Psyllid ID: psy93

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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---
Protein Sequence
MLEQGFSNEQEVNQLYQARLRSYTGHFKIPEIEDMPFMSLGGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGGDRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEQQQGRGGSGGYGSPGQAYGNAIIDFEALAAAVGNAVVGNVTGVDNKGSAMDFDQGGRSGGGGGRRNDSASSGWSRREGGAGRWGPSVDHGSRRGGSGGGGPTDYQPKRRN
Secondary Structure (PSIPRED)
ccccccccccccccEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEEccccEEEEEEccHHHHHHHHHHHccccccccEEEEEEccccccEEEccccccccHHHHHHHHcccccEEEEEEEEccccccEEEEEEEEccHHHHHHHHHHHHccccccccccccEEEEccccccccccHHHHHHHcccccccccccccccccccccEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHcccccccHHHHHHcccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHHHHHHHHHHHcccccccccccccccHHccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccHHHcccccccccccEEEEEccccccccHHHHHHHHHHcccEEEEEEEccccEEEEEcccHHHHHHHHHHHccccccccEEEEEEEccccEEEEEcccccccHHHHHHHHcccccEEEEEEEEEcccccccEEEEEEccHHHHHHHHHHHcccEEEEEEccccEEEEccccccccccccHHHHHHHcHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MLEQGFSNEQEVNQLYQARLRSYtghfkipeiedmpfmslggrgggrgggvggrggyrgnrpdgrgsdmnesrmggggggdryfTEKIMAiqgptldlppsepqnkdikfaNNCRLYlgniggditenDIIELfkpygetqELFINKEKMFGFIRMDYKHNADKAkakldghvlkgrslkirfapinaAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVdergnskcEGIVEFARKPAAAQALRRCAEGCFFltqslrpvivepleltdeidglsertinkktpefykqrqvgprfatvnsFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEQqqgrggsggygspgqaygNAIIDFEALAAAVGNAVVGnvtgvdnkgsamdfdqggrsgggggrrndsassgwsrreggagrwgpsvdhgsrrggsggggptdyqpkrrn
Flexible Loop (DISEMBL)
mleqgfsnEQEVNQLYQARLRSYTGHFKIPEIEDMPFMSLGGRGGGrgggvggrggyrgnrpdgrgsdmnesrmgggGGGDRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKakldghvlkgrsLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLtqslrpvivepleltdeidglsertinkktpefykqrqvgprfatVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEQQQGRGGSGGYGSPGQAYGNAIIDFEALAAAVGNAVVGNVTGVDNKGSAMDFdqggrsgggggrrndsassgwsrreggagrwgpsvdhgsrrggsggggptdyqpkrrn
Low Complexity Region (SEG)
MLEQGFSNEQEVNQLYQARLRSYTGHFKIPEIEDMPFMSLggrgggrgggvggrggyrgnrpdgrgSDMNESRMggggggDRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEqqqgrggsggygspgqaygNAIIDFEalaaavgnavvgnvtgvdnKGSAMDFDQggrsgggggrrndsassgWSRREGGAGRWGPSVDHgsrrggsggggPTDYQPKRRN
Disordered region (IsUnstruct)
**************LYQARLRSYTGHFKIPEIEDM************************************************************************IKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEH***************************************************************************************QAYGNAIIDFEALAAAVGNAVVGNVTGV*******************************************************************
Disordered Region (DISOPRED)
*************QLYQARLRSYTGHFKIPEIEDMPFM*****************************************************************************LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV*********************PEFYKQRQVGPRFATVNSFEFEYGSRWKQLHE*****************IDRERQK******************************************************************************************************************************************************************
Disordered Region (DISEMBL)
MLEQGFSNEQEVNQLYQARLRSYTGHFKIPEIEDMPFMSLGGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGGDRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEQQQGRGGSGGYGSPGQAYGNAIIDFEALAAAVGNAVVGNVTGVDNKGSAMDFDQG*******************************************************
Disordered Region (DISPRO)
****GFSNEQEVNQLYQARLRSYTGHFKIPEIEDMPF******************************************GDRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEQQQG************AYGNAIIDFEALAAAVGNAVVGNVTGVDNKGSAMDFDQGGRSGGGG******ASS***********W***************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLEQGFSNEQEVNQLYQARLRSYTGHFKIPEIEDMPFMSLGGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGGDRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxNSMFLVEQQQGRGGSGGYGSPGQAYGNAIIDFEALAAAVGNAVVGNVTGVDNKGSAMDFDQGGRSGGGGGRRNDSASSGWSRREGGAGRWGPSVDHGSRRGGSGGGGPTDYQPKRRN
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	503	2.2.26 [Sep-21-2011]
Q9GRW7	697	Protein no-on-transient A	N/A	N/A	0.628	0.453	0.502	7e-97
Q9GRX4	698	Protein no-on-transient A	N/A	N/A	0.628	0.452	0.497	5e-95
Q04047	700	Protein no-on-transient A	no	N/A	0.622	0.447	0.491	2e-94
Q9U1N0	535	Hrp65 protein OS=Chironom	N/A	N/A	0.610	0.573	0.479	4e-89
P23246	707	Splicing factor, proline-	yes	N/A	0.526	0.374	0.474	5e-63
Q8VIJ6	699	Splicing factor, proline-	yes	N/A	0.526	0.379	0.474	6e-63
Q5ZK88	523	Paraspeckle component 1 O	no	N/A	0.479	0.460	0.482	1e-62
Q1LZD9	520	Paraspeckle component 1 O	no	N/A	0.479	0.463	0.482	3e-62
Q4KLH4	522	Paraspeckle component 1 O	no	N/A	0.479	0.461	0.482	7e-62
Q8R326	523	Paraspeckle component 1 O	no	N/A	0.479	0.460	0.482	7e-62

>sp|Q9GRW7|NONA_DROVI Protein no-on-transient A OS=Drosophila virilis GN=nonA PE=2 SV=1

 Score =  354 bits (909), Expect = 7e-97,   Method: Compositional matrix adjust.
 Identities = 173/344 (50%), Positives = 238/344 (69%), Gaps = 28/344 (8%)

Query: 79  GGDRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYG 138
           G D ++++++ +I GPT +LPP E   ++ KF+   RLY+GN+  DIT+ ++ E+FKPYG
Sbjct: 251 GDDFFYSQRLRSISGPTHELPPIEVA-QETKFSGRNRLYVGNLTNDITDEELREMFKPYG 309

Query: 139 ETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSC 198
           E  E+F N EK F F+++DY  NA+KAK  LDG + KGR +++RFAP    ++V NLT  
Sbjct: 310 EIGEIFSNLEKNFTFLKVDYHINAEKAKRPLDGSMRKGRHVRVRFAPNATILRVSNLTPF 369

Query: 199 VTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQS 258
           V+NELL  +F +FG IERA + VD+RG    EG VEFA+K +A+  LR C E CFFLT S
Sbjct: 370 VSNELLYKSFEIFGPIERASITVDDRGKHLGEGTVEFAKKSSASACLRLCNEKCFFLTAS 429

Query: 259 LRPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHEL 318
           LRP +VEP+E+ D+ DGL E+ +NKK  EF ++R VGPRFA +NSFE EYGSRWKQLH+L
Sbjct: 430 LRPCLVEPMEVNDDNDGLPEKALNKKLQEFNQERSVGPRFADLNSFEHEYGSRWKQLHDL 489

Query: 319 ---------------------------YEHETEMLRKELAQREIDRERQKAEWEMKERQA 351
                                      YE ETE+LR+EL +RE D ER+K EWEM+E+QA
Sbjct: 490 FKSKQDALKRELKMEEEKLDAQMEYARYEQETELLRQELRKRESDNERKKLEWEMREKQA 549

Query: 352 EELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEQQ 395
           EE+++R+EE M++H  EMQ R+ +QEED+RRRQ +N++F+  QQ
Sbjct: 550 EEMRKREEETMRRHQTEMQSRMVRQEEDMRRRQQENTLFMQAQQ 593

Required for normal vision and courtship behavior in Drosophila.
Drosophila virilis (taxid: 7244)

>sp|Q9GRX4|NONA_DROLR Protein no-on-transient A OS=Drosophila littoralis GN=nonA PE=2 SV=1

 Score =  348 bits (894), Expect = 5e-95,   Method: Compositional matrix adjust.
 Identities = 171/344 (49%), Positives = 235/344 (68%), Gaps = 28/344 (8%)

Query: 79  GGDRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYG 138
           G D +  +++ +I GPT +LPP E   ++ KF+   RLY+GN+  DIT+ ++ E+FKPYG
Sbjct: 247 GDDFFIAQRLRSISGPTHELPPIEVA-QETKFSGRNRLYVGNLTNDITDEELREMFKPYG 305

Query: 139 ETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSC 198
           E  E+F N EK F F+++DY  NA+KAK  LDG + KGR L++RFAP    ++V NLT  
Sbjct: 306 EIGEIFSNLEKNFTFLKVDYHINAEKAKRALDGSMRKGRQLRVRFAPNATILRVSNLTPF 365

Query: 199 VTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQS 258
           V+NELL  +F +FG IERA + VD+RG    EG VEFA+K +A+  LR C E CFFLT S
Sbjct: 366 VSNELLYKSFEIFGPIERASITVDDRGKHLGEGTVEFAKKSSASACLRLCNEKCFFLTAS 425

Query: 259 LRPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHEL 318
           LRP +VEP+E+ D+ DGL E+ +NKK  EF ++R VGPRFA +NSFE EYGSRWKQLH+L
Sbjct: 426 LRPCLVEPMEVNDDNDGLPEKALNKKLQEFNQERSVGPRFADLNSFEHEYGSRWKQLHDL 485

Query: 319 YE---------------------------HETEMLRKELAQREIDRERQKAEWEMKERQA 351
           ++                            ETE+ R+EL +RE D ER+K EWEM+E+QA
Sbjct: 486 FKSKQDALKRELKMEEEKLDAQMEYARYGQETELSRQELRKRESDNERKKLEWEMREKQA 545

Query: 352 EELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEQQ 395
           EE+++R+EE M++H  EMQ R+ +QEED+RRRQ +N++F+  QQ
Sbjct: 546 EEMRKREEETMRRHQTEMQSRMVRQEEDMRRRQQENTLFMQAQQ 589

Required for normal vision and courtship behavior in Drosophila.

