Q 008920          224 LLRTIFVGNL--PLKV--------KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKS  293 (548)
Q Consensus       224 ~~rtVfVgNL--P~~~--------tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s  293 (548)
                      ++++|+|.||  |..+        .+++|+++|++||.|.+|.|+.+..+               +.+.++|||||+|.+
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~---------------~~~~~~G~~fV~f~~   68 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDG---------------VEVPGCGKIFVEFTS   68 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTT---------------BCCTTTTEEEEEESS
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCC---------------CCcCCcEEEEEEECC
Confidence            4689999998  4444        34799999999999999999554311               112467999999999


Q ss_pred             HHHHHHHH-HhcceeecCceeEeecCC
Q 008920          294 EQSTEAAL-AFNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       294 ~e~A~~Al-~lng~~~~gr~I~V~~a~  319 (548)
                      .++|.+|+ .|||..|.|+.|.|.++.
T Consensus        69 ~~~A~~Ai~~lnG~~f~GR~i~v~~~~   95 (105)
T 3v4m_A           69 VFDCQKAMQGLTGRKFANRVVVTKYCD   95 (105)
T ss_dssp             HHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             HHHHHHHHHHhCCCEeCCCEEEEEEeC
Confidence            99999999 699999999999999875

>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=99.10  E-value=2.4e-10  Score=101.11  Aligned_cols=83  Identities=17%  Similarity=0.166  Sum_probs=67.9

Q ss_pred             cccEEEEcCCCC--C---CcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHH
Q 008920          224 LLRTIFVGNLPL--K---VKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (548)
Q Consensus       224 ~~rtVfVgNLP~--~---~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~  298 (548)
                      .+++|+|.||-.  +   -.+++|+++|++||.|.+|.|+.+......             ++.++|||||+|.+.++|.
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 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEE-------------DAEIIVKIFVEFSIASETH   85 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSST-------------TCEEEEEEEEEESSHHHHH
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCccc-------------CCcceEEEEEEECCHHHHH
Confidence            358999999942  2   247899999999999999999776532111             2236799999999999999


Q ss_pred             HHH-HhcceeecCceeEeecCC
Q 008920          299 AAL-AFNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       299 ~Al-~lng~~~~gr~I~V~~a~  319 (548)
                      +|+ .|||..|.|+.|.|.++.
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 699999999999999875

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.08  E-value=1.1e-09  Score=93.91  Aligned_cols=65  Identities=22%  Similarity=0.215  Sum_probs=57.6

Q ss_pred             CCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEeeecCC
Q 008920          346 FDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQNC  420 (548)
Q Consensus       346 ~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~Ak~~~  420 (548)
                      ..+++++|+++|++|    |.|..|.|+     +.++|||||+|.+.++|..||..++ .+.|++|+|.|+.+..
T Consensus        27 ~~~te~~L~~~F~~~----G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~-~~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKY----GEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEV-GLVDNPLKISWLEGQP   91 (100)
T ss_dssp             CSCCHHHHHHHHHTT----SCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCC-BCSSSBCEEECSSCCC
T ss_pred             CCCCHHHHHHHHHhc----CCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcC-CCCCCeEEEEEccCCC
Confidence            568999999999999    899999998     3579999999999999999998854 4679999999998753

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.97  E-value=3.3e-09  Score=91.02  Aligned_cols=75  Identities=15%  Similarity=0.117  Sum_probs=60.7

Q ss_pred             ccEEEEcCCC-------CCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHH
Q 008920          225 LRTIFVGNLP-------LKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQST  297 (548)
Q Consensus       225 ~rtVfVgNLP-------~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A  297 (548)
                      ...|.|.-.+       ..+++++|+++|++||.|..|.|+.                      .++|||||+|.+.++|
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            3466666554       4689999999999999999999841                      2679999999999999


Q ss_pred             HHHHHhcceeecCceeEeecCCCcc
Q 008920          298 EAALAFNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       298 ~~Al~lng~~~~gr~I~V~~a~~~~  322 (548)
                      ..||.. +..+.|+.|.|.++.++.
T Consensus        68 ~~Ai~~-~~~~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           68 ELAVQN-EVGLVDNPLKISWLEGQP   91 (100)
T ss_dssp             HHHHHT-CCBCSSSBCEEECSSCCC
T ss_pred             HHHHHh-cCCCCCCeEEEEEccCCC
Confidence            999964 344689999999987543

>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=98.96  E-value=1.1e-09  Score=113.90  Aligned_cols=75  Identities=16%  Similarity=0.272  Sum_probs=63.5

Q ss_pred             CCcccEEEEcC--CCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHH
Q 008920          222 GKLLRTIFVGN--LPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (548)
Q Consensus       222 ~~~~rtVfVgN--LP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~  299 (548)
                      .....+|||+|  |++.+|+++|.++|++||.|.+|.|..                       ++|||||+|.+.++|++
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----------------------~kgfaFV~f~~~~~A~~   71 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----------------------NKPYSFARYRTTEESKR   71 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-----------------------TCSEEEEEESSHHHHHH
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----------------------CCCEEEEEECCHHHHHH
Confidence            44568999999  588999999999999999999987721                       45899999999999999


Q ss_pred             HH-Hhcceeec---Cc--eeEeecCC
Q 008920          300 AL-AFNMAVIG---GN--HIRLDRAC  319 (548)
Q Consensus       300 Al-~lng~~~~---gr--~I~V~~a~  319 (548)
                      |+ .|||..+.   |+  .|.|.++.
T Consensus        72 Ai~~lnG~~~~~~~g~~~~ly~~~~~   97 (345)
T 3tht_A           72 AYVTLNGKEVVDDLGQKITLYLNFVE   97 (345)
T ss_dssp             HHHHTTTCEEECTTSCEEECEEEECS
T ss_pred             HHHHhCCCccccccCCceEEEEEEee
Confidence            99 59999884   45  67777764

>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=98.92  E-value=1.8e-09  Score=112.14  Aligned_cols=75  Identities=16%  Similarity=0.200  Sum_probs=64.2

Q ss_pred             CCCccEEEEeC--CCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-Ccc---
Q 008920          333 YDIKKTVFVGN--LPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKL---  406 (548)
Q Consensus       333 ~~~~~tLfV~N--Lp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l---  406 (548)
                      ..++.+|||+|  |++.+++++|+++|++|    |.|..|.++.      ++|||||+|.+.++|..||+.|| ..+   
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~----G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~   84 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKC----GLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDD   84 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTT----SCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECT
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhc----CCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccc
Confidence            45688999999  57899999999999999    8999887753      47999999999999999999988 555   


Q ss_pred             CCe--EEEEEeee
Q 008920          407 RDR--ELRLSHAQ  417 (548)
Q Consensus       407 ~Gr--~I~V~~Ak  417 (548)
                      .|+  .|.|.|+.
T Consensus        85 ~g~~~~ly~~~~~   97 (345)
T 3tht_A           85 LGQKITLYLNFVE   97 (345)
T ss_dssp             TSCEEECEEEECS
T ss_pred             cCCceEEEEEEee
Confidence            355  68888884

>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=98.89  E-value=3.5e-09  Score=93.01  Aligned_cols=77  Identities=10%  Similarity=0.059  Sum_probs=65.4

Q ss_pred             CccEEEEeCCCCCC----------CHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-
Q 008920          335 IKKTVFVGNLPFDV----------KDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-  403 (548)
Q Consensus       335 ~~~tLfV~NLp~~~----------teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-  403 (548)
                      ++++|.|.||=...          .++||++.|++|    |.|..|.|.++.    ++|||||+|.+.++|..|+..|| 
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kf----G~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG   77 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKH----GGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHG   77 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTT----TCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTT
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhcc----CCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCC
Confidence            57889999983322          146899999999    999999987663    58999999999999999999888 


Q ss_pred             CccCCeEEEEEeeecC
Q 008920          404 LKLRDRELRLSHAQQN  419 (548)
Q Consensus       404 ~~l~Gr~I~V~~Ak~~  419 (548)
                      ..|+||.|.|.|+...
T Consensus        78 ~~f~GR~i~v~~~~~~   93 (114)
T 3s6e_A           78 RWFAGKMITAAYVPLP   93 (114)
T ss_dssp             CEETTEECEEEEECHH
T ss_pred             CEECCEEEEEEEEcHH
Confidence            9999999999999653

>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=98.87  E-value=4.5e-09  Score=92.35  Aligned_cols=75  Identities=17%  Similarity=0.138  Sum_probs=62.3

Q ss_pred             cccEEEEcCCCC--C--------CcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecC
Q 008920          224 LLRTIFVGNLPL--K--------VKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKS  293 (548)
Q Consensus       224 ~~rtVfVgNLP~--~--------~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s  293 (548)
                      .+++|.|.||=.  +        -.+++|+++|++||.|.+|.|..+.                     .+|||||+|.+
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~---------------------~~G~~fV~f~~   64 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS---------------------AQGNVYVKCPS   64 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC---------------------TTCCEEEECSS
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC---------------------CcEEEEEEECC
Confidence            457899999833  2        1246889999999999999983211                     46999999999


Q ss_pred             HHHHHHHH-HhcceeecCceeEeecCC
Q 008920          294 EQSTEAAL-AFNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       294 ~e~A~~Al-~lng~~~~gr~I~V~~a~  319 (548)
                      .++|.+|+ .|||..|.|+.|.|.++.
T Consensus        65 ~e~A~~Ai~~lnG~~f~GR~i~v~~~~   91 (114)
T 3s6e_A           65 IAAAIAAVNALHGRWFAGKMITAAYVP   91 (114)
T ss_dssp             HHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             HHHHHHHHHHhCCCEECCEEEEEEEEc
Confidence            99999999 699999999999999975

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.68  E-value=5.8e-08  Score=86.08  Aligned_cols=76  Identities=21%  Similarity=0.203  Sum_probs=67.3

Q ss_pred             cCCCccEEEEeCCCCC-CCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECC-HHHHHHHHHHcC---Ccc
Q 008920          332 LYDIKKTVFVGNLPFD-VKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT-REAANLVIKRRN---LKL  406 (548)
Q Consensus       332 ~~~~~~tLfV~NLp~~-~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~-~e~A~~Al~~ln---~~l  406 (548)
                      .......|||+||++. ++.++|+++|+.|    |.|.+|.|+++..      .|||.|.+ ..+|..|+..++   ..|
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~----G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i   83 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNH----GEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQL   83 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSS----CCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCT
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhc----CCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEE
Confidence            4567899999999999 9999999999999    8999999998854      69999999 899999998884   889


Q ss_pred             CCeEEEEEeee
Q 008920          407 RDRELRLSHAQ  417 (548)
Q Consensus       407 ~Gr~I~V~~Ak  417 (548)
                      .|..+.+....
T Consensus        84 ~g~~~~~evL~   94 (121)
T 1owx_A           84 RNKEVTWEVLE   94 (121)
T ss_dssp             TSSSEEEEECC
T ss_pred             eCcEEEEEECC
Confidence            99888887653

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.62  E-value=6.8e-08  Score=81.01  Aligned_cols=70  Identities=20%  Similarity=0.305  Sum_probs=59.7

Q ss_pred             cEEEEcCCCC----CCcH----HHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHH
Q 008920          226 RTIFVGNLPL----KVKK----KTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQST  297 (548)
Q Consensus       226 rtVfVgNLP~----~~te----e~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A  297 (548)
                      -||+|.-+|.    .+-.    .+|.+.|.+||.|..|+|..                         +.+||+|.+.++|
T Consensus         8 ~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~-------------------------d~~fVtF~d~~sA   62 (91)
T 2dnr_A            8 GTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVE-------------------------DKMWVTFLEGSSA   62 (91)
T ss_dssp             CEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECS-------------------------SSEEEEESSHHHH
T ss_pred             CeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEec-------------------------CCEEEEECChHHH
Confidence            5888888772    3333    67889999999999999932                         3499999999999


Q ss_pred             HHHHHhcceeecCceeEeecCCC
Q 008920          298 EAALAFNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       298 ~~Al~lng~~~~gr~I~V~~a~~  320 (548)
                      .+||.|||..+.|+.|.|.++.+
T Consensus        63 laAi~mnG~~v~Gr~LkV~lkt~   85 (91)
T 2dnr_A           63 LNVLSLNGKELLNRTITIALKSP   85 (91)
T ss_dssp             HHGGGGTTCEETTEEEEEEECCC
T ss_pred             HHHHhcCCeEeCCeEEEEEeCCC
Confidence            99999999999999999999864

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.56  E-value=1.8e-07  Score=78.39  Aligned_cols=74  Identities=20%  Similarity=0.275  Sum_probs=61.8

Q ss_pred             CCccEEEEeCCCC----CCCH----HHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCc
Q 008920          334 DIKKTVFVGNLPF----DVKD----EEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLK  405 (548)
Q Consensus       334 ~~~~tLfV~NLp~----~~te----edL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~  405 (548)
                      ++..||+|..++.    .+-+    .+|.+.|.+|    |.|..|+|+.|.        +||+|.+.++|.+||.+.+..
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~----G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~mnG~~   72 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASF----GEVILIRFVEDK--------MWVTFLEGSSALNVLSLNGKE   72 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTT----CCEEEEEECSSS--------EEEEESSHHHHHHGGGGTTCE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhC----CCeEEEEEecCC--------EEEEECChHHHHHHHhcCCeE
Confidence            4567888887762    3333    6788999999    999999999873        899999999999999944499


Q ss_pred             cCCeEEEEEeeecC
Q 008920          406 LRDRELRLSHAQQN  419 (548)
Q Consensus       406 l~Gr~I~V~~Ak~~  419 (548)
                      ++||.|+|.++.+.
T Consensus        73 v~Gr~LkV~lkt~d   86 (91)
T 2dnr_A           73 LLNRTITIALKSPS   86 (91)
T ss_dssp             ETTEEEEEEECCCS
T ss_pred             eCCeEEEEEeCCCC
Confidence            99999999999875

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.54  E-value=1.5e-07  Score=83.37  Aligned_cols=73  Identities=11%  Similarity=0.037  Sum_probs=61.5

Q ss_pred             cccEEEEcCCCCC-CcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecC-HHHHHHHH
Q 008920          224 LLRTIFVGNLPLK-VKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKS-EQSTEAAL  301 (548)
Q Consensus       224 ~~rtVfVgNLP~~-~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s-~e~A~~Al  301 (548)
                      ..+.|||+||+.. ++.++|+++|+.||.|..|.|..+.                       ..|||.|.+ +.+|..|+
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            4579999999999 9999999999999999999984322                       369999999 78999888


Q ss_pred             -Hh--cceeecCceeEeecCC
Q 008920          302 -AF--NMAVIGGNHIRLDRAC  319 (548)
Q Consensus       302 -~l--ng~~~~gr~I~V~~a~  319 (548)
                       .+  ++..|.|..+.+....
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             56  4788888887776653

>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=98.35  E-value=5.8e-07  Score=75.80  Aligned_cols=70  Identities=17%  Similarity=0.231  Sum_probs=58.8

Q ss_pred             ccEEEEcCCCCC-----CcH----HHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHH
Q 008920          225 LRTIFVGNLPLK-----VKK----KTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQ  295 (548)
Q Consensus       225 ~rtVfVgNLP~~-----~te----e~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e  295 (548)
                      .-||+|.-++..     +-.    .+|.+.|..||.|..|+|..                         .-+||+|.+.+
T Consensus        15 D~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~-------------------------d~~fVtF~d~~   69 (95)
T 1ufw_A           15 DATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQ-------------------------GQMLVTFADSH   69 (95)
T ss_dssp             TCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEET-------------------------TEEEEECSCSH
T ss_pred             CCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEec-------------------------CcEEEEEcChH
Confidence            369999988743     222    56889999999999999943                         23999999999


Q ss_pred             HHHHHHHhcceeecCceeEeecCC
Q 008920          296 STEAALAFNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       296 ~A~~Al~lng~~~~gr~I~V~~a~  319 (548)
                      +|.+||.|||..+.|+.|.|.+-.
T Consensus        70 sAl~AI~ldG~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           70 SALSVLDVDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHGGGSEETTEEEEEECCC
T ss_pred             HHHHHHhcCCeeeCCeEEEEeccC
Confidence            999999999999999999998753

>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=98.35  E-value=7.1e-07  Score=86.29  Aligned_cols=67  Identities=13%  Similarity=0.046  Sum_probs=59.8

Q ss_pred             CCHHHHHHHHhccCCCCCCeEEEEEeecC----CCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeeec
Q 008920          348 VKDEEIYQLFCGLNDLESSVEAVRVIRHP----HMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQ  418 (548)
Q Consensus       348 ~teedL~~~F~~~g~~~G~I~~VrI~~d~----~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak~  418 (548)
                      ..+++|.+.|+.|    |.|..|.|+++.    .++.++|++||+|.+.++|.+|+..|+ ..|.||.|.|.|+..
T Consensus       141 e~~~dl~~e~~~~----G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKF----GAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTT----SCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHcc----CCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            4578999999999    999999999654    345899999999999999999999888 999999999999864

>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=98.30  E-value=1.2e-06  Score=84.59  Aligned_cols=70  Identities=19%  Similarity=0.197  Sum_probs=58.9

Q ss_pred             CcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-HhcceeecCceeEe
Q 008920          237 VKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRL  315 (548)
Q Consensus       237 ~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng~~~~gr~I~V  315 (548)
                      -.+++|.+.|+.||.|.+|.|+.+...+.             .++.++|++||+|.+.++|.+|+ .|||..|.||.|.|
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~-------------~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~  207 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEE-------------EDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVA  207 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSS-------------TTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcc-------------cCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEE
Confidence            35689999999999999999966543221             13457899999999999999999 69999999999999


Q ss_pred             ecCC
Q 008920          316 DRAC  319 (548)
Q Consensus       316 ~~a~  319 (548)
                      .++.
T Consensus       208 ~~~~  211 (222)
T 3dxb_A          208 EVYD  211 (222)
T ss_dssp             EECC
T ss_pred             EEcC
Confidence            9975

>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=98.24  E-value=1.7e-06  Score=72.93  Aligned_cols=73  Identities=19%  Similarity=0.219  Sum_probs=60.9

Q ss_pred             CCCccEEEEeCCCCC-----CCH----HHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC
Q 008920          333 YDIKKTVFVGNLPFD-----VKD----EEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN  403 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~-----~te----edL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln  403 (548)
                      .++..||+|..++..     +.+    .+|.+.|..|    |.|..|+|+.|.        +||+|.+.++|.+||.+.+
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~----G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~ldG   79 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSY----GTIVLVRINQGQ--------MLVTFADSHSALSVLDVDG   79 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHH----SCCSEEEEETTE--------EEEECSCSHHHHHHHHGGG
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHC----CCEEEEEEecCc--------EEEEEcChHHHHHHHhcCC
Confidence            456789999988743     222    5688999999    899999999883        9999999999999999444


Q ss_pred             CccCCeEEEEEeee
Q 008920          404 LKLRDRELRLSHAQ  417 (548)
Q Consensus       404 ~~l~Gr~I~V~~Ak  417 (548)
                      ..++||.|+|.+-.
T Consensus        80 ~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           80 MKVKGRAVKISGPS   93 (95)
T ss_dssp             SEETTEEEEEECCC
T ss_pred             eeeCCeEEEEeccC
Confidence            99999999998743

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.98  E-value=2.5e-05  Score=67.40  Aligned_cols=71  Identities=20%  Similarity=0.139  Sum_probs=64.0

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhc-----CCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHH
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKF-----GEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~f-----G~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~  299 (548)
                      .++|-|-|||-.+++..|+.|+..|     |.|..|.++.+-                       +=|+|+|.+...|-+
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            4899999999999999999999999     999999985432                       569999999999999


Q ss_pred             HH-HhcceeecCceeEeecC
Q 008920          300 AL-AFNMAVIGGNHIRLDRA  318 (548)
Q Consensus       300 Al-~lng~~~~gr~I~V~~a  318 (548)
                      |. +|+|..|.|+.|+|.-.
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 99999999999999764

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.75  E-value=0.00012  Score=62.57  Aligned_cols=88  Identities=20%  Similarity=0.189  Sum_probs=73.1

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhh-c----CCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHH
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIK-F----GEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~-f----G~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~  298 (548)
                      ...+|.|.|||..+.++.|.-+|+. -    |+|.+|...                        . +-|+|+|.+...|+
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~------------------------~-~~AvItF~d~~va~   61 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRL------------------------G-CGGVLTFREPADAE   61 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEE------------------------T-TEEEEEESSHHHHH
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEc------------------------C-CcEEEEEcChHHHH
Confidence            3478999999999999999999996 2    688888772                        1 46999999999999


Q ss_pred             HHHHhcceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCC
Q 008920          299 AALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVK  349 (548)
Q Consensus       299 ~Al~lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~t  349 (548)
                      ..|+...+.|.+..|.|....+.             ...+|++.+|+..++
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            99988788899999999876432             357899999998775

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.36  E-value=0.0012  Score=56.40  Aligned_cols=75  Identities=21%  Similarity=0.182  Sum_probs=63.7

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhc---cCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCG---LNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDREL  411 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~---~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I  411 (548)
                      ...+|.|.|||..+.++.|.-+|+.   -|.  |.|..|....        +-|+|+|.+...|+..|..-.+.|.|..|
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGG--G~V~~v~~~~--------~~AvItF~d~~va~rVL~k~~H~L~~~~L   76 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGG--GPVLSWQRLG--------CGGVLTFREPADAERVLAQADHELHGAQL   76 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCC--CCEEEEEEET--------TEEEEEESSHHHHHHHHTCSCCBSSSSBC
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCC--ceeeEEEEcC--------CcEEEEEcChHHHHHHhcCCcceecCeEE
Confidence            4689999999999999999999977   232  8999887643        47899999999999999987899999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      .|....+.
T Consensus        77 sV~P~~~~   84 (104)
T 2dhx_A           77 SLRPAPPR   84 (104)
T ss_dssp             EEEECCCC
T ss_pred             EEEcCCCC
Confidence            99765543

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.27  E-value=0.00079  Score=58.08  Aligned_cols=77  Identities=13%  Similarity=0.138  Sum_probs=63.7

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccC-CCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLN-DLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g-~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      +..++|-|-|||..+++..|+.++.++. ...|.|..|.++.|      -|-|+|+|.+...|-+|.-.++ ..|.|+.|
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD------H~GAivef~d~~~AgKasLaL~G~ef~gr~L   92 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD------FNGAIIIFRDSKFAAKMLMILNGSQFQGKVI   92 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT------TTEEEEECSCHHHHHHHHHHHSSEEETTEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC------CCceEEEEccchhhHHHHhhcCCeeecCeEE
Confidence            3468899999999999999999998871 22368999988888      3579999999999988865555 99999999


Q ss_pred             EEEee
Q 008920          412 RLSHA  416 (548)
Q Consensus       412 ~V~~A  416 (548)
                      +|.-.
T Consensus        93 r~gTv   97 (117)
T 2l9w_A           93 RSGTI   97 (117)
T ss_dssp             EEECH
T ss_pred             EecCH
Confidence            99743

>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=96.77  E-value=0.0029  Score=54.11  Aligned_cols=73  Identities=12%  Similarity=0.060  Sum_probs=60.6

Q ss_pred             ccEEEEcCCCCCC-c----HHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHH
Q 008920          225 LRTIFVGNLPLKV-K----KKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (548)
Q Consensus       225 ~rtVfVgNLP~~~-t----ee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~  299 (548)
                      ..+|+|.||+..+ .    .+.+..+|..|+++.+..+..                       +-.-..|.|.++++|..
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            4789999998865 2    367899999999998866521                       33457899999999999


Q ss_pred             HH-HhcceeecCceeEeecCCC
Q 008920          300 AL-AFNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       300 Al-~lng~~~~gr~I~V~~a~~  320 (548)
                      |- .||+..|.|..|+|.++++
T Consensus        62 AR~~Lh~~~f~g~~~r~YFgq~   83 (104)
T 1wey_A           62 ARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             HHHTSTTSEETTEECEEECCCC
T ss_pred             HHHHhccceecCceeEEEecCC
Confidence            97 7999999999999999874

>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=96.63  E-value=0.0077  Score=52.77  Aligned_cols=73  Identities=15%  Similarity=0.154  Sum_probs=59.5

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      ..+-|.|-+.|... ...|..+|+.||.|......          .             ...+-+|.|.+..+|++||..
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~----------~-------------~~NWihI~Y~s~~~A~rAL~k   78 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS----------N-------------TGNWMHIRYQSKLQARKALSK   78 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC----------S-------------SSSEEEEEESSHHHHHHHHTT
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC----------C-------------CCCeEEEEeCCHHHHHHHHHh
Confidence            35789999999886 57888999999999887751          0             235899999999999999999


Q ss_pred             cceeecC-ceeEeecCCC
Q 008920          304 NMAVIGG-NHIRLDRACP  320 (548)
Q Consensus       304 ng~~~~g-r~I~V~~a~~  320 (548)
                      ||..|.| -.|-|.++..
T Consensus        79 NG~ii~g~~mIGV~p~~d   96 (119)
T 1wwh_A           79 DGRIFGESIMIGVKPCID   96 (119)
T ss_dssp             TTCEETTTEECEEEECCC
T ss_pred             CCeEecCCEEEEEEECCC
Confidence            9999985 5677777643

>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=96.45  E-value=0.011  Score=49.35  Aligned_cols=71  Identities=23%  Similarity=0.220  Sum_probs=53.4

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~ln  304 (548)
                      +.|.|++||+.+|++++.+.+..+..+....+.......  .+             ..-.-|||.|.+.+++.... .++
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~--~~-------------~~~SRaYi~f~~~e~v~~f~~~~~   66 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSL--YP-------------HMYARAYINFKNQEDIILFRDRFD   66 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSS--TT-------------CCCEEEEEEESSSHHHHHHHHHHT
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCC--CC-------------CcceEEEEEeCCHHHHHHHHHHhC
Confidence            469999999999999999999999877666553322211  11             13357999999999988888 589


Q ss_pred             ceeecCc
Q 008920          305 MAVIGGN  311 (548)
Q Consensus       305 g~~~~gr  311 (548)
                      |..|.+.
T Consensus        67 g~~F~D~   73 (91)
T 1uw4_A           67 GYVFLDN   73 (91)
T ss_dssp             TCEEECT
T ss_pred             CcEEEcC
Confidence            9888553

>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=96.41  E-value=0.0082  Score=50.67  Aligned_cols=52  Identities=19%  Similarity=0.359  Sum_probs=42.5

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      .+.++| ++|..+...||.++|+.||.| .|..+.                        -..|||.|.+++.|..||.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~Wid------------------------DTsAlvvf~~~~~a~~al~   67 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWID------------------------DTSAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEE------------------------TTEEEEECSCHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEc------------------------CCeEEEEecCHHHHHHHHH
Confidence            456666 999999999999999999965 444422                        1489999999999999985

>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=95.79  E-value=0.053  Score=45.24  Aligned_cols=66  Identities=17%  Similarity=0.200  Sum_probs=51.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCC--CCceEEEEEECCHHHHHHHHHHcC-Ccc
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMR--VGKGIAYVLFKTREAANLVIKRRN-LKL  406 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg--~srG~AFV~F~~~e~A~~Al~~ln-~~l  406 (548)
                      .+|.|++||+.+|++++.+.++.+    ..+.....+....+.  ..-.-|||.|.+.+++....+..+ ..+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~----~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F   70 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPM----PEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVF   70 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSC----CCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCc----ccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEE
Confidence            478999999999999999999998    677776666544322  233469999999999988887776 444

>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=95.69  E-value=0.02  Score=48.87  Aligned_cols=74  Identities=15%  Similarity=0.083  Sum_probs=59.2

Q ss_pred             ccEEEEeCCCCCC-C----HHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCe
Q 008920          336 KKTVFVGNLPFDV-K----DEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDR  409 (548)
Q Consensus       336 ~~tLfV~NLp~~~-t----eedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr  409 (548)
                      .++|+|.||+..+ .    .+.++.+|..|    +.+........-      .=..|.|.+.++|.+|-..|+ ..+.|.
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~----~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~   74 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTY----DKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGK   74 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTT----CSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhh----CcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCc
Confidence            4789999998765 2    25779999999    666666555442      146899999999999988887 999999


Q ss_pred             EEEEEeeecC
Q 008920          410 ELRLSHAQQN  419 (548)
Q Consensus       410 ~I~V~~Ak~~  419 (548)
                      .|+|-|+++.
T Consensus        75 ~~r~YFgq~~   84 (104)
T 1wey_A           75 EMKLYFAQTL   84 (104)
T ss_dssp             ECEEECCCCS
T ss_pred             eeEEEecCCC
Confidence            9999999843

>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=95.67  E-value=0.011  Score=50.12  Aligned_cols=51  Identities=20%  Similarity=0.389  Sum_probs=41.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      +.++| ++|..+...||.++|+.||.| .|..+.                        -..|||.|.+++.|..||.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv-~I~Wid------------------------DTsAlvvf~~~~~a~~al~   57 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWID------------------------DTSAFVSLSQPEQVKIAVN   57 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEE------------------------TTEEEEEEEEECHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCE-EEEEEc------------------------CCeEEEEecCHHHHHHHHH
Confidence            44555 999999999999999999944 444421                        1479999999999999995

>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=95.12  E-value=0.06  Score=45.41  Aligned_cols=55  Identities=20%  Similarity=0.433  Sum_probs=44.7

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHc
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR  402 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~l  402 (548)
                      ....++| ++|..+.-.||.++|+.|    |.| .|..+-|-       -|||.|.+++.|..||.++
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~f----ggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAF----GNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTT----CSC-CCEEEETT-------EEEEECSCHHHHHHHHHHH
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhcc----CCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhc
Confidence            3456666 999999999999999999    532 45555552       7999999999999999866

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=94.75  E-value=0.049  Score=48.42  Aligned_cols=87  Identities=20%  Similarity=0.122  Sum_probs=56.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeeccc--CCCCCccchhhhhhhccC-CCcceEEEEecCHHHHHHHHH
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPII--DTKIPRKGAILQKQINEN-ADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~--~~~~prkga~~~~~~~~g-~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ..|.|=+.|...+ ..|..+|++||.|..-.-+..+..  ....+.      .+.... ....+..|.|.+..+|.+||.
T Consensus         8 ~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~------~k~yP~f~g~NWikItYds~~~A~rAL~   80 (132)
T 3p3d_A            8 LAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQD------RQFVPIFSGNSWTKITYDNPASAVDALL   80 (132)
T ss_dssp             CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------------CCCCCEETTEEEEEBSSHHHHHHHHT
T ss_pred             eEEEEEecCHHHH-HHHHHHHHhhceEeeecccccccccccccccc------ccccCccCCCcEEEEEcCCHHHHHHHHH
Confidence            4678888877665 567789999999855211000000  000000      000000 134688999999999999999


Q ss_pred             hcceeecCceeEeecCC
Q 008920          303 FNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~  319 (548)
                      .||..|.|..|-|.++.
T Consensus        81 ~NG~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           81 ENGAVFNGVLLGVIPYT   97 (132)
T ss_dssp             TTTCEETTEECEEEECC
T ss_pred             hCCeEeCcEEEEEEECC
Confidence            99999999988887764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=94.37  E-value=0.07  Score=44.99  Aligned_cols=72  Identities=14%  Similarity=0.158  Sum_probs=48.5

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      +-.|.|+.||+.+|++++.+.++.+-.+....+     .....+.          ....-.-|||.|.+.+++.... .+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~f-----v~G~~s~----------~~~~~SRAYI~F~~~edv~~F~~~f   73 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEF-----FAADLSL----------YPHLYSRAYINFRNPDDILLFRDRF   73 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCC-----CCCCSSS----------CCSCCCCCEEEESCHHHHHHHHHHS
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEE-----eCCccCC----------CCCcceEEEEEeCCHHHHHHHHHHc
Confidence            346999999999999998888776554422222     1111111          0112346999999999999888 58