Drosophila littoralis (taxid: 47316)

>sp|Q04047|NONA_DROME Protein no-on-transient A OS=Drosophila melanogaster GN=nonA PE=1 SV=2

 Score =  346 bits (887), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 168/342 (49%), Positives = 232/342 (67%), Gaps = 29/342 (8%)

Query: 81  DRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGET 140
           D + T+++ +I GPT +L P E    + KF+   RLY+GN+  DIT++++ E+FKPYGE 
Sbjct: 270 DFFITQRLRSISGPTFELEPVEVP-TETKFSGRNRLYVGNLTNDITDDELREMFKPYGEI 328

Query: 141 QELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVT 200
            E+F N +K F F+++DY  NA+KAK  LDG + KGR L++RFAP    ++V NLT  V+
Sbjct: 329 SEIFSNLDKNFTFLKVDYHPNAEKAKRALDGSMRKGRQLRVRFAPNATILRVSNLTPFVS 388

Query: 201 NELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLR 260
           NELL  +F +FG IERA + VD+RG    EGIVEFA+K +A+  LR C E CFFLT SLR
Sbjct: 389 NELLYKSFEIFGPIERASITVDDRGKHMGEGIVEFAKKSSASACLRMCNEKCFFLTASLR 448

Query: 261 PVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHEL-- 318
           P +V+P+E+ D+ DGL E+  NKK P+F ++R +GPRFA  NSFE EYGSRWKQLH L  
Sbjct: 449 PCLVDPMEVNDDTDGLPEKAFNKKMPDFNQERSIGPRFADPNSFEHEYGSRWKQLHNLFK 508

Query: 319 -------------------------YEHETEMLRKELAQREIDRERQKAEWEMKERQAEE 353
                                    YE ETE+LR+EL +RE+D ER+K EWEM+E+QAEE
Sbjct: 509 TKQDALKRELKMEEDKLEAQMEYARYEQETELLRQELRKREVDNERKKLEWEMREKQAEE 568

Query: 354 LKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEQQ 395
           +++R+EE M++H  EMQ  + +QEED+ RRQ + ++F+  QQ
Sbjct: 569 MRKREEETMRRHQTEMQSHMNRQEEDMLRRQQE-TLFMKAQQ 609

Required for normal vision and courtship behavior in Drosophila.

Drosophila melanogaster (taxid: 7227)

>sp|Q9U1N0|HRP65_CHITE Hrp65 protein OS=Chironomus tentans GN=HRP65 PE=1 SV=1

 Score =  329 bits (843), Expect = 4e-89,   Method: Compositional matrix adjust.
 Identities = 161/336 (47%), Positives = 230/336 (68%), Gaps = 29/336 (8%)

Query: 87  KIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFIN 146
           K+  + GPT DLP  E   ++IKF+   RLY+GN+  D+TE ++ ELF PYGE  E FIN
Sbjct: 88  KLKNLAGPTHDLP--ELVCEEIKFSGRNRLYIGNLTSDVTEEELKELFSPYGEISEAFIN 145

Query: 147 KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLEL 206
            EK F F+++DY+ NA++AK  LDG + K + ++IRFAP    I+VKNLT  V+NELL  
Sbjct: 146 AEKNFAFLKIDYRANAERAKKDLDGRMRKNKPIRIRFAPNATTIRVKNLTPFVSNELLFK 205

Query: 207 AFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP 266
           +F VFG +ERA++IVD+RG +  EGIVEFARK  A  AL+ C+E C+FLT SLRP +VE 
Sbjct: 206 SFEVFGQVERAVIIVDDRGKTTGEGIVEFARKSGAMSALKYCSEKCYFLTSSLRPCVVET 265

Query: 267 LELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELY------- 319
            +  DE DG  E+++ +K+ ++YK RQ GPRFA + SFE E+G++WKQ++++Y       
Sbjct: 266 FDHIDETDGFPEKSLMRKSNDYYKARQNGPRFAEMGSFEHEFGTKWKQMYDMYKQKHDAL 325

Query: 320 --------------------EHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDE 359
                               EHETE LR++L +RE DR+RQK EWE +ERQA+E + RDE
Sbjct: 326 KREMQLEEEKLEAQMEYAKFEHETESLREQLRKREQDRDRQKKEWEDRERQADESRIRDE 385

Query: 360 ELMKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEQQ 395
           + M++  ++MQ+R+ +Q+E++RRRQ +NS+F+  QQ
Sbjct: 386 QQMRRQQDDMQMRMQRQDEEMRRRQQENSLFMQAQQ 421

Component of nuclear connecting fibers associated with the transport of ribonucleoprotein particles from either the chromosome to the nuclear pore complex or their transient retention in the nucleoplasm.

Chironomus tentans (taxid: 7153)

>sp|P23246|SFPQ_HUMAN Splicing factor, proline- and glutamine-rich OS=Homo sapiens GN=SFPQ PE=1 SV=2

 Score =  242 bits (617), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 130/274 (47%), Positives = 178/274 (64%), Gaps = 9/274 (3%)

Query: 110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL 169
           +   CRL++GN+  DITE++   LF  YGE  E+FINK K FGFI+++ +  A+ AKA+L
Sbjct: 293 YTQRCRLFVGNLPADITEDEFKRLFAKYGEPGEVFINKGKGFGFIKLESRALAEIAKAEL 352

Query: 170 DGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKC 229
           D   ++GR L++RFA   AA+ V+NL+  V+NELLE AF  FG IERA+VIVD+RG S  
Sbjct: 353 DDTPMRGRQLRVRFATHAAALSVRNLSPYVSNELLEEAFSQFGPIERAVVIVDDRGRSTG 412

Query: 230 EGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFY 289
           +GIVEFA KPAA +A  RC+EG F LT + RPVIVEPLE  D+ DGL E+ + +K P + 
Sbjct: 413 KGIVEFASKPAARKAFERCSEGVFLLTTTPRPVIVEPLEQLDDEDGLPEK-LAQKNPMYQ 471

Query: 290 KQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKER 349
           K+R+  PRFA   +FE+EY  RWK L E+ + + E + K +   + D+   + E    E 
Sbjct: 472 KERETPPRFAQHGTFEYEYSQRWKSLDEMEKQQREQVEKNMKDAK-DKLESEMEDAYHEH 530

Query: 350 QA----EELKRRDEELMKK---HAEEMQLRLAQQ 376
           QA    ++L RR EEL +    H +EMQ R   Q
Sbjct: 531 QANLLRQDLMRRQEELRRMEELHNQEMQKRKEMQ 564

DNA- and RNA binding protein, involved in several nuclear processes. Essential pre-mRNA splicing factor required early in spliceosome formation and for splicing catalytic step II, probably as an heteromer with NONO. Binds to pre-mRNA in spliceosome C complex, and specifically binds to intronic polypyrimidine tracts. Interacts with U5 snRNA, probably by binding to a purine-rich sequence located on the 3' side of U5 snRNA stem 1b. May be involved in a pre-mRNA coupled splicing and polyadenylation process as component of a snRNP-free complex with SNRPA/U1A. The SFPQ-NONO heteromer associated with MATR3 may play a role in nuclear retention of defective RNAs. SFPQ may be involved in homologous DNA pairing; in vitro, promotes the invasion of ssDNA between a duplex DNA and produces a D-loop formation. The SFPQ-NONO heteromer may be involved in DNA unwinding by modulating the function of topoisomerase I/TOP1; in vitro, stimulates dissociation of TOP1 from DNA after cleavage and enhances its jumping between separate DNA helices. The SFPQ-NONO heteromer may be involved in DNA nonhomologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination and may stabilize paired DNA ends; in vitro, the complex strongly stimulates DNA end joining, binds directly to the DNA substrates and cooperates with the Ku70/G22P1-Ku80/XRCC5 (Ku) dimer to establish a functional preligation complex. SFPQ is involved in transcriptional regulation. Transcriptional repression is probably mediated by an interaction of SFPQ with SIN3A and subsequent recruitment of histone deacetylases (HDACs). The SFPQ-NONO/SF-1 complex binds to the CYP17 promoter and regulates basal and cAMP-dependent transcriptional avtivity. SFPQ isoform Long binds to the DNA binding domains (DBD) of nuclear hormone receptors, like RXRA and probably THRA, and acts as transcriptional corepressor in absence of hormone ligands. Binds the DNA sequence 5'-CTGAGTC-3' in the insulin-like growth factor response element (IGFRE) and inhibits IGF-I-stimulated transcriptional activity.

Homo sapiens (taxid: 9606)

>sp|Q8VIJ6|SFPQ_MOUSE Splicing factor, proline- and glutamine-rich OS=Mus musculus GN=Sfpq PE=1 SV=1

 Score =  242 bits (617), Expect = 6e-63,   Method: Compositional matrix adjust.
 Identities = 130/274 (47%), Positives = 179/274 (65%), Gaps = 9/274 (3%)

Query: 110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL 169
           +   CRL++GN+  DITE++   LF  YGE  E+FINK K FGFI+++ +  A+ AKA+L
Sbjct: 285 YTQRCRLFVGNLPADITEDEFKRLFAKYGEPGEVFINKGKGFGFIKLESRALAEIAKAEL 344

Query: 170 DGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKC 229
           D   ++GR L++RFA   AA+ V+NL+  V+NELLE AF  FG IERA+VIVD+RG S  
Sbjct: 345 DDTPMRGRQLRVRFATHAAALSVRNLSPYVSNELLEEAFSQFGPIERAVVIVDDRGRSTG 404

Query: 230 EGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFY 289
           +GIVEFA KPAA +A  RC+EG F LT + RPVIVEPLE  D+ DGL E+ + +K P + 
Sbjct: 405 KGIVEFASKPAARKAFERCSEGVFLLTTTPRPVIVEPLEQLDDEDGLPEK-LAQKNPMYQ 463

Query: 290 KQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKER 349
           K+R+  PRFA   +FE+EY  RWK L E+ + + E + K +   + D+   + E    E 
Sbjct: 464 KERETPPRFAQHGTFEYEYSQRWKSLDEMEKQQREQVEKNMKDAK-DKLESEMEDAYHEH 522

Query: 350 QA----EELKRRDEELMKK---HAEEMQLRLAQQ 376
           QA    ++L RR EEL +    H++EMQ R   Q
Sbjct: 523 QANLLRQDLMRRQEELRRMEELHSQEMQKRKEMQ 556

DNA- and RNA binding protein, involved in several nuclear processes. Essential pre-mRNA splicing factor required early in spliceosome formation and for splicing catalytic step II, probably as an heteromer with NONO. Binds to pre-mRNA in spliceosome C complex, and specifically binds to intronic polypyrimidine tracts. Interacts with U5 snRNA, probably by binding to a purine-rich sequence located on the 3' side of U5 snRNA stem 1b. May be involved in a pre-mRNA coupled splicing and polyadenylation process as component of a snRNP-free complex with SNRPA/U1A. The SFPQ-NONO heteromer associated with MATR3 may play a role in nuclear retention of defective RNAs. SFPQ may be involved in homologous DNA pairing; in vitro, promotes the invasion of ssDNA between a duplex DNA and produces a D-loop formation. The SFPQ-NONO heteromer may be involved in DNA unwinding by modulating the function of topoisomerase I/TOP1; in vitro, stimulates dissociation of TOP1 from DNA after cleavage and enhances its jumping between separate DNA helices. The SFPQ-NONO heteromer may be involved in DNA nonhomologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination and may stabilize paired DNA ends; in vitro, the complex strongly stimulates DNA end joining, binds directly to the DNA substrates and cooperates with the Ku70/G22P1-Ku80/XRCC5 (Ku) dimer to establish a functional preligation complex. SFPQ is involved in transcriptional regulation. Transcriptional repression is probably mediated by an interaction of SFPQ with SIN3A and subsequent recruitment of histone deacetylases (HDACs). The SFPQ-NONO-NR5A1 complex binds to the CYP17 promoter and regulates basal and cAMP-dependent transcriptional avtivity. SFPQ isoform Long binds to the DNA binding domains (DBD) of nuclear hormone receptors, like RXRA and probably THRA, and acts as transcriptional corepressor in absence of hormone ligands. Binds the DNA sequence 5'-CTGAGTC-3' in the insulin-like growth factor response element (IGFRE) and inhibits IGF-I-stimulated transcriptional activity.