Q ss_pred             cceeecCc
Q 008920          304 NMAVIGGN  311 (548)
Q Consensus       304 ng~~~~gr  311 (548)
                      +|..|.+.
T Consensus        74 ~g~~F~D~   81 (97)
T 2l08_A           74 DGYIFLDS   81 (97)
T ss_dssp             TTEEEECT
T ss_pred             CCcEEEeC
Confidence            99888553

>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=93.98  E-value=0.073  Score=45.02  Aligned_cols=53  Identities=21%  Similarity=0.406  Sum_probs=44.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHc
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR  402 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~l  402 (548)
                      ..++| ++|..+.-.||.++|+.|    | -..|..+-|-       -|||.|.+++.|..||.++
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~f----g-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i   59 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAF----G-NIQISWIDDT-------SAFVSLSQPEQVKIAVNTS   59 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTS----E-EEEEEEEETT-------EEEEEEEEECHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHHhcc----C-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhc
Confidence            45566 999999999999999999    6 3456666662       7999999999999999876

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=93.89  E-value=0.03  Score=60.01  Aligned_cols=56  Identities=20%  Similarity=0.259  Sum_probs=41.7

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      .|+|||. .|..+++.+|.++|++||+|.++.+    +.+                  ..-||.|+|.+.+++..++..
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~----~~~------------------~g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFF----YES------------------FGLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEE----ECS------------------SSEEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEE----Ecc------------------CCeEEEEEeCCHHHHHHHHhc
Confidence            4899997 7999999999999999999999988    221                  225999999999999988743

>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=93.85  E-value=0.2  Score=43.86  Aligned_cols=73  Identities=8%  Similarity=0.031  Sum_probs=58.7

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCC-eEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRD-RELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~G-r~I~V  413 (548)
                      ....|.|-+.|... -..|...|..|    |.|+......      ...+-+|.|.+..+|++||..++..|.| -.|-|
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~----G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV   91 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQY----GNILKHVMSN------TGNWMHIRYQSKLQARKALSKDGRIFGESIMIGV   91 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTT----SCEEEEEECS------SSSEEEEEESSHHHHHHHHTTTTCEETTTEECEE
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhh----CcEEEeccCC------CCCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEE
Confidence            46788898998874 66788889999    8999887621      2458999999999999999998888875 67777


Q ss_pred             Eeeec
Q 008920          414 SHAQQ  418 (548)
Q Consensus       414 ~~Ak~  418 (548)
                      .++..
T Consensus        92 ~p~~d   96 (119)
T 1wwh_A           92 KPCID   96 (119)
T ss_dssp             EECCC
T ss_pred             EECCC
Confidence            77653

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=92.96  E-value=0.19  Score=42.41  Aligned_cols=65  Identities=15%  Similarity=0.151  Sum_probs=45.9

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCC--CceEEEEEECCHHHHHHHHHHcC
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV--GKGIAYVLFKTREAANLVIKRRN  403 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~--srG~AFV~F~~~e~A~~Al~~ln  403 (548)
                      .+-+|.|+.||+.+|++++.+.++.+.    .+.....+....+..  .-.-|||.|.+.++.....+..+
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~----~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~   74 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLP----AHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFD   74 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCS----SEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHST
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcC----ccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcC
Confidence            456899999999999999998888762    333333322222211  12358999999999999888776

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=87.42  E-value=0.45  Score=42.22  Aligned_cols=80  Identities=11%  Similarity=0.186  Sum_probs=55.5

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEE-EEEeecC--------CCC-----CCceEEEEEECCHHHHHHHHH
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEA-VRVIRHP--------HMR-----VGKGIAYVLFKTREAANLVIK  400 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~-VrI~~d~--------~tg-----~srG~AFV~F~~~e~A~~Al~  400 (548)
                      ....|.|-+.|... ...|.+.|+.|    |.|.. +.+....        ...     ...++-.|+|.+..+|.+||.
T Consensus         6 ~e~~VtVFGFp~~~-~~~VI~~Fs~~----G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~   80 (132)
T 3p3d_A            6 GELAILVFGYPETM-ANQVIAYFQEF----GTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL   80 (132)
T ss_dssp             --CEEEEECCCGGG-HHHHHHHHGGG----SCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT
T ss_pred             CceEEEEEecCHHH-HHHHHHHHHhh----ceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH
Confidence            34567777887754 45677789999    77765 2111100        000     134588999999999999999


Q ss_pred             HcCCccCCeEEEEEeeecC
Q 008920          401 RRNLKLRDRELRLSHAQQN  419 (548)
Q Consensus       401 ~ln~~l~Gr~I~V~~Ak~~  419 (548)
                      ..+..|.|.-|-|.++.+.
T Consensus        81 ~NG~ii~G~mIGV~Py~~~   99 (132)
T 3p3d_A           81 ENGAVFNGVLLGVIPYTKD   99 (132)
T ss_dssp             TTTCEETTEECEEEECCHH
T ss_pred             hCCeEeCcEEEEEEECCHH
Confidence            9999999998888888653

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=87.14  E-value=0.33  Score=51.95  Aligned_cols=57  Identities=12%  Similarity=0.175  Sum_probs=42.4

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHc
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR  402 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~l  402 (548)
                      .+.|||. .|..+++.+|.++|++|    |.|.++.+..+.  |   -||.|+|.+.+++..++...
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~----g~i~~~~~~~~~--g---~~~~vef~~~~~~~~~~~~~  109 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQF----GPINNHFFYESF--G---LYAVVEFCQKESIGSLQNGT  109 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGG----SCCCCEEEECSS--S---EEEEEECC---CCHHHHSSC
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhc----CCcceEEEEccC--C---eEEEEEeCCHHHHHHHHhcc
Confidence            5789998 78899999999999999    899998776552  2   59999999999998776543

>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=80.73  E-value=3.4  Score=44.61  Aligned_cols=52  Identities=21%  Similarity=0.376  Sum_probs=42.0

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|+ +|..+...+|.++|+.||.| .|+.+                        +...|||.|.+.+.|..++.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~wi------------------------ddt~a~V~~~~~~~a~~~l~  491 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWI------------------------DDTSAFVSLSQPEQVQIAVN  491 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEEC------------------------SSSEEEEECSCHHHHHHHHH
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEE------------------------cCCeEEEEECCHHHHHHHHH
Confidence            4577776 99999999999999999965 45442                        22479999999999999984

---

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	548
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-14
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	4e-11
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	9e-08
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	8e-11
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-07
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	9e-11
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	5e-07
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	6e-10
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	6e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	8e-10
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	8e-04
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-09
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	9e-06
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-09
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-07
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	4e-09
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	0.003
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	4e-09
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	6e-05
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	4e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	4e-06
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	6e-09
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-05
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	8e-09
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-06
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-09
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-05
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	9e-09
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-08
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-06
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-08
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	6e-04
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-08
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-05
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-08
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-06
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-08
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-06
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-08
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-07
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-08
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-05
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-08
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	4e-06
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-08
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-06
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-08
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-04
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-08
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-07
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	5e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	5e-08
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	6e-08
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	7e-05
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	8e-08
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	6e-06
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	9e-08
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-07
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-07
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	4e-07
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-07
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-04
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-07
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	0.002
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	2e-07
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	7e-05
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-07
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	0.003
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-07
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-06
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-07
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-04
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-07
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-05
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-07
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-05
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-07
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-04
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-07
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	3e-04
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	4e-07
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-05
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	4e-07
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	8e-05
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	6e-07
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	5e-05
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-07
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-05
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	8e-07
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-05
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	8e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	0.001
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	9e-07
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-04
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	9e-07
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-04
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-04
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-06
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	3e-05
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-06
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-06
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-06
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-04
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	4e-06
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	5e-06
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	0.001
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	8e-06
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-05
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-04
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-05
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	3e-05
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	5e-05
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	1e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	3e-04
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	3e-04
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-04
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	4e-04
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	4e-04
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	7e-04
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	9e-04
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	0.001
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	0.001
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	0.002
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	0.002

>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 = 69.6 bits (169), Expect = 2e-14
 Identities = 28/207 (13%), Positives = 74/207 (35%), Gaps = 30/207 (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 PFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNL 404
             D ++  +   F         +E + ++        +G A+V F   ++ + ++ ++  
Sbjct: 106 KEDTEEHHLRDYFEQ----YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH 161

Query: 405 KLRDRELRLSHAQQNCTPSKRKDVAPA 431
            +      +  A        ++++A A
Sbjct: 162 TVNGHNCEVRKAL------SKQEMASA 182

>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 = 56.9 bits (137), Expect = 4e-11
 Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 5/83 (6%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
           +++VG+L  DV +  +Y+ F     + S    +RV R    R   G AYV F+    A  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILS----IRVCRDMITRRSLGYAYVNFQQPADAER 57

Query: 398 VIKRRN-LKLRDRELRLSHAQQN 419
            +   N   ++ + +R+  +Q++
Sbjct: 58  ALDTMNFDVIKGKPVRIMWSQRD 80

>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 = 47.2 bits (112), Expect = 9e-08
 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

>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 = 56.1 bits (135), Expect = 8e-11
 Identities = 15/78 (19%), Positives = 33/78 (42%), Gaps = 4/78 (5%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
           +F+G L +    E + + F    +    V+   V+R P  +  +G  +V F  +   + V
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGE----VKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 58

Query: 399 IKRRNLKLRDRELRLSHA 416
           + +   +L  + +    A
Sbjct: 59  LAQSRHELDSKTIDPKVA 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 = 45.7 bits (108), Expect = 4e-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

>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 = 56.6 bits (136), Expect = 9e-11
 Identities = 23/97 (23%), Positives = 40/97 (41%), Gaps = 4/97 (4%)

Query: 321 PRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV 380
           P ++     +P     +TVF   L   ++  ++   F  +      V  VR+I   + R 
Sbjct: 3   PVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGK----VRDVRIISDRNSRR 58

Query: 381 GKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQ 417
            KGIAYV F   ++  L I     +L    + +  +Q
Sbjct: 59  SKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQ 95

>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 = 45.8 bits (108), Expect = 5e-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

>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 = 53.9 bits (129), Expect = 6e-10
 Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 4/80 (5%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           + +F+G L F+  DE +   F     L        V+R P+ +  +G  +V + T E  +
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTD----CVVMRDPNTKRSRGFGFVTYATVEEVD 62

Query: 397 LVIKRRNLKLRDRELRLSHA 416
             +  R  K+  R +    A
Sbjct: 63  AAMNARPHKVDGRVVEPKRA 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 = 42.3 bits (99), Expect = 6e-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

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.2 bits (127), Expect = 8e-10
 Identities = 10/83 (12%), Positives = 32/83 (38%), Gaps = 5/83 (6%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
            ++V++   P D   ++I +       + +      + +     +     +V+F + E+A
Sbjct: 6   NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSI-----FVVFDSIESA 60

Query: 396 NLVIKRRNLKLRDRELRLSHAQQ 418
              ++    K ++ +L +     
Sbjct: 61  KKFVETPGQKYKETDLLILFKDD 83

>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 = 36.3 bits (83), Expect = 8e-04
 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

>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 = 52.8 bits (126), Expect = 2e-09
 Identities = 17/98 (17%), Positives = 36/98 (36%), Gaps = 8/98 (8%)

Query: 320 PPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMR 379
            P ++ K E        + +F+G L F+  +E +   +         +    V+R P  +
Sbjct: 8   VPLERKKREKEQF----RKLFIGGLSFETTEESLRNYYEQWGK----LTDCVVMRDPASK 59

Query: 380 VGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQ 417
             +G  +V F +    +  +  R   +  R +    A 
Sbjct: 60  RSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAV 97

>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 = 42.4 bits (99), Expect = 9e-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

>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 = 51.5 bits (123), Expect = 3e-09
 Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 5/81 (6%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            + V  LP D+ D E+Y LF  +  + +     R++R        G A+V F +   +  
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINT----CRIMRDYKTGYSYGYAFVDFTSEMDSQR 59

Query: 398 VIKRRN-LKLRDRELRLSHAQ 417
            IK  N + +R++ L++S+A+
Sbjct: 60  AIKVLNGITVRNKRLKVSYAR 80

>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 = 45.8 bits (108), Expect = 3e-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

>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 = 52.0 bits (124), Expect = 4e-09
 Identities = 22/90 (24%), Positives = 34/90 (37%), Gaps = 4/90 (4%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
             +FVG LP+   D  + + F G  D    +E   VI        +G  +V    R AA 
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGFGD----IEEAVVITDRQTGKSRGYGFVTMADRAAAE 66

Query: 397 LVIKRRNLKLRDRELRLSHAQQNCTPSKRK 426
              K  N  +  R+  ++ A     P   +
Sbjct: 67  RACKDPNPIIDGRKANVNLAYLGAKPRSLQ 96

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.5 bits (81), Expect = 0.003
 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

>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 = 52.3 bits (125), Expect = 4e-09
 Identities = 19/91 (20%), Positives = 38/91 (41%), Gaps = 8/91 (8%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           + +++ NLP+ +  EE+Y +F            +R IR  +    +G AYV+++    A 
Sbjct: 8   RILYIRNLPYKITAEEMYDIF-------GKYGPIRQIRVGNTPETRGTAYVVYEDIFDAK 60

Query: 397 LVIKRRN-LKLRDRELRLSHAQQNCTPSKRK 426
                 +   + +R L + +   N    K  
Sbjct: 61  NACDHLSGFNVCNRYLVVLYYNANRAFQKMD 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 = 40.4 bits (94), Expect = 6e-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

>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 = 51.3 bits (122), Expect = 4e-09
 Identities = 19/80 (23%), Positives = 42/80 (52%), Gaps = 4/80 (5%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
           +F+GNL  ++ ++ +Y  F     +    +  +++R P     KG A++ F + +A++  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVIL---QTPKIMRDPDTGNSKGYAFINFASFDASDAA 57

Query: 399 IKRRN-LKLRDRELRLSHAQ 417
           I+  N   L +R + +S+A 
Sbjct: 58  IEAMNGQYLCNRPITVSYAF 77

>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 = 43.2 bits (101), 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

>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 = 51.1 bits (122), Expect = 6e-09
 Identities = 22/89 (24%), Positives = 39/89 (43%), Gaps = 12/89 (13%)

Query: 334 DIKKT-VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK 390
            IK T ++V NLP  + D+++  +F   G      S+    ++R       +G+A+V + 
Sbjct: 3   SIKDTNLYVTNLPRTITDDQLDTIFGKYG------SIVQKNILRDKLTGRPRGVAFVRYN 56

Query: 391 TREAANLVIKRRN---LKLRDRELRLSHA 416
            RE A   I   N    +   + L +  A
Sbjct: 57  KREEAQEAISALNNVIPEGGSQPLSVRLA 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 = 41.9 bits (98), Expect = 1e-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

>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 = 50.5 bits (120), Expect = 8e-09
 Identities = 12/78 (15%), Positives = 30/78 (38%), Gaps = 4/78 (5%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
           +FVG L  +   E++   F         V+   ++        +G  +V F++ +    V
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGK----VDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 57

Query: 399 IKRRNLKLRDRELRLSHA 416
            +    ++ ++ +    A
Sbjct: 58  CEIHFHEINNKMVECKKA 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 = 43.9 bits (103), 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

>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 = 50.4 bits (120), Expect = 8e-09
 Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 4/78 (5%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
           +F+G L +D   +++   F    ++        +   P     +G  +VLFK  E+ + V
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVD----CTLKLDPITGRSRGFGFVLFKESESVDKV 57

Query: 399 IKRRNLKLRDRELRLSHA 416
           + ++  KL  + +    A
Sbjct: 58  MDQKEHKLNGKVIDPKRA 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 = 41.1 bits (96), 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

>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 = 50.4 bits (120), Expect = 9e-09
 Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 5/80 (6%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            + V N+PF V  +EI   F G   +  SV     +++    +  G A V F++R+ A  
Sbjct: 11  IIKVQNMPFTVSIDEILDFFYGYQVIPGSV----CLKYNEKGMPTGEAMVAFESRDEATA 66

Query: 398 VIKRRN-LKLRDRELRLSHA 416
            +   N   +  R+++L   
Sbjct: 67  AVIDLNDRPIGSRKVKLVLG 86

>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 = 50.1 bits (119), Expect = 1e-08
 Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
           K  + V  LP ++  EE   LF  + ++ES       I    +       +V +   + A
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLG----YGFVNYIDPKDA 57

Query: 396 NLVIKRRN-LKLRDRELRLSHAQ 417
              I   N L+L+ + +++S+A+
Sbjct: 58  EKAINTLNGLRLQTKTIKVSYAR 80

>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 = 43.9 bits (103), Expect = 2e-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

>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 = 50.0 bits (119), Expect = 1e-08
 Identities = 14/81 (17%), Positives = 30/81 (37%), Gaps = 5/81 (6%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
             + V  LP+   ++++ + F    ++      V+V +       KG  +V F   E   
Sbjct: 9   SDLIVLGLPWKTTEQDLKEYFSTFGEVLM----VQVKKDLKTGHSKGFGFVRFTEYETQV 64

Query: 397 LVIKRRNLKLRDRELRLSHAQ 417
            V+ +R+  +  R        
Sbjct: 65  KVMSQRH-MIDGRWCDCKLPN 84

>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 = 6e-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

>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 = 50.1 bits (119), Expect = 2e-08
 Identities = 15/83 (18%), Positives = 35/83 (42%), Gaps = 5/83 (6%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            +F+G +P   K EEI +    + +    V              +G A+V +++  AA +
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKN--RGFAFVEYESHRAAAM 60

Query: 398 VIKRRN---LKLRDRELRLSHAQ 417
             ++     ++L   ++ +  A+
Sbjct: 61  ARRKLMPGRIQLWGHQIAVDWAE 83

>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 = 3e-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

>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 = 49.2 bits (117), Expect = 2e-08
 Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 4/78 (5%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
           +FVG L  D  +E+I + F G       VE++ +         +G  ++ FK  E    +
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFG----EVESIELPMDNKTNKRRGFCFITFKEEEPVKKI 57

Query: 399 IKRRNLKLRDRELRLSHA 416
           ++++   +   +  +  A
Sbjct: 58  MEKKYHNVGLSKCEIKVA 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 = 43.4 bits (102), Expect = 2e-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

>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 = 49.2 bits (117), Expect = 2e-08
 Identities = 16/80 (20%), Positives = 37/80 (46%), Gaps = 5/80 (6%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
           +F+G LP  + D+++ +L          ++A  +++     + KG A+  +      +  
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGP----LKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 59

Query: 399 IKRRN-LKLRDRELRLSHAQ 417
           I   N ++L D++L +  A 
Sbjct: 60  IAGLNGMQLGDKKLLVQRAS 79

>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 = 42.3 bits (99), Expect = 6e-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

>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 = 49.3 bits (117), Expect = 2e-08
 Identities = 15/85 (17%), Positives = 36/85 (42%), Gaps = 2/85 (2%)

Query: 340 FVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVI 399
           F+ NL F   +E +  +F  +  ++S     +      + +  G  +V +K  E A   +
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTI-SKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 400 KRRN-LKLRDRELRLSHAQQNCTPS 423
           K+     +   +L +  +++   P+
Sbjct: 61  KQLQGHTVDGHKLEVRISERATKPA 85

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.6 bits (110), Expect = 2e-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

>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 = 49.6 bits (118), Expect = 3e-08
 Identities = 18/86 (20%), Positives = 28/86 (32%), Gaps = 5/86 (5%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
              + V N+PF     EI +LF   +            +       +G  +V F T++ A
Sbjct: 8   TSKILVRNIPFQANQREIRELF---STFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 396 NLVIKR--RNLKLRDRELRLSHAQQN 419
                    +  L  R L L  A   
Sbjct: 65  KKAFNALCHSTHLYGRRLVLEWADSE 90

>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 = 1e-05
 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

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.7 bits (118), Expect = 3e-08
 Identities = 24/94 (25%), Positives = 39/94 (41%), Gaps = 8/94 (8%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
            T F+GNLP+DV +E I + F GLN               +    KG  Y  F+  ++  
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLNI----SAVRLPREPSNPERLKGFGYAEFEDLDSLL 71

Query: 397 LVIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAP 430
             +      L ++ +R+  A      ++ KD  P
Sbjct: 72  SALSLNEESLGNKRIRVDVAD----QAQDKDSGP 101

>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 = 43.6 bits (102), Expect = 4e-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

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.8 bits (116), Expect = 3e-08
 Identities = 19/80 (23%), Positives = 33/80 (41%), Gaps = 6/80 (7%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
           + V NL F V D +I +LF     L+ +      + +       G A V F+ +  A   
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKA-----AVHYDRSGRSLGTADVHFERKADALKA 57

Query: 399 IKRRN-LKLRDRELRLSHAQ 417
           +K+ N + L  R + +    
Sbjct: 58  MKQYNGVPLDGRPMNIQLVT 77

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.4 bits (102), Expect = 3e-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

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 3e-08
 Identities = 17/82 (20%), Positives = 32/82 (39%), Gaps = 7/82 (8%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            ++V  LP  +  +E+ QLF     + +     R++      V +G+ ++ F  R  A  
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIIT----SRILVDQVTGVSRGVGFIRFDKRIEAEE 63

Query: 398 VIKRRN---LKLRDRELRLSHA 416
            IK  N          + +  A
Sbjct: 64  AIKGLNGQKPSGATEPITVKFA 85

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.1 bits (88), Expect = 2e-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

>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 = 49.0 bits (116), Expect = 4e-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 = 46.7 bits (110), Expect = 2e-07
 Identities = 12/81 (14%), Positives = 33/81 (40%), Gaps = 1/81 (1%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLES-SVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
           + ++VGN+PF + +E +   F     L   +      +    +   K  A++ F++ +  
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 396 NLVIKRRNLKLRDRELRLSHA 416
              +    +  + + L++   
Sbjct: 62  TQAMAFDGIIFQGQSLKIRRP 82

>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 = 48.5 bits (115), Expect = 5e-08
 Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 5/83 (6%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
           TV+VG L   V +  +++LF     + ++      +   H        +V F + E A+ 
Sbjct: 11  TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQG----YGFVEFLSEEDADY 66

Query: 398 VIKRRN-LKLRDRELRLSHAQQN 419
            IK  + +KL  + +R++ A  +
Sbjct: 67  AIKIMDMIKLYGKPIRVNKASAH 89

>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 = 48.5 bits (115), Expect = 5e-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

>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 = 48.5 bits (115), Expect = 6e-08
 Identities = 20/83 (24%), Positives = 35/83 (42%), Gaps = 8/83 (9%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            ++VGNLP D++ ++I  +F           A+R I   + R G   A+V F+    A  
Sbjct: 16  RIYVGNLPPDIRTKDIEDVF-------YKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAED 68

Query: 398 VIKRRN-LKLRDRELRLSHAQQN 419
            +  R+        LR+   +  
Sbjct: 69  AVYGRDGYDYDGYRLRVEFPRSG 91

>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 = 39.7 bits (92), Expect = 7e-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

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.0 bits (114), Expect = 8e-08
 Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 5/82 (6%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
            T++VGNL F   +E+IY+LF    D    ++ + +      +   G  +V + +R  A 
Sbjct: 8   CTLYVGNLSFYTTEEQIYELFSKSGD----IKKIIMGLDKMKKTACGFCFVEYYSRADAE 63

Query: 397 LVIKRRN-LKLRDRELRLSHAQ 417
             ++  N  +L DR +R     
Sbjct: 64  NAMRYINGTRLDDRIIRTDWDA 85

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.6 bits (100), Expect = 6e-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

>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 = 47.7 bits (113), Expect = 9e-08
 Identities = 22/91 (24%), Positives = 35/91 (38%), Gaps = 10/91 (10%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           +T++VGNL  DV +  I QLF                            +V F     A 
Sbjct: 9   RTLYVGNLSRDVTEVLILQLF------SQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAA 62

Query: 397 LVIKRRN-LKLRDRELRLSHAQQNCTPSKRK 426
             +   N  K+  +E++++ A    TPS +K
Sbjct: 63  AALAAMNGRKILGKEVKVNWAT---TPSSQK 90

>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 = 2e-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

>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 = 47.7 bits (113), Expect = 1e-07
 Identities = 22/93 (23%), Positives = 40/93 (43%), Gaps = 9/93 (9%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
           K+ ++VG L  +V D+ ++  F    D+      +      H       A+V F+  E A
Sbjct: 5   KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG----FAFVEFELAEDA 60

Query: 396 NLVIKRRN-LKLRDRELRLSHAQQNCTPSKRKD 427
              I   N  +L  R +R++ A+    P + K+
Sbjct: 61  AAAIDNMNESELFGRTIRVNLAK----PMRIKE 89

>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 = 45.8 bits (108), Expect = 4e-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

>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 = 47.7 bits (113), Expect = 1e-07
 Identities = 18/85 (21%), Positives = 33/85 (38%), Gaps = 5/85 (5%)

Query: 334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRE 393
           D   T+ V NL  D ++ ++ +LF     +      + + +       KG A++ F  RE
Sbjct: 6   DDNATIRVTNLSEDTRETDLQELFRPFGSISR----IYLAKDKTTGQSKGFAFISFHRRE 61

Query: 394 AANLVIKRRN-LKLRDRELRLSHAQ 417
            A   I   +        L +  A+
Sbjct: 62  DAARAIAGVSGFGYDHLILNVEWAK 86

>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 = 38.5 bits (89), Expect = 2e-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

>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 = 47.4 bits (112), Expect = 1e-07
 Identities = 16/83 (19%), Positives = 37/83 (44%), Gaps = 4/83 (4%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
             T+++ NL   +K +E+ +     + + S    +  I        +G A+V+FK   +A
Sbjct: 3   NHTIYINNLNEKIKKDELKKSL---HAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 59

Query: 396 NLVIKRRN-LKLRDRELRLSHAQ 417
              ++        D+ +R+ +A+
Sbjct: 60  TNALRSMQGFPFYDKPMRIQYAK 82

>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 = 35.0 bits (80), Expect = 0.002
 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

>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 = 46.8 bits (110), Expect = 2e-07
 Identities = 17/79 (21%), Positives = 28/79 (35%), Gaps = 6/79 (7%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
           TV V NLP      ++Y+ F         +  V V            A + F   + A  
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGP----IIHVDVADSLKKN--FRFARIEFARYDGALA 55

Query: 398 VIKRRNLKLRDRELRLSHA 416
            I + +  +   E+ +SH 
Sbjct: 56  AITKTHKVVGQNEIIVSHL 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 = 39.1 bits (90), Expect = 7e-05
 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

>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 = 47.1 bits (111), Expect = 2e-07
 Identities = 30/88 (34%), Positives = 45/88 (51%), Gaps = 11/88 (12%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           KTVF+ NL FD ++E + ++     DL+     VRV+ HP     KG A+  F T+EAA 
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKY----VRVVLHPDTEHSKGCAFAQFMTQEAAQ 64

Query: 397 LVIKRRN-------LKLRDRELRLSHAQ 417
             +   +       LKL  R+L++  A 
Sbjct: 65  KCLAAASLEAEGGGLKLDGRQLKVDLAV 92

>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 = 0.003
 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

>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 = 46.5 bits (110), Expect = 2e-07
 Identities = 21/85 (24%), Positives = 38/85 (44%), Gaps = 11/85 (12%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
           +  +FVGNLP D+ +EE+ +LF                    +   KG  ++  +TR  A
Sbjct: 8   RSRLFVGNLPPDITEEEMRKLFE----------KYGKAGEVFIHKDKGFGFIRLETRTLA 57

Query: 396 NLVIKRRN-LKLRDRELRLSHAQQN 419
            +     + + LR ++LR+  A  +
Sbjct: 58  EIAKVELDNMPLRGKQLRVRFACHS 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 = 44.2 bits (104), Expect = 2e-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

>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 = 45.9 bits (108), Expect = 3e-07
 Identities = 15/81 (18%), Positives = 29/81 (35%), Gaps = 5/81 (6%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
           T+++ N P       I  L   +N     V     +        +  AY+   ++E A  
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDIN----VVALSIRLPSLRFNTSRRFAYIDVTSKEDARY 58

Query: 398 VIKRRN-LKLRDRELRLSHAQ 417
            +++ N LK+    L    + 
Sbjct: 59  CVEKLNGLKIEGYTLVTKVSN 79

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 39.0 bits (90), 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

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.6 bits (110), Expect = 3e-07
 Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 5/82 (6%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
             +FV NL +   +E++ +LF         +  +        +  KG A+V F   E A 
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGP----LSELHYPIDSLTKKPKGFAFVTFMFPEHAV 64

Query: 397 LVIKRRN-LKLRDRELRLSHAQ 417
                 +    + R L +  + 
Sbjct: 65  KAYAEVDGQVFQGRMLHVLPST 86

>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 = 40.5 bits (94), Expect = 4e-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

>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 = 46.3 bits (109), Expect = 3e-07
 Identities = 13/80 (16%), Positives = 35/80 (43%), Gaps = 5/80 (6%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            +FV ++  + +++EI + FC        ++ + +         KG A V ++T + A  
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCD----YGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 64

Query: 398 VIKRRN-LKLRDRELRLSHA 416
             +  N  ++  + +++   
Sbjct: 65  AKEALNGAEIMGQTIQVDWC 84

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 41.2 bits (96), Expect = 2e-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

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 46.2 bits (109), Expect = 3e-07
 Identities = 17/82 (20%), Positives = 38/82 (46%), Gaps = 10/82 (12%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           +T+   NL F++ ++E+ ++F          +A+ +         KGIAY+ FK+   A 
Sbjct: 17  RTLLAKNLSFNITEDELKEVFE---------DALEIRLVSQDGKSKGIAYIEFKSEADAE 67

Query: 397 LVIKRRN-LKLRDRELRLSHAQ 417
             ++ +   ++  R + L +  
Sbjct: 68  KNLEEKQGAEIDGRSVSLYYTG 89

>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 = 38.1 bits (88), Expect = 2e-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

>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 = 46.3 bits (109), Expect = 4e-07
 Identities = 20/92 (21%), Positives = 43/92 (46%), Gaps = 5/92 (5%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
            ++VFVGN+P++  +E++  +F  +      V + R++        KG  +  ++ +E A
Sbjct: 8   LRSVFVGNIPYEATEEQLKDIFSEVGP----VVSFRLVYDRETGKPKGYGFCEYQDQETA 63

Query: 396 NLVIKRRN-LKLRDRELRLSHAQQNCTPSKRK 426
              ++  N  +   R LR+ +A       + K
Sbjct: 64  LSAMRNLNGREFSGRALRVDNAASEKNKEELK 95

>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 = 38.2 bits (88), Expect = 3e-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

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 45.9 bits (108), Expect = 4e-07
 Identities = 14/81 (17%), Positives = 33/81 (40%), Gaps = 2/81 (2%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           + + + NL  ++ DE +  L        S  +                A+++F+ +++A 
Sbjct: 5   REIMIRNLSTELLDENL--LRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 62

Query: 397 LVIKRRNLKLRDRELRLSHAQ 417
             ++     L +RE+ +S A 
Sbjct: 63  RALQMNRSLLGNREISVSLAD 83

>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

>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 = 45.5 bits (107), Expect = 4e-07
 Identities = 12/77 (15%), Positives = 26/77 (33%), Gaps = 5/77 (6%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
             + V  L     + ++ ++F     +                     A+V F+  + A 
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG----FAFVYFENVDDAK 65

Query: 397 LVIKRRN-LKLRDRELR 412
              +R N ++L  R +R
Sbjct: 66  EAKERANGMELDGRRIR 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 = 39.3 bits (91), Expect = 8e-05
 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

>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 = 45.3 bits (107), Expect = 6e-07
 Identities = 15/83 (18%), Positives = 31/83 (37%), Gaps = 11/83 (13%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
           TV+ G +   + D+ + Q F     +      +RV            ++V F T E+A  
Sbjct: 20  TVYCGGIASGLTDQLMRQTFSPFGQIME----IRVFPEKGY------SFVRFSTHESAAH 69

Query: 398 VIKRRN-LKLRDRELRLSHAQQN 419
            I   N   +    ++    +++
Sbjct: 70  AIVSVNGTTIEGHVVKCYWGKES 92

>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 = 40.3 bits (94), Expect = 5e-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