Mus musculus (taxid: 10090)

>sp|Q5ZK88|PSPC1_CHICK Paraspeckle component 1 OS=Gallus gallus GN=PSPC1 PE=2 SV=1

 Score =  240 bits (613), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 122/253 (48%), Positives = 170/253 (67%), Gaps = 12/253 (4%)

Query: 110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL 169
           +   CRL++GN+  DITE D   LF+ YGE  E+FIN+++ FGFIR++ +  A+ AKA+L
Sbjct: 77  YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAEL 136

Query: 170 DGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKC 229
           DG +LK R L+IRFA   AA+ VKNL+  V+NELLE AF  FG +ERA+V+VD+RG +  
Sbjct: 137 DGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVERAVVVVDDRGRATG 196

Query: 230 EGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFY 289
           +G VEFA KP A +AL RC++G F LT + RPV+VEP+E  D+ DGL E+ + +KT +++
Sbjct: 197 KGFVEFAAKPPARKALERCSDGAFLLTTTPRPVVVEPMEQFDDEDGLPEKLM-QKTQQYH 255

Query: 290 KQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKER 349
           K+R+  PRFA   +FEFEY SRWK L E+     E  ++E   R I   ++K E EM   
Sbjct: 256 KEREQPPRFAQPGTFEFEYASRWKALDEM-----EKQQREQVDRNIREAKEKLEAEM--- 307

Query: 350 QAEELKRRDEELM 362
              E  R + +LM
Sbjct: 308 ---EAARHEHQLM 317

Together with NONO, required for the formation of nuclear paraspeckles. Acts as a coactivator during transcriptional activation. Binds to RNA.

Gallus gallus (taxid: 9031)

>sp|Q1LZD9|PSPC1_BOVIN Paraspeckle component 1 OS=Bos taurus GN=PSPC1 PE=2 SV=1

 Score =  239 bits (611), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 122/253 (48%), Positives = 170/253 (67%), Gaps = 12/253 (4%)

Query: 110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL 169
           +   CRL++GN+  DITE+D   LF+ YGE  E+FIN+++ FGFIR++ +  A+ AKA+L
Sbjct: 75  YTQRCRLFVGNLPTDITEDDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAEL 134

Query: 170 DGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKC 229
           DG +LK R L+IRFA   AA+ VKNL+  V+NELLE AF  FG +E+A+V+VD+RG +  
Sbjct: 135 DGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATG 194

Query: 230 EGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFY 289
           +G VEFA KP A +AL RC +G F LT + RPVIVEP+E  D+ DGL E+ + +KT +++
Sbjct: 195 KGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLM-QKTQQYH 253

Query: 290 KQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKER 349
           K+R+  PRFA   +FEFEY SRWK L E+     E  ++E   R I   ++K E EM   
Sbjct: 254 KEREQPPRFAQPGTFEFEYASRWKALDEM-----EKQQREQVDRNIREAKEKLEAEM--- 305

Query: 350 QAEELKRRDEELM 362
              E  R + +LM
Sbjct: 306 ---EAARHEHQLM 315

Together with NONO, required for the formation of nuclear paraspeckles. Regulates, cooperatively with NONO and SFPQ, androgen receptor-mediated gene transcription activity in Sertoli cell line. Binds to poly(A), poly(G) and poly(U) RNA homopolymers.

Bos taurus (taxid: 9913)

>sp|Q4KLH4|PSPC1_RAT Paraspeckle component 1 OS=Rattus norvegicus GN=Pspc1 PE=2 SV=1

 Score =  238 bits (608), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 122/253 (48%), Positives = 169/253 (66%), Gaps = 12/253 (4%)

Query: 110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL 169
           +   CRL++GN+  DITE D   LF+ YGE  E+FIN+++ FGFIR++ +  A+ AKA+L
Sbjct: 77  YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAEL 136

Query: 170 DGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKC 229
           DG +LK R L+IRFA   AA+ VKNL+  V+NELLE AF  FG +E+A+V+VD+RG +  
Sbjct: 137 DGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATG 196

Query: 230 EGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFY 289
           +G VEFA KP A +AL RC +G F LT + RPVIVEP+E  D+ DGL E+ + +KT +++
Sbjct: 197 KGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLM-QKTQQYH 255

Query: 290 KQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKER 349
           K+R+  PRFA   +FEFEY SRWK L E+     E  ++E   R I   ++K E EM   
Sbjct: 256 KEREQPPRFAQPGTFEFEYASRWKALDEM-----EKQQREQVDRNIREAKEKLEAEM--- 307

Query: 350 QAEELKRRDEELM 362
              E  R + +LM
Sbjct: 308 ---EAARHEHQLM 317

Together with NONO, required for the formation of nuclear paraspeckles. Regulates, cooperatively with NONO and SFPQ, androgen receptor-mediated gene transcription activity in Sertoli cell line. Binds to poly(A), poly(G) and poly(U) RNA homopolymers.

Rattus norvegicus (taxid: 10116)

>sp|Q8R326|PSPC1_MOUSE Paraspeckle component 1 OS=Mus musculus GN=Pspc1 PE=1 SV=1

 Score =  238 bits (607), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 122/253 (48%), Positives = 169/253 (66%), Gaps = 12/253 (4%)

Query: 110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL 169
           +   CRL++GN+  DITE D   LF+ YGE  E+FIN+++ FGFIR++ +  A+ AKA+L
Sbjct: 77  YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAEL 136

Query: 170 DGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKC 229
           DG +LK R L+IRFA   AA+ VKNL+  V+NELLE AF  FG +E+A+V+VD+RG +  
Sbjct: 137 DGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATG 196

Query: 230 EGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFY 289
           +G VEFA KP A +AL RC +G F LT + RPVIVEP+E  D+ DGL E+ + +KT +++
Sbjct: 197 KGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLM-QKTQQYH 255

Query: 290 KQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKER 349
           K+R+  PRFA   +FEFEY SRWK L E+     E  ++E   R I   ++K E EM   
Sbjct: 256 KEREQPPRFAQPGTFEFEYASRWKALDEM-----EKQQREQVDRNIREAKEKLEAEM--- 307

Query: 350 QAEELKRRDEELM 362
              E  R + +LM
Sbjct: 308 ---EAARHEHQLM 317

Together with NONO, required for the formation of nuclear paraspeckles. Regulates, cooperatively with NONO and SFPQ, androgen receptor-mediated gene transcription activity in Sertoli cell line. Binds to poly(A), poly(G) and poly(U) RNA homopolymers.

Mus musculus (taxid: 10090)

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	503
242020088	522	Hrp65 protein, putative [Pediculus human	0.654	0.630	0.578	1e-115
193605913	547	PREDICTED: hrp65 protein-like [Acyrthosi	0.767	0.705	0.507	1e-107
91094279	495	PREDICTED: similar to splicing factor pr	0.701	0.713	0.537	1e-106
383861809	566	PREDICTED: hrp65 protein-like [Megachile	0.630	0.560	0.557	1e-101
380023432	563	PREDICTED: hrp65 protein-like [Apis flor	0.632	0.564	0.557	1e-100
321454568	472	hypothetical protein DAPPUDRAFT_204255 [	0.610	0.650	0.547	1e-100
328792621	563	PREDICTED: hrp65 protein-like [Apis mell	0.632	0.564	0.557	1e-100
307200250	589	Hrp65 protein [Harpegnathos saltator]	0.719	0.614	0.496	1e-100
350412928	571	PREDICTED: hrp65 protein-like [Bombus im	0.632	0.556	0.548	3e-99
390177481	698	GA27079, isoform B [Drosophila pseudoobs	0.624	0.449	0.523	4e-99

>gi|242020088|ref|XP_002430488.1| Hrp65 protein, putative [Pediculus humanus corporis] gi|212515645|gb|EEB17750.1| Hrp65 protein, putative [Pediculus humanus corporis]

 Score =  421 bits (1083), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 213/368 (57%), Positives = 266/368 (72%), Gaps = 39/368 (10%)

Query: 81  DRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGET 140
           D    ++I  I GPT++LPP + + K  KF+  CRLY+GN+  D+TE +I +LF PYGET
Sbjct: 127 DDRLIDRIATISGPTIELPPVDAKEK--KFSGRCRLYIGNLANDVTEEEIKQLFAPYGET 184

Query: 141 QELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVT 200
            E+FIN EKMF F+R+DY+ NA+KAK +LDG + KGR LK+RFAP +AAIKVKNL   VT
Sbjct: 185 SEIFINSEKMFAFVRVDYRSNAEKAKRELDGFMRKGRPLKVRFAPHSAAIKVKNLNQWVT 244

Query: 201 NELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLR 260
           NELLE AF VFG+IERA+VI DERG S  EGIVEFARKP A QALRRC EGC+F+T SLR
Sbjct: 245 NELLEWAFQVFGEIERAVVIGDERGKSTGEGIVEFARKPGATQALRRCTEGCYFITSSLR 304

Query: 261 PVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHEL-- 318
           PVIVEPL+  D+IDG SE+++ KK PEF+K+R+VGPRFA   SFEFEYG+RWKQLHEL  
Sbjct: 305 PVIVEPLDQVDDIDGYSEKSLFKKGPEFFKEREVGPRFANHGSFEFEYGTRWKQLHELYK 364

Query: 319 -------------------------YEHETEMLRKELAQREIDRERQKAEWEMKERQAEE 353
                                    YEHETE+LR++L  RE D+ERQK EWE+KERQAEE
Sbjct: 365 QKEEALRREMKMEEEKLEAQMEYAKYEHETELLREQLRLREQDKERQKREWELKERQAEE 424