>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 = 45.2 bits (107), Expect = 8e-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

>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 = 39.9 bits (93), Expect = 7e-05
 Identities = 16/86 (18%), Positives = 30/86 (34%), Gaps = 14/86 (16%)

Query: 334 DIKKTVFVGNL-PFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            +   VF+GNL    VK  ++  +F     +                V KG A+V +   
Sbjct: 13  SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVG------------CSVHKGFAFVQYVNE 60

Query: 393 EAANLVIKRRN-LKLRDRELRLSHAQ 417
             A   +   +   +  + L ++ A 
Sbjct: 61  RNARAAVAGEDGRMIAGQVLDINLAA 86

>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 = 44.7 bits (105), Expect = 8e-07
 Identities = 12/80 (15%), Positives = 32/80 (40%), Gaps = 4/80 (5%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           K +FVG +  D ++  +   F         +E + ++        +G A+V F   ++ +
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGK----IEVIEIMTDRGSGKKRGFAFVTFDDHDSVD 58

Query: 397 LVIKRRNLKLRDRELRLSHA 416
            ++ ++   +      +  A
Sbjct: 59  KIVIQKYHTVNGHNCEVRKA 78

>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 = 41.2 bits (96), 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

>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 = 45.1 bits (106), Expect = 8e-07
 Identities = 18/82 (21%), Positives = 37/82 (45%), Gaps = 5/82 (6%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            +FVG L FD  ++ + Q+F         +  V V++    +  +G  +V F+  + A  
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQ----ISEVVVVKDRETQRSRGFGFVTFENIDDAKD 62

Query: 398 VIKRRN-LKLRDRELRLSHAQQ 418
            +   N   +  R++R+  A +
Sbjct: 63  AMMAMNGKSVDGRQIRVDQAGK 84

>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 = 35.9 bits (82), Expect = 0.001
 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

>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 = 44.6 bits (105), Expect = 9e-07
 Identities = 17/82 (20%), Positives = 32/82 (39%), Gaps = 11/82 (13%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           K ++V NL     +E I + F            ++      ++  +  A+V F  RE A 
Sbjct: 9   KILYVRNLMLSTSEEMIEKEF----------NNIKPGAVERVKKIRDYAFVHFSNREDAV 58

Query: 397 LVIKRRN-LKLRDRELRLSHAQ 417
             +K  N   L    + ++ A+
Sbjct: 59  EAMKALNGKVLDGSPIEVTLAK 80

>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 = 2e-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 = 45.1 bits (106), Expect = 9e-07
 Identities = 17/82 (20%), Positives = 37/82 (45%), Gaps = 7/82 (8%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           K + V N+PF  +D ++ Q+F     +        V    + R  KG  +V F+    A+
Sbjct: 12  KRLHVSNIPFRFRDPDLRQMFGQFGKILD------VEIIFNERGSKGFGFVTFENSADAD 65

Query: 397 LVIKRRN-LKLRDRELRLSHAQ 417
              ++ +   +  R++ +++A 
Sbjct: 66  RAREKLHGTVVEGRKIEVNNAT 87

>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 = 37.7 bits (87), Expect = 3e-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

>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 = 46.1 bits (108), Expect = 1e-06
 Identities = 23/114 (20%), Positives = 51/114 (44%), Gaps = 8/114 (7%)

Query: 320 PPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMR 379
             +     +  P  D+ + + V  +P  V + ++ QLF         +E+V+++     R
Sbjct: 26  QQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGP----IESVKIVCDRETR 81

Query: 380 VGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQQNCTPSKRKDVAPAV 432
             +G  +V F++  +A   I   N   + ++ L+++ A    +  +R  +A AV
Sbjct: 82  QSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA---SGHQRPGIAGAV 132

>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 = 39.5 bits (91), Expect = 2e-04
 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

>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 = 2e-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

>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 = 40.9 bits (95), Expect = 3e-05
 Identities = 12/88 (13%), Positives = 33/88 (37%), Gaps = 5/88 (5%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLE----SSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
             ++V  L   V  +++   F     ++    +    + +         KG A V ++  
Sbjct: 9   SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 68

Query: 393 EAANLVIKRRN-LKLRDRELRLSHAQQN 419
             A   ++  +    +  +L++S A++ 
Sbjct: 69  PTAKAAVEWFDGKDFQGSKLKVSLARKK 96

>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 = 43.9 bits (103), Expect = 2e-06
 Identities = 17/86 (19%), Positives = 30/86 (34%), Gaps = 13/86 (15%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
             ++VG L  +     + + F               IR      G   AY+ +++ +AA 
Sbjct: 18  TRLWVGGLGPNTSLAALAREFD----------RFGSIRTIDHVKGDSFAYIQYESLDAAQ 67

Query: 397 LVIKRRN---LKLRDRELRLSHAQQN 419
               +     L   DR LR+  A+  
Sbjct: 68  AACAKMRGFPLGGPDRRLRVDFAKSG 93

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 2e-06
 Identities = 14/81 (17%), Positives = 36/81 (44%), Gaps = 5/81 (6%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            +F+ +LP +  D+++ Q+F    ++ S     +V       + K   +V +    +A  
Sbjct: 20  NLFIYHLPQEFGDQDLLQMFMPFGNVVS----AKVFIDKQTNLSKCFGFVSYDNPVSAQA 75

Query: 398 VIKRRN-LKLRDRELRLSHAQ 417
            I+  N  ++  + L++   +
Sbjct: 76  AIQSMNGFQIGMKRLKVQLKR 96

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.5 bits (102), Expect = 3e-06
 Identities = 20/81 (24%), Positives = 41/81 (50%), Gaps = 7/81 (8%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            +F+ NL   + ++ +Y  F    ++ S     +V+   +    KG  +V F+T+EAA  
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILS----CKVVCDENG--SKGYGFVHFETQEAAER 63

Query: 398 VIKRRN-LKLRDRELRLSHAQ 417
            I++ N + L DR++ +   +
Sbjct: 64  AIEKMNGMLLNDRKVFVGRFK 84

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.5 bits (89), Expect = 2e-04
 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

>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 = 43.1 bits (101), Expect = 3e-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

>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 = 43.1 bits (101), Expect = 4e-06
 Identities = 16/81 (19%), Positives = 33/81 (40%), Gaps = 10/81 (12%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
             VFVG    D+ ++E+ + F          + + V      R     A+V F   + A 
Sbjct: 6   SGVFVGRCTGDMTEDELREFF------SQYGDVMDVFIPKPFR---AFAFVTFADDQIAQ 56

Query: 397 LVIKRRNLKLRDRELRLSHAQ 417
            +    +L ++   + +S+A+
Sbjct: 57  SLCG-EDLIIKGISVHISNAE 76

>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 = 42.9 bits (100), Expect = 5e-06
 Identities = 21/103 (20%), Positives = 36/103 (34%), Gaps = 11/103 (10%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
           K    + N+PF +   ++ Q   G+       E    +   +   G G A V FK  + A
Sbjct: 8   KVCAHITNIPFSITKMDVLQFLEGIPV----DENAVHVLVDNNGQGLGQALVQFKNEDDA 63

Query: 396 NLVIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAPAVNSPPKK 438
               +    KL  RE  +            +D+     +PP +
Sbjct: 64  RKSERLHRKKLNGREAFVH-------VVTLEDMREIEKNPPAQ 99

>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 = 36.4 bits (83), Expect = 0.001
 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

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.7 bits (100), Expect = 8e-06
 Identities = 13/94 (13%), Positives = 32/94 (34%), Gaps = 11/94 (11%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
             + V NL + V  + ++Q+F        +V  +      +    +  A + +    +A 
Sbjct: 8   LRIIVENLFYPVTLDVLHQIFSK----FGTVLKIITFTKNN----QFQALLQYADPVSAQ 59

Query: 397 LVIKR---RNLKLRDRELRLSHAQQNCTPSKRKD 427
                   +N+      LR+  ++      K  +
Sbjct: 60  HAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNN 93

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.3 bits (96), Expect = 3e-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

>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 = 39.3 bits (91), Expect = 1e-04
 Identities = 19/94 (20%), Positives = 31/94 (32%), Gaps = 10/94 (10%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            V +  LP+   + +IY  F  LN           I         G A V F T E A  
Sbjct: 17  CVHMRGLPYRATENDIYNFFSPLNP------MRVHIEIGPDGRVTGEADVEFATHEDAVA 70

Query: 398 VIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAPA 431
            + +    ++ R + L       + +      P+
Sbjct: 71  AMAKDKANMQHRYVELFLN----STAGTSGSGPS 100

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.4 bits (94), Expect = 3e-05
 Identities = 13/82 (15%), Positives = 35/82 (42%), Gaps = 12/82 (14%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            +++GNL   V  +++ QLF             ++     + +  G A+V +  +  A  
Sbjct: 3   KLYIGNLSPAVTADDLRQLF----------GDRKLPLAGQVLLKSGYAFVDYPDQNWAIR 52

Query: 398 VIKRRN--LKLRDRELRLSHAQ 417
            I+  +  ++L  + + + ++ 
Sbjct: 53  AIETLSGKVELHGKIMEVDYSV 74

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.9 bits (95), Expect = 3e-05
 Identities = 17/100 (17%), Positives = 30/100 (30%), Gaps = 14/100 (14%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
             V V  L   V + ++ +                 I +  M   K  A V F+  ++A 
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGT----------ICYVMMMPFKRQALVEFENIDSAK 65

Query: 397 LVIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAPAVNSPP 436
             +           + ++  Q     S  K +    NS P
Sbjct: 66  ECVTFAADV----PVYIAGQQAFFNYSTSKRITRPGNSGP 101

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.8 bits (92), Expect = 3e-05
 Identities = 11/75 (14%), Positives = 27/75 (36%), Gaps = 5/75 (6%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
           +++  L     D+++ +L      + S     + I        KG  +V F +  AA   
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVS----TKAILDKTTNKCKGYGFVDFDSPSAAQKA 56

Query: 399 IKRRN-LKLRDRELR 412
           +       ++ +  +
Sbjct: 57  VTALKASGVQAQMAK 71

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 5e-05
 Identities = 14/85 (16%), Positives = 32/85 (37%), Gaps = 10/85 (11%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
            T+ + N+P  V +E++  LF     +        V      +  + +A +   + E A 
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGV--------VKGFKFFQKDRKMALIQMGSVEEAV 62

Query: 397 LVIKRRNLK--LRDRELRLSHAQQN 419
             +   +      +  LR+S ++  
Sbjct: 63  QALIDLHNHDLGENHHLRVSFSKST 87

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.6 bits (89), Expect = 1e-04
 Identities = 18/82 (21%), Positives = 28/82 (34%), Gaps = 3/82 (3%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMR--VGKGIAYVLFKTRE 393
           K  VFV  L   + D E+ +            + V      +         AYV +   E
Sbjct: 8   KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE 67

Query: 394 AANLVIKRRN-LKLRDRELRLS 414
            A   I+  N + +  R L+ S
Sbjct: 68  DALRAIQCVNNVVVDGRTLKAS 89

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 3e-04
 Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 5/82 (6%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           K +++ NL   V + ++  LF          +   +         +G A++ F  +E A 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQ----EKKGPPIQFRMMTGRMRGQAFITFPNKEIAW 74

Query: 397 LVIKRRN-LKLRDRELRLSHAQ 417
             +   N  KL  + L +   +
Sbjct: 75  QALHLVNGYKLYGKILVIEFGK 96

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (86), Expect = 3e-04
 Identities = 15/84 (17%), Positives = 31/84 (36%), Gaps = 12/84 (14%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
             + V NLP D   +E++ L    +            ++ ++   K  A+V     E A 
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDL-----------KYCYVDRNKRTAFVTLLNGEQAQ 54

Query: 397 LVIKRRN-LKLRDRELRLSHAQQN 419
             I+  +    R ++L +     +
Sbjct: 55  NAIQMFHQYSFRGKDLIVQLQPTD 78

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.9 bits (87), Expect = 3e-04
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 4/81 (4%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            V +  LPF    EEI Q F GL  + + +      +           +V F ++E A  
Sbjct: 17  FVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA----FVQFASQEIAEK 72

Query: 398 VIKRRNLKLRDRELRLSHAQQ 418
            +K+   ++  R + +  + +
Sbjct: 73  ALKKHKERIGHRYIEIFKSSR 93

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.8 bits (87), Expect = 4e-04
 Identities = 12/81 (14%), Positives = 25/81 (30%), Gaps = 12/81 (14%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            V V  LP     +++        D+                   G+  V +  +E    
Sbjct: 17  RVLVSGLPPSGSWQDLKDHMREAGDV-----------CYADVQKDGMGMVEYLRKEDMEY 65

Query: 398 VIKRRN-LKLRDRELRLSHAQ 417
            +++ +  K R  E   S+ +
Sbjct: 66  ALRKLDDTKFRSHEGETSYIR 86

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.9 bits (85), Expect = 4e-04
 Identities = 13/82 (15%), Positives = 31/82 (37%), Gaps = 13/82 (15%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
            T++V     D+    +   F               I    M   +  A+V ++  E+A+
Sbjct: 6   NTLYVYGE--DMTPTLLRGAF----------SPFGNIIDLSMDPPRNCAFVTYEKMESAD 53

Query: 397 LVIKRRN-LKLRDRELRLSHAQ 417
             +   N  ++   +L+++ A+
Sbjct: 54  QAVAELNGTQVESVQLKVNIAR 75

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.1 bits (85), Expect = 7e-04
 Identities = 10/81 (12%), Positives = 27/81 (33%), Gaps = 6/81 (7%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            +++ NLP  + ++E+  +      + S+                   +   ++ E    
Sbjct: 20  NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVG-----FARMESTEKCEA 74

Query: 398 VIKRRNLK-LRDRELRLSHAQ 417
           VI   N K ++      +  +
Sbjct: 75  VIGHFNGKFIKTPPGVSAPTE 95

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 36.4 bits (83), Expect = 9e-04
 Identities = 13/84 (15%), Positives = 29/84 (34%), Gaps = 11/84 (13%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           + +F+ NLP +  +  +  LF                    +     IA+V F T   +N
Sbjct: 9   QILFLTNLPEETNEMMLSMLFNQFPG---------FKEVRLVPNRHDIAFVEFTTELQSN 59

Query: 397 LVIKRRNLK--LRDRELRLSHAQQ 418
              +            ++++ A++
Sbjct: 60  AAKEALQGFKITPTHAMKITFAKK 83

>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 = 36.1 bits (82), Expect = 0.001
 Identities = 14/81 (17%), Positives = 28/81 (34%), Gaps = 5/81 (6%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
             +F+GNL  +    E+      L            +        +   YV F++ E   
Sbjct: 14  FNLFIGNLNPNKSVAELKVAISELFAKN-----DLAVVDVRTGTNRKFGYVDFESAEDLE 68

Query: 397 LVIKRRNLKLRDRELRLSHAQ 417
             ++   LK+   E++L   +
Sbjct: 69  KALELTGLKVFGNEIKLEKPK 89

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.0 bits (82), Expect = 0.001
 Identities = 15/85 (17%), Positives = 34/85 (40%), Gaps = 13/85 (15%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
           + + +  LP +V + E+  L                + +  M  GK  A++   T EAA 
Sbjct: 9   RVLHIRKLPGEVTETEVIALG----------LPFGKVTNILMLKGKNQAFLELATEEAAI 58

Query: 397 LVIKRRNLK---LRDRELRLSHAQQ 418
            ++   +     LR++ + + ++  
Sbjct: 59  TMVNYYSAVTPHLRNQPIYIQYSNH 83

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.9 bits (79), Expect = 0.002
 Identities = 18/82 (21%), Positives = 33/82 (40%), Gaps = 12/82 (14%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
           + +  LP DV ++E++ L                +++  +   KG A+V     E A   
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSD-----------YELKYCFVDKYKGTAFVTLLNGEQAEAA 49

Query: 399 IKRRNLK-LRDRELRLSHAQQN 419
           I   +   LR+REL +     +
Sbjct: 50  INTFHQSRLRERELSVQLQPTD 71

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.9 bits (80), Expect = 0.002
 Identities = 10/91 (10%), Positives = 25/91 (27%), Gaps = 17/91 (18%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
            V V   P       I   F          +   +++H          ++ ++++  A  
Sbjct: 6   WVTVFGFPQAS-ASYILLQFA---------QYGNILKHVMSN-TGNWMHIRYQSKLQARK 54

Query: 398 VIKRRNLKLRDRELRLSHAQQNCTPSKRKDV 428
            + +      +  +          P   K+V
Sbjct: 55  ALSKDGRIFGESIMI------GVKPCIDKNV 79

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	548
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.97
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.72
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.72
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.72
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.72
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.71
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.71
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.71
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.71
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.7
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.7
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.7
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.7
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.7
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.69
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.69
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.69
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.69
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.69
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.69
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.68
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.68
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.68
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.68
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.68
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.67
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.67
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.67
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.67
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.67
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.67
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.67
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.67
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.67
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.67
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.66
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.66
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.66
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.66
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.66
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.66
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.66
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.66
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.66
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.66
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.66
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.65
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.65
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.65
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.65
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.65
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.65
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.65
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.65
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.64
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.64
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.64
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.64
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.64
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.64
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.64
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.64
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.64
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.64
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.64
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.64
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.63
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.63
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.63
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.63
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.63
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.63
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.63
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.62
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.62
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.62
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.61
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.61
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.61
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.61
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.6
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.6
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.6
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.6
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.6
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.6
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.6
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.59
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.59
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.59
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.59
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.58
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.58
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.58
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.58
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.58
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.57
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.57
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.57
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.57
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.57
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.56
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.56
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.56
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.55
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.55
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.55
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.55
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.54
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.54
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.54
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.54
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.54
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.54
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.54
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.54
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.53
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.53
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.53
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.53
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.53
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.53
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.52
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.52
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.52
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.52
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.52
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.52
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.51
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.51
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.51
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.51
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.51
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.51
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.51
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.5
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.5
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.49
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.49
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.49
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.49
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.49
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.49
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.48
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.48
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.48
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.47
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.47
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.45
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.45
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.44
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.44
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.42
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.41
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.4
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.39
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.34
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.33
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.32
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.26
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.22
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	99.2
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	99.19
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.19
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.16
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.14
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.07
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.04
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.96
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.95
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.95
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.59
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.41
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.26
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.09
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	95.46
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	94.96
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	91.33
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	80.54

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=8e-30  Score=238.87  Aligned_cols=172  Identities=15%  Similarity=0.335  Sum_probs=150.7

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      +.++|||+|||+.+|+++|.++|++||.|.+|.++.+..                 .+.++|||||+|.+.++|..|+.+
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~-----------------~~~~~g~afv~f~~~~~a~~a~~~   67 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN-----------------TKRSRGFGFVTYATVEEVDAAMNA   67 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----------------TCCEEEEEEEEESSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeeccc-----------------CCCccCceecccCCHHHHHHHHHh
Confidence            458999999999999999999999999999999865431                 345789999999999999999998


Q ss_pred             cceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCce
Q 008920          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG  383 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG  383 (548)
                      ++..+.++.+.+.+.........   .......++|||+|||+.+++++|+++|..|    |.|..|.|+.+..+|.++|
T Consensus        68 ~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~----G~v~~~~i~~~~~~~~~~g  140 (183)
T d1u1qa_          68 RPHKVDGRVVEPKRAVSREDSQR---PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY----GKIEVIEIMTDRGSGKKRG  140 (183)
T ss_dssp             CSCEETTEECEEEECCCTTGGGS---TTTTCCCSEEEEECCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEE
T ss_pred             cCCcccccchhhhhhhhcccccc---cccccccceeEEccCCCcCCHHHHhhhhccC----CceeeeeeecccccCccce
Confidence            88889999998887765433222   2234567899999999999999999999999    8999999999999999999


Q ss_pred             EEEEEECCHHHHHHHHHHcCCccCCeEEEEEeeecC
Q 008920          384 IAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQN  419 (548)
Q Consensus       384 ~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~Ak~~  419 (548)
                      ||||+|.+.++|.+||.+++..|.|+.|.|.+|.++
T Consensus       141 ~~fV~f~~~e~A~~Al~~~~~~~~G~~i~V~~A~~k  176 (183)
T d1u1qa_         141 FAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSK  176 (183)
T ss_dssp             EEEEEESCHHHHHHHHTSSCEEETTEEEEEEECCCH
T ss_pred             eEEEEECCHHHHHHHHHhCCCeECCEEEEEEecCCc
Confidence            999999999999999987668899999999998753

>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=99.72  E-value=1.3e-17  Score=138.18  Aligned_cols=82  Identities=16%  Similarity=0.259  Sum_probs=77.0

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      ...++|||+|||+.+++++|.++|+.|    |.|..|+|++|+.+|.++|||||+|.+.++|..||..+| ..|.|+.|+
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~----G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~   80 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDY----GEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ   80 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHc----CCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            346899999999999999999999999    899999999999999999999999999999999998877 999999999


Q ss_pred             EEeeecC
Q 008920          413 LSHAQQN  419 (548)
Q Consensus       413 V~~Ak~~  419 (548)
                      |.||.++
T Consensus        81 V~~a~~k   87 (88)
T d1rk8a_          81 VDWCFVK   87 (88)
T ss_dssp             EEESEEC
T ss_pred             EEEecCC
Confidence            9999875

>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=99.72  E-value=6.5e-18  Score=137.69  Aligned_cols=79  Identities=28%  Similarity=0.507  Sum_probs=75.4

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLS  414 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~  414 (548)
                      .++|||+|||+.+++++|+++|+.|    |.|..|.|++++.+|.++|||||+|.+.++|..||..|+ ..|.|+.|+|.
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~----G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~   77 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAI----GPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVS   77 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTT----SCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHh----CCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3679999999999999999999999    899999999999999999999999999999999998877 99999999999


Q ss_pred             eeec
Q 008920          415 HAQQ  418 (548)
Q Consensus       415 ~Ak~  418 (548)
                      ||+|
T Consensus        78 ~a~p   81 (82)
T d1b7fa1          78 YARP   81 (82)
T ss_dssp             ECCC
T ss_pred             EcCC
Confidence            9986

>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=99.72  E-value=1.4e-17  Score=138.39  Aligned_cols=84  Identities=23%  Similarity=0.326  Sum_probs=78.9

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      .+...+|||+|||..+++++|+++|+.|    |.|..|.|+.|..+|.++|||||+|.+.++|..||+.++ ..|+|+.|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~----G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i   80 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPF----GSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLIL   80 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTT----CCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHh----cccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            4456899999999999999999999999    999999999999999999999999999999999999888 99999999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      .|.||+|..
T Consensus        81 ~v~~akp~~   89 (90)
T d2cq0a1          81 NVEWAKPST   89 (90)
T ss_dssp             EEEESSCCC
T ss_pred             EEEeeeCCC
Confidence            999998753

>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=99.72  E-value=1.5e-17  Score=135.45  Aligned_cols=79  Identities=24%  Similarity=0.437  Sum_probs=75.2

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLS  414 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~  414 (548)
                      ..+|||+|||+.+++++|+++|+.|    |.|..|+|+.+..+|.++|||||+|.+.++|..|+..++ ..|.|+.|+|.
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~----G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~   77 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSI----GEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVS   77 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTT----SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHh----CCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3579999999999999999999999    899999999999999999999999999999999998777 99999999999


Q ss_pred             eeec
Q 008920          415 HAQQ  418 (548)
Q Consensus       415 ~Ak~  418 (548)
                      ||+|
T Consensus        78 ~AkP   81 (82)
T d1fxla1          78 YARP   81 (82)
T ss_dssp             ECCC
T ss_pred             EeeC
Confidence            9986

>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=99.71  E-value=2.9e-17  Score=137.46  Aligned_cols=83  Identities=24%  Similarity=0.386  Sum_probs=77.9

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ...+++|||+|||+.+++++|+++|+.|    |.|.+|.|+.++.+|.++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~----G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i   79 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKS----GDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRII   79 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEEC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHHH----CCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            4467899999999999999999999999    899999999999999999999999999999999999887 99999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      +|.|+...
T Consensus        80 ~V~~a~~~   87 (93)
T d1h2vz_          80 RTDWDAGF   87 (93)
T ss_dssp             EEEEESCC
T ss_pred             EEEEcCCC
Confidence            99998643

>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=2.5e-17  Score=140.39  Aligned_cols=84  Identities=25%  Similarity=0.425  Sum_probs=78.5

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLS  414 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~  414 (548)
                      ..++|||+|||+.+++++|+++|+.|    |.|.+|.|+.|..+|.++|||||+|.+.++|..||+.++..|.|+.|.|.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~----G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l~V~   84 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGF----GDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVN   84 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTT----SCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEE
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhc----ccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEEEEE
Confidence            34679999999999999999999999    89999999999999999999999999999999999999988999999999


Q ss_pred             eeecCCCC
Q 008920          415 HAQQNCTP  422 (548)
Q Consensus       415 ~Ak~~~~~  422 (548)
                      +|.....|
T Consensus        85 ~a~~~~~p   92 (103)
T d2cqda1          85 LAYLGAKP   92 (103)
T ss_dssp             ESTTTCCC
T ss_pred             EcCCCCCC
Confidence            99876544

>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=99.71  E-value=8e-18  Score=139.62  Aligned_cols=81  Identities=23%  Similarity=0.373  Sum_probs=76.8

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      ..++|||+|||+++++++|+++|+.|    |.|..|.|+.|+.+|.++|||||+|.+.++|..||..++ ..|+|+.|.|
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~----G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v   79 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPF----GDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV   79 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTT----SCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhC----CeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            46899999999999999999999999    899999999999999999999999999999999998877 9999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      .||.|.
T Consensus        80 ~~a~p~   85 (89)
T d2cqba1          80 NLAKPM   85 (89)
T ss_dssp             EECCCC
T ss_pred             EEeCCC
Confidence            999764

>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=3.2e-17  Score=146.81  Aligned_cols=84  Identities=21%  Similarity=0.430  Sum_probs=78.3

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      .+..++|||+|||+++++++|+++|+.|    |.|..|.|+++..+|.++|||||+|.+.++|..||..|| ..|+|+.|
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~----G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l  114 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERY----GPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRL  114 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHH----SCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhh----ccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            3445789999999999999999999999    999999999999999999999999999999999999887 99999999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      +|.||.+..
T Consensus       115 ~V~~a~~~~  123 (139)
T d1u6fa1         115 KVALAASGH  123 (139)
T ss_dssp             EEEESSCCC
T ss_pred             EEEEcCCCC
Confidence            999998653

>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=99.71  E-value=3.2e-17  Score=138.57  Aligned_cols=83  Identities=19%  Similarity=0.259  Sum_probs=77.8

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      ...++|||+|||+.+++++|+++|..|    |.|..|+|+.|..++.++|||||+|.+.++|..||..|+ ..|.|+.|+
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~----g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~   81 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAY----GPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLH   81 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTT----SCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhc----CCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            346789999999999999999999999    899999999999999999999999999999999999887 999999999


Q ss_pred             EEeeecCC
Q 008920          413 LSHAQQNC  420 (548)
Q Consensus       413 V~~Ak~~~  420 (548)
                      |.++.+..
T Consensus        82 V~~a~~~~   89 (99)
T d1whwa_          82 VLPSTIKK   89 (99)
T ss_dssp             EEECCCCS
T ss_pred             EEECCCCC
Confidence            99998753

>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=99.70  E-value=2.2e-17  Score=135.61  Aligned_cols=79  Identities=18%  Similarity=0.391  Sum_probs=71.4

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      ..++|||+|||+++|+++|.++|+.||.|..|.|+.+..                 +|.++|||||+|.+.++|+.||++
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~-----------------tg~~kG~afV~f~~~~~a~~ai~~   67 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN-----------------TKRSRGFGFVTYATVEEVDAAMNA   67 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----------------TCCEEEEEEEEESSHHHHHHHHHT
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeeccccc-----------------CCCcccEEEEEEcCHHHHHHHHHh
Confidence            357999999999999999999999999999999976542                 355789999999999999999999


Q ss_pred             cceeecCceeEeecCC
Q 008920          304 NMAVIGGNHIRLDRAC  319 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~  319 (548)
                      ++..|.|+.|.|..|.
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            9999999999998874

>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=99.70  E-value=2.7e-17  Score=135.13  Aligned_cols=79  Identities=23%  Similarity=0.445  Sum_probs=75.1

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLS  414 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~  414 (548)
                      ..++|||+|||+++++++|.++|+.|    |.|..|.|++|+.+|.++|||||+|.+.++|..||.+++..|.|+.|.|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~----G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~   80 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQW----GTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPK   80 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhh----ccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEE
Confidence            45789999999999999999999999    99999999999999999999999999999999999987799999999999


Q ss_pred             eee
Q 008920          415 HAQ  417 (548)
Q Consensus       415 ~Ak  417 (548)
                      .|.
T Consensus        81 ~A~   83 (84)
T d1l3ka1          81 RAV   83 (84)
T ss_dssp             ECC
T ss_pred             eee
Confidence            875

>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=99.70  E-value=2.2e-17  Score=134.20  Aligned_cols=77  Identities=26%  Similarity=0.438  Sum_probs=73.9

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEee
Q 008920          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHA  416 (548)
Q Consensus       338 tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~A  416 (548)
                      .|||+|||+.+|+++|+++|+.|    |.|..|+|++|+.+|.++|||||+|.++++|..||+.++ ..|.|+.|+|.||
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~----G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a   77 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPA----GPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   77 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEEC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHh----CCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            69999999999999999999999    899999999999999999999999999999999998887 9999999999998


Q ss_pred             ec
Q 008920          417 QQ  418 (548)
Q Consensus       417 k~  418 (548)
                      +.
T Consensus        78 ~~   79 (80)
T d1cvja1          78 QR   79 (80)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>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=99.70  E-value=2.2e-17  Score=138.19  Aligned_cols=83  Identities=24%  Similarity=0.381  Sum_probs=78.0

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      +..++|||+|||+.+++++|+++|+.|    |.|..|.|++++.+|.++|||||+|.+.++|..||..|+ ..|.|+.|+
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~----G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   82 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQA----GPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIR   82 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTT----SCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHh----CCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            345799999999999999999999999    899999999999999999999999999999999999888 999999999


Q ss_pred             EEeeecCC
Q 008920          413 LSHAQQNC  420 (548)
Q Consensus       413 V~~Ak~~~  420 (548)
                      |.||.+..
T Consensus        83 V~~A~~~~   90 (93)
T d1x5ua1          83 VNKASAHN   90 (93)
T ss_dssp             EEETTTTS
T ss_pred             EEEcCCCC
Confidence            99998753

>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=99.70  E-value=3e-17  Score=136.68  Aligned_cols=82  Identities=18%  Similarity=0.279  Sum_probs=75.8

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRL  413 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V  413 (548)
                      ....+|||+|||+++|+++|+++|+.|    |.|..|.|++|+.+|.++|||||+|.+.++|..||..+ ..|+|+.|.|
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~----G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~-~~l~Gr~i~v   80 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTF----GEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR-HMIDGRWCDC   80 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGG----SCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC-EEETTEEEEE
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhh----cccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC-CccCCEEeEE
Confidence            356789999999999999999999999    99999999999999999999999999999999999854 5799999999


Q ss_pred             EeeecCC
Q 008920          414 SHAQQNC  420 (548)
Q Consensus       414 ~~Ak~~~  420 (548)
                      .+|.++.
T Consensus        81 ~~a~~k~   87 (90)
T d2cqga1          81 KLPNSKQ   87 (90)
T ss_dssp             ECCCTTC
T ss_pred             EeCCCCC
Confidence            9998753

>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=99.69  E-value=1.6e-17  Score=141.26  Aligned_cols=79  Identities=25%  Similarity=0.283  Sum_probs=71.6