Query: 354 LKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSMF---------LVEQQQGRG-GSGG 403
            +R DEE+M++ AEEMQLR+ +QEE+LRRRQ +N++F         L +Q+Q  G G GG
Sbjct: 425 QRRSDEEMMRRQAEEMQLRIHRQEEELRRRQQENTLFMQAHQLNSLLDQQEQALGSGPGG 484

Query: 404 YGSPGQAY 411
           Y S G+ +
Sbjct: 485 YDSAGRGH 492

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193605913|ref|XP_001947323.1| PREDICTED: hrp65 protein-like [Acyrthosiphon pisum]

 Score =  395 bits (1014), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 214/422 (50%), Positives = 274/422 (64%), Gaps = 36/422 (8%)

Query: 80  GDRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGE 139
            D  + E++M I GPT +LP ++   +  KF + CRLY+GN+  D TE ++IE+FKPYGE
Sbjct: 128 ADALWNERLMQIMGPTHELPQTDTTER--KFLSQCRLYIGNLV-DCTEEELIEMFKPYGE 184

Query: 140 TQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCV 199
             E F+NKEKMF FIR+DY+ NA+KAK +LDG   KGR LKIRFAPI AAIKVKNLT  V
Sbjct: 185 VSENFLNKEKMFAFIRLDYRTNAEKAKRELDGQTRKGRMLKIRFAPIAAAIKVKNLTPFV 244

Query: 200 TNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSL 259
           +NELLE AF +FGDIER  V+VDERGNS  EGI+EF+RK AA+ AL+RC+EGCFFLT SL
Sbjct: 245 SNELLEYAFSIFGDIERCQVMVDERGNSTGEGIIEFSRKNAASNALKRCSEGCFFLTSSL 304

Query: 260 RPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHEL- 318
           RP +VE  E  D  DGL ++ + KKT +F KQR VGPRFA  NSFE E+G+RWKQL EL 
Sbjct: 305 RPCVVETYEFVDSSDGLPDKLLPKKTMDFQKQRDVGPRFANPNSFEHEFGTRWKQLAELY 364

Query: 319 --------------------------YEHETEMLRKELAQREIDRERQKAEWEMKERQAE 352
                                     YEHETEMLR++L QRE+DRERQK EWEMKERQAE
Sbjct: 365 KSKEDALKREMKLEEEKLEAQMEYARYEHETEMLREQLRQREMDRERQKMEWEMKERQAE 424

Query: 353 ELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEQQQGRGGSGGYGSPGQAYG 412
           + + R+ ++ ++ +E++ +R+  Q+E++RRRQ DNS F+ + + G G     G P    G
Sbjct: 425 DQRLREGDIFRRQSEDLSMRMHHQDEEMRRRQQDNSSFMQDHRGGPGKPQFDGPPIPVEG 484

Query: 413 NAIIDFEALAAAVGNAVVGNVTGV--DNKGSAMD---FDQGGRSGGGGGRRNDSASSGWS 467
            ++ + EA+ A  G      V     DN+G       FD G R G  GGR      +G  
Sbjct: 485 MSVRELEAITAQGGMESTPFVETFVRDNQGVLPPPGLFDAGPR-GDRGGRWGQDRRNGQD 543

Query: 468 RR 469
           RR
Sbjct: 544 RR 545

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91094279|ref|XP_970760.1| PREDICTED: similar to splicing factor proline- and glutamine-rich [Tribolium castaneum] gi|270014396|gb|EFA10844.1| hypothetical protein TcasGA2_TC001621 [Tribolium castaneum]

 Score =  392 bits (1007), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 208/387 (53%), Positives = 258/387 (66%), Gaps = 34/387 (8%)

Query: 58  RGNR-PDGRGSDMNESRMGGGGGGDRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRL 116
           R NR P G   + N +  G  G  D+   EK+  + GPT DLPP +   K  KF+   RL
Sbjct: 88  RPNRGPGGPHGNQNFNEHGPPGRIDK-INEKLANMNGPTFDLPPLDHSEK--KFSGRTRL 144

Query: 117 YLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKG 176
           Y+GNIG D+TE+D+ ELF+PYGET E F+NKEK F FIR+DY+ NA+KAK +LDG + KG
Sbjct: 145 YVGNIGNDVTEDDLTELFRPYGETSEHFVNKEKNFAFIRVDYRANAEKAKRELDGILFKG 204

Query: 177 RSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFA 236
           ++LKIRFAP  + +KVKNLT  V+NELL  +F VFG++ERA VIVDERG    EGIVEFA
Sbjct: 205 KNLKIRFAPNGSTVKVKNLTPFVSNELLYYSFSVFGEVERAYVIVDERGKPVGEGIVEFA 264

Query: 237 RKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGP 296
           RK  A  A+RRC+EGCFFLT SLRPVIVE  E  D+ DG  E+ +NKK PEF K R+VGP
Sbjct: 265 RKGCALNAVRRCSEGCFFLTTSLRPVIVESYEPMDDSDGYPEKYLNKKNPEFSKSREVGP 324

Query: 297 RFATVNSFEFEYGSRWKQLHEL---------------------------YEHETEMLRKE 329
           RFA+VNSFE+EYG RWKQLHEL                           YEHETEMLR +
Sbjct: 325 RFASVNSFEYEYGMRWKQLHELFAQKEEAMKKEYEMEKEKLEAQMEFARYEHETEMLRDQ 384

Query: 330 LAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSM 389
           L  RE+DR+RQK EWEMKER AEE ++R+EE M++  EEMQ R+  QEE++RRRQ +N++
Sbjct: 385 LRAREMDRDRQKHEWEMKERLAEEQRQRNEEQMRRQQEEMQNRMMHQEEEMRRRQQENNL 444

Query: 390 FLVEQQQG---RGGSGGYGSPGQAYGN 413
           F+   Q     +     Y  P   Y N
Sbjct: 445 FMQAHQLDNMLQQEEQAYEEPSGMYNN 471

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383861809|ref|XP_003706377.1| PREDICTED: hrp65 protein-like [Megachile rotundata]

 Score =  375 bits (963), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 193/346 (55%), Positives = 246/346 (71%), Gaps = 29/346 (8%)

Query: 76  GGGGGDRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFK 135
           G    D    E+IMAI GPT DLPP E   K  KF+   RLY+GN+  D+TE +I ++F+
Sbjct: 114 GNRSQDDRLMERIMAISGPTHDLPPQETTEK--KFSGRNRLYIGNLTNDVTEEEIQQMFQ 171

Query: 136 PYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNL 195
            YGE  ELF+NKEK F F+RMDY+ NA+KAK +LDG + KGR+LK+RFAP ++ IK+KNL
Sbjct: 172 QYGEISELFVNKEKNFAFLRMDYRVNAEKAKHELDGTMRKGRALKVRFAPHSSTIKIKNL 231

Query: 196 TSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFL 255
           T  ++NELLE AF VFG+IERAIVIVD+RG S  EGIVEF RKP+A  ALR+C EGC+FL
Sbjct: 232 TPWISNELLERAFSVFGEIERAIVIVDDRGKSTGEGIVEFCRKPSAQLALRKCTEGCYFL 291

Query: 256 TQSLRPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQL 315
           T SLRPV+VEP E  D++DG  ++ + +K PEF+K R +GPRFA + SFE EYG+RWKQL
Sbjct: 292 TASLRPVVVEPFEQQDDVDGYPDKNLPRKNPEFFKARDIGPRFAQIGSFEHEYGTRWKQL 351

Query: 316 HEL---------------------------YEHETEMLRKELAQREIDRERQKAEWEMKE 348
           HEL                           YEHETE+LR++L  RE DRERQK EWEMKE
Sbjct: 352 HELYKQKEEALKREMAMEEEKLEAQMEFARYEHETELLREQLRMREADRERQKREWEMKE 411

Query: 349 RQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEQ 394
           RQAEE + R+EEL ++  EEM +R+ +QEE+L RRQ +N++F+ EQ
Sbjct: 412 RQAEEQRTREEELRRRQQEEMAMRIRRQEEELHRRQQENNLFMQEQ 457

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380023432|ref|XP_003695527.1| PREDICTED: hrp65 protein-like [Apis florea]

 Score =  371 bits (952), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 194/348 (55%), Positives = 247/348 (70%), Gaps = 30/348 (8%)

Query: 74  MGGGGGGDRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIEL 133
           MG     DR   E+IMAI GPT +LP  E   K  KF+   RLY+GN+  D+TE +I ++
Sbjct: 113 MGNRSQDDR-LMERIMAISGPTHELPSQETTEK--KFSGRNRLYIGNLTNDVTEEEIQQM 169

Query: 134 FKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVK 193
           F+ YGE  ELF+NKEK F F+RMDY+ NA+KAK +LDG + KGR+LK+RFAP ++ IKVK
Sbjct: 170 FQQYGEISELFVNKEKNFAFLRMDYRVNAEKAKHELDGTMRKGRALKVRFAPHSSTIKVK 229

Query: 194 NLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCF 253
           NLT  ++NELLE AF VFG+IERAIVIVD+RG S  EGIVEF RKP+A  ALR+C EGC+
Sbjct: 230 NLTPWISNELLERAFSVFGEIERAIVIVDDRGKSTGEGIVEFCRKPSAQLALRKCTEGCY 289

Query: 254 FLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWK 313
           FLT SLRPV+VEP E  D+IDG  ++ + +K PEF+K R +GPRFA + SFE EYG+RWK
Sbjct: 290 FLTASLRPVVVEPFEQQDDIDGYPDKNLPRKNPEFFKARDIGPRFAQIGSFEHEYGTRWK 349

Query: 314 QLHEL---------------------------YEHETEMLRKELAQREIDRERQKAEWEM 346
           QLHEL                           YEHETE+LR++L  RE DRERQK EWEM
Sbjct: 350 QLHELYKQKEEALKREMAMEEEKLEAQMEFARYEHETELLREQLRMREADRERQKREWEM 409

Query: 347 KERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEQ 394
           KERQAEE + R+EEL ++  EEM +R+ +Q+E+L RRQ +N++F+ EQ
Sbjct: 410 KERQAEEQRTREEELRRRQQEEMAMRIRRQDEELHRRQQENNLFMQEQ 457

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321454568|gb|EFX65733.1| hypothetical protein DAPPUDRAFT_204255 [Daphnia pulex]

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 184/336 (54%), Positives = 236/336 (70%), Gaps = 29/336 (8%)

Query: 86  EKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFI 145
           EK+  +   T++LP       + KF+   RLY+GN+G DI E D+ E F  YGE  E+F+
Sbjct: 75  EKLATLSNSTVELPIR--SFTETKFSGRSRLYVGNLGNDIVEQDLKEYFSAYGEIAEVFL 132

Query: 146 NKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLE 205
           NKEK F F+R+DY+ N++KAK +LDG VLKGR+L++R AP +AA++VKNL+  VTNELLE
Sbjct: 133 NKEKGFAFVRLDYRSNSEKAKRELDGKVLKGRTLRVRSAPHSAAVRVKNLSPFVTNELLE 192

Query: 206 LAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE 265
            AF +FGDIERAIV+ +ERG S  EG+VEF RKP A  A+RRC +GCFFLT SLRPV+VE
Sbjct: 193 KAFSIFGDIERAIVVANERGQSTNEGVVEFVRKPGAQAAIRRCTDGCFFLTSSLRPVVVE 252

Query: 266 PLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHEL------- 318
           P+E  D+ DG SER   KKTPEF K+R+ GPRFA  NSF+F YG RWKQL EL       
Sbjct: 253 PMEQLDDEDGFSERAFTKKTPEFSKEREAGPRFAEPNSFQFTYGQRWKQLLELYKQKMDA 312

Query: 319 --------------------YEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRD 358
                               YEHETE+LR++L QRE DRERQK +WEMKERQ EE + R+
Sbjct: 313 VERELKIEEDKLVSQMEYARYEHETELLREQLRQREQDRERQKRDWEMKERQHEESRLRE 372

Query: 359 EELMKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEQ 394
           EE +++  +EMQ RL QQE+++RRRQ +N+MF+ EQ
Sbjct: 373 EETLRRQQDEMQHRLRQQEDEMRRRQQENTMFMQEQ 408

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328792621|ref|XP_001121935.2| PREDICTED: hrp65 protein-like [Apis mellifera]

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 194/348 (55%), Positives = 247/348 (70%), Gaps = 30/348 (8%)

Query: 74  MGGGGGGDRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIEL 133
           MG     DR   E+IMAI GPT +LP  E   K  KF+   RLY+GN+  D+TE +I ++
Sbjct: 113 MGNRSQDDR-LMERIMAISGPTHELPSQETTEK--KFSGRNRLYIGNLTNDVTEEEIQQM 169

Query: 134 FKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVK 193
           F+ YGE  ELF+NKEK F F+RMDY+ NA+KAK +LDG + KGR+LK+RFAP ++ IKVK
Sbjct: 170 FQQYGEISELFVNKEKNFAFLRMDYRVNAEKAKHELDGTMRKGRALKVRFAPHSSTIKVK 229

Query: 194 NLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCF 253
           NLT  ++NELLE AF VFG+IERAIVIVD+RG S  EGIVEF RKP+A  ALR+C EGC+
Sbjct: 230 NLTPWISNELLERAFSVFGEIERAIVIVDDRGKSTGEGIVEFCRKPSAQLALRKCTEGCY 289

Query: 254 FLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWK 313
           FLT SLRPV+VEP E  D+IDG  ++ + +K PEF+K R +GPRFA + SFE EYG+RWK
Sbjct: 290 FLTASLRPVVVEPFEQQDDIDGYPDKNLPRKNPEFFKARDIGPRFAQIGSFEHEYGTRWK 349

Query: 314 QLHEL---------------------------YEHETEMLRKELAQREIDRERQKAEWEM 346
           QLHEL                           YEHETE+LR++L  RE DRERQK EWEM
Sbjct: 350 QLHELYKQKEEALKREMAMEEEKLEAQMEFARYEHETELLREQLRMREADRERQKREWEM 409

Query: 347 KERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEQ 394
           KERQAEE + R+EEL ++  EEM +R+ +Q+E+L RRQ +N++F+ EQ
Sbjct: 410 KERQAEEQRTREEELRRRQQEEMAMRIRRQDEELHRRQQENNLFMQEQ 457

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307200250|gb|EFN80529.1| Hrp65 protein [Harpegnathos saltator]

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 203/409 (49%), Positives = 263/409 (64%), Gaps = 47/409 (11%)

Query: 81  DRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGET 140
           D    E+IMAI GPT +LPP E   K  KF+   RLY+GN+  D+TE +I  +F+ YGE 
Sbjct: 143 DDRLMERIMAISGPTHELPPQEMTEK--KFSGRNRLYIGNLTNDVTEEEIQTMFRKYGEI 200

Query: 141 QELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVT 200
            ELF+NKEK F F+RMDY+ NA+KAK +LDG V KGR+LK+RFAP ++ IK+KNLT  ++
Sbjct: 201 SELFVNKEKSFAFLRMDYRINAEKAKHELDGTVRKGRALKVRFAPHSSTIKIKNLTPWIS 260

Query: 201 NELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLR 260
           NELLE AF VFG++ERAIVIVD+RG S  EG+VE+ RKP+A  ALR+C EGC+FLT SLR
Sbjct: 261 NELLEKAFSVFGEVERAIVIVDDRGKSTGEGVVEYCRKPSAQLALRKCTEGCYFLTASLR 320

Query: 261 PVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHEL-- 318
           PV+VEP E  D++DG  ++ + +K PEF+K R +GPRFA + SFE EYG+RWKQLHEL  
Sbjct: 321 PVVVEPFEQQDDVDGYPDKNLPRKNPEFFKARDIGPRFAQLGSFEHEYGTRWKQLHELYK 380

Query: 319 -------------------------YEHETEMLRKELAQREIDRERQKAEWEMKERQAEE 353
                                    YEHETE+LR++L  RE DRERQK EWEMKERQAEE
Sbjct: 381 QKEEALKREMAMEEEKLEAQMEFARYEHETELLREQLRMREADRERQKREWEMKERQAEE 440

Query: 354 LKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEQ----------------QQG 397
            + R+EEL ++  EEM +R+ +QEE+L RRQ +N++F+ EQ                   
Sbjct: 441 QRTREEELRRRQQEEMAIRIRRQEEELHRRQQENNLFMQEQAIRSSGGGLGGGKNYDSVS 500

Query: 398 RGGSGGYGSPGQAYGNAIIDFEALAAAVGNAVVGNVTGV-DNKGSAMDF 445
                GYG P    G   +D ++   A      GN  G  D++G  MD 
Sbjct: 501 NNDRDGYGQPDGGSG-IPVDPKSFMDAYNTMDRGNRGGYNDDRGQIMDL 548

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350412928|ref|XP_003489819.1| PREDICTED: hrp65 protein-like [Bombus impatiens]

 Score =  369 bits (946), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 193/352 (54%), Positives = 249/352 (70%), Gaps = 34/352 (9%)

Query: 74  MGGGGGGDRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIEL 133
           MG     DR   E+IMAI GPT DLPP  P+  + KF+   RLY+GN+  D+TE +I ++
Sbjct: 114 MGNRSQDDR-LMERIMAISGPTHDLPP--PETTEKKFSGRNRLYIGNLSNDVTEEEIQQI 170

Query: 134 FKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL----KGRSLKIRFAPINAA 189
           F+ YGE  ELF+NKEK F F+RMDY+ NA+KAK +LDG  +    KGR+LK+RFAP ++ 
Sbjct: 171 FQQYGEISELFVNKEKNFAFLRMDYRVNAEKAKHELDGKNVFTNSKGRALKVRFAPHSST 230

Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCA 249
           +KVKNLT  +TNELLE AF VFG+IERAIVI D++G S  EGIVEF RKP+A  ALR+C 
Sbjct: 231 VKVKNLTPWITNELLERAFSVFGEIERAIVIADDKGKSTGEGIVEFCRKPSAQLALRKCT 290

Query: 250 EGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYG 309
           EGC+FLT SLRPV+V+P EL D+IDG S++ + +K  EF+  R +GPRFA + SFE+EYG
Sbjct: 291 EGCYFLTASLRPVVVKPFELLDDIDGYSDKNLPRKNQEFFTARDIGPRFAKIGSFEYEYG 350

Query: 310 SRWKQLHEL---------------------------YEHETEMLRKELAQREIDRERQKA 342
           +RWKQLHEL                           YEHETE+LR++L  RE DRERQK 
Sbjct: 351 TRWKQLHELYEQKEEALKREMAMEEEKLEAQMEFARYEHETELLREQLRMREADRERQKR 410

Query: 343 EWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEQ 394
           EWEMKERQAEE + R+EEL ++  EEM +R+ +QEE+L RRQ +N++F+ EQ
Sbjct: 411 EWEMKERQAEEQRTREEELRRRQQEEMAMRIRRQEEELHRRQQENNLFMQEQ 462

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|390177481|ref|XP_003736389.1| GA27079, isoform B [Drosophila pseudoobscura pseudoobscura] gi|388859061|gb|EIM52462.1| GA27079, isoform B [Drosophila pseudoobscura pseudoobscura]

 Score =  368 bits (944), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 179/342 (52%), Positives = 241/342 (70%), Gaps = 28/342 (8%)

Query: 81  DRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGET 140
           D +  +++ AI GPTL+LPP E   ++ KF+   RLY+GN+ GDIT+N++ E+FKPYGE 
Sbjct: 280 DFFIAQRLRAIAGPTLELPPVEVP-EETKFSGRNRLYVGNLTGDITDNELREMFKPYGEI 338

Query: 141 QELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVT 200
            E+F N EK F F+++DY  NA+KAK  LDG + KGR L++RFAP    ++V+NLT  V+
Sbjct: 339 GEIFSNIEKNFTFLKVDYHVNAEKAKRALDGTMRKGRQLRVRFAPNATILRVRNLTPFVS 398

Query: 201 NELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLR 260
           NELL  +F +FG IERA + VD+RG    EGIVEFA+K +A   LR C E CFFLT SLR
Sbjct: 399 NELLYKSFEIFGPIERASITVDDRGKHTGEGIVEFAKKSSANACLRFCNEKCFFLTASLR 458

Query: 261 PVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHEL-- 318
           P +VEP+E+ D+ DGL E+ +NKK  EF ++R VGPRFA +NSFE EYGSRWKQLH+L  
Sbjct: 459 PCLVEPMEVNDDNDGLPEKALNKKLQEFNQERSVGPRFADLNSFEHEYGSRWKQLHDLYK 518

Query: 319 -------------------------YEHETEMLRKELAQREIDRERQKAEWEMKERQAEE 353
                                    YE ETE+LR+EL +RE+D ER+K EWEM+E+QAEE
Sbjct: 519 SKQDTLKRELKMEEEKLDAQMQYARYEQETELLRQELRKREVDNERKKIEWEMREKQAEE 578

Query: 354 LKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSMFLVEQQ 395
           +++RDE+ M++H  EMQ R+A+QEED+RRRQ +N++F+  QQ
Sbjct: 579 MRKRDEDTMRRHQTEMQTRMARQEEDMRRRQQENTLFIQAQQ 620