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      ..+||||+|||+++|+++|+++|+.||.|.+|+|+.+.                 .+|.++|||||+|.+.++|.+||+|
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-----------------NSRRSKGIAYVEFCEIQSVPLAIGL   79 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSC-----------------CSSSCCCCEEEEESCGGGHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecC-----------------CCccccceEEEEECCHHHHHHHHHH
Confidence            45799999999999999999999999999999995543                 2456889999999999999999999


Q ss_pred             cceeecCceeEeecCC
Q 008920          304 NMAVIGGNHIRLDRAC  319 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~  319 (548)
                      ||..|.|+.|.|.++.
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            9999999999999874

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=3.2e-17  Score=137.19  Aligned_cols=81  Identities=22%  Similarity=0.342  Sum_probs=72.7

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||+++|+++|+++|+.||.|.+|.|+.++                 .+|.++|||||+|.+.++|+.|| .
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~-----------------~tg~~kg~afV~f~~~~~A~~Ai~~   70 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDR-----------------VTGQHQGYGFVEFLSEEDADYAIKI   70 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCS-----------------SSCSBCSCEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecc-----------------cccccccceEEEECCHHHHHHHHHH
Confidence            35799999999999999999999999999999986543                 24567899999999999999999 6


Q ss_pred             hcceeecCceeEeecCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~  321 (548)
                      ||+..|.|+.|.|.++.+.
T Consensus        71 l~g~~~~g~~l~V~~A~~~   89 (93)
T d1x5ua1          71 MDMIKLYGKPIRVNKASAH   89 (93)
T ss_dssp             SSSCBCSSCBCEEEETTTT
T ss_pred             cCCCEECCEEEEEEEcCCC
Confidence            9999999999999999764

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=6.1e-17  Score=134.49  Aligned_cols=81  Identities=25%  Similarity=0.411  Sum_probs=71.6

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      +...+||||+|||.++|+++|.++|+.||+|..|.|+.+..                   ..+|||||+|.+.++|..|+
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            34468999999999999999999999999999999865431                   24689999999999999999


Q ss_pred             -HhcceeecCceeEeecCCCc
Q 008920          302 -AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 -~lng~~~~gr~I~V~~a~~~  321 (548)
                       .|||..|.|+.|+|.++.++
T Consensus        66 ~~l~~~~~~g~~i~v~~a~~~   86 (90)
T d2cqia1          66 AAMNGRKILGKEVKVNWATTP   86 (90)
T ss_dssp             HHHTTEEETTEEEEEEECCCT
T ss_pred             HHcCCCEECCEEEEEEEcCCC
Confidence             59999999999999999764

>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=99.69  E-value=3.1e-17  Score=133.59  Aligned_cols=79  Identities=22%  Similarity=0.330  Sum_probs=71.2

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      .++|||+|||+++|+++|.++|++||.|.+|.|..++                 .+|.++|||||+|.+.++|+.|| .|
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-----------------KTGYSYGYAFVDFTSEMDSQRAIKVL   64 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEET-----------------TTTEECSEEEEEESSHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeec-----------------ccCCccccceEEECCHHHHHHHHHHh
Confidence            4789999999999999999999999999999986544                 23457899999999999999999 59


Q ss_pred             cceeecCceeEeecCCC
Q 008920          304 NMAVIGGNHIRLDRACP  320 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~  320 (548)
                      ||..|.|+.|.|.++.|
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

>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=99.69  E-value=5.5e-17  Score=137.98  Aligned_cols=83  Identities=17%  Similarity=0.348  Sum_probs=78.0

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      ++.++|||+|||+++++++|+++|+.|    |.|..|.++.+..+|.++|||||+|.+.++|..||..|+ ..|+|+.|+
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~----G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~   91 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPF----GNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLK   91 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGG----SCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhh----ccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEE
Confidence            456789999999999999999999999    899999999999999999999999999999999998777 999999999


Q ss_pred             EEeeecCC
Q 008920          413 LSHAQQNC  420 (548)
Q Consensus       413 V~~Ak~~~  420 (548)
                      |.||.+..
T Consensus        92 V~~a~~k~   99 (102)
T d2cpza1          92 VQLKRSKN   99 (102)
T ss_dssp             EECCCCSC
T ss_pred             EEEeCCCC
Confidence            99998764

>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=99.69  E-value=5.4e-17  Score=136.03  Aligned_cols=84  Identities=24%  Similarity=0.413  Sum_probs=76.7

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCC-CCCCceEEEEEECCHHHHHHHHHHc-C-CccCCe
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPH-MRVGKGIAYVLFKTREAANLVIKRR-N-LKLRDR  409 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~-tg~srG~AFV~F~~~e~A~~Al~~l-n-~~l~Gr  409 (548)
                      .....+|||+|||+.+++++|+.+|+.|    |.|..|+|+++.. +|.++|||||+|.+.++|..||..| + ..|.|+
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~----G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr   80 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTF----GELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGR   80 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTT----SCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHh----CCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCE
Confidence            3456889999999999999999999999    8999999998864 8999999999999999999999876 6 889999


Q ss_pred             EEEEEeeecCC
Q 008920          410 ELRLSHAQQNC  420 (548)
Q Consensus       410 ~I~V~~Ak~~~  420 (548)
                      .|.|.||.+..
T Consensus        81 ~l~V~~A~~~~   91 (94)
T d2cpha1          81 RLVLEWADSEV   91 (94)
T ss_dssp             BCEEEECCCCC
T ss_pred             EEEEEEcCCCC
Confidence            99999998764

>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=99.68  E-value=3.6e-17  Score=134.56  Aligned_cols=79  Identities=20%  Similarity=0.446  Sum_probs=75.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEe
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSH  415 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~  415 (548)
                      .+|||+|||+.+++++|+++|+.|    |.|..|+|++|+.+|.++|||||+|.+.++|..|+..++ ..|.|+.|.|.|
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~----G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~   77 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSF----GPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR   77 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSS----SCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhc----CccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            469999999999999999999999    899999999999999999999999999999999999887 999999999999


Q ss_pred             eecC
Q 008920          416 AQQN  419 (548)
Q Consensus       416 Ak~~  419 (548)
                      |.+.
T Consensus        78 A~~~   81 (85)
T d2u2fa_          78 ASVG   81 (85)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9864

>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=99.68  E-value=3.1e-17  Score=135.96  Aligned_cols=80  Identities=29%  Similarity=0.438  Sum_probs=72.1

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      .+||||+|||+++|+++|.++|+.||+|.+|.|+.++.                 +|.++|||||+|.+.++|+.|| .|
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~-----------------~~~~kg~afV~f~~~~~A~~ai~~l   67 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-----------------TEKHRGFAFVEFELAEDAAAAIDNM   67 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSS-----------------SCCCSSEEEECCSSHHHHHHHHHHH
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccc-----------------cccccceeEEEECCHHHHHHHHHHc
Confidence            57999999999999999999999999999999965442                 3557899999999999999999 69


Q ss_pred             cceeecCceeEeecCCCc
Q 008920          304 NMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~  321 (548)
                      |+..|.|+.|.|.++.+.
T Consensus        68 ~~~~i~g~~l~v~~a~p~   85 (89)
T d2cqba1          68 NESELFGRTIRVNLAKPM   85 (89)
T ss_dssp             TTEEETTEEEEEEECCCC
T ss_pred             CCCEECCEEEEEEEeCCC
Confidence            999999999999999754

>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=99.68  E-value=6.1e-17  Score=131.71  Aligned_cols=78  Identities=18%  Similarity=0.290  Sum_probs=70.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~ln  304 (548)
                      ++|||+|||+++++++|.++|+.||.|..|+|+.+.                 ..+.++|||||+|.+.++|+.|+ .||
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~-----------------~~~~~~g~afv~f~~~~~a~~a~~~l~   65 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDK-----------------ITGQSLGYGFVNYIDPKDAEKAINTLN   65 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-----------------TTCCEEEEEEEEESSHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeec-----------------cCCCceeeEEEEECCHHHHHHHHHHhC
Confidence            679999999999999999999999999999996543                 13457899999999999999999 599


Q ss_pred             ceeecCceeEeecCCC
Q 008920          305 MAVIGGNHIRLDRACP  320 (548)
Q Consensus       305 g~~~~gr~I~V~~a~~  320 (548)
                      |..|.|+.|.|.++.|
T Consensus        66 g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1          66 GLRLQTKTIKVSYARP   81 (82)
T ss_dssp             TCEETTEECEEEECCC
T ss_pred             CCEECCEEEEEEEeeC
Confidence            9999999999999864

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=6.4e-17  Score=135.28  Aligned_cols=80  Identities=20%  Similarity=0.303  Sum_probs=72.1

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      .++||||+|||+++|+++|.++|+.||+|.+|.|+.++.                 ++.++|||||+|.+.++|..|| .
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~-----------------~~~~kg~afV~f~~~~~A~~Ai~~   68 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-----------------KKTACGFCFVEYYSRADAENAMRY   68 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----------------TCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccc-----------------cccccceEEEEECCHHHHHHHHHH
Confidence            468999999999999999999999999999999966542                 3457799999999999999999 5


Q ss_pred             hcceeecCceeEeecCCC
Q 008920          303 FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~  320 (548)
                      ||+..|.|+.|.|.|+..
T Consensus        69 l~g~~~~gr~i~V~~a~~   86 (93)
T d1h2vz_          69 INGTRLDDRIIRTDWDAG   86 (93)
T ss_dssp             TTTSEETTEECEEEEESC
T ss_pred             hCCCEECCEEEEEEEcCC
Confidence            999999999999999854

>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=99.68  E-value=8.2e-17  Score=131.52  Aligned_cols=77  Identities=22%  Similarity=0.232  Sum_probs=68.6

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++|+++|+++|+.||.|.+|.|+.++.                 ++.++|||||+|.+.++|..||
T Consensus         6 p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~-----------------~~~~~g~afV~f~~~~~A~~Ai   68 (83)
T d2cqca1           6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQ-----------------SRRSRGFAFVYFENVDDAKEAK   68 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSS-----------------SSSEEEEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCcccccccccc-----------------ccccccceEEEECCHHHHHHHH
Confidence            34568999999999999999999999999999999966442                 3457799999999999999999


Q ss_pred             -HhcceeecCceeEe
Q 008920          302 -AFNMAVIGGNHIRL  315 (548)
Q Consensus       302 -~lng~~~~gr~I~V  315 (548)
                       .||+..|.|+.|+|
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             59999999999987

>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=99.67  E-value=5.4e-17  Score=138.49  Aligned_cols=82  Identities=17%  Similarity=0.368  Sum_probs=76.8

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLS  414 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~  414 (548)
                      ..++|||+|||+++++++|+++|.+|    |.|..|.|++|..++.++|||||+|.+.++|..||.+++..|.|+.|.|.
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~----G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~   94 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQW----GKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPK   94 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSS----CCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhh----CcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEE
Confidence            34789999999999999999999999    99999999999999999999999999999999999876789999999999


Q ss_pred             eeecCC
Q 008920          415 HAQQNC  420 (548)
Q Consensus       415 ~Ak~~~  420 (548)
                      +|.++.
T Consensus        95 ~a~~ke  100 (103)
T d1x4ba1          95 RAVARE  100 (103)
T ss_dssp             CCSSCC
T ss_pred             ECcccC
Confidence            998753

>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=99.67  E-value=1.1e-16  Score=130.75  Aligned_cols=76  Identities=21%  Similarity=0.392  Sum_probs=72.2

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      ++.++|||+|||+.+|+++|+++|+.|    |.|.+|.|+.++.+|.++|||||+|.+.++|..||..++ ..|.|+.|+
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~   82 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKY----GPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR   82 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTT----SCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHh----CCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeE
Confidence            356899999999999999999999999    899999999999999999999999999999999998777 999999998


Q ss_pred             E
Q 008920          413 L  413 (548)
Q Consensus       413 V  413 (548)
                      |
T Consensus        83 V   83 (83)
T d2cqca1          83 V   83 (83)
T ss_dssp             E
T ss_pred             C
Confidence            7

>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=99.67  E-value=5.3e-17  Score=138.55  Aligned_cols=80  Identities=20%  Similarity=0.404  Sum_probs=72.3

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhc
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~ln  304 (548)
                      .++|||+|||+++|+++|+++|++||.|..|.|+.++.                 ++.++|||||+|.+.++|..||+++
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~-----------------~~~~kg~aFV~f~~~~~a~~al~~~   82 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPA-----------------SKRSRGFGFVTFSSMAEVDAAMAAR   82 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTT-----------------TSSCCSEEEEECSSHHHHHHHHTSC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeeccccc-----------------CCCccCeEEEEECCHHHHHHHHHhC
Confidence            47899999999999999999999999999999966542                 3457899999999999999999999


Q ss_pred             ceeecCceeEeecCCCc
Q 008920          305 MAVIGGNHIRLDRACPP  321 (548)
Q Consensus       305 g~~~~gr~I~V~~a~~~  321 (548)
                      +..|.|+.|.|.++.+.
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

>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=99.67  E-value=8.1e-17  Score=133.49  Aligned_cols=82  Identities=22%  Similarity=0.452  Sum_probs=76.8

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      ..++|||+|||+.+++++|.++|..|    |.|..|.++.+..+|.++|||||+|.+.++|..||..++ ..|+|+.|.|
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~----G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V   79 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKY----GQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRV   79 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHH----SCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhcc----ccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            35779999999999999999999999    899999999998999999999999999999999998777 9999999999


Q ss_pred             EeeecCC
Q 008920          414 SHAQQNC  420 (548)
Q Consensus       414 ~~Ak~~~  420 (548)
                      .||.+..
T Consensus        80 ~~a~~~~   86 (90)
T d1x5sa1          80 DQAGKSS   86 (90)
T ss_dssp             EEEECCC
T ss_pred             EEcCCCC
Confidence            9998754

>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=99.67  E-value=4.3e-17  Score=130.92  Aligned_cols=75  Identities=23%  Similarity=0.475  Sum_probs=71.0

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEee
Q 008920          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHA  416 (548)
Q Consensus       338 tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~A  416 (548)
                      .|||+|||+++++++|.++|++|    |.|..|.|++++.++.++|||||+|.+.++|..||.+.+..|.|+.|.|..|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~----G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKF----GEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTT----SCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhh----ccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeEC
Confidence            48999999999999999999999    9999999999999999999999999999999999987669999999999754

>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=99.67  E-value=2.2e-17  Score=133.46  Aligned_cols=76  Identities=20%  Similarity=0.429  Sum_probs=72.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEee
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHA  416 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~A  416 (548)
                      ++|||+|||+++++++|+++|+.|    |.|..|.|++|+.+|.++|||||+|.+.++|.+||.+.+..|+|+.|.|.+|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~----G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQF----GEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTT----SCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHh----CCcceeeeecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            479999999999999999999999    8999999999999999999999999999999999986559999999999987

>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=99.67  E-value=8.8e-17  Score=129.94  Aligned_cols=76  Identities=18%  Similarity=0.382  Sum_probs=69.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhcc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNM  305 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~lng  305 (548)
                      ++|||+|||+++|+++|.++|+.||.|..+.++.++.                 ++.++|||||+|.++++|.+|+.+|+
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~-----------------~~~~~g~afV~f~~~e~~~~al~~~~   65 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRG-----------------SGKKRGFAFVTFDDHDSVDKIVIQKY   65 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTT-----------------TCCEEEEEEEEESSHHHHHHHHHCSC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCC-----------------CcccccEEEEEEcCHHHHHHHHHhCC
Confidence            6899999999999999999999999999999865442                 34578999999999999999999999


Q ss_pred             eeecCceeEeecC
Q 008920          306 AVIGGNHIRLDRA  318 (548)
Q Consensus       306 ~~~~gr~I~V~~a  318 (548)
                      ..|.|+.|.|..|
T Consensus        66 ~~l~Gr~i~V~~A   78 (79)
T d1l3ka2          66 HTVNGHNCEVRKA   78 (79)
T ss_dssp             CEETTEECEEEEC
T ss_pred             CEECCEEEEEEEC
Confidence            9999999999876

>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=99.67  E-value=1.3e-16  Score=130.97  Aligned_cols=77  Identities=23%  Similarity=0.402  Sum_probs=72.2

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCC--eEEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRD--RELR  412 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~G--r~I~  412 (548)
                      .++|||+|||+++++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.+.++|..||+.++ ..+.|  ++|.
T Consensus         6 ~t~lfV~nlp~~~te~~l~~~F~~~----G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~   81 (85)
T d1b7fa2           6 DTNLYVTNLPRTITDDQLDTIFGKY----GSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLS   81 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHTSS----SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhh----CCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEE
Confidence            4679999999999999999999999    899999999999999999999999999999999998887 77766  8999


Q ss_pred             EEee
Q 008920          413 LSHA  416 (548)
Q Consensus       413 V~~A  416 (548)
                      |.||
T Consensus        82 V~~A   85 (85)
T d1b7fa2          82 VRLA   85 (85)
T ss_dssp             EEEC
T ss_pred             EEEC
Confidence            9997

>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=99.67  E-value=1.1e-16  Score=131.35  Aligned_cols=78  Identities=17%  Similarity=0.395  Sum_probs=71.9

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCC---CCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEE
Q 008920          339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMR---VGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLS  414 (548)
Q Consensus       339 LfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg---~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~  414 (548)
                      |||+|||+++++++|+++|+.|    |.|..|.|+++..++   .++|||||+|.+.++|..||..++ ..|+|+.|.|.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~----G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~   76 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKV----GAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR   76 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTT----SCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CEEcCCCCCCCHHHHHHHHHHh----CCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            8999999999999999999999    899999999987655   578999999999999999999888 99999999999


Q ss_pred             eeecCC
Q 008920          415 HAQQNC  420 (548)
Q Consensus       415 ~Ak~~~  420 (548)
                      ||....
T Consensus        77 ~a~~~~   82 (85)
T d2cpfa1          77 ISERAT   82 (85)
T ss_dssp             CSSCSS
T ss_pred             ECCCCC
Confidence            986543

>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=99.67  E-value=9.6e-17  Score=130.35  Aligned_cols=76  Identities=29%  Similarity=0.425  Sum_probs=69.6

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhcc
Q 008920          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (548)
Q Consensus       227 tVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng  305 (548)
                      +|||+|||+.+|+++|.++|+.||+|.+|+|+.++.                 +|.++|||||+|.++++|..|| .|||
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~-----------------tg~~~g~aFV~f~~~~~a~~ai~~l~g   64 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMI-----------------TRRSLGYAYVNFQQPADAERALDTMNF   64 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----------------TCCEEEEEEEEESSHHHHHHHHTTSTT
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEeccc-----------------ccCCCCceEEEECCHHHHHHHHHHcCC
Confidence            699999999999999999999999999999976542                 3457899999999999999999 6999


Q ss_pred             eeecCceeEeecCC
Q 008920          306 AVIGGNHIRLDRAC  319 (548)
Q Consensus       306 ~~~~gr~I~V~~a~  319 (548)
                      ..|.|+.|.|.++.
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

>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=99.66  E-value=1.1e-16  Score=132.52  Aligned_cols=80  Identities=20%  Similarity=0.268  Sum_probs=71.5

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      +.++|||+|||.++|+++|.++|+.||.|.+|+|+.++.                 +|.++|||||+|.+.++|+.|| .
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~-----------------tg~~~g~afV~f~~~~~A~~A~~~   68 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR-----------------TGFSKGYALVEYETHKQALAAKEA   68 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----------------TSSEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCccccccccccc-----------------ccccccceeEEECCHHHHHHHHHH
Confidence            357999999999999999999999999999999976542                 3557899999999999999999 5


Q ss_pred             hcceeecCceeEeecCCC
Q 008920          303 FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~  320 (548)
                      |||..|.|+.|.|+|+.+
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            999999999999999853

>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=99.66  E-value=2.8e-17  Score=132.28  Aligned_cols=75  Identities=21%  Similarity=0.435  Sum_probs=71.7

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEee
Q 008920          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHA  416 (548)
Q Consensus       338 tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~A  416 (548)
                      .|||+|||+++|+++|+++|+.|    |.|..|.|+.++.++.++|||||+|.+.++|.+||+.++..|+|+.|.|..|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~----G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGF----GEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHH----SCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHh----CCcccccccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEEC
Confidence            59999999999999999999999    9999999999999999999999999999999999988779999999999865

>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=99.66  E-value=1.1e-16  Score=133.02  Aligned_cols=81  Identities=20%  Similarity=0.219  Sum_probs=72.4

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ...+|||+|||.++++++|.++|+.||.|.+|.|+.+.                 .+|.++|||||+|.+.++|..|| .
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-----------------TTGQSKGFAFISFHRREDAARAIAG   69 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECS-----------------SSCSEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccc-----------------cccccccceeEEECCHHHHHHHHHH
Confidence            35799999999999999999999999999999996544                 23557899999999999999999 5


Q ss_pred             hcceeecCceeEeecCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~  321 (548)
                      |||..|.|+.|.|.++.+.
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            9999999999999999753

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.3e-16  Score=131.05  Aligned_cols=77  Identities=23%  Similarity=0.401  Sum_probs=72.1

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCC--eEEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRD--RELR  412 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~G--r~I~  412 (548)
                      .++|||+|||+.+++++|+++|++|    |.|..|+|++|+.+|.++|||||+|.+.++|..|++.|| ..|.|  ++|.
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~----G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~   81 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQY----GRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPIT   81 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHh----CCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEE
Confidence            4679999999999999999999999    999999999999999999999999999999999998887 88887  5699


Q ss_pred             EEee
Q 008920          413 LSHA  416 (548)
Q Consensus       413 V~~A  416 (548)
                      |.||
T Consensus        82 V~~A   85 (85)
T d1fxla2          82 VKFA   85 (85)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9987

>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=99.66  E-value=7.6e-17  Score=129.45  Aligned_cols=75  Identities=27%  Similarity=0.473  Sum_probs=67.6

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhcce
Q 008920          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMA  306 (548)
Q Consensus       227 tVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~lng~  306 (548)
                      .|||+|||+++|+++|.++|++||+|..|.|+.++.                 ++.++|||||+|.++++|+.||.+++.
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~-----------------t~~~kg~afV~f~~~~~a~~Al~~~~~   63 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPI-----------------TGRSRGFGFVLFKESESVDKVMDQKEH   63 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTT-----------------TTBCCSEEEEEESSHHHHHHHHHTCCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCC-----------------CCCcCceEEEEECCHHHHHHHHhcCCC
Confidence            389999999999999999999999999999965442                 345789999999999999999999999


Q ss_pred             eecCceeEeecC
Q 008920          307 VIGGNHIRLDRA  318 (548)
Q Consensus       307 ~~~gr~I~V~~a  318 (548)
                      .|.|+.|.|..|
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

>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=99.66  E-value=6.8e-17  Score=137.38  Aligned_cols=80  Identities=26%  Similarity=0.382  Sum_probs=75.0

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLS  414 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~  414 (548)
                      ..++|||+|||+.+++++|+++|+.|    |.|..|+|+++..+|.++|||||+|.+.++|..||.+.+..|.|+.|.|.
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~----G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l~V~   92 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAV----GKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQ   92 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTT----SCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCC----CeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEE
Confidence            35789999999999999999999999    99999999999999999999999999999999999755599999999999


Q ss_pred             eeec
Q 008920          415 HAQQ  418 (548)
Q Consensus       415 ~Ak~  418 (548)
                      ++.+
T Consensus        93 ~a~~   96 (101)
T d2cq4a1          93 ASQA   96 (101)
T ss_dssp             EHHH
T ss_pred             ECCC
Confidence            9864

>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=99.66  E-value=3.5e-17  Score=132.30  Aligned_cols=76  Identities=18%  Similarity=0.346  Sum_probs=69.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhcc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNM  305 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~lng  305 (548)
                      +.|||+|||+++|+++|.++|++||.|.+|.|+.++.                 +|.++|||||+|.+.++|++||++++
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-----------------TKRSRGFGFVTFMDQAGVDKVLAQSR   63 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCC-----------------SSSCSSEEEECCCCTTHHHHHHHTTT
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccC-----------------CCCccceEEEEECCHHHHHHHHHcCC
Confidence            5799999999999999999999999999999966542                 34578999999999999999999999


Q ss_pred             eeecCceeEeecC
Q 008920          306 AVIGGNHIRLDRA  318 (548)
Q Consensus       306 ~~~~gr~I~V~~a  318 (548)
                      ..|.|+.|.|..|
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

>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=99.66  E-value=2.6e-16  Score=130.64  Aligned_cols=79  Identities=24%  Similarity=0.382  Sum_probs=72.9

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      ..++|||+|||..+++++|+++|+.|    |.|..|.|+.+..++  +|||||+|.+.++|..|+..++ ..|.|+.|+|
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~----G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v   80 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQI----GPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKV   80 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHH----SCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhc----CCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            46799999999999999999999999    899999999986554  7899999999999999998877 8999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      .||.++
T Consensus        81 ~~a~~~   86 (90)
T d2cqia1          81 NWATTP   86 (90)
T ss_dssp             EECCCT
T ss_pred             EEcCCC
Confidence            999864

>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=99.66  E-value=8.7e-17  Score=131.28  Aligned_cols=77  Identities=25%  Similarity=0.496  Sum_probs=72.1

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCCCCCeEEE-EEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEee
Q 008920          339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAV-RVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHA  416 (548)
Q Consensus       339 LfV~NLp~~~teedL~~~F~~~g~~~G~I~~V-rI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~A  416 (548)
                      |||+|||+++++++|+++|+.|    |.|..+ .|+++..+|.++|||||+|.+.++|..||..++ ..|.|++|+|.||
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~----G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a   76 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAF----GVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA   76 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTT----SCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             CEEcCCCCcCcHHHHHHHHHHh----CceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEe
Confidence            8999999999999999999999    888664 789999999999999999999999999998887 9999999999999


Q ss_pred             ecC
Q 008920          417 QQN  419 (548)
Q Consensus       417 k~~  419 (548)
                      .++
T Consensus        77 ~~k   79 (83)
T d1x5ta1          77 FKK   79 (83)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            865

>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=99.66  E-value=7.6e-17  Score=131.03  Aligned_cols=78  Identities=18%  Similarity=0.282  Sum_probs=67.8

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEe
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSH  415 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~  415 (548)
                      ++|||+|||+++|+++|+++|+.|    |.|..+.++.+..+|.++|||||+|.+.++|..||..++ ..|.|+.|.|.|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~----G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~   77 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDI----NVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKV   77 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHT----TCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHh----CcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            689999999999999999999999    899988888888899999999999999999999998877 999999999999


Q ss_pred             eec
Q 008920          416 AQQ  418 (548)
Q Consensus       416 Ak~  418 (548)
                      +.|
T Consensus        78 a~P   80 (81)
T d2ghpa1          78 SNP   80 (81)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            987

>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=99.66  E-value=7.7e-17  Score=137.30  Aligned_cols=80  Identities=24%  Similarity=0.506  Sum_probs=76.0

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLS  414 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~  414 (548)
                      .++|||+|||+++++++|.++|+.|    |.|..|.|+.++.+|.++|||||+|.+.++|..||..|+ ..|.|+.|.|.
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~----G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~   83 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEV----GPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVD   83 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTT----SCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEE
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhcc----ccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            4689999999999999999999999    899999999999999999999999999999999999887 99999999999


Q ss_pred             eeecC
Q 008920          415 HAQQN  419 (548)
Q Consensus       415 ~Ak~~  419 (548)
                      ||.+.
T Consensus        84 ~a~~~   88 (104)
T d1p1ta_          84 NAASE   88 (104)
T ss_dssp             ETTCT
T ss_pred             ECCCC
Confidence            98764

>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=99.65  E-value=8.4e-17  Score=132.56  Aligned_cols=80  Identities=26%  Similarity=0.431  Sum_probs=68.2

Q ss_pred             ccEEEEcCCCCCCc-HHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          225 LRTIFVGNLPLKVK-KKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~t-ee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      .++|||+|||+++| +++|.++|+.||.|.+|+|....                ..++.++|||||+|.+.++|..||+|
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~----------------~~~~~~kg~afV~f~~~~~a~~Al~~   67 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQ----------------KEHSFNNCCAFMVFENKDSAERALQM   67 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCC----------------C---CCCEEEEEEESSHHHHHHHGGG
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeeccc----------------CCccccceeeeEEECCHHHHHHHHhc
Confidence            58999999999986 56699999999999999984321                12456889999999999999999999


Q ss_pred             cceeecCceeEeecCCC
Q 008920          304 NMAVIGGNHIRLDRACP  320 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~  320 (548)
                      |+..|.|+.|.|.++.+
T Consensus        68 n~~~~~gr~l~V~~a~~   84 (86)
T d2ghpa3          68 NRSLLGNREISVSLADK   84 (86)
T ss_dssp             TTEEETTEEEEEEECCC
T ss_pred             CCCEECCEEEEEEEcCC
Confidence            99999999999999864

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.65  E-value=1.6e-16  Score=133.04  Aligned_cols=82  Identities=22%  Similarity=0.393  Sum_probs=71.7

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||+++++++|..+|+.||.|.+|+|+.+..                .+|.++|||||+|.+.++|..|| .
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----------------GTGAHRGFGFVDFITKQDAKKAFNA   70 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCS----------------SSCSSCSEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccc----------------cCCCcccEEEEEECCHHHHHHHHHH
Confidence            357899999999999999999999999999999854331                24568899999999999999999 5


Q ss_pred             h-cceeecCceeEeecCCCc
Q 008920          303 F-NMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 l-ng~~~~gr~I~V~~a~~~  321 (548)
                      | |+..|.|+.|.|.|+...
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            6 899999999999999753

>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=99.65  E-value=3.2e-16  Score=130.89  Aligned_cols=81  Identities=20%  Similarity=0.366  Sum_probs=71.7

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+.+++++|.++|+.||+|.+|.|+.+.                   +.++|||||+|.+.++|..||
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~-------------------~~~kg~afV~f~~~~~a~~Ai   68 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE-------------------RGSKGFGFVTFENSADADRAR   68 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT-------------------TTTCCEEEEEESCHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc-------------------cCCcceeEEEECCHHHHHHHH
Confidence            3446789999999999999999999999999999995543                   125699999999999999999


Q ss_pred             -HhcceeecCceeEeecCCCc
Q 008920          302 -AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 -~lng~~~~gr~I~V~~a~~~  321 (548)
                       .||+..|.|+.|.|.++.+.
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             59999999999999999753

>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=99.65  E-value=2.6e-16  Score=132.86  Aligned_cols=82  Identities=16%  Similarity=0.199  Sum_probs=72.6

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||+++++++|.++|..||.|.+|+|+.++                 .++.++|||||+|.+.++|+.|| .
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~-----------------~tg~~~g~afV~f~~~~~a~~A~~~   69 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDS-----------------LTKKPKGFAFVTFMFPEHAVKAYAE   69 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCT-----------------TTCCCCSEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccc-----------------cccccCcceEEEECCHHHHHHHHHH
Confidence            35789999999999999999999999999999985543                 23457899999999999999999 5


Q ss_pred             hcceeecCceeEeecCCCcc
Q 008920          303 FNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~~  322 (548)
                      ||+..|.|+.|.|.++.+..
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            99999999999999997653

>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=99.65  E-value=2.4e-16  Score=127.36  Aligned_cols=77  Identities=16%  Similarity=0.383  Sum_probs=72.8

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEe
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSH  415 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~  415 (548)
                      .++|||+|||+++|+++|.++|+.|    |.|..+.++.++.++.++|||||+|.+.++|.+|+.+.+..|+|+.|.|.+
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~----G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V~~   77 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQY----GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK   77 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTT----SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEE
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHh----ccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4789999999999999999999999    899999999999999999999999999999999998656999999999987


Q ss_pred             e
Q 008920          416 A  416 (548)
Q Consensus       416 A  416 (548)
                      |
T Consensus        78 A   78 (79)
T d1l3ka2          78 A   78 (79)
T ss_dssp             C
T ss_pred             C
Confidence            6

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.65  E-value=2e-16  Score=129.84  Aligned_cols=78  Identities=21%  Similarity=0.310  Sum_probs=69.3