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	503
FB|FBgn0015520	642	nonA-l "nonA-like" [Drosophila	0.614	0.481	0.473	9.3e-75
FB|FBgn0004227	700	nonA "no on or off transient A	0.600	0.431	0.474	5.1e-74
UNIPROTKB|Q9GRW7	697	nonA "Protein no-on-transient	0.600	0.433	0.477	6.5e-74
UNIPROTKB|Q9GRX4	698	nonA "Protein no-on-transient	0.600	0.432	0.481	1.1e-73
UNIPROTKB|Q9U1N0	535	HRP65 "Hrp65 protein" [Chirono	0.610	0.573	0.440	1.4e-69
UNIPROTKB|Q5ZK88	523	PSPC1 "Paraspeckle component 1	0.568	0.546	0.446	1.3e-61
UNIPROTKB|F1P555	647	SFPQ "Uncharacterized protein"	0.546	0.425	0.473	1.6e-61
MGI|MGI:1918764	699	Sfpq "splicing factor proline/	0.546	0.393	0.470	2.1e-61
RGD|727923	699	Sfpq "splicing factor proline/	0.546	0.393	0.470	2.1e-61
UNIPROTKB|F1LQW3	606	Sfpq "Protein Sfpq" [Rattus no	0.546	0.453	0.470	2.1e-61

FB|FBgn0015520 nonA-l "nonA-like" [Drosophila melanogaster (taxid:7227)]

 Score = 754 (270.5 bits), Expect = 9.3e-75, P = 9.3e-75
 Identities = 158/334 (47%), Positives = 222/334 (66%)

Query:    81 DRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGET 140
             D +  ++++ I GPT +LPP E    D KF    RLY+GN+  D T++D+ E+FKPYGE 
Sbjct:   245 DFFIAQRLLDISGPTHELPPIELPT-DNKFVGRNRLYVGNLTSDTTDDDLREMFKPYGEI 303

Query:   141 QELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVT 200
              ++F N EK F F+R+DY  NA+KAK  LDG + KGR L++RFAP NA ++V NL   V+
Sbjct:   304 GDIFSNPEKNFTFLRLDYYQNAEKAKRALDGSLRKGRVLRVRFAP-NAIVRVTNLNQFVS 362

Query:   201 NELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLR 260
             NELL  +F +FG IERA++ VD+RG    EGIVEFA+K +A+  LR C E CFFLT SLR
Sbjct:   363 NELLHQSFEIFGPIERAVICVDDRGKHTGEGIVEFAKKSSASACLRLCNEKCFFLTASLR 422

Query:   261 PVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYE 320
             P +VEP+E+ ++ DGL ++T+NKK+ EF  +R VGPRFA +NSFE EYGSRWKQLH+L++
Sbjct:   423 PCLVEPMEVNNDNDGLPDKTLNKKSLEFRHERSVGPRFACLNSFEHEYGSRWKQLHDLFK 482

Query:   321 HETEMLRKELAQRE--IDRERQKAEWEMK-ERQAEELKRR--DEELMK-------KHAEE 368
              + + L++EL   E  ++ + + A +E + E   +ELK+R  D E MK       K AEE
Sbjct:   483 SKQDSLKRELKMEEDKLEAQMEYARYEQETELLRQELKKRELDNERMKLEWEMREKQAEE 542

Query:   369 MQLR-----------LAQQEEDLRRRQNDNSMFL 391
             ++ R           L + EED+R RQ +N + +
Sbjct:   543 IRKREEEYMHRYQNQLLRHEEDMRARQQENDLLM 576

GO:0003729 "mRNA binding" evidence=ISS

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

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0008187 "poly-pyrimidine tract binding" evidence=ISS

GO:0000166 "nucleotide binding" evidence=IEA

FB|FBgn0004227 nonA "no on or off transient A" [Drosophila melanogaster (taxid:7227)]

 Score = 747 (268.0 bits), Expect = 5.1e-74, P = 5.1e-74
 Identities = 151/318 (47%), Positives = 215/318 (67%)

Query:    81 DRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGET 140
             D + T+++ +I GPT +L P E    + KF+   RLY+GN+  DIT++++ E+FKPYGE 
Sbjct:   270 DFFITQRLRSISGPTFELEPVEVPT-ETKFSGRNRLYVGNLTNDITDDELREMFKPYGEI 328

Query:   141 QELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVT 200
              E+F N +K F F+++DY  NA+KAK  LDG + KGR L++RFAP    ++V NLT  V+
Sbjct:   329 SEIFSNLDKNFTFLKVDYHPNAEKAKRALDGSMRKGRQLRVRFAPNATILRVSNLTPFVS 388

Query:   201 NELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLR 260
             NELL  +F +FG IERA + VD+RG    EGIVEFA+K +A+  LR C E CFFLT SLR
Sbjct:   389 NELLYKSFEIFGPIERASITVDDRGKHMGEGIVEFAKKSSASACLRMCNEKCFFLTASLR 448

Query:   261 PVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYE 320
             P +V+P+E+ D+ DGL E+  NKK P+F ++R +GPRFA  NSFE EYGSRWKQLH L++
Sbjct:   449 PCLVDPMEVNDDTDGLPEKAFNKKMPDFNQERSIGPRFADPNSFEHEYGSRWKQLHNLFK 508

Query:   321 HETEMLRKEL--------AQREIDRERQKAEW---EMKERQAE-ELKRRDEELMKKHAEE 368
              + + L++EL        AQ E  R  Q+ E    E+++R+ + E K+ + E+ +K AEE
Sbjct:   509 TKQDALKRELKMEEDKLEAQMEYARYEQETELLRQELRKREVDNERKKLEWEMREKQAEE 568

Query:   369 MQLRLAQQEEDLRRRQND 386
             M+ R   +EE +RR Q +
Sbjct:   569 MRKR---EEETMRRHQTE 583

GO:0005634 "nucleus" evidence=IDA

GO:0045433 "male courtship behavior, veined wing generated song production" evidence=NAS;IMP;TAS

GO:0007601 "visual perception" evidence=NAS;IMP;TAS

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0008187 "poly-pyrimidine tract binding" evidence=ISS

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

GO:0003729 "mRNA binding" evidence=ISS;NAS;TAS

GO:0007632 "visual behavior" evidence=NAS

GO:0042331 "phototaxis" evidence=NAS

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0071011 "precatalytic spliceosome" evidence=IDA

UNIPROTKB|Q9GRW7 nonA "Protein no-on-transient A" [Drosophila virilis (taxid:7244)]

 Score = 746 (267.7 bits), Expect = 6.5e-74, P = 6.5e-74
 Identities = 152/318 (47%), Positives = 219/318 (68%)

Query:    81 DRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGET 140
             D ++++++ +I GPT +LPP E   ++ KF+   RLY+GN+  DIT+ ++ E+FKPYGE 
Sbjct:   253 DFFYSQRLRSISGPTHELPPIEVA-QETKFSGRNRLYVGNLTNDITDEELREMFKPYGEI 311

Query:   141 QELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVT 200
              E+F N EK F F+++DY  NA+KAK  LDG + KGR +++RFAP    ++V NLT  V+
Sbjct:   312 GEIFSNLEKNFTFLKVDYHINAEKAKRPLDGSMRKGRHVRVRFAPNATILRVSNLTPFVS 371

Query:   201 NELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLR 260
             NELL  +F +FG IERA + VD+RG    EG VEFA+K +A+  LR C E CFFLT SLR
Sbjct:   372 NELLYKSFEIFGPIERASITVDDRGKHLGEGTVEFAKKSSASACLRLCNEKCFFLTASLR 431

Query:   261 PVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYE 320
             P +VEP+E+ D+ DGL E+ +NKK  EF ++R VGPRFA +NSFE EYGSRWKQLH+L++
Sbjct:   432 PCLVEPMEVNDDNDGLPEKALNKKLQEFNQERSVGPRFADLNSFEHEYGSRWKQLHDLFK 491

Query:   321 HETEMLRKEL--------AQREIDRERQKAEW---EMKERQAE-ELKRRDEELMKKHAEE 368
              + + L++EL        AQ E  R  Q+ E    E+++R+++ E K+ + E+ +K AEE
Sbjct:   492 SKQDALKRELKMEEEKLDAQMEYARYEQETELLRQELRKRESDNERKKLEWEMREKQAEE 551

Query:   369 MQLRLAQQEEDLRRRQND 386
             M+ R   +EE +RR Q +
Sbjct:   552 MRKR---EEETMRRHQTE 566

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|Q9GRX4 nonA "Protein no-on-transient A" [Drosophila littoralis (taxid:47316)]

 Score = 744 (267.0 bits), Expect = 1.1e-73, P = 1.1e-73
 Identities = 153/318 (48%), Positives = 217/318 (68%)

Query:    81 DRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGET 140
             D +  +++ +I GPT +LPP E   ++ KF+   RLY+GN+  DIT+ ++ E+FKPYGE 
Sbjct:   249 DFFIAQRLRSISGPTHELPPIEVA-QETKFSGRNRLYVGNLTNDITDEELREMFKPYGEI 307

Query:   141 QELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVT 200
              E+F N EK F F+++DY  NA+KAK  LDG + KGR L++RFAP    ++V NLT  V+
Sbjct:   308 GEIFSNLEKNFTFLKVDYHINAEKAKRALDGSMRKGRQLRVRFAPNATILRVSNLTPFVS 367

Query:   201 NELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLR 260
             NELL  +F +FG IERA + VD+RG    EG VEFA+K +A+  LR C E CFFLT SLR
Sbjct:   368 NELLYKSFEIFGPIERASITVDDRGKHLGEGTVEFAKKSSASACLRLCNEKCFFLTASLR 427

Query:   261 PVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYE 320
             P +VEP+E+ D+ DGL E+ +NKK  EF ++R VGPRFA +NSFE EYGSRWKQLH+L++
Sbjct:   428 PCLVEPMEVNDDNDGLPEKALNKKLQEFNQERSVGPRFADLNSFEHEYGSRWKQLHDLFK 487

Query:   321 HETEMLRKEL--------AQREIDRERQKAEW---EMKERQAE-ELKRRDEELMKKHAEE 368
              + + L++EL        AQ E  R  Q+ E    E+++R+++ E K+ + E+ +K AEE
Sbjct:   488 SKQDALKRELKMEEEKLDAQMEYARYGQETELSRQELRKRESDNERKKLEWEMREKQAEE 547

Query:   369 MQLRLAQQEEDLRRRQND 386
             M+ R   +EE +RR Q +
Sbjct:   548 MRKR---EEETMRRHQTE 562

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|Q9U1N0 HRP65 "Hrp65 protein" [Chironomus tentans (taxid:7153)]

 Score = 705 (253.2 bits), Expect = 1.4e-69, P = 1.4e-69
 Identities = 140/318 (44%), Positives = 214/318 (67%)

Query:    81 DRYFTEKIMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGET 140
             D     K+  + GPT DLP  E   ++IKF+   RLY+GN+  D+TE ++ ELF PYGE 
Sbjct:    82 DFIVNSKLKNLAGPTHDLP--ELVCEEIKFSGRNRLYIGNLTSDVTEEELKELFSPYGEI 139