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||+++++++|.++|+.||.|..|+|+.++.                 +|.++|||||+|.+.++|..|| .
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~-----------------~g~~~g~afV~f~~~~~A~~Ai~~   67 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKL-----------------TGRPRGVAFVRYNKREEAQEAISA   67 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTT-----------------TCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccc-----------------cccCceeEEEEECCHHHHHHHHHH
Confidence            457899999999999999999999999999999976542                 3457899999999999999999 5


Q ss_pred             hcceeecC--ceeEeecC
Q 008920          303 FNMAVIGG--NHIRLDRA  318 (548)
Q Consensus       303 lng~~~~g--r~I~V~~a  318 (548)
                      ||+..+.|  ++|.|.+|
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

>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=99.65  E-value=3.5e-16  Score=130.11  Aligned_cols=80  Identities=16%  Similarity=0.240  Sum_probs=70.3

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      ..++|||+|||+++|+++|+++|+.||.|.+|.|+.++.                 +|.++|||||+|.+.++|..||+ 
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~-----------------tg~srG~aFV~f~~~~~a~~al~-   68 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLK-----------------TGHSKGFGFVRFTEYETQVKVMS-   68 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSS-----------------SCSEEEEEEEEESSHHHHHHHHH-
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCC-----------------CcccCCEEEEEECCHHHHHHHHh-
Confidence            347899999999999999999999999999999976542                 35688999999999999999997 


Q ss_pred             cceeecCceeEeecCCCc
Q 008920          304 NMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~  321 (548)
                      ++..|.|+.|.|.++.+.
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            345899999999998754

>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=99.65  E-value=2.6e-16  Score=133.76  Aligned_cols=80  Identities=19%  Similarity=0.350  Sum_probs=72.2

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      .++|||+|||+++++++|.++|+.||.|.+|.++.++.                 +|.++|||||+|.+.++|..|| .|
T Consensus        18 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~-----------------~g~~kG~afV~f~~~~~A~~Ai~~l   80 (102)
T d2cpza1          18 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQ-----------------TNLSKCFGFVSYDNPVSAQAAIQSM   80 (102)
T ss_dssp             TCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSS-----------------SCSEEEEEEEECSSHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecc-----------------cCCCccceEEEeCCHHHHHHHHHHh
Confidence            47899999999999999999999999999999866442                 3557899999999999999999 69


Q ss_pred             cceeecCceeEeecCCCc
Q 008920          304 NMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~  321 (548)
                      ||..|.|+.|.|.++.+.
T Consensus        81 ng~~~~g~~i~V~~a~~k   98 (102)
T d2cpza1          81 NGFQIGMKRLKVQLKRSK   98 (102)
T ss_dssp             TTCEETTEECEEECCCCS
T ss_pred             CCCEECCEEEEEEEeCCC
Confidence            999999999999999754

>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=99.64  E-value=8.3e-17  Score=137.09  Aligned_cols=81  Identities=22%  Similarity=0.391  Sum_probs=72.5

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||+++|+++|.++|+.||.|.+|+|+.++.                 +|.++|||||+|.+.++|..|| .
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~-----------------tg~~~g~afV~f~~~~~a~~ai~~   69 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRE-----------------TGKPKGYGFCEYQDQETALSAMRN   69 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETT-----------------TTEEEEEEEEECSCHHHHHHHHHH
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccc-----------------eeccCCceEEEECCHHHHHHHHHH
Confidence            457999999999999999999999999999999976542                 3457899999999999999999 5


Q ss_pred             hcceeecCceeEeecCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~  321 (548)
                      ||+..|.|+.|.|.++.+.
T Consensus        70 l~~~~~~g~~i~V~~a~~~   88 (104)
T d1p1ta_          70 LNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             SSSBSCSSSCBEEEETTCT
T ss_pred             cCCCEECCEEEEEEECCCC
Confidence            8999999999999998653

>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=99.64  E-value=2e-16  Score=130.15  Aligned_cols=76  Identities=12%  Similarity=0.163  Sum_probs=69.4

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhc
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~ln  304 (548)
                      .++|||+|||+++|+++|.++|+.||+|..|.|+.+.                  +|.++|||||+|.++++|+.||+++
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~------------------~~~~kG~afV~f~~~e~a~~al~~~   67 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL------------------HKAFKGSIFVVFDSIESAKKFVETP   67 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT------------------TCCEEEEEEEEESCHHHHHHHHTCC
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec------------------cCCcceEEEEEEcCHHHHHHHHHHC
Confidence            5799999999999999999999999999999986532                  3457899999999999999999999


Q ss_pred             ceeecCceeEeecC
Q 008920          305 MAVIGGNHIRLDRA  318 (548)
Q Consensus       305 g~~~~gr~I~V~~a  318 (548)
                      +..|.|+.|.|.+.
T Consensus        68 ~~~~~g~~l~v~~~   81 (85)
T d1zh5a2          68 GQKYKETDLLILFK   81 (85)
T ss_dssp             CCEETTEECEEEEG
T ss_pred             CCEECCEEEEEEEc
Confidence            99999999999875

>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=99.64  E-value=2.6e-16  Score=127.14  Aligned_cols=75  Identities=25%  Similarity=0.374  Sum_probs=71.5

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEee
Q 008920          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHA  416 (548)
Q Consensus       338 tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~A  416 (548)
                      .|||+|||+.+++++|+++|+.|    |.|..|.|+.+. +|.++|||||+|.+.++|..|+..+| ..|.|++|+|.+|
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~----G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a   76 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEF----GTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV   76 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHH----SCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHh----CCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            59999999999999999999999    899999999995 89999999999999999999998877 9999999999998


Q ss_pred             e
Q 008920          417 Q  417 (548)
Q Consensus       417 k  417 (548)
                      .
T Consensus        77 ~   77 (78)
T d1no8a_          77 T   77 (78)
T ss_dssp             C
T ss_pred             e
Confidence            5

>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=99.64  E-value=1.6e-16  Score=129.06  Aligned_cols=78  Identities=15%  Similarity=0.170  Sum_probs=66.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~ln  304 (548)
                      +||||+|||+++|+++|.++|+.||.|..+.++.+.                 ..|.++|||||+|.+.++|+.|+ .||
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~-----------------~~~~~~g~afV~f~~~e~A~~Ai~~l~   64 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSL-----------------RFNTSRRFAYIDVTSKEDARYCVEKLN   64 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC------------------------CCEEEEECSSHHHHHHHHHHHT
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeeccc-----------------ccccccceeEEEECCHHHHHHHHHHhC
Confidence            799999999999999999999999999887763322                 23557899999999999999999 599


Q ss_pred             ceeecCceeEeecCCC
Q 008920          305 MAVIGGNHIRLDRACP  320 (548)
Q Consensus       305 g~~~~gr~I~V~~a~~  320 (548)
                      |..|.|+.|.|.++.|
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            9999999999999864

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=1.5e-16  Score=130.79  Aligned_cols=79  Identities=18%  Similarity=0.323  Sum_probs=71.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-hc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-FN  304 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-ln  304 (548)
                      ..|||+|||+++|+++|.++|+.||+|.+|+|+.++.                 +|.++|||||+|.++++|..|+. ||
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~-----------------tg~~rg~aFV~f~~~~~A~~a~~~l~   64 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSA-----------------TGLSKGYAFCEYVDINVTDQAIAGLN   64 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCS-----------------SSCCCCEEEEEESSSHHHHHHHHTSS
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeecccc-----------------ccccceeEEEEECCHHHHHHHHHHhC
Confidence            4699999999999999999999999999999966542                 35678999999999999999995 99


Q ss_pred             ceeecCceeEeecCCCc
Q 008920          305 MAVIGGNHIRLDRACPP  321 (548)
Q Consensus       305 g~~~~gr~I~V~~a~~~  321 (548)
                      +..|.|+.|.|.++.+.
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            99999999999999753

>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=99.64  E-value=2.3e-16  Score=127.51  Aligned_cols=75  Identities=16%  Similarity=0.291  Sum_probs=67.9

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhcc
Q 008920          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (548)
Q Consensus       227 tVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng  305 (548)
                      .|||+|||+++++++|.++|+.||.|.+|+|+.+.                  +|.++|||||+|.+.++|+.|+ .|||
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------------------SGRSLGTADVHFERKADALKAMKQYNG   63 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS------------------CCCSCCEEEEEESCHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee------------------ccccceeEEEEECCHHHHHHHHHHhCC
Confidence            49999999999999999999999999999995432                  3457899999999999999999 5999


Q ss_pred             eeecCceeEeecCC
Q 008920          306 AVIGGNHIRLDRAC  319 (548)
Q Consensus       306 ~~~~gr~I~V~~a~  319 (548)
                      ..|.|+.|.|.++.
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

>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=99.64  E-value=4.6e-16  Score=132.41  Aligned_cols=82  Identities=21%  Similarity=0.322  Sum_probs=70.3

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+.+++++|.++|+.||.|.+|+|+.+.                 .+|.++|||||+|.+.++|+.||+
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-----------------QTGKSRGYGFVTMADRAAAERACK   70 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCS-----------------SSCCCCSEEEEEESSHHHHHHHHT
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccc-----------------cccccCCeEEEEECCHHHHHHHHH
Confidence            345789999999999999999999999999999996543                 235688999999999999999996


Q ss_pred             hcceeecCceeEeecCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~  321 (548)
                      ..+..|.|+.|.|.++...
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            4334799999999998654

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.64  E-value=3.6e-16  Score=139.83  Aligned_cols=82  Identities=23%  Similarity=0.357  Sum_probs=73.1

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...++|||+|||+++|+++|.++|+.||.|.+|.|+.++.                 +|.++|||||+|.+.++|..|| 
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 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRE-----------------TRQSRGYGFVKFQSGSSAQQAIA  102 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETT-----------------TTEEEEEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccc-----------------cccccceeeEEECCHHHHHHHHH
Confidence            3457999999999999999999999999999999976542                 3457899999999999999999 


Q ss_pred             HhcceeecCceeEeecCCCc
Q 008920          302 AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~  321 (548)
                      .||+..|.|+.|.|.++...
T Consensus       103 ~lng~~~~gr~l~V~~a~~~  122 (139)
T d1u6fa1         103 GLNGFNILNKRLKVALAASG  122 (139)
T ss_dssp             HTTTEECSSCEEEEEESSCC
T ss_pred             HhCCCEECCEEEEEEEcCCC
Confidence            59999999999999998754

>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=99.64  E-value=7.9e-16  Score=128.46  Aligned_cols=82  Identities=21%  Similarity=0.407  Sum_probs=74.4

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+.+++++|+++|+.|    |.|..|.|+.+..  .++|||||+|.+.++|..||..++ ..|.|+.|
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~----G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l   81 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQF----GKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKI   81 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGT----SCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhc----ceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            3346789999999999999999999999    8999999999853  478999999999999999998877 99999999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      .|.||.++.
T Consensus        82 ~V~~A~~r~   90 (93)
T d2cq3a1          82 EVNNATARV   90 (93)
T ss_dssp             EEEECCSSC
T ss_pred             EEEecCcCC
Confidence            999998753

>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=99.64  E-value=2.9e-16  Score=128.95  Aligned_cols=77  Identities=23%  Similarity=0.334  Sum_probs=68.2

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      .++|||+|||+.+|+++|+++|++||+|.+|+|+.++.                 +|.++|||||+|.+.++|..|+ .|
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 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQV-----------------TGVSRGVGFIRFDKRIEAEEAIKGL   68 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----------------TCCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccc-----------------cccCCCeeEEEEcCHHHHHHHHHHh
Confidence            46899999999999999999999999999999976542                 3457899999999999999999 59


Q ss_pred             cceeecCc--eeEeecC
Q 008920          304 NMAVIGGN--HIRLDRA  318 (548)
Q Consensus       304 ng~~~~gr--~I~V~~a  318 (548)
                      ||..+.|+  +|.|.||
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            99999984  6888875

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=3.3e-16  Score=128.33  Aligned_cols=79  Identities=19%  Similarity=0.278  Sum_probs=69.2

Q ss_pred             EEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhcce
Q 008920          228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMA  306 (548)
Q Consensus       228 VfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng~  306 (548)
                      |||+|||+++|+++|.++|+.||.|.+|.|+.++.+..              .+.++|||||+|.+.++|..|| .||+.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~--------------~~~~kG~afV~f~~~~~A~~A~~~~~~~   66 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAG--------------VLLSMGFGFVEYKKPEQAQKALKQLQGH   66 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTC--------------CEEEEEEEEEEESSHHHHHHHHHHSTTC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceeccccccc--------------ccccceEEEEEECCHHHHHHHHHHhCCC
Confidence            79999999999999999999999999999977653211              1236799999999999999999 69999


Q ss_pred             eecCceeEeecCCC
Q 008920          307 VIGGNHIRLDRACP  320 (548)
Q Consensus       307 ~~~gr~I~V~~a~~  320 (548)
                      .|.|+.|.|.++..
T Consensus        67 ~~~g~~i~V~~a~~   80 (85)
T d2cpfa1          67 TVDGHKLEVRISER   80 (85)
T ss_dssp             EETTEECEEECSSC
T ss_pred             EECCEEEEEEECCC
Confidence            99999999999854

>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=99.64  E-value=4.9e-16  Score=130.31  Aligned_cols=83  Identities=34%  Similarity=0.515  Sum_probs=76.0

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-------Cc
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-------LK  405 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-------~~  405 (548)
                      ....++|||+|||+.+++++|+++|..|    |.|..+.++.+..++.++|||||+|.+.++|..||..++       ..
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~----G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~   80 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQF----GDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLK   80 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTT----SCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEE
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhcc----ccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcE
Confidence            3456799999999999999999999999    899999999999999999999999999999999998764       46


Q ss_pred             cCCeEEEEEeeecC
Q 008920          406 LRDRELRLSHAQQN  419 (548)
Q Consensus       406 l~Gr~I~V~~Ak~~  419 (548)
                      |.|+.|+|.||.++
T Consensus        81 ~~gr~l~v~~a~~k   94 (98)
T d1x4ha1          81 LDGRQLKVDLAVTR   94 (98)
T ss_dssp             SSSCEEEEECCCCC
T ss_pred             ECCEEEEEEECCCC
Confidence            88999999999875

>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=99.63  E-value=3.3e-16  Score=129.68  Aligned_cols=77  Identities=22%  Similarity=0.383  Sum_probs=69.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~ln  304 (548)
                      .+|||+|||+++|+++|.++|+.||.|.+|.|+.+.                   +.++|||||+|.+.++|+.|| .||
T Consensus         9 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~-------------------~~~kg~afV~f~~~~~A~~Ai~~l~   69 (89)
T d1cvja2           9 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-------------------NGSKGYGFVHFETQEAAERAIEKMN   69 (89)
T ss_dssp             TEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT-------------------TBCCSCEEEEESCHHHHHHHTTSSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec-------------------CCCcceeEEEECCHHHHHHHHHHcC
Confidence            589999999999999999999999999999995432                   226799999999999999999 599


Q ss_pred             ceeecCceeEeecCCCc
Q 008920          305 MAVIGGNHIRLDRACPP  321 (548)
Q Consensus       305 g~~~~gr~I~V~~a~~~  321 (548)
                      |..|.|+.|.|.++.+.
T Consensus        70 g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2          70 GMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             EEEETTEEEEEEECCCT
T ss_pred             CCEECCEEEEEEECCCC
Confidence            99999999999999754

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.63  E-value=3.3e-16  Score=125.82  Aligned_cols=74  Identities=26%  Similarity=0.290  Sum_probs=66.9

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhcc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNM  305 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~lng  305 (548)
                      +||||+|||+++++++|+++|+.||.|..|+|+.++.                   ..+|||||+|.++++|++||.+|+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~-------------------~~~~~afV~F~~~~~a~~Al~~~~   61 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK-------------------KNFRFARIEFARYDGALAAITKTH   61 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT-------------------SSSEEEEEEESSHHHHHHHHTTTT
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc-------------------ccceEEEEEEcchHHhHHHHHhcC
Confidence            5899999999999999999999999999999965431                   245799999999999999999999


Q ss_pred             eeecCceeEeecC
Q 008920          306 AVIGGNHIRLDRA  318 (548)
Q Consensus       306 ~~~~gr~I~V~~a  318 (548)
                      ..|+|+.|.|..+
T Consensus        62 ~~i~g~~i~V~~~   74 (75)
T d2ghpa2          62 KVVGQNEIIVSHL   74 (75)
T ss_dssp             CEETTEECEEEEC
T ss_pred             cEECCEEEEEEEC
Confidence            9999999999865

>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=99.63  E-value=4.2e-16  Score=134.68  Aligned_cols=100  Identities=18%  Similarity=0.253  Sum_probs=80.8

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      .+++|||+|||+++|+++|.++|+.||.|.+|+|..                    ++.++|||||+|.+.++|..|| .
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~--------------------~~~~kG~afV~f~~~~~A~~Ai~~   65 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--------------------TPETRGTAYVVYEDIFDAKNACDH   65 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC--------------------STTTTTEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc--------------------cCCcCCeEEEEECCHHHHHHHHHH
Confidence            468999999999999999999999999999999843                    2236799999999999999999 6


Q ss_pred             hcceeecCceeEeecCCCcccccCCCCCCcCCCccEEEEeCCCCCCCHHHHHHHHhcc
Q 008920          303 FNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGL  360 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~~k~~~~~~~~~~~~~~tLfV~NLp~~~teedL~~~F~~~  360 (548)
                      |||..|.|+.|.|.++......                 ..+.....++.+..++..|
T Consensus        66 l~g~~~~gr~l~V~~a~~~~~~-----------------~~~~~~~~~~~~~~~~~~~  106 (114)
T d2f9da1          66 LSGFNVCNRYLVVLYYNANRAF-----------------QKMDTKKKEEQLKLLKEKY  106 (114)
T ss_dssp             HTTCEETTEECEEEECCHHHHT-----------------TTSCHHHHHHHHHHHHHHH
T ss_pred             hCCCEECCEEEEEEEcCCCchh-----------------hhhHHHHHHHHHHHHHHHh
Confidence            9999999999999998642111                 0112223467778888777

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=2.2e-16  Score=130.75  Aligned_cols=81  Identities=23%  Similarity=0.424  Sum_probs=71.4

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      +.++|||+|||+++|+++|.++|+.||.|..|.++.+.                 .++.++|||||+|.++++|+.|| .
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~-----------------~~~~~~g~afV~f~~~~~a~~Ai~~   66 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDR-----------------ETQRSRGFGFVTFENIDDAKDAMMA   66 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCS-----------------SSCSCCSEEEEECSSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeecccc-----------------ccccccceEEEEECCHHHHHHHHHH
Confidence            35789999999999999999999999999999885433                 23457899999999999999999 6


Q ss_pred             hcceeecCceeEeecCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~  321 (548)
                      ||+..|.|+.|.|.++.+.
T Consensus        67 l~~~~~~g~~l~V~~a~~~   85 (90)
T d1x5sa1          67 MNGKSVDGRQIRVDQAGKS   85 (90)
T ss_dssp             HTTCCTTSCCCEEEEEECC
T ss_pred             cCCCEECCEEEEEEEcCCC
Confidence            9999999999999998653

>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=99.63  E-value=1.1e-16  Score=133.45  Aligned_cols=80  Identities=20%  Similarity=0.279  Sum_probs=71.0

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+++|+++|+++|+.||.|.+|.|+..                  .+|.++|||||+|.+.++|+.||+
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~------------------~~g~~kg~afv~F~~~e~a~~Al~   72 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV------------------RTGTNRKFGYVDFESAEDLEKALE   72 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE------------------EEETTTTEEEEEESSHHHHHHHHH
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec------------------CCCCccEEeEEeeCCHHHHHHHHh
Confidence            34579999999999999999999999999988877432                  245688999999999999999999


Q ss_pred             hcceeecCceeEeecCCC
Q 008920          303 FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~  320 (548)
                      ||+..|.|+.|.|.++..
T Consensus        73 ~~g~~~~g~~i~V~~ak~   90 (91)
T d1fjeb1          73 LTGLKVFGNEIKLEKPKG   90 (91)
T ss_dssp             GGGEEETTEEEEEECCCC
T ss_pred             cCCcEECCEEEEEEecCC
Confidence            999999999999999853

>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=99.63  E-value=2.7e-16  Score=129.47  Aligned_cols=81  Identities=17%  Similarity=0.353  Sum_probs=69.4

Q ss_pred             CccEEEEeCCCCCCC-HHHHHHHHhccCCCCCCeEEEEEeec-CCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEE
Q 008920          335 IKKTVFVGNLPFDVK-DEEIYQLFCGLNDLESSVEAVRVIRH-PHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELR  412 (548)
Q Consensus       335 ~~~tLfV~NLp~~~t-eedL~~~F~~~g~~~G~I~~VrI~~d-~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~  412 (548)
                      ..++|||+|||++++ +++|+++|+.|    |.|..|+|+.+ ..++.++|||||+|.+.++|..||++.+..|+|+.|+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~----G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~   78 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGF----GSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREIS   78 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGG----SCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhh----hhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEE
Confidence            368999999999986 55699999999    99999998774 4689999999999999999999997444999999999


Q ss_pred             EEeeecC
Q 008920          413 LSHAQQN  419 (548)
Q Consensus       413 V~~Ak~~  419 (548)
                      |.||.++
T Consensus        79 V~~a~~k   85 (86)
T d2ghpa3          79 VSLADKK   85 (86)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCC
Confidence            9999864

>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=99.63  E-value=2e-16  Score=127.25  Aligned_cols=75  Identities=23%  Similarity=0.364  Sum_probs=67.0

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhcce
Q 008920          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMA  306 (548)
Q Consensus       227 tVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~lng~  306 (548)
                      .|||+|||+++|+++|+++|++||.|..|.|+.++.                 ++.++|||||+|.+.++|++||++++.
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~-----------------t~~~rG~~FV~f~~~~~a~~al~~~~~   63 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNK-----------------TNKRRGFCFITFKEEEPVKKIMEKKYH   63 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTT-----------------TCCTTCCEEEEESSSHHHHHHTTCSSC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCccccccccccc-----------------ccccccEEEEEECCHHHHHHHHhhCCC
Confidence            499999999999999999999999999999965442                 345789999999999999999988888


Q ss_pred             eecCceeEeecC
Q 008920          307 VIGGNHIRLDRA  318 (548)
Q Consensus       307 ~~~gr~I~V~~a  318 (548)
                      .|.|+.|.|..|
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

>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=99.62  E-value=2.8e-16  Score=125.44  Aligned_cols=75  Identities=21%  Similarity=0.373  Sum_probs=67.0

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhcce
Q 008920          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMA  306 (548)
Q Consensus       227 tVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~lng~  306 (548)
                      .|||+|||+++|+++|.++|+.||.|..+.++.++.                 ++.++|||||+|.+.++|+.||++|+.
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~-----------------~~~~~~~afV~F~~~~~a~~al~~~~~   63 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKT-----------------TNRHRGFGFVTFESEDIVEKVCEIHFH   63 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTT-----------------CTTSCCEEEEECSCHHHHHHHHHCSSC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecc-----------------ccccCceeEEEECCHHHHHHHHhcCCC
Confidence            389999999999999999999999999988755331                 345779999999999999999999999


Q ss_pred             eecCceeEeecC
Q 008920          307 VIGGNHIRLDRA  318 (548)
Q Consensus       307 ~~~gr~I~V~~a  318 (548)
                      .|.|+.|.|.+|
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

>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=99.62  E-value=5.7e-16  Score=128.25  Aligned_cols=78  Identities=24%  Similarity=0.472  Sum_probs=72.2

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLS  414 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~  414 (548)
                      ..+|||+|||+++++++|+++|+.|    |.|..|.|+.+.  +.++|||||+|.+.++|..||+.|+ ..|+|+.|.|.
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~----G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~   81 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAF----GNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVG   81 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTT----SCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhc----CCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            4579999999999999999999999    899999999985  3478999999999999999999887 99999999999


Q ss_pred             eeecC
Q 008920          415 HAQQN  419 (548)
Q Consensus       415 ~Ak~~  419 (548)
                      ||.+.
T Consensus        82 ~a~~~   86 (89)
T d1cvja2          82 RFKSR   86 (89)
T ss_dssp             ECCCT
T ss_pred             ECCCC
Confidence            99864

>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=99.62  E-value=1.1e-15  Score=129.99  Aligned_cols=82  Identities=29%  Similarity=0.410  Sum_probs=70.2

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      ..++|||+|||+++|+++|+++|+.|| |..++++.+.                ..++.++|||||+|.+.++|++|+.|
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~----------------~~~g~~~g~afV~f~~~e~a~~~~~~   76 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREP----------------SNPERLKGFGYAEFEDLDSLLSALSL   76 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCS----------------SCTTSBCSCEEEEESSHHHHHHHHGG
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeee----------------ccCCCcceeeeEEECCHHHHHHHHHc
Confidence            358999999999999999999999999 6677764332                12456789999999999999988899


Q ss_pred             cceeecCceeEeecCCCcc
Q 008920          304 NMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~  322 (548)
                      |+..|.|+.|.|.++.+..
T Consensus        77 ~~~~~~gr~l~V~~a~~~~   95 (104)
T d1wi8a_          77 NEESLGNKRIRVDVADQAQ   95 (104)
T ss_dssp             GTCEETTEECEEEECCCCC
T ss_pred             CCCEECCEEEEEEECCCCC
Confidence            9999999999999987643

>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=99.61  E-value=3.1e-16  Score=125.17  Aligned_cols=75  Identities=16%  Similarity=0.340  Sum_probs=70.7

Q ss_pred             EEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEee
Q 008920          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHA  416 (548)
Q Consensus       338 tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~A  416 (548)
                      .|||+|||+++|+++|+++|+.|    |.|..+.++.+..++.++|||||+|.+.++|..||++.+..|+|+.|+|.+|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~----G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQF----GKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTT----SCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHh----CCcceeeeeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEEC
Confidence            49999999999999999999999    8999999999999999999999999999999999984449999999999986

>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=99.61  E-value=4.9e-16  Score=131.14  Aligned_cols=92  Identities=16%  Similarity=0.189  Sum_probs=72.7

Q ss_pred             CCCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       221 ~~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      ++...++|||+|||+.+|+++|.+||..||.|..+.+.....         ..+.....+|.++|||||+|.+.++|..|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~---------~~~~~d~~~~~~~g~afV~f~~~~~a~~A   74 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPM---------IHIYLDKETGKPKGDATVSYEDPPTAKAA   74 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBS---------EECCBCTTTCSBCSEEEEEBSSHHHHHHH
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccce---------eEEeeccccccccceeeEEecCHHHHHHH
Confidence            334568999999999999999999999999986554422110         01112234567889999999999999999


Q ss_pred             H-HhcceeecCceeEeecCCCc
Q 008920          301 L-AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       301 l-~lng~~~~gr~I~V~~a~~~  321 (548)
                      | .|||..|.|+.|.|.++.+.
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 59999999999999999753

>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=99.61  E-value=5.1e-16  Score=126.63  Aligned_cols=77  Identities=30%  Similarity=0.420  Sum_probs=67.2

Q ss_pred             EEEcCCCCCCcHHHHHHHhhhcCCeeEE-EEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhcc
Q 008920          228 IFVGNLPLKVKKKTLIKEFIKFGEIDSV-RIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (548)
Q Consensus       228 VfVgNLP~~~tee~L~~~Fs~fG~I~sV-ri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng  305 (548)
                      |||+|||+++|+++|.++|++||.|..+ .|+.+.                 .+|.++|||||+|.+.++|..|| .||+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~-----------------~~g~~~g~afV~f~~~~~a~~Ai~~~~g   63 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDP-----------------DTGNSKGYAFINFASFDASDAAIEAMNG   63 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCT-----------------TTCSCCSEEEEEBSSHHHHHHHHHTTTT
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeec-----------------cccccCceEEEEECCHHHHHHHHHhCCC
Confidence            8999999999999999999999998664 554322                 24568899999999999999999 5999


Q ss_pred             eeecCceeEeecCCCc
Q 008920          306 AVIGGNHIRLDRACPP  321 (548)
Q Consensus       306 ~~~~gr~I~V~~a~~~  321 (548)
                      ..|.|+.|.|.++.+.
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            9999999999998754

>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=99.61  E-value=2e-15  Score=123.97  Aligned_cols=75  Identities=24%  Similarity=0.354  Sum_probs=67.8

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      .++|||+|||+++|+++|.++|+.||.|..+.+.                       .++|||||+|.+.++|..|| .|
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~-----------------------~~rg~afV~f~~~~~A~~Ai~~l   64 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK-----------------------KIRDYAFVHFSNREDAVEAMKAL   64 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE-----------------------ECSSEEEEEESSHHHHHHHHHHH
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc-----------------------cccEEEEEEeCCHHHHHHHHHHc
Confidence            4799999999999999999999999999887762                       15689999999999999999 59


Q ss_pred             cceeecCceeEeecCCCcc
Q 008920          304 NMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~  322 (548)
                      |+..|.|+.|.|.++.|+.
T Consensus        65 ~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1          65 NGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             SSEEETTEEEEEECCCCCC
T ss_pred             CCCEECCEEEEEEeccCCC
Confidence            9999999999999997653

>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=99.60  E-value=7.3e-16  Score=130.65  Aligned_cols=79  Identities=22%  Similarity=0.276  Sum_probs=69.7

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      +.++|||+|||+++++++|.++|+.||.|..+.+..+.                  .+.++|||||+|.+.++|..|| .
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~------------------~~~~~g~afV~f~~~~~A~~Ai~~   78 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS------------------SGTSRGVGFARMESTEKCEAVIGH   78 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS------------------SSCEEEEEEEEESCHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc------------------ccccccceeEEeCCHHHHHHHHHH
Confidence            35799999999999999999999999999999885432                  3347799999999999999999 5


Q ss_pred             hcceeecCceeEeecCCC
Q 008920          303 FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~  320 (548)
                      |||..|.|+++.|.++.|
T Consensus        79 lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          79 FNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             HBTCCCCCCTTSCCCSSC
T ss_pred             hCCCEECCcCCccCCCCC
Confidence            999999999999987753

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.60  E-value=6.9e-16  Score=129.51  Aligned_cols=78  Identities=28%  Similarity=0.294  Sum_probs=68.7

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ....++|||+|||+++|+++|+++|+.||.|..+..                      ++.++|||||+|.+.++|..||
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~----------------------~~~~~~~afV~f~~~~~A~~A~   70 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----------------------DGKSKGIAYIEFKSEADAEKNL   70 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE----------------------TTEEEEEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee----------------------cCccccEEEEEeCCHHHHHHHH
Confidence            345689999999999999999999999998866643                      2347799999999999999999


Q ss_pred             -HhcceeecCceeEeecCCCc
Q 008920          302 -AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 -~lng~~~~gr~I~V~~a~~~  321 (548)
                       .||+..|.|+.|.|.++.+.
T Consensus        71 ~~l~~~~~~gr~i~V~~a~~k   91 (96)
T d1fjca_          71 EEKQGAEIDGRSVSLYYTGEK   91 (96)
T ss_dssp             HHTTEEEETTEEEEEEECSSS
T ss_pred             HHcCCCEECCEEEEEEEeCCC
Confidence             59999999999999999754

>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=99.60  E-value=1.2e-15  Score=125.42  Aligned_cols=78  Identities=18%  Similarity=0.343  Sum_probs=72.3

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEe
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSH  415 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~  415 (548)
                      .++|||+|||+++|+++|.++|+.|    |.|..|.|+.+ .+|.++|||||+|.+.++|..||++.+..+.|+.|.|.|
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~----G~v~~v~l~~~-~~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~   80 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDK----GQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILF   80 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTS----CCEEEEEEEEC-TTCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEE
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHh----cccccceeeee-ccCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEE
Confidence            5789999999999999999999999    89999999888 489999999999999999999998766999999999998


Q ss_pred             eec
Q 008920          416 AQQ  418 (548)
Q Consensus       416 Ak~  418 (548)
                      ...
T Consensus        81 ~~d   83 (85)
T d1zh5a2          81 KDD   83 (85)
T ss_dssp             GGG
T ss_pred             cCC
Confidence            653