Query:   141 QELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVT 200
              E FIN EK F F+++DY+ NA++AK  LDG + K + ++IRFAP    I+VKNLT  V+
Sbjct:   140 SEAFINAEKNFAFLKIDYRANAERAKKDLDGRMRKNKPIRIRFAPNATTIRVKNLTPFVS 199

Query:   201 NELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLR 260
             NELL  +F VFG +ERA++IVD+RG +  EGIVEFARK  A  AL+ C+E C+FLT SLR
Sbjct:   200 NELLFKSFEVFGQVERAVIIVDDRGKTTGEGIVEFARKSGAMSALKYCSEKCYFLTSSLR 259

Query:   261 PVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYE 320
             P +VE  +  DE DG  E+++ +K+ ++YK RQ GPRFA + SFE E+G++WKQ++++Y+
Sbjct:   260 PCVVETFDHIDETDGFPEKSLMRKSNDYYKARQNGPRFAEMGSFEHEFGTKWKQMYDMYK 319

Query:   321 HETEMLRKE--LAQREIDRERQKAEWEMK-ERQAEELKRR--DEELMKKHAEEMQLRLAQ 375
              + + L++E  L + +++ + + A++E + E   E+L++R  D +  KK  E+ + +  +
Sbjct:   320 QKHDALKREMQLEEEKLEAQMEYAKFEHETESLREQLRKREQDRDRQKKEWEDRERQADE 379

Query:   376 Q----EEDLRRRQNDNSM 389
                  E+ +RR+Q+D  M
Sbjct:   380 SRIRDEQQMRRQQDDMQM 397

GO:0003723 "RNA binding" evidence=NAS

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0006406 "mRNA export from nucleus" evidence=NAS

UNIPROTKB|Q5ZK88 PSPC1 "Paraspeckle component 1" [Gallus gallus (taxid:9031)]

 Score = 630 (226.8 bits), Expect = 1.3e-61, P = 1.3e-61
 Identities = 138/309 (44%), Positives = 206/309 (66%)

Query:    93 GPTLDLPPS-EPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMF 151
             G T+D+    +P  K   +   CRL++GN+  DITE D   LF+ YGE  E+FIN+++ F
Sbjct:    61 GFTIDIKSFLKPGEKS--YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGF 118

Query:   152 GFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVF 211
             GFIR++ +  A+ AKA+LDG +LK R L+IRFA   AA+ VKNL+  V+NELLE AF  F
Sbjct:   119 GFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQF 178

Query:   212 GDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTD 271
             G +ERA+V+VD+RG +  +G VEFA KP A +AL RC++G F LT + RPV+VEP+E  D
Sbjct:   179 GPVERAVVVVDDRGRATGKGFVEFAAKPPARKALERCSDGAFLLTTTPRPVVVEPMEQFD 238

Query:   272 EIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKEL- 330
             + DGL E+ + +KT +++K+R+  PRFA   +FEFEY SRWK L E+ + + E + + + 
Sbjct:   239 DEDGLPEKLM-QKTQQYHKEREQPPRFAQPGTFEFEYASRWKALDEMEKQQREQVDRNIR 297

Query:   331 -AQREIDRERQKAEWE-----MKE---RQAEELKR----RDEELMKKHAEEMQLRLAQQE 377
              A+ +++ E + A  E     M++   R+ EEL+R    R++EL K+  +++QLR    E
Sbjct:   298 EAKEKLEAEMEAARHEHQLMLMRQDLMRRQEELRRLEELRNQELQKR--KQIQLR---HE 352

Query:   378 EDLRRRQND 386
             E+ RRR+ +
Sbjct:   353 EEHRRREEE 361

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

UNIPROTKB|F1P555 SFPQ "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 629 (226.5 bits), Expect = 1.6e-61, P = 1.6e-61
 Identities = 136/287 (47%), Positives = 185/287 (64%)

Query:   110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL 169
             +   CRL++GN+  DIT+ D   LF  YGE  E+FINK K FGFI+++ +  A+ AKA+L
Sbjct:   233 YTQRCRLFVGNLPADITDEDFKRLFAKYGEPGEVFINKGKGFGFIKLESRALAEIAKAEL 292

Query:   170 DGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKC 229
             D   ++GR L++RFA   AA+ V+NL+  V+NELLE AF  FG +ERA+VIVD+RG S  
Sbjct:   293 DDTPMRGRQLRVRFATHAAALSVRNLSPYVSNELLEEAFSQFGPVERAVVIVDDRGRSTG 352

Query:   230 EGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFY 289
             +GIVEFA KPAA +A  RC EG F LT + RPVIVEPLE  D+ DGL E+ + +K P + 
Sbjct:   353 KGIVEFASKPAARKAFERCTEGVFLLTTTPRPVIVEPLEQLDDEDGLPEK-LAQKNPMYQ 411

Query:   290 KQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKER 349
             K+R+  PRFA   SFEFEY  RWK L E+ + + E + K +   + D+   + E    E 
Sbjct:   412 KERETPPRFAQPGSFEFEYSQRWKSLDEMEKQQREQVAKNMKDAK-DKLESEMEDAYHEH 470

Query:   350 QA----EELKRRDEELMKK---HAEEMQLRLA---QQEEDLRRRQND 386
             QA    ++L RR EEL +    H +EMQ R     +QEE+ RRR+ +
Sbjct:   471 QANLLRQDLMRRQEELRRMEELHNQEMQKRKEIQLRQEEERRRREEE 517

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000380 "alternative mRNA splicing, via spliceosome" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IEA

GO:0042382 "paraspeckles" evidence=IEA

MGI|MGI:1918764 Sfpq "splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)" [Mus musculus (taxid:10090)]

 Score = 628 (226.1 bits), Expect = 2.1e-61, P = 2.1e-61
 Identities = 135/287 (47%), Positives = 188/287 (65%)

Query:   110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL 169
             +   CRL++GN+  DITE++   LF  YGE  E+FINK K FGFI+++ +  A+ AKA+L
Sbjct:   285 YTQRCRLFVGNLPADITEDEFKRLFAKYGEPGEVFINKGKGFGFIKLESRALAEIAKAEL 344

Query:   170 DGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKC 229
             D   ++GR L++RFA   AA+ V+NL+  V+NELLE AF  FG IERA+VIVD+RG S  
Sbjct:   345 DDTPMRGRQLRVRFATHAAALSVRNLSPYVSNELLEEAFSQFGPIERAVVIVDDRGRSTG 404

Query:   230 EGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFY 289
             +GIVEFA KPAA +A  RC+EG F LT + RPVIVEPLE  D+ DGL E+ + +K P + 
Sbjct:   405 KGIVEFASKPAARKAFERCSEGVFLLTTTPRPVIVEPLEQLDDEDGLPEK-LAQKNPMYQ 463

Query:   290 KQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKER 349
             K+R+  PRFA   +FE+EY  RWK L E+ + + E + K +   + D+   + E    E 
Sbjct:   464 KERETPPRFAQHGTFEYEYSQRWKSLDEMEKQQREQVEKNMKDAK-DKLESEMEDAYHEH 522

Query:   350 QA----EELKRRDEELMKK---HAEEMQLRLA---QQEEDLRRRQND 386
             QA    ++L RR EEL +    H++EMQ R     +QEE+ RRR+ +
Sbjct:   523 QANLLRQDLMRRQEELRRMEELHSQEMQKRKEMQLRQEEERRRREEE 569

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000380 "alternative mRNA splicing, via spliceosome" evidence=ISO

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005654 "nucleoplasm" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0016363 "nuclear matrix" evidence=ISO

GO:0042382 "paraspeckles" evidence=ISO

RGD|727923 Sfpq "splicing factor proline/glutamine-rich" [Rattus norvegicus (taxid:10116)]

 Score = 628 (226.1 bits), Expect = 2.1e-61, P = 2.1e-61
 Identities = 135/287 (47%), Positives = 188/287 (65%)

Query:   110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL 169
             +   CRL++GN+  DITE++   LF  YGE  E+FINK K FGFI+++ +  A+ AKA+L
Sbjct:   285 YTQRCRLFVGNLPADITEDEFKRLFAKYGEPGEVFINKGKGFGFIKLESRALAEIAKAEL 344

Query:   170 DGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKC 229
             D   ++GR L++RFA   AA+ V+NL+  V+NELLE AF  FG IERA+VIVD+RG S  
Sbjct:   345 DDTPMRGRQLRVRFATHAAALSVRNLSPYVSNELLEEAFSQFGPIERAVVIVDDRGRSTG 404

Query:   230 EGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFY 289
             +GIVEFA KPAA +A  RC+EG F LT + RPVIVEPLE  D+ DGL E+ + +K P + 
Sbjct:   405 KGIVEFASKPAARKAFERCSEGVFLLTTTPRPVIVEPLEQLDDEDGLPEK-LAQKNPMYQ 463

Query:   290 KQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKER 349
             K+R+  PRFA   +FE+EY  RWK L E+ + + E + K +   + D+   + E    E 
Sbjct:   464 KERETPPRFAQHGTFEYEYSQRWKSLDEMEKQQREQVEKNMKDAK-DKLESEMEDAYHEH 522

Query:   350 QA----EELKRRDEELMKK---HAEEMQLRLA---QQEEDLRRRQND 386
             QA    ++L RR EEL +    H++EMQ R     +QEE+ RRR+ +
Sbjct:   523 QANLLRQDLMRRQEELRRMEELHSQEMQKRKEMQLRQEEERRRREEE 569

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0000380 "alternative mRNA splicing, via spliceosome" evidence=ISO

GO:0005654 "nucleoplasm" evidence=ISO

GO:0016363 "nuclear matrix" evidence=ISO

GO:0042382 "paraspeckles" evidence=ISO

UNIPROTKB|F1LQW3 Sfpq "Protein Sfpq" [Rattus norvegicus (taxid:10116)]

 Score = 628 (226.1 bits), Expect = 2.1e-61, P = 2.1e-61
 Identities = 135/287 (47%), Positives = 188/287 (65%)

Query:   110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL 169
             +   CRL++GN+  DITE++   LF  YGE  E+FINK K FGFI+++ +  A+ AKA+L
Sbjct:   192 YTQRCRLFVGNLPADITEDEFKRLFAKYGEPGEVFINKGKGFGFIKLESRALAEIAKAEL 251

Query:   170 DGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKC 229
             D   ++GR L++RFA   AA+ V+NL+  V+NELLE AF  FG IERA+VIVD+RG S  
Sbjct:   252 DDTPMRGRQLRVRFATHAAALSVRNLSPYVSNELLEEAFSQFGPIERAVVIVDDRGRSTG 311