>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=99.60  E-value=1.6e-15  Score=128.82  Aligned_cols=82  Identities=32%  Similarity=0.519  Sum_probs=72.5

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecC-CCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP-HMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELR  412 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~-~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~  412 (548)
                      .+.++|||+|||+++++++|+++|+.|    | |..+.++.+. .++.++|||||+|.+.++|++|+.+.+..|.|+.|+
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~----g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~   87 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGL----N-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIR   87 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTS----C-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHh----c-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEE
Confidence            456899999999999999999999999    7 7788887765 478899999999999999998887555999999999


Q ss_pred             EEeeecCC
Q 008920          413 LSHAQQNC  420 (548)
Q Consensus       413 V~~Ak~~~  420 (548)
                      |.||.+..
T Consensus        88 V~~a~~~~   95 (104)
T d1wi8a_          88 VDVADQAQ   95 (104)
T ss_dssp             EEECCCCC
T ss_pred             EEECCCCC
Confidence            99998753

>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=99.60  E-value=1.6e-15  Score=127.05  Aligned_cols=81  Identities=21%  Similarity=0.385  Sum_probs=69.6

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH-
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~-  302 (548)
                      +.++|||+|||+++|+++|+++|+.||.|.++.++.+.                 ..+.++|||||+|.+.++|..||. 
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~-----------------~~~~~~g~afV~F~~~~~a~~ai~~   69 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHP-----------------DTEHSKGCAFAQFMTQEAAQKCLAA   69 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCS-----------------SSCCBCSEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeecccc-----------------ccccccceEEEEEcCHHHHHHHHHH
Confidence            45799999999999999999999999999999885433                 134578999999999999999994 


Q ss_pred             hc------ceeecCceeEeecCCCc
Q 008920          303 FN------MAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 ln------g~~~~gr~I~V~~a~~~  321 (548)
                      ||      |..|.|+.|.|.++.+.
T Consensus        70 l~~~~~~~g~~~~gr~l~v~~a~~k   94 (98)
T d1x4ha1          70 ASLEAEGGGLKLDGRQLKVDLAVTR   94 (98)
T ss_dssp             HCTTTTTCCEESSSCEEEEECCCCC
T ss_pred             cccccccCCcEECCEEEEEEECCCC
Confidence            54      77899999999998753

>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=99.60  E-value=1.5e-15  Score=131.19  Aligned_cols=78  Identities=22%  Similarity=0.436  Sum_probs=71.5

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      .+++|||+|||+.+++++|+++|+.|    |.|..|+|..+   +.++|||||+|.+.++|..||+.|+ ..|.|+.|.|
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~----G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   78 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKY----GPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVV   78 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTT----SCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhc----CCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            46899999999999999999999999    99999999865   5678999999999999999998877 9999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      .|+.+.
T Consensus        79 ~~a~~~   84 (114)
T d2f9da1          79 LYYNAN   84 (114)
T ss_dssp             EECCHH
T ss_pred             EEcCCC
Confidence            998653

>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=99.60  E-value=2.4e-16  Score=133.44  Aligned_cols=83  Identities=18%  Similarity=0.260  Sum_probs=77.4

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      .+++++|||+|||.++++++|+++|+.|    |.|..+.++.+..+|.++|||||+|.+.++|..||..++ ..|.|+.|
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~----G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l   90 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARF----QEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKIL   90 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHH----HHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhc----cceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEE
Confidence            3467899999999999999999999999    899999999888899999999999999999999999887 99999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      +|.||+++
T Consensus        91 ~V~~ak~k   98 (102)
T d2cpxa1          91 VIEFGKNK   98 (102)
T ss_dssp             EEEECCCC
T ss_pred             EEEeCCCc
Confidence            99999875

>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=99.59  E-value=1.3e-15  Score=128.44  Aligned_cols=82  Identities=16%  Similarity=0.223  Sum_probs=74.3

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCe--------EEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-C
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSV--------EAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-L  404 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I--------~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~  404 (548)
                      ....+|||+|||+.+++++|+++|..|    |.|        ..+.+..+..+|.++|||||+|.+.++|..||..++ .
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~----G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~   81 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQC----GVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   81 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTT----SCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHC----ceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCC
Confidence            346899999999999999999999999    666        356778888899999999999999999999999877 9


Q ss_pred             ccCCeEEEEEeeecC
Q 008920          405 KLRDRELRLSHAQQN  419 (548)
Q Consensus       405 ~l~Gr~I~V~~Ak~~  419 (548)
                      .|.|+.|+|.||+++
T Consensus        82 ~~~gr~i~V~~a~~~   96 (101)
T d2cpea1          82 DFQGSKLKVSLARKK   96 (101)
T ss_dssp             EETTEECEEECSSCC
T ss_pred             EECCEEEEEEEcCCC
Confidence            999999999999864

>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=99.59  E-value=6.5e-16  Score=132.49  Aligned_cols=75  Identities=17%  Similarity=0.247  Sum_probs=67.8

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      +..++|||+|||+++++++|.++|+.||.|..|.|.                       .++|||||+|.+.++|+.|| 
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~-----------------------~~kg~afV~f~~~~~A~~A~~   64 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-----------------------EGGITAIVEFLEPLEARKAFR   64 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-----------------------SSSSCEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee-----------------------ccCceEEEEEcCHHHHHHHHH
Confidence            345899999999999999999999999999998872                       15689999999999999999 


Q ss_pred             HhcceeecCceeEeecCCC
Q 008920          302 AFNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~  320 (548)
                      .|||..|.|+.|.|.|+..
T Consensus        65 ~lng~~~~gr~l~v~~a~~   83 (111)
T d1whxa_          65 HLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             HHTTCBSSSSBCEEEEEET
T ss_pred             HHcCCccCCCeEEEEECCC
Confidence            6999999999999999753

>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=99.59  E-value=1.3e-15  Score=127.72  Aligned_cols=82  Identities=21%  Similarity=0.337  Sum_probs=73.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCC-eEEEEEeecC-CCCCCceEEEEEECCHHHHHHHHHHcC---CccCCeEE
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESS-VEAVRVIRHP-HMRVGKGIAYVLFKTREAANLVIKRRN---LKLRDREL  411 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~-I~~VrI~~d~-~tg~srG~AFV~F~~~e~A~~Al~~ln---~~l~Gr~I  411 (548)
                      +.|||+|||.++++++|+++|+.|    |. |..|.|+.+. .+|.++|||||+|.++++|..|++.|+   ..++|+.|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~----g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i   77 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKV----TEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   77 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHH----STTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHh----CCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEE
Confidence            579999999999999999999999    74 9999999886 468999999999999999999998874   66789999


Q ss_pred             EEEeeecCCCC
Q 008920          412 RLSHAQQNCTP  422 (548)
Q Consensus       412 ~V~~Ak~~~~~  422 (548)
                      .|.||.|...+
T Consensus        78 ~V~~A~p~~~~   88 (96)
T d2disa1          78 AVDWAEPEIDV   88 (96)
T ss_dssp             EEEESCSSCST
T ss_pred             EEEEcCCCCCC
Confidence            99999876444

>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=99.59  E-value=2.1e-15  Score=126.73  Aligned_cols=73  Identities=18%  Similarity=0.352  Sum_probs=67.7

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      .++|||+|||..+++++|.++|+.||.|.+|+|..                       .+|||||+|.+.++|..|+ .|
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~-----------------------~kg~afV~f~~~~~A~~Ai~~l   74 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP-----------------------EKGYSFVRFSTHESAAHAIVSV   74 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEET-----------------------TTTEEEEEESSHHHHHHHHHHH
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEe-----------------------cceEEEEEECCHHHHHHHHHHh
Confidence            47999999999999999999999999999999842                       4589999999999999999 69


Q ss_pred             cceeecCceeEeecCCC
Q 008920          304 NMAVIGGNHIRLDRACP  320 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~  320 (548)
                      |+..|.|+.|+|.|+.+
T Consensus        75 ~~~~i~g~~l~v~~ak~   91 (96)
T d1x4ga1          75 NGTTIEGHVVKCYWGKE   91 (96)
T ss_dssp             TTCEETTEECEEECCCC
T ss_pred             CCCEECCEEEEEEEcCC
Confidence            99999999999999864

>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=99.58  E-value=3.1e-15  Score=125.19  Aligned_cols=77  Identities=22%  Similarity=0.416  Sum_probs=68.6

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||+++|+++|.++|+.||.|..|.+..                    ++.++|||||+|.+.++|..|| .
T Consensus        13 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~--------------------~~~~~g~afV~f~~~e~a~~Ai~~   72 (95)
T d1x4aa1          13 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN--------------------RRGGPPFAFVEFEDPRDAEDAVYG   72 (95)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC--------------------SSSSSCCEEEEESCHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecc--------------------cccccceEEEEECCHHHHHHHHHH
Confidence            457899999999999999999999999999888732                    1236699999999999999999 5


Q ss_pred             hcceeecCceeEeecCCC
Q 008920          303 FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~  320 (548)
                      ||+..|.|+.|.|.++.+
T Consensus        73 l~g~~~~g~~l~V~~a~~   90 (95)
T d1x4aa1          73 RDGYDYDGYRLRVEFPRS   90 (95)
T ss_dssp             HTTCEETTEECEEECCCC
T ss_pred             hCCCEECCEEEEEEeccC
Confidence            999999999999999864

>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=99.58  E-value=3.7e-15  Score=124.74  Aligned_cols=82  Identities=22%  Similarity=0.414  Sum_probs=72.5

Q ss_pred             CcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCe
Q 008920          331 PLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDR  409 (548)
Q Consensus       331 ~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr  409 (548)
                      +...+.++|||+|||+.+++++|+++|..|    |.|..|.+..+   +.++|||||+|.+.++|..||..|+ ..|.|+
T Consensus         9 p~~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~   81 (95)
T d1x4aa1           9 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKY----GAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGY   81 (95)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHhcC----CceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            334566789999999999999999999999    89999887655   4568999999999999999998877 999999


Q ss_pred             EEEEEeeecC
Q 008920          410 ELRLSHAQQN  419 (548)
Q Consensus       410 ~I~V~~Ak~~  419 (548)
                      .|.|.||++.
T Consensus        82 ~l~V~~a~~~   91 (95)
T d1x4aa1          82 RLRVEFPRSG   91 (95)
T ss_dssp             ECEEECCCCC
T ss_pred             EEEEEeccCC
Confidence            9999998753

>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=99.58  E-value=5e-15  Score=125.98  Aligned_cols=85  Identities=25%  Similarity=0.346  Sum_probs=75.6

Q ss_pred             CcCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeE
Q 008920          331 PLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRE  410 (548)
Q Consensus       331 ~~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~  410 (548)
                      +......+|||+|||+++|+++|+++|..|    |.|..+.++.+..++.++|||||+|.+.++|.+||++.+..|+||.
T Consensus        10 ~~~~~~~~v~v~nLP~~~te~dI~~~F~~~----g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~   85 (104)
T d1wg5a_          10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGL----EIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRY   85 (104)
T ss_dssp             SSCSCCCEEEEESCCTTCCHHHHHHHTTTC----CEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhc----CCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceE
Confidence            344556789999999999999999999999    8888877777778899999999999999999999985559999999


Q ss_pred             EEEEeeecC
Q 008920          411 LRLSHAQQN  419 (548)
Q Consensus       411 I~V~~Ak~~  419 (548)
                      |.|.++.+.
T Consensus        86 i~V~~~~~~   94 (104)
T d1wg5a_          86 IEIFKSSRA   94 (104)
T ss_dssp             CEEEEECTT
T ss_pred             EEEEECCHH
Confidence            999999865

>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=99.58  E-value=1.6e-15  Score=128.70  Aligned_cols=81  Identities=16%  Similarity=0.205  Sum_probs=69.7

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      .....+|||+|||+++|+++|++||..||.| .|.++.+.                  ++..+|||||+|.+.++|+.||
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~~-~v~~~~~~------------------~g~~~G~afVeF~~~~~a~~Al   72 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP------------------DGRVTGEADVEFATHEDAVAAM   72 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS------------------SSCEEEEEEEECSSSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCcc-eeeeEEec------------------CCcceEEEEEEECCHHHHHHHH
Confidence            3445799999999999999999999999854 67664432                  3457899999999999999999


Q ss_pred             HhcceeecCceeEeecCCCc
Q 008920          302 AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~~  321 (548)
                      ++|+..|.||.|.|.++...
T Consensus        73 ~~~~~~i~gR~I~V~~s~~~   92 (102)
T d1weza_          73 AKDKANMQHRYVELFLNSTA   92 (102)
T ss_dssp             TTSSCCSSSSCCEEEEECCC
T ss_pred             HcCCCEECCEEEEEEEcCCC
Confidence            99999999999999998754

>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=99.58  E-value=1.9e-15  Score=124.87  Aligned_cols=76  Identities=20%  Similarity=0.323  Sum_probs=67.4

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      ..++|||+|||+++|+++|+++|++||.|..|+++.                      .++|||||+|.+.++|+.||. 
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            468999999999999999999999999999987621                      256899999999999999986 


Q ss_pred             cceeecCceeEeecCCCcc
Q 008920          304 NMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~  322 (548)
                      ++..|.|+.|.|.++.++.
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            7889999999999997653

>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=99.57  E-value=2.2e-15  Score=127.19  Aligned_cols=75  Identities=27%  Similarity=0.466  Sum_probs=67.2

Q ss_pred             CCcccEEEEcCCC-CCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          222 GKLLRTIFVGNLP-LKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       222 ~~~~rtVfVgNLP-~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      ....++|||+||| ..+++++|+.+|++||.|..|.|                         ++|||||+|.+.++|..|
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            3445789999996 57889999999999999999998                         458999999999999999


Q ss_pred             H-HhcceeecCceeEeecCCCc
Q 008920          301 L-AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       301 l-~lng~~~~gr~I~V~~a~~~  321 (548)
                      | .|||..|.|+.|.|.++.++
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 59999999999999999754

>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=99.57  E-value=3.8e-16  Score=130.10  Aligned_cols=80  Identities=19%  Similarity=0.279  Sum_probs=72.7

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRL  413 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V  413 (548)
                      ....+|||+|||+++++++|+++|+.|    |.|..|.|+.+ .+|.++|||||+|.+.++|..||++.+..|.|+.|+|
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~----G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V   85 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISEL----FAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKL   85 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHH----HHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEE
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcC----CcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEE
Confidence            356799999999999999999999999    89999988765 6899999999999999999999985449999999999


Q ss_pred             Eeeec
Q 008920          414 SHAQQ  418 (548)
Q Consensus       414 ~~Ak~  418 (548)
                      .+|+.
T Consensus        86 ~~ak~   90 (91)
T d1fjeb1          86 EKPKG   90 (91)
T ss_dssp             ECCCC
T ss_pred             EecCC
Confidence            99975

>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=99.57  E-value=2.6e-15  Score=123.55  Aligned_cols=74  Identities=27%  Similarity=0.481  Sum_probs=67.9

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      .++|||+|||.++++++|.++|+.||.|.+|.+..                       .+|||||+|.+.++|..|+ .|
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            46899999999999999999999999999999832                       4589999999999999999 59


Q ss_pred             cceeecCceeEeecCCCc
Q 008920          304 NMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~  321 (548)
                      ||..|.|+.|.|.++.+.
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

>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=99.57  E-value=4.4e-15  Score=126.34  Aligned_cols=82  Identities=17%  Similarity=0.195  Sum_probs=70.1

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      ...+|||+|||+++|+++|++||..||.|..+.++...                 .++.++|||||+|.++++|++||++
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~-----------------~~~~~kG~afV~F~~~e~a~~a~~~   76 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-----------------FQGRSTGEAFVQFASQEIAEKALKK   76 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-----------------SSSCBCSEEEEEESSHHHHHHHHTT
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeC-----------------CCCCcceEEEEEeCCHHHHHHHHhh
Confidence            34689999999999999999999999988776553322                 2345789999999999999999999


Q ss_pred             cceeecCceeEeecCCCcc
Q 008920          304 NMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~~  322 (548)
                      |+..|.|+.|.|.++.+..
T Consensus        77 ~~~~i~gR~i~V~~~~~~~   95 (104)
T d1wg5a_          77 HKERIGHRYIEIFKSSRAE   95 (104)
T ss_dssp             TTCCSSSSCCEEEEECTTT
T ss_pred             CCCEEcceEEEEEECCHHH
Confidence            9999999999999987653

>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=99.57  E-value=3.4e-15  Score=125.41  Aligned_cols=75  Identities=23%  Similarity=0.375  Sum_probs=69.7

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      ..++|||+|||..+++++|+++|+.|    |.|.+|+|+.+      +|||||+|.+.++|..||..|+ ..|.|+.|+|
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~f----G~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v   86 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPF----GQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKC   86 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHH----SCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHh----CCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            45789999999999999999999999    99999999976      7899999999999999998776 9999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      .|+++.
T Consensus        87 ~~ak~~   92 (96)
T d1x4ga1          87 YWGKES   92 (96)
T ss_dssp             ECCCCC
T ss_pred             EEcCCC
Confidence            999764

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=4.3e-15  Score=125.99  Aligned_cols=81  Identities=22%  Similarity=0.298  Sum_probs=71.9

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELR  412 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~  412 (548)
                      .....+|||+|||+++|+++|+++|..|    | |..|.++.+. ++.++|||||+|.+.++|+.||++.+..|.||.|+
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~----~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~   85 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPL----N-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVE   85 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSC----C-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhcc----C-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEE
Confidence            4456799999999999999999999998    6 5578888884 68999999999999999999998555999999999


Q ss_pred             EEeeecC
Q 008920          413 LSHAQQN  419 (548)
Q Consensus       413 V~~Ak~~  419 (548)
                      |.++.+.
T Consensus        86 V~~s~~~   92 (102)
T d1weza_          86 LFLNSTA   92 (102)
T ss_dssp             EEEECCC
T ss_pred             EEEcCCC
Confidence            9998864

>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=99.56  E-value=3.3e-15  Score=126.76  Aligned_cols=79  Identities=13%  Similarity=0.162  Sum_probs=68.0

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeE-EEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDS-VRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~s-Vri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...+|||+|||+++|+++|.+||..||.|.. +.++..                  .+|.++|||||+|.+.++|+.||.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~------------------~~g~~~G~afV~F~s~~~a~~Al~   68 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD------------------NNGQGLGQALVQFKNEDDARKSER   68 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCC------------------TTSSCSSCEEEECSSHHHHHHHGG
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeC------------------CCCCcCccEEEEECCHHHHHHHHh
Confidence            3578999999999999999999999999876 444221                  245688999999999999999999


Q ss_pred             hcceeecCceeEeecCCC
Q 008920          303 FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~  320 (548)
                      +|+..|.|+.|.|.++..
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

>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=99.56  E-value=1.2e-15  Score=129.02  Aligned_cols=81  Identities=19%  Similarity=0.218  Sum_probs=71.8

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      .+++|||+|||.++++++|.++|+.||.|..+.++.+.                 .+|.++|||||+|.+.++|..|| .
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~-----------------~~g~~~g~~fV~f~~~~~A~~Ai~~   79 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRM-----------------MTGRMRGQAFITFPNKEIAWQALHL   79 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEE-----------------ECSSSCSEEEEECSSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeeccc-----------------ccccccccceEEeccHHHHHHHHHH
Confidence            46899999999999999999999999999888775433                 24567899999999999999999 5


Q ss_pred             hcceeecCceeEeecCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~  321 (548)
                      |||..|.|+.|.|.++.+.
T Consensus        80 l~g~~~~g~~l~V~~ak~k   98 (102)
T d2cpxa1          80 VNGYKLYGKILVIEFGKNK   98 (102)
T ss_dssp             STTCBCSSCBCEEEECCCC
T ss_pred             hCCCEECCEEEEEEeCCCc
Confidence            9999999999999999764

>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=99.55  E-value=1.6e-15  Score=123.08  Aligned_cols=74  Identities=15%  Similarity=0.190  Sum_probs=65.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~ln  304 (548)
                      .+|||+|||.++|+++|.++|++||.|.++.+..                       ++|||||+|.+.++|..|| .||
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            3699999999999999999999999987766632                       4589999999999999999 599


Q ss_pred             ce-eecCceeEeecCCCcc
Q 008920          305 MA-VIGGNHIRLDRACPPR  322 (548)
Q Consensus       305 g~-~~~gr~I~V~~a~~~~  322 (548)
                      |. .|.|+.|.|.++.+..
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 6999999999998643

>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=99.55  E-value=5.6e-15  Score=121.73  Aligned_cols=76  Identities=20%  Similarity=0.167  Sum_probs=66.4

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      +++||||+|||+++++++|.++|+.||.|..+.++.                     +.++|||||+|.+.++|..|+ .
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~---------------------~~~~~~afV~f~~~~~A~~A~~~   67 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF---------------------QKDRKMALIQMGSVEEAVQALID   67 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC---------------------SSSTTCEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee---------------------ecccceeEEEECCHHHHHHHHHh
Confidence            368999999999999999999999999998877632                     125689999999999999999 6


Q ss_pred             hcceee-cCceeEeecCCC
Q 008920          303 FNMAVI-GGNHIRLDRACP  320 (548)
Q Consensus       303 lng~~~-~gr~I~V~~a~~  320 (548)
                      |||..| .|+.|+|.++.+
T Consensus        68 l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2          68 LHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             HTTCBSSSSCBCEEEECSS
T ss_pred             ccCCEecCCCEEEEEeCCC
Confidence            999887 589999999853

>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=99.55  E-value=2.9e-15  Score=124.08  Aligned_cols=78  Identities=22%  Similarity=0.355  Sum_probs=66.6

Q ss_pred             ccEEEEcCCCCCCcHHHH---HHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          225 LRTIFVGNLPLKVKKKTL---IKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L---~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      .++|||+|||+++++++|   .++|++||.|..|.|+.++.+..              .+...|||||+|.+.++|..|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~--------------~~~~~g~aFV~f~~~~~A~~Ai   73 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAG--------------SQGPSASAYVTYIRSEDALRAI   73 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCS--------------SSCCCEEEEEEESSHHHHHHHH
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCC--------------CCCcceEEEEecccchhHHHHH
Confidence            368999999999999999   67899999999999976653321              1235699999999999999999


Q ss_pred             -HhcceeecCceeEee
Q 008920          302 -AFNMAVIGGNHIRLD  316 (548)
Q Consensus       302 -~lng~~~~gr~I~V~  316 (548)
                       .|||..|.|+.|+|.
T Consensus        74 ~~lng~~~~gr~lkvS   89 (89)
T d2cpia1          74 QCVNNVVVDGRTLKAS   89 (89)
T ss_dssp             HHHTTEEETTEEEEEE
T ss_pred             HHhCCCEECCEEEEEC
Confidence             599999999999873

>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=99.55  E-value=2.9e-15  Score=126.89  Aligned_cols=79  Identities=15%  Similarity=0.326  Sum_probs=72.8

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      ..++|||+|||+++++++|+++|+.|    |.|..+.++.+ .++.++|||||+|.+.++|..||..|| ..|.|++|.|
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~----G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v   91 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPF----GQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVS   91 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTT----SCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhc----ccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCcc
Confidence            45789999999999999999999999    89999999988 578999999999999999999998777 9999999998


Q ss_pred             Eeeec
Q 008920          414 SHAQQ  418 (548)
Q Consensus       414 ~~Ak~  418 (548)
                      .++.|
T Consensus        92 ~~~~P   96 (101)
T d1x5oa1          92 APTEP   96 (101)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            87765

>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=99.54  E-value=3.6e-15  Score=123.83  Aligned_cols=78  Identities=26%  Similarity=0.331  Sum_probs=67.7

Q ss_pred             cccEEEEcCCCCCCcHHHHH----HHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHH
Q 008920          224 LLRTIFVGNLPLKVKKKTLI----KEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~----~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~  299 (548)
                      +++||||+|||+.+++++|.    .+|+.||.|.+|.+..                    ++.++|||||+|.+.++|..
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~--------------------~~~~~g~afV~F~~~~~A~~   61 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--------------------SLKMRGQAFVIFKEVSSATN   61 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--------------------HHHHTTCEEEEESSHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee--------------------eccCCCceEEEECCHHHHHH
Confidence            46899999999999999886    4689999999988722                    23467999999999999999


Q ss_pred             HH-HhcceeecCceeEeecCCCc
Q 008920          300 AL-AFNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       300 Al-~lng~~~~gr~I~V~~a~~~  321 (548)
                      |+ .+|+..|.|+.|.|.++...
T Consensus        62 A~~~~~~~~~~g~~l~v~~ak~~   84 (91)
T d1nu4a_          62 ALRSMQGFPFYDKPMRIQYAKTD   84 (91)
T ss_dssp             HHHHHTTCEETTEECEEEECSSC
T ss_pred             HHHHhCCCEECCEEEEEEEeCCC
Confidence            99 59999999999999998643

>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=99.54  E-value=7.1e-15  Score=123.23  Aligned_cols=79  Identities=22%  Similarity=0.396  Sum_probs=70.5

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....++|||+|||+++++++|+++|..|    |.|..+.     .++.++|||||+|.+.++|..||..|+ ..|.|+.|
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~----g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i   83 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDA----LEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV   83 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSE----EEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----ccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEE
Confidence            4457899999999999999999999999    7776553     367889999999999999999999888 99999999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      .|.|+.++.
T Consensus        84 ~V~~a~~k~   92 (96)
T d1fjca_          84 SLYYTGEKG   92 (96)
T ss_dssp             EEEECSSSC
T ss_pred             EEEEeCCCC
Confidence            999998764

>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=99.54  E-value=1.1e-14  Score=118.76  Aligned_cols=74  Identities=23%  Similarity=0.281  Sum_probs=65.6

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      +++||||+|||.++|+++|.++|+.||.|..|+|+.                      ..+|||||+|.+.++|..|+ .
T Consensus         7 P~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~----------------------~~~g~afV~f~~~~~A~~A~~~   64 (83)
T d2b0ga1           7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVP----------------------NRHDIAFVEFTTELQSNAAKEA   64 (83)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECT----------------------TTCSCEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeec----------------------ccceeEEEecCCHHHHHHHHHH
Confidence            468999999999999999999999999999999832                      13589999999999999999 5


Q ss_pred             hcceeec-CceeEeecCC
Q 008920          303 FNMAVIG-GNHIRLDRAC  319 (548)
Q Consensus       303 lng~~~~-gr~I~V~~a~  319 (548)
                      |||..|. |+.|.|.|+.
T Consensus        65 l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1          65 LQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             HTTCBSSTTCBCEEEECC
T ss_pred             hCCcEeCCCcEEEEEEec
Confidence            8998884 6899999974

>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=99.54  E-value=5.3e-15  Score=121.26  Aligned_cols=77  Identities=23%  Similarity=0.352  Sum_probs=68.2

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEE-EEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAV-RVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~V-rI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      ...+|||+|||+++++++|+++|..|    |.|..+ .+..+ .++.++|||||+|.+.++|..||..++ ..|.||+|+
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~----~~~~~~~~~~~~-~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~   82 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGY----QVIPGSVCLKYN-EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVK   82 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTS----CCCTTTCEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhc----ccceeEEEEEeC-CCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEE
Confidence            45679999999999999999999999    677654 44444 689999999999999999999999887 999999999


Q ss_pred             EEee
Q 008920          413 LSHA  416 (548)
Q Consensus       413 V~~A  416 (548)
                      |.++
T Consensus        83 v~l~   86 (86)
T d2cqpa1          83 LVLG   86 (86)
T ss_dssp             EEES
T ss_pred             EEEC
Confidence            9875

>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=99.54  E-value=9.4e-15  Score=119.17  Aligned_cols=76  Identities=21%  Similarity=0.380  Sum_probs=68.3

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-Ccc-CCeE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKL-RDRE  410 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l-~Gr~  410 (548)
                      .+++++|||+|||..+++++|..+|+.|    |.|..|+|+++.     +|||||+|.+.++|..|+..|+ ..| +|+.
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~----G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~   75 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQF----PGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHA   75 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTS----TTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCB
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccC----ccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcE
Confidence            3467899999999999999999999999    899999998662     6899999999999999999887 666 5699


Q ss_pred             EEEEeee
Q 008920          411 LRLSHAQ  417 (548)
Q Consensus       411 I~V~~Ak  417 (548)
                      |.|.||+
T Consensus        76 i~v~~ak   82 (83)
T d2b0ga1          76 MKITFAK   82 (83)
T ss_dssp             CEEEECC
T ss_pred             EEEEEec
Confidence            9999986

>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=99.54  E-value=1.6e-14  Score=118.50  Aligned_cols=76  Identities=25%  Similarity=0.273  Sum_probs=67.6

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      ..++|||+|||+.+++++|.++|+.|    |.|..+.+..      ++|||||+|.+.++|..||..|+ ..|.|+.|.|
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~----g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V   76 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNI----KPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   76 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTT----STTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhccc----ceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEE
Confidence            45789999999999999999999999    7777776643      47899999999999999998877 9999999999


Q ss_pred             EeeecCC
Q 008920          414 SHAQQNC  420 (548)
Q Consensus       414 ~~Ak~~~  420 (548)
                      .||+|..
T Consensus        77 ~~akP~~   83 (86)
T d2cpda1          77 TLAKPVD   83 (86)
T ss_dssp             ECCCCCC
T ss_pred             EeccCCC
Confidence            9998753

>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=99.54  E-value=1.2e-14  Score=124.19  Aligned_cols=75  Identities=20%  Similarity=0.293  Sum_probs=66.8

Q ss_pred             ccEEEEcCCCC-CCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          225 LRTIFVGNLPL-KVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       225 ~rtVfVgNLP~-~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      +++|||+|||+ .+|+++|.++|+.||.|..|.|+.+                      .+|||||+|.+.++|..|| .
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            47999999965 5999999999999999999999432                      3589999999999999999 5


Q ss_pred             hcceeecCceeEeecCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~  321 (548)
                      |||..|.|+.|.|.++...
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            9999999999999998643

>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=99.54  E-value=8.2e-15  Score=122.77  Aligned_cols=81  Identities=20%  Similarity=0.340  Sum_probs=68.0

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCC-eeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGE-IDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~-I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ++.|||+|||.++++++|.++|+.||+ |..|.|+.+..                ..+.++|||||+|.+.++|..|+ .
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 88898854321                23568899999999999999999 4


Q ss_pred             hc--ceeecCceeEeecCCCc
Q 008920          303 FN--MAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 ln--g~~~~gr~I~V~~a~~~  321 (548)
                      |+  +..+.|+.|.|.|+.+.
T Consensus        65 l~~~~~~~~g~~i~V~~A~p~   85 (96)
T d2disa1          65 LMPGRIQLWGHQIAVDWAEPE   85 (96)
T ss_dssp             TTTCCSCBTTBCCEEEESCSS
T ss_pred             HcCCCeEECCEEEEEEEcCCC
Confidence            64  45668999999999764

>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=99.53  E-value=5.7e-15  Score=122.28  Aligned_cols=76  Identities=25%  Similarity=0.287  Sum_probs=68.4

Q ss_pred             CccEEEEeCCCCCCCHHHH---HHHHhccCCCCCCeEEEEEeecCCCCCC---ceEEEEEECCHHHHHHHHHHcC-CccC
Q 008920          335 IKKTVFVGNLPFDVKDEEI---YQLFCGLNDLESSVEAVRVIRHPHMRVG---KGIAYVLFKTREAANLVIKRRN-LKLR  407 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL---~~~F~~~g~~~G~I~~VrI~~d~~tg~s---rG~AFV~F~~~e~A~~Al~~ln-~~l~  407 (548)
                      ..++|||+|||+.+++++|   .++|++|    |.|..|.|++++.++.+   .|||||+|.+.++|..|++.|| ..|.
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~----G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~   82 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKF----GKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVD   82 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTT----SCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhccc----CCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEEC
Confidence            3578999999999999999   6789999    99999999999876554   4999999999999999998887 9999


Q ss_pred             CeEEEEE
Q 008920          408 DRELRLS  414 (548)
Q Consensus       408 Gr~I~V~  414 (548)
                      |+.|+|+
T Consensus        83 gr~lkvS   89 (89)
T d2cpia1          83 GRTLKAS   89 (89)
T ss_dssp             TEEEEEE
T ss_pred             CEEEEEC
Confidence            9999985

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.53  E-value=8.2e-15  Score=120.13  Aligned_cols=76  Identities=22%  Similarity=0.332  Sum_probs=65.4

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeE-EEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDS-VRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~s-Vri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      .++|||+|||+++++++|.++|..||.|.. +.+..+                  .++.++|||||+|.+.++|+.|| .
T Consensus         9 ~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~------------------~~g~~~G~afV~f~~~e~a~~Ai~~   70 (86)
T d2cqpa1           9 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN------------------EKGMPTGEAMVAFESRDEATAAVID   70 (86)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC------------------SSSCEEEEEEEEESCHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeC------------------CCCCcceEEEEEEcCcHHHHHHHHH
Confidence            468999999999999999999999999865 344222                  14567899999999999999999 5


Q ss_pred             hcceeecCceeEeecC
Q 008920          303 FNMAVIGGNHIRLDRA  318 (548)
Q Consensus       303 lng~~~~gr~I~V~~a  318 (548)
                      ||+..|.|+.|.|.++
T Consensus        71 l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1          71 LNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             TTTCEETTEECEEEES
T ss_pred             cCCCEECCEEEEEEEC
Confidence            9999999999999864

>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=99.53  E-value=1.3e-14  Score=116.19  Aligned_cols=74  Identities=23%  Similarity=0.293  Sum_probs=67.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEee
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHA  416 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~A  416 (548)
                      .+|||+|||+.+++++|+++|..|    |.|..|+|+.+...  ..|||||+|.+.++|.+||.+.+..|+|+.|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~----G~I~~v~~~~~~~~--~~~~afV~F~~~~~a~~Al~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHC----GPIIHVDVADSLKK--NFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGG----SCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcC----CceEEEEEEeeccc--cceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            479999999999999999999999    99999999998643  467999999999999999976569999999999875

>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=99.53  E-value=1.5e-14  Score=119.06  Aligned_cols=79  Identities=19%  Similarity=0.263  Sum_probs=68.7

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-Ccc-CCeE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKL-RDRE  410 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l-~Gr~  410 (548)
                      .+++++|||+|||+++++++|+++|..|    |.|..+.+...    .++|||||+|.+.++|..|+..|+ ..| .|+.
T Consensus         7 ~pPs~tL~V~NLp~~~te~~l~~~F~~~----G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~   78 (88)
T d2adca2           7 FPPSATLHLSNIPPSVSEEDLKVLFSSN----GGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHH   78 (88)
T ss_dssp             CCSCSEEEEECCCTTCCHHHHHHHHHTT----SCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHhhcc----CCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCE
Confidence            3567899999999999999999999999    88888776544    357899999999999999998777 666 5899


Q ss_pred             EEEEeeecC
Q 008920          411 LRLSHAQQN  419 (548)
Q Consensus       411 I~V~~Ak~~  419 (548)
                      |+|.|+++.
T Consensus        79 l~v~~sk~~   87 (88)
T d2adca2          79 LRVSFSKST   87 (88)
T ss_dssp             CEEEECSSC
T ss_pred             EEEEeCCCC
Confidence            999999763

>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=99.53  E-value=8.7e-15  Score=120.36  Aligned_cols=75  Identities=29%  Similarity=0.529  Sum_probs=69.5

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      ..++|||+|||.++++++|+++|+.|    |.|..|.++.+      +|||||+|.+.++|..|+..|+ ..|.|+.|+|
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~----G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V   76 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKY----GKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV   76 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTT----CCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHh----CCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            35679999999999999999999999    89999999866      6899999999999999999887 9999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      .||.+.
T Consensus        77 ~~A~~~   82 (86)
T d2cpja1          77 RFACHS   82 (86)
T ss_dssp             EESSCC
T ss_pred             EECCCc
Confidence            999865

>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=99.53  E-value=9.9e-15  Score=117.99  Aligned_cols=73  Identities=16%  Similarity=0.272  Sum_probs=65.8

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-  301 (548)
                      ...+||||+|||  +|+++|+++|++||.|.+|.+..                       .+|||||+|.+.++|..|+ 
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            345799999996  89999999999999999998832                       4589999999999999999 


Q ss_pred             HhcceeecCceeEeecCCC
Q 008920          302 AFNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       302 ~lng~~~~gr~I~V~~a~~  320 (548)
                      .||+..|.|+.|.|.|+.+
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            6999999999999999964

>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=99.52  E-value=4.5e-15  Score=120.40  Aligned_cols=73  Identities=21%  Similarity=0.314  Sum_probs=65.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC--CccCCeEEEEE
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN--LKLRDRELRLS  414 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln--~~l~Gr~I~V~  414 (548)
                      ++|||+|||+++++++|+++|.+|    |.|..+.++..      +|||||+|.+.++|..||+.++  ..|.|+.|+|.
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~----G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~   71 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDR----KLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   71 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHT----TCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHh----CcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEE
Confidence            469999999999999999999999    88877766654      7899999999999999998876  46999999999


Q ss_pred             eeecC
Q 008920          415 HAQQN  419 (548)
Q Consensus       415 ~Ak~~  419 (548)
                      ||.++
T Consensus        72 ~a~~k   76 (80)
T d2cqha1          72 YSVSK   76 (80)
T ss_dssp             ECCCC
T ss_pred             EcCCc
Confidence            99875

>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=99.52  E-value=3.2e-15  Score=123.17  Aligned_cols=72  Identities=19%  Similarity=0.228  Sum_probs=66.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEe
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSH  415 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~  415 (548)
                      ++|||+|||+.+++++|+++|+.|    |.|..|.|+.+       |||||+|.+.++|..||..|+ ..|.|+.|.|.|
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~----G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~   69 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREA----GDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   69 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGG----SCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCB
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhh----ccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeE
Confidence            369999999999999999999999    89999998754       799999999999999998777 999999999999


Q ss_pred             eecC
Q 008920          416 AQQN  419 (548)
Q Consensus       416 Ak~~  419 (548)
                      +.+.
T Consensus        70 ~~~~   73 (87)
T d3begb1          70 IRVK   73 (87)
T ss_dssp             CEEE
T ss_pred             EecC
Confidence            8754

>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=99.52  E-value=9e-15  Score=125.24  Aligned_cols=75  Identities=24%  Similarity=0.219  Sum_probs=68.5

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      ..++|||+|||+.+++++|+++|+.|    |.|..|.|..      .+|||||+|.+.++|..||..|| ..|.|+.|.|
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~f----G~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v   78 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRF----GSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYL   78 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTT----SCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhcc----CCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEE
Confidence            45799999999999999999999999    8999998743      47899999999999999998887 9999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      .|+...
T Consensus        79 ~~a~~~   84 (111)
T d1whxa_          79 EWAPIG   84 (111)
T ss_dssp             EEEETT
T ss_pred             EECCCC
Confidence            999765

>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=99.52  E-value=4.2e-15  Score=117.80  Aligned_cols=70  Identities=14%  Similarity=0.249  Sum_probs=66.4

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEE
Q 008920          339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELR  412 (548)
Q Consensus       339 LfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~  412 (548)
                      |||+|||+++++++|+++|..|    |.|..+.+++++.++.++|||||+|.+.++|..|+..|| ..|.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~----G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPY----GKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTT----SCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhh----ccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            7999999999999999999999    899999999999999999999999999999999998887 889998763

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=1.6e-14  Score=121.67  Aligned_cols=74  Identities=22%  Similarity=0.407  Sum_probs=66.5

Q ss_pred             CCccEEEEeCCC-CCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          334 DIKKTVFVGNLP-FDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       334 ~~~~tLfV~NLp-~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      ....+|||+||| ..+++++|+++|.+|    |.|..|.|        ++|||||+|.+.++|..||..|| ..|.|+.|
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~----G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l   80 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKY----GKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVL   80 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTS----SCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEEC
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhc----CCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            345679999996 578899999999999    99999988        36899999999999999999888 99999999


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      +|.|+.+.
T Consensus        81 ~V~~a~~~   88 (98)
T d1wf2a_          81 DINLAAEP   88 (98)
T ss_dssp             EEEETTSC
T ss_pred             EEEECCCC
Confidence            99999753

>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=99.52  E-value=6.4e-15  Score=121.59  Aligned_cols=76  Identities=21%  Similarity=0.329  Sum_probs=67.2

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLS  414 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~  414 (548)
                      ..++|||+|||+.+++++|+++|+.|    |.|..|+++.     .++|||||+|.+.++|+.||. .++.|.|+.|.|.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~----G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l~v~   73 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQY----GDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG-EDLIIKGISVHIS   73 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTT----SCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT-CEEEETTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHc----CCceEEEEee-----ccCceEEEEECCHHHHHHHHh-CCCEECCEEeEEE
Confidence            46899999999999999999999999    8999987654     358899999999999999985 3488999999999


Q ss_pred             eeecCC
Q 008920          415 HAQQNC  420 (548)
Q Consensus       415 ~Ak~~~  420 (548)
                      ||.++.
T Consensus        74 ~a~~k~   79 (88)
T d1wf0a_          74 NAEPKH   79 (88)
T ss_dssp             CCCCCC
T ss_pred             eCCCCC
Confidence            997653

>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=99.51  E-value=5.1e-15  Score=117.30  Aligned_cols=70  Identities=16%  Similarity=0.239  Sum_probs=62.2

Q ss_pred             EEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhcce
Q 008920          228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMA  306 (548)
Q Consensus       228 VfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng~  306 (548)
                      |||+|||+++|+++|+++|+.||.|..+++..++.                 ++.++|||||+|.+.++|+.|+ .|||.
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~-----------------~~~~~g~afV~f~~~~~A~~Ai~~lng~   63 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKT-----------------TNKCKGYGFVDFDSPSAAQKAVTALKAS   63 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSS-----------------SCSCCSEEEEEESCHHHHHHHHHHHHHH
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccc-----------------cccccceeEEEECCHHHHHHHHHHhCCC
Confidence            89999999999999999999999999998865432                 3457899999999999999999 69999


Q ss_pred             eecCceeE
Q 008920          307 VIGGNHIR  314 (548)
Q Consensus       307 ~~~gr~I~  314 (548)
                      .|.|+.|+
T Consensus        64 ~~~Gr~~k   71 (72)
T d1x4ea1          64 GVQAQMAK   71 (72)
T ss_dssp             TCCEESCC
T ss_pred             EECCEECc
Confidence            99998763

>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=99.51  E-value=9.5e-15  Score=121.22  Aligned_cols=79  Identities=22%  Similarity=0.421  Sum_probs=69.7

Q ss_pred             CccEEEEeCCCCCCCHHHHHH----HHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCe
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQ----LFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDR  409 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~----~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr  409 (548)
                      +.++|||+|||+.+++++|++    +|+.|    |.|..|.+..   ++.++|||||+|.+.++|..|+..++ ..|.|+
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~----G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~   74 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRF----GQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK   74 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGG----SCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhccc----ccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCE
Confidence            468999999999999999865    57888    8999988754   46789999999999999999998887 999999


Q ss_pred             EEEEEeeecCC
Q 008920          410 ELRLSHAQQNC  420 (548)
Q Consensus       410 ~I~V~~Ak~~~  420 (548)
                      .|+|.||++..
T Consensus        75 ~l~v~~ak~~~   85 (91)
T d1nu4a_          75 PMRIQYAKTDS   85 (91)
T ss_dssp             ECEEEECSSCC
T ss_pred             EEEEEEeCCCc
Confidence            99999998753

>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=99.51  E-value=7.6e-15  Score=124.47  Aligned_cols=82  Identities=22%  Similarity=0.283  Sum_probs=71.2

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEE
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRL  413 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V  413 (548)
                      ....||||+|||+++++++|+++|..|    |.|..+.++.+..+|.++|||||+|.+.++|..||.+.+..|+|+.|.|
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~----g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V   81 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGI----PVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFV   81 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTS----CCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhccc----ceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEE
Confidence            346789999999999999999999999    7787655555557899999999999999999999975449999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      .++...
T Consensus        82 ~~~~~~   87 (103)
T d2cpya1          82 HVVTLE   87 (103)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            998653

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=2.8e-14  Score=117.53  Aligned_cols=77  Identities=14%  Similarity=0.253  Sum_probs=68.1

Q ss_pred             CCcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       222 ~~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ...+++|||+|||+++++++|.++|+.||.|.+|++..                       ++|||||+|.+.++|..|+
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            34678999999999999999999999999999998832                       4589999999999999998


Q ss_pred             H---hcceeecCceeEeecCCCc
Q 008920          302 A---FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       302 ~---lng~~~~gr~I~V~~a~~~  321 (548)
                      .   +++..+.|+.|.|.++...
T Consensus        62 ~~~~~~~~~~~g~~l~v~~sk~~   84 (88)
T d2cq1a1          62 NYYSAVTPHLRNQPIYIQYSNHK   84 (88)
T ss_dssp             HHHHHSCCEETTEECEEEECSCS
T ss_pred             HHHccCCCccCCCEEEEEECCCC
Confidence            4   4678999999999998643

>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=99.51  E-value=6.8e-15  Score=121.16  Aligned_cols=70  Identities=10%  Similarity=0.087  Sum_probs=64.0

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhcc
Q 008920          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (548)
Q Consensus       227 tVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng  305 (548)
                      .|||+|||+++++++|.++|+.||.|..|.|+                        ..|||||+|.+.++|+.|| .|||
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~------------------------~~g~afV~f~~~~~a~~Ai~~l~g   57 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVY------------------------RDGTGVVEFVRKEDMTYAVRKLDN   57 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEEC------------------------TTSEEEEEESSHHHHHHHHHHHTT
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccc------------------------ccceeeEEeCCHHHHHHHHHHhCC
Confidence            59999999999999999999999999999882                        2379999999999999999 6999


Q ss_pred             eeecCceeEeecCCC
Q 008920          306 AVIGGNHIRLDRACP  320 (548)
Q Consensus       306 ~~~~gr~I~V~~a~~  320 (548)
                      ..|.|+.|.|.++..
T Consensus        58 ~~~~g~~i~v~~~~~   72 (87)
T d3begb1          58 TKFRSHEGETAYIRV   72 (87)
T ss_dssp             CBCCCTTSCCCBCEE
T ss_pred             CEECCcEeEEeEEec
Confidence            999999999988753

>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=99.51  E-value=2.7e-14  Score=121.88  Aligned_cols=75  Identities=23%  Similarity=0.365  Sum_probs=68.8

Q ss_pred             ccEEEEeCCCC-CCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          336 KKTVFVGNLPF-DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       336 ~~tLfV~NLp~-~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      ..+|||+|||+ .+++++|+++|+.|    |.|..|.|+++.     +|||||+|.+.++|..||..++ ..|.|+.|.|
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~f----G~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v   72 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVY----GDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI   72 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHH----TCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhc----cccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            47899999965 59999999999999    999999999884     7899999999999999998887 9999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      .|++..
T Consensus        73 ~~s~~~   78 (109)
T d2adca1          73 TLSKHQ   78 (109)
T ss_dssp             ECCSCC
T ss_pred             EECCCC
Confidence            998755

>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=99.51  E-value=6.2e-15  Score=127.17  Aligned_cols=80  Identities=16%  Similarity=0.277  Sum_probs=68.5

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHh
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~l  303 (548)
                      ..++|||+|||+++|+++|.+||+.||.|..+.++.+.                 .+|.++|||||+|.+.++|++||.+
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~-----------------~~g~~~G~afVeF~~~e~a~~al~~   79 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYG-----------------PNGKATGEGFVEFRNEADYKAALCR   79 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEEC-----------------TTSSEEEEEEEEBSSSHHHHHHHTS
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecC-----------------cccceeeEEEEEECCHHHHHHHHHc
Confidence            45799999999999999999999999988664443221                 2456789999999999999999999


Q ss_pred             cceeecCceeEeecCCC
Q 008920          304 NMAVIGGNHIRLDRACP  320 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~  320 (548)
                      |+..|+|+.|.|.++..
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=99.50  E-value=2e-14  Score=118.61  Aligned_cols=73  Identities=12%  Similarity=0.242  Sum_probs=63.3

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hh
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~l  303 (548)
                      .++|||+|||+++++++|.++|..|| +..+.+                       +..+|||||+|.+.++|+.|| .|
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~-----------------------~~~kg~afV~f~~~~~A~~Ai~~l   60 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV-----------------------DRNKRTAFVTLLNGEQAQNAIQMF   60 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE-----------------------EGGGTEEEECCSCHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee-----------------------eccCCceEEEECCHHHHHHHHHHh
Confidence            47899999999999999999999999 333333                       125689999999999999999 69


Q ss_pred             cceeecCceeEeecCCCc
Q 008920          304 NMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       304 ng~~~~gr~I~V~~a~~~  321 (548)
                      |+..|.|+.|.|.++...
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

>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=99.50  E-value=2.7e-14  Score=122.23  Aligned_cols=77  Identities=21%  Similarity=0.217  Sum_probs=67.6

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ...+|||+|||+.+|+++|.++|+.||.|..|.|+...                     ++|||||+|.+.++|+.|| .
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            35689999999999999999999999999999985432                     5699999999999999999 6


Q ss_pred             hcceee--cCceeEeecCCCc
Q 008920          303 FNMAVI--GGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~--~gr~I~V~~a~~~  321 (548)
                      ||+..|  .|++|.|.++.+.
T Consensus        65 ln~~~l~~~~~~l~v~~s~~~   85 (108)
T d2adba1          65 LDGQNIYNACCTLRIDFSKLT   85 (108)
T ss_dssp             HHSCCSSTTCCCCEEEECSSC
T ss_pred             HCCCEeccCCcEEEEEecCCc
Confidence            999988  4678999988653

>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=99.49  E-value=3.9e-14  Score=113.42  Aligned_cols=69  Identities=13%  Similarity=0.262  Sum_probs=61.5

Q ss_pred             EEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhcce
Q 008920          228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMA  306 (548)
Q Consensus       228 VfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng~  306 (548)
                      |||+|||+++++++|.++|++|| +..+.+                       +.++|||||+|.+.++|..|+ .|||.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~-----------------------~~~~g~afv~f~~~~~A~~Ai~~ln~~   56 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-----------------------DKYKGTAFVTLLNGEQAEAAINTFHQS   56 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE-----------------------ETTTTEEEEEESSHHHHHHHHHHHTTE
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee-----------------------cccceeEEEEECCHHHHHHHHHHhCCc
Confidence            79999999999999999999999 545444                       126799999999999999999 69999


Q ss_pred             eecCceeEeecCCC
Q 008920          307 VIGGNHIRLDRACP  320 (548)
Q Consensus       307 ~~~gr~I~V~~a~~  320 (548)
                      .|.|+.|.|.++..
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

>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=99.49  E-value=2.2e-14  Score=120.92  Aligned_cols=73  Identities=11%  Similarity=0.085  Sum_probs=66.5

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||+++++++|.++|+.||.|..|.|.                        ..|||||+|.+.++|+.|| .
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~------------------------~~g~afV~f~~~~~a~~Ai~~   69 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ------------------------KDGMGMVEYLRKEDMEYALRK   69 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEE------------------------TTTEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhccccccccc------------------------ccceEEEEECCHHHHHHHHHH
Confidence            35789999999999999999999999999999882                        3489999999999999999 6


Q ss_pred             hcceeecCceeEeecCCC
Q 008920          303 FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~  320 (548)
                      ||+..|.|+.|.|.++..
T Consensus        70 lng~~~~g~~i~v~~~~~   87 (98)
T d1wg4a_          70 LDDTKFRSHEGETSYIRV   87 (98)
T ss_dssp             HSSEEEECTTSCEEEEEE
T ss_pred             hCCCEeCCeEEEEEEEec
Confidence            999999999999988754

>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=99.49  E-value=4.1e-14  Score=116.50  Aligned_cols=77  Identities=18%  Similarity=0.269  Sum_probs=69.5

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHc--C-CccCCe
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR--N-LKLRDR  409 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~l--n-~~l~Gr  409 (548)
                      ..++++|||+|||+.+++++|+++|+.|    |.|..|.++.+      +|||||+|.+.++|..|+..+  + ..+.|+
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~----G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~   74 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPF----GKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQ   74 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTT----SCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcc----ccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCC
Confidence            4578999999999999999999999999    89999998865      579999999999999999754  3 789999


Q ss_pred             EEEEEeeecC
Q 008920          410 ELRLSHAQQN  419 (548)
Q Consensus       410 ~I~V~~Ak~~  419 (548)
                      +|+|.|+..+
T Consensus        75 ~l~v~~sk~~   84 (88)
T d2cq1a1          75 PIYIQYSNHK   84 (88)
T ss_dssp             ECEEEECSCS
T ss_pred             EEEEEECCCC
Confidence            9999999754

>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=99.49  E-value=2.4e-14  Score=115.66  Aligned_cols=73  Identities=14%  Similarity=0.236  Sum_probs=66.6

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      ..++|||+||+  +|+++|+++|++|    |.|..|.+..+      +|||||+|.+.++|..|+..+| ..|.|+.|+|
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~----G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V   71 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPF----GNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKV   71 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTT----CCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEE
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhcc----CccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEE
Confidence            45799999996  8999999999999    89999998755      6799999999999999998887 9999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      .|+++.
T Consensus        72 ~~a~~~   77 (79)
T d2bz2a1          72 NIARKQ   77 (79)
T ss_dssp             EECCSS
T ss_pred             EEecCC
Confidence            999864

>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=99.49  E-value=1.1e-14  Score=125.48  Aligned_cols=82  Identities=17%  Similarity=0.282  Sum_probs=72.2

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELR  412 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~  412 (548)
                      .....+|||+|||+.+|+++|.++|+.|    |.|..+.++.+..+|.++|||||+|.+.++|.+||.+.+..|+||.|.
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~----g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~   90 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKL----DIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQ   90 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSS----CBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhc----cccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEE
Confidence            4456799999999999999999999999    788776666666789999999999999999999998555999999999


Q ss_pred             EEeeec
Q 008920          413 LSHAQQ  418 (548)
Q Consensus       413 V~~Ak~  418 (548)
                      |..+.+
T Consensus        91 V~~~~~   96 (112)
T d1wela1          91 VHPITK   96 (112)
T ss_dssp             EEEECH
T ss_pred             EEEcCh
Confidence            998864

>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=99.49  E-value=3.4e-14  Score=117.27  Aligned_cols=74  Identities=22%  Similarity=0.269  Sum_probs=64.0

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      ...+|||+|||+++++++|+++|..|    | +..+.+      +..+|||||+|.+.++|..||..|| ..|.|+.|.|
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~----G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V   72 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDY----D-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIV   72 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS----C-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhc----C-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            35789999999999999999999999    6 333333      3458999999999999999998888 9999999999


Q ss_pred             EeeecC
Q 008920          414 SHAQQN  419 (548)
Q Consensus       414 ~~Ak~~  419 (548)
                      .|+...
T Consensus        73 ~~a~~~   78 (88)
T d1wg1a_          73 QLQPTD   78 (88)
T ss_dssp             EECCCC
T ss_pred             EEcCCC
Confidence            999765

>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=99.48  E-value=3.5e-14  Score=119.60  Aligned_cols=77  Identities=17%  Similarity=0.165  Sum_probs=69.6

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEE
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDREL  411 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I  411 (548)
                      .....+|||+|||+.+++++|+++|+.|    |.|..|.|..       +|||||+|.+.++|..||+.|| ..|.|+.|
T Consensus        12 ~~~~~~i~V~Nlp~~~~~~~L~~~F~~~----G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i   80 (98)
T d1wg4a_          12 RRSDFRVLVSGLPPSGSWQDLKDHMREA----GDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEG   80 (98)
T ss_dssp             CSCSCEEEEECCCSSCCHHHHHHHHTTS----SCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhh----cccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEE
Confidence            3456789999999999999999999999    8999999864       4799999999999999998887 99999999


Q ss_pred             EEEeeecCC
Q 008920          412 RLSHAQQNC  420 (548)
Q Consensus       412 ~V~~Ak~~~  420 (548)
                      .|.|+.+..
T Consensus        81 ~v~~~~~~~   89 (98)
T d1wg4a_          81 ETSYIRVYP   89 (98)
T ss_dssp             CEEEEEEEC
T ss_pred             EEEEEecCC
Confidence            999998753

>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=99.48  E-value=4.6e-14  Score=118.44  Aligned_cols=77  Identities=18%  Similarity=0.336  Sum_probs=69.1

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCC--e
Q 008920          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRD--R  409 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~G--r  409 (548)
                      ..+.++|||+|||+++++++|+++|+.|    |.|..|+++++      ++||||+|.+.++|..|++.|+ ..|.|  +
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~----G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~   83 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRF----GSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDR   83 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTT----SCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSC
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhh----cccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCce
Confidence            3467899999999999999999999999    89999998765      6799999999999999998887 77776  6


Q ss_pred             EEEEEeeecC
Q 008920          410 ELRLSHAQQN  419 (548)
Q Consensus       410 ~I~V~~Ak~~  419 (548)
                      +|+|.||++.
T Consensus        84 ~l~v~~ak~~   93 (97)
T d1whya_          84 RLRVDFAKSG   93 (97)
T ss_dssp             BCEEEECCCC
T ss_pred             EEEEEeCCCC
Confidence            8999999864

>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=99.48  E-value=4.7e-14  Score=118.38  Aligned_cols=74  Identities=27%  Similarity=0.416  Sum_probs=66.6

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-H
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~  302 (548)
                      ..++|||+|||+++++++|+++|+.||.|..|++..                       .++||||+|.+.++|..|+ .
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~-----------------------~~~~afV~f~~~~~A~~A~~~   72 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK-----------------------GDSFAYIQYESLDAAQAACAK   72 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS-----------------------SSCCEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeec-----------------------cccEEEeccCCHHHHHHHHHH
Confidence            468999999999999999999999999999998832                       4589999999999999999 6


Q ss_pred             hcceeecC--ceeEeecCCC
Q 008920          303 FNMAVIGG--NHIRLDRACP  320 (548)
Q Consensus       303 lng~~~~g--r~I~V~~a~~  320 (548)
                      ||+..|.|  +.|+|.|+.+
T Consensus        73 l~~~~i~g~~~~l~v~~ak~   92 (97)
T d1whya_          73 MRGFPLGGPDRRLRVDFAKS   92 (97)
T ss_dssp             HTTCBCSSSSCBCEEEECCC
T ss_pred             hCCCEeCCCceEEEEEeCCC
Confidence            99999987  4899999864

>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=99.47  E-value=1.4e-13  Score=116.93  Aligned_cols=78  Identities=13%  Similarity=0.138  Sum_probs=70.0

Q ss_pred             cCCCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHc--C-CccCC
Q 008920          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR--N-LKLRD  408 (548)
Q Consensus       332 ~~~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~l--n-~~l~G  408 (548)
                      ...++++|||+|||..+++++|.++|..|    |.|..|.|.++      +|||||+|.+.++|..||..+  + ..+.|
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~f----G~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g   80 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKF----GTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAG   80 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTT----SCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhc----ccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEee
Confidence            34578899999999999999999999999    89999998765      689999999999999999866  3 77899


Q ss_pred             eEEEEEeeecC
Q 008920          409 RELRLSHAQQN  419 (548)
Q Consensus       409 r~I~V~~Ak~~  419 (548)
                      ++|.|.|+...
T Consensus        81 ~~l~v~~s~~~   91 (104)
T d1wexa_          81 QQAFFNYSTSK   91 (104)
T ss_dssp             SBCEEEECSSS
T ss_pred             EEEEEEEcCCC
Confidence            99999999764

>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=99.47  E-value=3.4e-14  Score=119.85  Aligned_cols=77  Identities=18%  Similarity=0.272  Sum_probs=67.8

Q ss_pred             CCCcccEEEEcCCCCC-CcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHH
Q 008920          221 EGKLLRTIFVGNLPLK-VKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (548)
Q Consensus       221 ~~~~~rtVfVgNLP~~-~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~  299 (548)
                      .....++|||+|||.+ +|+++|.++|+.||.|..|.|+.                       ++|||||+|.+.++|..
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~-----------------------~k~~afV~f~~~~~A~~   70 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR-----------------------MKSQAFIEMETREDAMA   70 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET-----------------------TTTEEEEECSSHHHHHH
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEee-----------------------cCCcEEEEecchHHHHH
Confidence            3445689999999985 89999999999999999999842                       45899999999999999


Q ss_pred             HHH---hcceeecCceeEeecCCC
Q 008920          300 ALA---FNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       300 Al~---lng~~~~gr~I~V~~a~~  320 (548)
                      |+.   +++..|.|+.|.|.++..
T Consensus        71 Ai~~~~~~~~~~~gr~l~V~~s~~   94 (99)
T d1x4fa1          71 MVDHCLKKALWFQGRCVKVDLSEK   94 (99)
T ss_dssp             HHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             HHHHHhcCCceECCEEEEEEEcCC
Confidence            984   688899999999999864

>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=99.45  E-value=1.7e-15  Score=125.47  Aligned_cols=82  Identities=21%  Similarity=0.404  Sum_probs=68.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhcc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNM  305 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~lng  305 (548)
                      |+|||+|||+++|+++|.++|+.||.|..+.+.....            ......+.++|||||+|.+.++|+.|++|||
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~------------~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g   69 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNP------------VLAVQINQDKNFAFLEFRSVDETTQAMAFDG   69 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCS------------EEECCEETTTTEEEEEESSCTTTTTGGGGSS
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccce------------eeecccCCCceEEEEEeCCHHHHHHHHhhCC
Confidence            6899999999999999999999999988776632110            1122345688999999999999999999999


Q ss_pred             eeecCceeEeecCC
Q 008920          306 AVIGGNHIRLDRAC  319 (548)
Q Consensus       306 ~~~~gr~I~V~~a~  319 (548)
                      ..|.|+.|.|.++.
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            99999999998754

>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=99.45  E-value=2.5e-13  Score=115.28  Aligned_cols=76  Identities=18%  Similarity=0.212  Sum_probs=66.9

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ..+++|||+|||..+|+++|.++|+.||.|..|+|..                       .+|||||+|.+.++|+.||.
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~-----------------------~k~~AfV~f~~~e~A~~ai~   69 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-----------------------FKRQALVEFENIDSAKECVT   69 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET-----------------------TTTEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe-----------------------cceeEEEEeCCHHHHHHHHH
Confidence            4578999999999999999999999999999998832                       45899999999999999994


Q ss_pred             -h--cceeecCceeEeecCCCc
Q 008920          303 -F--NMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 -l--ng~~~~gr~I~V~~a~~~  321 (548)
                       +  ++..+.|+.|.|.++...
T Consensus        70 ~~~~~~~~~~g~~l~v~~s~~~   91 (104)
T d1wexa_          70 FAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             HHHHSCCBSSSSBCEEEECSSS
T ss_pred             HHcCCCcEEeeEEEEEEEcCCC
Confidence             4  566789999999998653

>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=99.44  E-value=1.1e-13  Score=118.21  Aligned_cols=77  Identities=14%  Similarity=0.144  Sum_probs=69.0

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-Ccc--CCeEE
Q 008920          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKL--RDREL  411 (548)
Q Consensus       335 ~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l--~Gr~I  411 (548)
                      +..+|||+|||+.+|+++|+++|+.|    |.|..|.|+.+.    .+|||||+|.+.++|..||..++ ..|  .|+.|
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~----G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l   77 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKF----GTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTL   77 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTT----SCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCC
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccC----CcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEE
Confidence            46789999999999999999999999    999999998774    48999999999999999998877 555  67899


Q ss_pred             EEEeeecC
Q 008920          412 RLSHAQQN  419 (548)
Q Consensus       412 ~V~~Ak~~  419 (548)
                      .|.|+++.
T Consensus        78 ~v~~s~~~   85 (108)
T d2adba1          78 RIDFSKLT   85 (108)
T ss_dssp             EEEECSSC
T ss_pred             EEEecCCc
Confidence            99999765

>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=99.44  E-value=1.8e-13  Score=109.49  Aligned_cols=71  Identities=27%  Similarity=0.404  Sum_probs=62.8

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeee
Q 008920          339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQ  417 (548)
Q Consensus       339 LfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak  417 (548)
                      |||+|||+++++++|+++|.+|    | +..+.+      +.++|||||+|.+.++|..|+..|| ..|.|++|.|.|+.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~----g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~   69 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDY----E-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQP   69 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTS----C-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECC
T ss_pred             CEEeCCCCcCCHHHHHHHHhcc----c-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeC
Confidence            7999999999999999999999    6 555543      4568999999999999999998887 99999999999997


Q ss_pred             cCC
Q 008920          418 QNC  420 (548)
Q Consensus       418 ~~~  420 (548)
                      ...
T Consensus        70 ~d~   72 (75)
T d1wi6a1          70 TDA   72 (75)
T ss_dssp             STT
T ss_pred             CCC
Confidence            653

>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=99.42  E-value=1.6e-13  Score=115.67  Aligned_cols=79  Identities=18%  Similarity=0.352  Sum_probs=68.9

Q ss_pred             CcCCCccEEEEeCCCCC-CCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHH--cC-Ccc
Q 008920          331 PLYDIKKTVFVGNLPFD-VKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKR--RN-LKL  406 (548)
Q Consensus       331 ~~~~~~~tLfV~NLp~~-~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~--ln-~~l  406 (548)
                      +....+++|||+|||.+ +|+++|..+|+.|    |.|..|.|+.+      +|||||+|.+.++|..|+..  ++ ..|
T Consensus        13 ~~~~~~~~l~v~nLp~~~~te~~l~~~F~~f----G~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~   82 (99)
T d1x4fa1          13 QKQELGRVIHLSNLPHSGYSDSAVLKLAEPY----GKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWF   82 (99)
T ss_dssp             CSSCCCCEEEEESCCCSSCCSHHHHTTTTTT----SCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCS
T ss_pred             cCCCCCCEEEEeCCcCCccCHHHHHhhhccc----cceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceE
Confidence            33456789999999985 8999999999999    99999999866      68999999999999999973  34 789


Q ss_pred             CCeEEEEEeeecC
Q 008920          407 RDRELRLSHAQQN  419 (548)
Q Consensus       407 ~Gr~I~V~~Ak~~  419 (548)
                      .|+.|.|.||+..
T Consensus        83 ~gr~l~V~~s~~~   95 (99)
T d1x4fa1          83 QGRCVKVDLSEKY   95 (99)
T ss_dssp             SSSCCEEEEECSC
T ss_pred             CCEEEEEEEcCCc
Confidence            9999999999754

>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=99.41  E-value=2.2e-13  Score=112.55  Aligned_cols=75  Identities=17%  Similarity=0.256  Sum_probs=66.2

Q ss_pred             CcccEEEEcCCCCC-CcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLK-VKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (548)
Q Consensus       223 ~~~rtVfVgNLP~~-~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al  301 (548)
                      ..+++|||+|||.. +|+++|.++|+.||.|.+|.|+.                       .++||||+|.+.++|..|+
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            34689999999986 88999999999999999999832                       4479999999999999999


Q ss_pred             H-h--cceeecCceeEeecCCC
Q 008920          302 A-F--NMAVIGGNHIRLDRACP  320 (548)
Q Consensus       302 ~-l--ng~~~~gr~I~V~~a~~  320 (548)
                      . +  ++..+.|++|.|.++..
T Consensus        63 ~~l~~~~~~~~gr~l~V~~s~~   84 (89)
T d1x4da1          63 DYYTTTPALVFGKPVRVHLSQK   84 (89)
T ss_dssp             HHHHHSCCEETTEECEEEEECC
T ss_pred             HHHhhCCCccCCceEEEEECCC
Confidence            4 4  68889999999999864

>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=99.40  E-value=2.3e-13  Score=112.49  Aligned_cols=77  Identities=12%  Similarity=0.162  Sum_probs=68.7

Q ss_pred             CCCccEEEEeCCCCC-CCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHc--C-CccCC
Q 008920          333 YDIKKTVFVGNLPFD-VKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR--N-LKLRD  408 (548)
Q Consensus       333 ~~~~~tLfV~NLp~~-~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~l--n-~~l~G  408 (548)
                      .+.+++|||+|||.. +|++||.++|+.|    |.|..|.|+.+      ++||||+|.+.++|..|+..+  + ..+.|
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~f----G~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~g   74 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPF----GVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFG   74 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGG----SCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETT
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhh----CCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCC
Confidence            457899999999986 7899999999999    99999999876      469999999999999999865  3 78999


Q ss_pred             eEEEEEeeecC
Q 008920          409 RELRLSHAQQN  419 (548)
Q Consensus       409 r~I~V~~Ak~~  419 (548)
                      ++|.|.||...
T Consensus        75 r~l~V~~s~~~   85 (89)
T d1x4da1          75 KPVRVHLSQKY   85 (89)
T ss_dssp             EECEEEEECCC
T ss_pred             ceEEEEECCCc
Confidence            99999999753

>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=99.39  E-value=4.8e-13  Score=123.47  Aligned_cols=82  Identities=17%  Similarity=0.361  Sum_probs=72.6

Q ss_pred             CcccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       223 ~~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...++|||+|||+.+|+++|.++|+.||.|..|.|+.+.                 .+|.++|||||+|.+.++|..||.
T Consensus        95 ~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~-----------------~~~~~~g~~fV~f~~~e~A~~Al~  157 (183)
T d1u1qa_          95 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-----------------GSGKKRGFAFVTFDDHDSVDKIVI  157 (183)
T ss_dssp             CCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-----------------TTCCEEEEEEEEESCHHHHHHHHT
T ss_pred             cccceeEEccCCCcCCHHHHhhhhccCCceeeeeeeccc-----------------ccCccceeEEEEECCHHHHHHHHH
Confidence            345799999999999999999999999999999996643                 134577999999999999999999


Q ss_pred             hcceeecCceeEeecCCCc
Q 008920          303 FNMAVIGGNHIRLDRACPP  321 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~~~  321 (548)
                      +++..|.|+.|.|.++.++
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

>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=99.34  E-value=1.5e-14  Score=119.68  Aligned_cols=77  Identities=14%  Similarity=0.431  Sum_probs=65.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEE-----eecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEE
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRV-----IRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDREL  411 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI-----~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I  411 (548)
                      ++|||+|||+.+++++|.++|+.|    |.|..+.+     +.+..++.++|||||+|.+.++|..|+.+.+..|.|+.|
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~----g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l   77 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQ----MRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSL   77 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHH----HTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhh----CcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEE
Confidence            689999999999999999999999    55554443     345567889999999999999999999744499999999


Q ss_pred             EEEeee
Q 008920          412 RLSHAQ  417 (548)
Q Consensus       412 ~V~~Ak  417 (548)
                      +|.+++
T Consensus        78 ~V~r~k   83 (90)
T d1u2fa_          78 KIRRPH   83 (90)
T ss_dssp             CCBCTT
T ss_pred             EECCCC
Confidence            997544

>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=99.33  E-value=9.9e-13  Score=111.84  Aligned_cols=76  Identities=12%  Similarity=0.031  Sum_probs=66.3

Q ss_pred             cccEEEEcCCCCCC-c----HHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHH
Q 008920          224 LLRTIFVGNLPLKV-K----KKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (548)
Q Consensus       224 ~~rtVfVgNLP~~~-t----ee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~  298 (548)
                      ...+|||+||+.++ +    +++|..+|+.||.|.+|.++.                       ++|||||+|.+.++|.
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            35789999999876 3    367999999999999998832                       5689999999999999


Q ss_pred             HHH-HhcceeecCceeEeecCCCcc
Q 008920          299 AAL-AFNMAVIGGNHIRLDRACPPR  322 (548)
Q Consensus       299 ~Al-~lng~~~~gr~I~V~~a~~~~  322 (548)
                      .|+ .|||..|.|+.|.|.|+.+..
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 599999999999999997543

>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=99.32  E-value=1.2e-12  Score=111.28  Aligned_cols=76  Identities=14%  Similarity=0.071  Sum_probs=67.2

Q ss_pred             CccEEEEeCCCCCC-CH----HHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCC
Q 008920          335 IKKTVFVGNLPFDV-KD----EEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRD  408 (548)
Q Consensus       335 ~~~tLfV~NLp~~~-te----edL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~G  408 (548)
                      ...+|||+||+.++ ++    ++|..+|+.|    |.|..|.+++.      +|||||+|.+.++|..|+..|| ..|.|
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~----G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g   73 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTY----DKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLG   73 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTT----CSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETT
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhccc----ccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCC
Confidence            46789999999886 33    5699999999    99999998754      7799999999999999999998 99999


Q ss_pred             eEEEEEeeecCC
Q 008920          409 RELRLSHAQQNC  420 (548)
Q Consensus       409 r~I~V~~Ak~~~  420 (548)
                      +.|.|.||++..
T Consensus        74 ~~l~v~~a~~~~   85 (104)
T d1weya_          74 KEMKLYFAQTLH   85 (104)
T ss_dssp             EECEEECCCCSS
T ss_pred             CEeEEeecccCC
Confidence            999999998653

>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=99.26  E-value=7.1e-12  Score=101.67  Aligned_cols=72  Identities=15%  Similarity=0.168  Sum_probs=61.6

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHHhc
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~ln  304 (548)
                      .+.|||++||++++++. ..+|++||.|.++++.                       ..+|||||.|.++++|++||.+|
T Consensus         4 ~~wV~V~G~p~~~~~~i-l~~F~~~G~I~~~~~~-----------------------~~~~~~fV~f~~~~~A~~Al~~n   59 (81)
T d1wwha1           4 DTWVTVFGFPQASASYI-LLQFAQYGNILKHVMS-----------------------NTGNWMHIRYQSKLQARKALSKD   59 (81)
T ss_dssp             GGEEEEECCCGGGHHHH-HHHHHTTSCEEEEEEC-----------------------SSSSEEEEEESSHHHHHHHHTTT
T ss_pred             ccEEEEECCChHHHHHH-HHHHHhhhhhheEEec-----------------------CCCCEEEEEEcccHHHHHHHhcC
Confidence            46899999999998654 4689999999999872                       15689999999999999999999


Q ss_pred             ceeecCce-eEeecCCC
Q 008920          305 MAVIGGNH-IRLDRACP  320 (548)
Q Consensus       305 g~~~~gr~-I~V~~a~~  320 (548)
                      |..|.|+. |.|.++..
T Consensus        60 G~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1          60 GRIFGESIMIGVKPCID   76 (81)
T ss_dssp             TCEETTTEECEEEECCC
T ss_pred             CCeECCcEEEEEEeCCC
Confidence            99999985 56887754

>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=99.22  E-value=5.8e-12  Score=108.42  Aligned_cols=72  Identities=17%  Similarity=0.167  Sum_probs=60.9

Q ss_pred             ccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCH-HHHHHHH-H
Q 008920          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSE-QSTEAAL-A  302 (548)
Q Consensus       225 ~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~-e~A~~Al-~  302 (548)
                      ...+||||||+.+|+++|+.+|+.||+|.+|.|+.                       .+|||||.|.+. ++|..|+ .
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            45679999999999999999999999999999832                       458999999996 6788787 6


Q ss_pred             hcceeecCceeEeecCC
Q 008920          303 FNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       303 lng~~~~gr~I~V~~a~  319 (548)
                      +++..+.++.+.|.+..
T Consensus        68 ~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          68 ANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             TTTSCBCTTSSSEEEEE
T ss_pred             hcCCceecCceEEEEee
Confidence            89988888777666653

>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=99.20  E-value=1.5e-12  Score=110.74  Aligned_cols=74  Identities=15%  Similarity=0.219  Sum_probs=66.2

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhcc
Q 008920          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (548)
Q Consensus       227 tVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng  305 (548)
                      .++|.+++.++++++|.++|++||.|.+|.|+.+.                  ++.++|||||+|.+.++|..|+ .|||
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            58889999999999999999999999999994322                  3557899999999999999999 6999


Q ss_pred             eeecCceeEeecC
Q 008920          306 AVIGGNHIRLDRA  318 (548)
Q Consensus       306 ~~~~gr~I~V~~a  318 (548)
                      ..|.|+.|.|.++
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

>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=99.19  E-value=1.6e-12  Score=110.44  Aligned_cols=75  Identities=16%  Similarity=0.087  Sum_probs=69.8

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEe
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSH  415 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~  415 (548)
                      ..++|.+++..+++++|.++|++|    |.|..|.|+++ .+|.++|||||+|.+.++|..|+..|| ..|.|+.|.|.|
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~----G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~  102 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKY----GEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL  102 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHT----CCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             chHHhhhhhhhhhHHHHHHHhccC----CCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEE
Confidence            458889999899999999999999    99999999877 689999999999999999999998887 999999999998


Q ss_pred             e
Q 008920          416 A  416 (548)
Q Consensus       416 A  416 (548)
                      +
T Consensus       103 s  103 (104)
T d1jmta_         103 S  103 (104)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.19  E-value=1.4e-11  Score=103.92  Aligned_cols=63  Identities=16%  Similarity=0.296  Sum_probs=55.0

Q ss_pred             CcccEEEEcC--CCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHH
Q 008920          223 KLLRTIFVGN--LPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (548)
Q Consensus       223 ~~~rtVfVgN--LP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~A  300 (548)
                      ...++|||.|  ||.++|+++|..+|++||.|..|.++.                       .+|||||+|.+.++|..|
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~-----------------------~k~~aFV~f~~~e~A~~A   72 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----------------------NKPYSFARYRTTEESKRA   72 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT-----------------------TCSCEEEEESSHHHHHHH
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeecc-----------------------CccEEEEEECCHHHHHHH
Confidence            3457888855  999999999999999999999998732                       458999999999999999


Q ss_pred             H-Hhcceee
Q 008920          301 L-AFNMAVI  308 (548)
Q Consensus       301 l-~lng~~~  308 (548)
                      + .|||..+
T Consensus        73 ~~~lng~~i   81 (101)
T d2cq2a1          73 YVTLNGKEV   81 (101)
T ss_dssp             HHHTTTCEE
T ss_pred             HHHhCCCCC
Confidence            9 6999876

>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=99.16  E-value=2.1e-11  Score=104.86  Aligned_cols=73  Identities=21%  Similarity=0.208  Sum_probs=62.8

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCH-HHHHHHHHHcC-CccCCeEEEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR-EAANLVIKRRN-LKLRDRELRL  413 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~-e~A~~Al~~ln-~~l~Gr~I~V  413 (548)
                      ...+||+|||+.+|+++|+++|+.|    |.|.+|.|+.+      +|||||.|.+. ++|..|+..++ ..|.++.+.|
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~f----G~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v   80 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNH----GEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEV   80 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSS----CCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhc----CChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEE
Confidence            4566999999999999999999999    99999999865      78999999985 78889998887 7777777777


Q ss_pred             Eeeec
Q 008920          414 SHAQQ  418 (548)
Q Consensus       414 ~~Ak~  418 (548)
                      .|+..
T Consensus        81 ~~~~~   85 (113)
T d1owxa_          81 TWEVL   85 (113)
T ss_dssp             EEEEC
T ss_pred             EEeec
Confidence            77654

>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=99.14  E-value=4e-11  Score=100.74  Aligned_cols=77  Identities=18%  Similarity=0.303  Sum_probs=65.5

Q ss_pred             CcccEEEEcCC--CCCC---------cHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEe
Q 008920          223 KLLRTIFVGNL--PLKV---------KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVF  291 (548)
Q Consensus       223 ~~~rtVfVgNL--P~~~---------tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F  291 (548)
                      +.+++|+|.||  |.++         .+++|...|+.||.|..|.+...                     ..+|||||+|
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~---------------------~~~G~~fV~f   64 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR---------------------HPDGVASVSF   64 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT---------------------CTTCEEEEEC
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC---------------------CCccEEEEEE
Confidence            45789999999  6543         24689999999999999988332                     2569999999


Q ss_pred             cCHHHHHHHH-HhcceeecCceeEeecCCC
Q 008920          292 KSEQSTEAAL-AFNMAVIGGNHIRLDRACP  320 (548)
Q Consensus       292 ~s~e~A~~Al-~lng~~~~gr~I~V~~a~~  320 (548)
                      .+.++|..|+ .|||..|.|+.|.|.++.+
T Consensus        65 ~~~e~A~~A~~~lng~~~~gr~i~v~~~~g   94 (99)
T d2dita1          65 RDPEEADYCIQTLDGRWFGGRQITAQAWDG   94 (99)
T ss_dssp             SCHHHHHHHHHHSTTCEETTEECEEEECCS
T ss_pred             CCHHHHHHHHHHhCCcEECCEEEEEEEeCC
Confidence            9999999999 6999999999999999864

>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=99.07  E-value=8e-11  Score=99.23  Aligned_cols=64  Identities=16%  Similarity=0.196  Sum_probs=56.4

Q ss_pred             CCCccEEEEeC--CCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-Ccc
Q 008920          333 YDIKKTVFVGN--LPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKL  406 (548)
Q Consensus       333 ~~~~~tLfV~N--Lp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l  406 (548)
                      ..++.+|||.|  ||..+|+++|+++|++|    |.|..|.++.+      +|||||+|.+.++|..|+..|| ..|
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~----G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKC----GLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHH----SCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhh----CcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            44678888855  99999999999999999    89999988765      6799999999999999999888 555

>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=99.04  E-value=2.4e-10  Score=95.83  Aligned_cols=79  Identities=16%  Similarity=0.278  Sum_probs=67.1

Q ss_pred             CCCccEEEEeCC--CCCC---------CHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHH
Q 008920          333 YDIKKTVFVGNL--PFDV---------KDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKR  401 (548)
Q Consensus       333 ~~~~~tLfV~NL--p~~~---------teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~  401 (548)
                      ....++|+|.||  |.++         ..++|+..|+.|    |.|..|.++.+    .++|||||.|.+.++|..|+..
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~----G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~   76 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKF----GQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQT   76 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGT----SCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHH
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCc----ccEEEEeccCC----CCccEEEEEECCHHHHHHHHHH
Confidence            446789999999  5432         136889999999    89999988765    3579999999999999999999


Q ss_pred             cC-CccCCeEEEEEeeecC
Q 008920          402 RN-LKLRDRELRLSHAQQN  419 (548)
Q Consensus       402 ln-~~l~Gr~I~V~~Ak~~  419 (548)
                      || ..|+||.|.|.|+.+.
T Consensus        77 lng~~~~gr~i~v~~~~g~   95 (99)
T d2dita1          77 LDGRWFGGRQITAQAWDGT   95 (99)
T ss_dssp             STTCEETTEECEEEECCSC
T ss_pred             hCCcEECCEEEEEEEeCCc
Confidence            98 9999999999998764

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.96  E-value=2.9e-10  Score=96.13  Aligned_cols=81  Identities=14%  Similarity=0.151  Sum_probs=68.8

Q ss_pred             CCccEEEEeCC--CCCCC--------HHHHHHHHhccCCCCCCeEEEEEeecCCC--CCCceEEEEEECCHHHHHHHHHH
Q 008920          334 DIKKTVFVGNL--PFDVK--------DEEIYQLFCGLNDLESSVEAVRVIRHPHM--RVGKGIAYVLFKTREAANLVIKR  401 (548)
Q Consensus       334 ~~~~tLfV~NL--p~~~t--------eedL~~~F~~~g~~~G~I~~VrI~~d~~t--g~srG~AFV~F~~~e~A~~Al~~  401 (548)
                      .++++|+|.||  |..+.        .+||++.|++|    |.|..|.|+++..+  ....|++||.|.+.++|..|+..
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~----G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~   77 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKY----GLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQG   77 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTT----SCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHH
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhccc----CceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHH
Confidence            35789999999  55443        36799999999    99999999987654  34568999999999999999988


Q ss_pred             cC-CccCCeEEEEEeeec
Q 008920          402 RN-LKLRDRELRLSHAQQ  418 (548)
Q Consensus       402 ln-~~l~Gr~I~V~~Ak~  418 (548)
                      |+ ..++||.|.|.|+.+
T Consensus        78 l~Gr~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          78 LTGRKFANRVVVTKYCDP   95 (104)
T ss_dssp             HSSCCSSSSCCEEEEECH
T ss_pred             HCCCEECCeEEEEEEcCH
Confidence            88 999999999999864

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.95  E-value=3.8e-10  Score=95.36  Aligned_cols=81  Identities=14%  Similarity=0.124  Sum_probs=65.6

Q ss_pred             cccEEEEcCC--CCCC--------cHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecC
Q 008920          224 LLRTIFVGNL--PLKV--------KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKS  293 (548)
Q Consensus       224 ~~rtVfVgNL--P~~~--------tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s  293 (548)
                      ++++|+|.||  |..+        ..++|++.|++||.|.+|.|...+..  .             .....|++||+|.+
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~--~-------------~~~~~g~vfV~f~~   67 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDG--V-------------EVPGCGKIFVEFTS   67 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTS--S-------------SCTTCCEEEEEESC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCC--C-------------ccCCceEEEEEECC
Confidence            4688999999  4443        34679999999999999998543321  1             12356899999999


Q ss_pred             HHHHHHHH-HhcceeecCceeEeecCC
Q 008920          294 EQSTEAAL-AFNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       294 ~e~A~~Al-~lng~~~~gr~I~V~~a~  319 (548)
                      .++|..|+ .|||..|.||.|.|.++.
T Consensus        68 ~e~A~~A~~~l~Gr~f~gR~v~v~f~~   94 (104)
T d1o0pa_          68 VFDCQKAMQGLTGRKFANRVVVTKYCD   94 (104)
T ss_dssp             HHHHHHHHHHHSSCCSSSSCCEEEEEC
T ss_pred             HHHHHHHHHHHCCCEECCeEEEEEEcC
Confidence            99999999 699999999999999875

>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=98.95  E-value=5.5e-10  Score=90.26  Aligned_cols=72  Identities=7%  Similarity=0.043  Sum_probs=60.1

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeE-EEEE
Q 008920          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRE-LRLS  414 (548)
Q Consensus       336 ~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~-I~V~  414 (548)
                      .+.|+|++||++++++.| ++|++|    |.|.++++..+      +|||||+|.+.++|.+||.+.+..|+|+. |.|.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~----G~I~~~~~~~~------~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~   72 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQY----GNILKHVMSNT------GNWMHIRYQSKLQARKALSKDGRIFGESIMIGVK   72 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTT----SCEEEEEECSS------SSEEEEEESSHHHHHHHHTTTTCEETTTEECEEE
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhh----hhhheEEecCC------CCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEE
Confidence            467999999999987655 579999    89999987543      78999999999999999975459999975 5688


Q ss_pred             eeec
Q 008920          415 HAQQ  418 (548)
Q Consensus       415 ~Ak~  418 (548)
                      .+.+
T Consensus        73 ~~~~   76 (81)
T d1wwha1          73 PCID   76 (81)
T ss_dssp             ECCC
T ss_pred             eCCC
Confidence            7764

>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=96.59  E-value=0.002  Score=51.48  Aligned_cols=69  Identities=17%  Similarity=0.309  Sum_probs=55.2

Q ss_pred             cEEEEcCCCCCCc---------HHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHH
Q 008920          226 RTIFVGNLPLKVK---------KKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQS  296 (548)
Q Consensus       226 rtVfVgNLP~~~t---------ee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~  296 (548)
                      -||.|.=+.....         -.+|.+.|..||+|.-||+..                         +...|+|.+-++
T Consensus        16 gTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~-------------------------d~mwVTF~dG~S   70 (95)
T d1ufwa_          16 ATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQ-------------------------GQMLVTFADSHS   70 (95)
T ss_dssp             CEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEET-------------------------TEEEEECSCSHH
T ss_pred             cEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeC-------------------------CeEEEEECCcHH
Confidence            4777754433322         247888999999999999832                         468999999999


Q ss_pred             HHHHHHhcceeecCceeEeecCC
Q 008920          297 TEAALAFNMAVIGGNHIRLDRAC  319 (548)
Q Consensus       297 A~~Al~lng~~~~gr~I~V~~a~  319 (548)
                      |.+|+.+++..+.|+.|.|....
T Consensus        71 AL~al~l~g~~v~G~~l~It~~~   93 (95)
T d1ufwa_          71 ALSVLDVDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHGGGSEETTEEEEEECCC
T ss_pred             HHHHhccCCeEEcceEEEEecCC
Confidence            99999999999999999997643

>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=96.41  E-value=0.0059  Score=49.05  Aligned_cols=70  Identities=21%  Similarity=0.214  Sum_probs=54.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-Hhc
Q 008920          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (548)
Q Consensus       226 rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~ln  304 (548)
                      +.|.|++||+++|++++.+.+...|.+....+......  ..+             ..-.-|||.|.+.+++.... .++
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s--~~~-------------~~~SRAYi~F~~~~~v~~F~~~f~   66 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTS--LYP-------------HMYARAYINFKNQEDIILFRDRFD   66 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCS--STT-------------CCCEEEEEEESSSHHHHHHHHHHT
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcC--CCC-------------CcceEEEEEeCCHHHHHHHHHHcC
Confidence            56999999999999999999999999887766442211  111             13357999999999998887 588


Q ss_pred             ceeecC
Q 008920          305 MAVIGG  310 (548)
Q Consensus       305 g~~~~g  310 (548)
                      |..|.+
T Consensus        67 g~~F~D   72 (91)
T d1uw4a_          67 GYVFLD   72 (91)
T ss_dssp             TCEEEC
T ss_pred             CcEEEc
Confidence            888854

>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=96.26  E-value=0.0037  Score=49.91  Aligned_cols=53  Identities=21%  Similarity=0.323  Sum_probs=48.0

Q ss_pred             HHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcCCccCCeEEEEEe
Q 008920          351 EEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSH  415 (548)
Q Consensus       351 edL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln~~l~Gr~I~V~~  415 (548)
                      .+|.+.|..|    |.|.-||++.+        -..|+|.+-..|.+|+.+.+..++|+.|.|..
T Consensus        39 ~~Llq~l~~~----GeViLvRFv~d--------~mwVTF~dG~SAL~al~l~g~~v~G~~l~It~   91 (95)
T d1ufwa_          39 TELMQTLGSY----GTIVLVRINQG--------QMLVTFADSHSALSVLDVDGMKVKGRAVKISG   91 (95)
T ss_dssp             HHHHHHHHHH----SCCSEEEEETT--------EEEEECSCSHHHHHHHHGGGSEETTEEEEEEC
T ss_pred             HHHHHHHhhC----CeEEEEEEeCC--------eEEEEECCcHHHHHHhccCCeEEcceEEEEec
Confidence            4677888999    89999999877        67999999999999999999999999999974

>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=96.09  E-value=0.013  Score=47.01  Aligned_cols=66  Identities=17%  Similarity=0.214  Sum_probs=52.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCC--ceEEEEEECCHHHHHHHHHHcC-Ccc
Q 008920          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVG--KGIAYVLFKTREAANLVIKRRN-LKL  406 (548)
Q Consensus       337 ~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~s--rG~AFV~F~~~e~A~~Al~~ln-~~l  406 (548)
                      .+|.|++||+.+|++++.+.++..    |.+.....+....+...  -.-|||.|.+.++.....+..+ ..+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~----~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F   70 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPM----PEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVF   70 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSC----CCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCc----CceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEE
Confidence            478999999999999999999987    88888877765443322  2359999999999988887766 444

>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=95.46  E-value=0.024  Score=42.99  Aligned_cols=60  Identities=17%  Similarity=0.161  Sum_probs=50.6

Q ss_pred             HHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC-CccCCeEEEEEeee
Q 008920          351 EEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN-LKLRDRELRLSHAQ  417 (548)
Q Consensus       351 edL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln-~~l~Gr~I~V~~Ak  417 (548)
                      +.|...|..+    |.|..|.|.... .|  .-.|-|...+..+|..|+..++ ..|++++|.|+|+.
T Consensus        11 q~L~~~f~~h----~~V~sv~l~~~~-dg--~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARH----GKVKSVELSPHT-DY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHH----SCEEEEEECSCC-ST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhh----eeEEEEEEEecc-CC--cEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            4566778898    899999887663 23  3379999999999999999999 99999999999975

>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=94.96  E-value=0.056  Score=40.89  Aligned_cols=61  Identities=21%  Similarity=0.331  Sum_probs=49.8

Q ss_pred             HHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHH-HhcceeecCceeEeec
Q 008920          239 KKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDR  317 (548)
Q Consensus       239 ee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al-~lng~~~~gr~I~V~~  317 (548)
                      .+.|.+.|..+|.|.+|.|..  .++                  ..-.|-|...+.++|..|+ .|+...|++..|.|.+
T Consensus        10 qq~L~~~f~~h~~V~sv~l~~--~~d------------------g~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~   69 (73)
T d2dgxa1          10 QQLLQEAFARHGKVKSVELSP--HTD------------------YQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSL   69 (73)
T ss_dssp             HHHHHHHHHHHSCEEEEEECS--CCS------------------TTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             HHHHHHHHHhheeEEEEEEEe--ccC------------------CcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEE
Confidence            345667899999999999822  221                  3357999999999999999 6999999999999988


Q ss_pred             CC
Q 008920          318 AC  319 (548)
Q Consensus       318 a~  319 (548)
                      +.
T Consensus        70 ~~   71 (73)
T d2dgxa1          70 AT   71 (73)
T ss_dssp             CC
T ss_pred             ec
Confidence            64

>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=91.33  E-value=0.24  Score=39.75  Aligned_cols=54  Identities=19%  Similarity=0.308  Sum_probs=44.3

Q ss_pred             cccEEEEcCCCCCCcHHHHHHHhhhcCCeeEEEEeeecccCCCCCccchhhhhhhccCCCcceEEEEecCHHHHHHHHH
Q 008920          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (548)
Q Consensus       224 ~~rtVfVgNLP~~~tee~L~~~Fs~fG~I~sVri~~~~~~~~~~prkga~~~~~~~~g~skG~AFV~F~s~e~A~~Al~  302 (548)
                      ...-||.-..|..+...+|.++|+.||.|.--.| .                        -.-|||.....++|..++.
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-d------------------------dTSa~V~L~~~e~~~~v~~   67 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-D------------------------DTSAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-E------------------------TTEEEEECSCHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceEEEEe-c------------------------CceEEEEecCHHHHHHHHH
Confidence            3456999999999999999999999998843333 1                        1379999999999999885

>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=80.54  E-value=2.4  Score=33.60  Aligned_cols=58  Identities=19%  Similarity=0.401  Sum_probs=46.0

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHhccCCCCCCeEEEEEeecCCCCCCceEEEEEECCHHHHHHHHHHcC
Q 008920          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRN  403 (548)
Q Consensus       334 ~~~~tLfV~NLp~~~teedL~~~F~~~g~~~G~I~~VrI~~d~~tg~srG~AFV~F~~~e~A~~Al~~ln  403 (548)
                      +....||.-.+|..+...||.++|+.|    |.|. |..+-|  |     -|||...+.++|..++..++
T Consensus        13 p~RdHVf~~tFP~~Wk~~dI~~lFSpf----G~V~-VswIdd--T-----Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          13 PKRDHVLHVTFPKEWKTSDLYQLFSAF----GNIQ-ISWIDD--T-----SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCSEEEEECCTTCCHHHHHHHHTTT----CSCC-CEEEET--T-----EEEEECSCHHHHHHHHHHHH
T ss_pred             CCcceeEEEeCCcccchhHHHHHhcCC----CceE-EEEecC--c-----eEEEEecCHHHHHHHHHHhc
Confidence            345678888999999999999999999    6553 434434  1     79999999999999986653