Query:   230 EGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFY 289
             +GIVEFA KPAA +A  RC+EG F LT + RPVIVEPLE  D+ DGL E+ + +K P + 
Sbjct:   312 KGIVEFASKPAARKAFERCSEGVFLLTTTPRPVIVEPLEQLDDEDGLPEK-LAQKNPMYQ 370

Query:   290 KQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKER 349
             K+R+  PRFA   +FE+EY  RWK L E+ + + E + K +   + D+   + E    E 
Sbjct:   371 KERETPPRFAQHGTFEYEYSQRWKSLDEMEKQQREQVEKNMKDAK-DKLESEMEDAYHEH 429

Query:   350 QA----EELKRRDEELMKK---HAEEMQLRLA---QQEEDLRRRQND 386
             QA    ++L RR EEL +    H++EMQ R     +QEE+ RRR+ +
Sbjct:   430 QANLLRQDLMRRQEELRRMEELHSQEMQKRKEMQLRQEEERRRREEE 476

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000380 "alternative mRNA splicing, via spliceosome" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IEA

GO:0042382 "paraspeckles" 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 EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	503
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	3e-40
cd12945	100	cd12945, NOPS_NONA_like, NOPS domain, including C-	1e-32
cd12589	80	cd12589, RRM2_PSP1, RNA recognition motif 2 in ver	1e-28
cd12590	80	cd12590, RRM2_PSF, RNA recognition motif 2 in vert	5e-28
cd12591	80	cd12591, RRM2_p54nrb, RNA recognition motif 2 in v	8e-27
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	3e-26
cd12931	90	cd12931, eNOPS_SF, NOPS domain, including C-termin	4e-25
pfam08075	52	pfam08075, NOPS, NOPS (NUC059) domain	2e-20
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	1e-18
cd12949	94	cd12949, NOPS_PSPC1, NOPS domain, including C-term	3e-17
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	8e-17
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	2e-16
cd12946	93	cd12946, NOPS_p54nrb_PSF_PSPC1, NOPS domain, inclu	2e-16
cd12948	97	cd12948, NOPS_PSF, NOPS domain, including C-termin	1e-14
cd12947	94	cd12947, NOPS_p54nrb, NOPS domain, including C-ter	1e-14
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	5e-14
smart00360	73	smart00360, RRM, RNA recognition motif	1e-13
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-12
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-11
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-10
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-10
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	4e-10
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-09
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-08
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-08
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	3e-08
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	3e-08
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	7e-08
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	9e-08
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	2e-07
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-07
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-07
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-07
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	4e-07
smart00360	73	smart00360, RRM, RNA recognition motif	6e-07
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	9e-07
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	9e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-06
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	1e-06
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-06
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-06
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	2e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	5e-06
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	1e-05
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	1e-05
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	1e-05
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	1e-05
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	1e-05
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-05
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	2e-05
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	2e-05
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	2e-05
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-05
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	3e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-05
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	4e-05
cd12331	79	cd12331, RRM_NRD1_SEB1_like, RNA recognition motif	5e-05
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	5e-05
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	6e-05
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	8e-05
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	9e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-04
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	1e-04
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-04
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	1e-04
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	1e-04
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	1e-04
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	1e-04
cd12410	93	cd12410, RRM2_RRT5, RNA recognition motif 2 in yea	2e-04
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	2e-04
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	2e-04
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	2e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-04
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	3e-04
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	4e-04
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	4e-04
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	4e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	4e-04
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	5e-04
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	5e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	5e-04
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	5e-04
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	5e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	6e-04
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	7e-04
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	8e-04
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	8e-04
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	9e-04
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	9e-04
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	0.001
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	0.001
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	0.001
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	0.001
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	0.001
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	0.001
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	0.001
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	0.001
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	0.001
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	0.001
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	0.001
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	0.001
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	0.001
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	0.001
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	0.001
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	0.002
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	0.002
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	0.002
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	0.002
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	0.002
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	0.002
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	0.002
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.003
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	0.003
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	0.003
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	0.003
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	0.003
cd12687	75	cd12687, RRM1_PTBPH3, RNA recognition motif 1 in p	0.003
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	0.004
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	0.004
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	0.004
PRK06958	182	PRK06958, PRK06958, single-stranded DNA-binding pr	0.004
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	0.004
cd12426	79	cd12426, RRM4_PTBPH3, RNA recognition motif 4 in p	0.004
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	0.004

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score =  139 bits (352), Expect = 3e-40
 Identities = 53/80 (66%), Positives = 66/80 (82%)

Query: 189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRC 248
           A++VKNL+  V+NELLE AF  FG++ERA+VIVD+RG S  EGIVEF+RKP A  A++RC
Sbjct: 1   ALRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKRC 60

Query: 249 AEGCFFLTQSLRPVIVEPLE 268
           +EGCF LT S RPV+VEPLE
Sbjct: 61  SEGCFLLTASPRPVVVEPLE 80

This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 80

>gnl|CDD|240580 cd12945, NOPS_NONA_like, NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSP1 homologs from invertebrate species

 Score =  119 bits (300), Expect = 1e-32
 Identities = 54/103 (52%), Positives = 71/103 (68%), Gaps = 4/103 (3%)

Query: 259 LRPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHEL 318
           LRP +VEP+E  D+ DGL E+++NKK PEF K+R +GPRFA  NSFE EYG+RWKQLHEL
Sbjct: 1   LRPCVVEPMEEIDDEDGLPEKSLNKKNPEFNKERSIGPRFAEPNSFEHEYGTRWKQLHEL 60

Query: 319 YEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEEL 361
           Y+ + E L++EL   E   E Q  E+   E + E L+   E+L
Sbjct: 61  YKQKEEALKRELKMEEEKLEAQ-MEYARYEHETELLR---EQL 99

The family contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction NOPS (NONA and PSP1) domain. This model corresponds to the NOPS domain, with a long helical C-terminal extension , found in Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA), Chironomus tentans hrp65 gene encoding protein Hrp65 and similar proteins. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. The NOPS domain specifically binds to the second RNA recognition motif (RRM2) domain of the partner DBHS protein via a substantial interaction surface. Its highly conserved C-terminal residues are critical for functional DBHS dimerization while the highly conserved C-terminal helical extension, forming a right-handed antiparallel heterodimeric coiled-coil, is essential for localization of these proteins to subnuclear bodies. Length = 100

>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)

 Score =  107 bits (269), Expect = 1e-28
 Identities = 50/80 (62%), Positives = 61/80 (76%)

Query: 189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRC 248
           A+ VKNL+  V+NELLE AF  FG +ERA+VIVD+RG    +G VEFA KPAA +AL RC
Sbjct: 1   ALTVKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKALERC 60

Query: 249 AEGCFFLTQSLRPVIVEPLE 268
           A+G F LT + RPVIVEP+E
Sbjct: 61  ADGAFLLTTTPRPVIVEPME 80

This subgroup corresponds to the RRM2 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score =  106 bits (265), Expect = 5e-28
 Identities = 51/80 (63%), Positives = 61/80 (76%)

Query: 189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRC 248
           A+ V+NL+  V+NELLE AF  FG +ERA+VIVD+RG S  +GIVEFA KPAA +A  RC
Sbjct: 1   ALSVRNLSPYVSNELLEEAFSQFGPVERAVVIVDDRGRSTGKGIVEFASKPAARKAFERC 60

Query: 249 AEGCFFLTQSLRPVIVEPLE 268
            EG F LT + RPVIVEPLE
Sbjct: 61  TEGVFLLTTTPRPVIVEPLE 80

This subgroup corresponds to the RRM2 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. It promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 80

>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score =  103 bits (257), Expect = 8e-27
 Identities = 47/80 (58%), Positives = 60/80 (75%)

Query: 189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRC 248
           A+ VKNL   V+NELLE AF +FG +ERA+VIVD+RG    +GIVEFA KP+A +AL RC
Sbjct: 1   ALTVKNLPQFVSNELLEEAFSMFGQVERAVVIVDDRGRPTGKGIVEFAGKPSARKALDRC 60

Query: 249 AEGCFFLTQSLRPVIVEPLE 268
           ++G F LT   RPV VEP++
Sbjct: 61  SDGAFLLTAFPRPVTVEPMD 80

This subgroup corresponds to the RRM2 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. It binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. p54nrb forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner. It also forms a heterodimer with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

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

 Score =  100 bits (252), Expect = 3e-26
 Identities = 42/70 (60%), Positives = 55/70 (78%)

Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHV 173
           CRL++GN+  DITE +  ELF  YGE  E+F+NKEK FGFIR+D + NA+KAKA+LDG +
Sbjct: 2   CRLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEKGFGFIRLDTRTNAEKAKAELDGIM 61

Query: 174 LKGRSLKIRF 183
            KGR L++RF
Sbjct: 62  RKGRQLRVRF 71

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

>gnl|CDD|240579 cd12931, eNOPS_SF, NOPS domain, including C-terminal helical extension region, in the p54nrb/PSF/PSP1 family

 Score = 98.5 bits (246), Expect = 4e-25
 Identities = 45/94 (47%), Positives = 61/94 (64%), Gaps = 6/94 (6%)

Query: 260 RPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELY 319
           RPV+VEPLE  DE DGL ER + KK   + K+R+VGPRFA   SFE+E+G RWK L+EL 
Sbjct: 2   RPVVVEPLEQRDEEDGLPERNV-KKNAGYQKEREVGPRFAPPGSFEYEFGQRWKALYEL- 59

Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQAEE 353
               E  ++E  ++E+   R+K E EM+  + E 
Sbjct: 60  ----EKQQREQLEKELKEAREKLEAEMEAARYEH 89

All members in this family contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRM1 and RRM2), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction NOPS (NONA and PSP1) domain with a long helical C-terminal extension. The NOPS domain specifically binds to RRM2 domain of the partner DBHS protein via a substantial interaction surface. Its highly conserved C-terminal residues are critical for functional DBHS dimerization while the highly conserved C-terminal helical extension, forming a right-handed antiparallel heterodimeric coiled-coil, is essential for localization of these proteins to subnuclear bodies. PSF has an additional large N-terminal domain that differentiates it from other family members. The p54nrb/PSF/PSP1 family includes 54 kDa nuclear RNA- and DNA-binding protein (p54nrb), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and paraspeckle protein 1 (PSP1), which are ubiquitously expressed and are well conserved in vertebrates. p54nrb, also termed NONO or NMT55, is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF, also termed POMp100, is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1, also termed PSPC1, is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species. For instance, the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. Length = 90

>gnl|CDD|149257 pfam08075, NOPS, NOPS (NUC059) domain

 Score = 84.0 bits (208), Expect = 2e-20
 Identities = 32/53 (60%), Positives = 42/53 (79%), Gaps = 1/53 (1%)

Query: 261 PVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWK 313
           PVIVEP+E  D+ DGL E+ + KK+P+++K+R+ GPRFA   SFE EYGSRWK
Sbjct: 1   PVIVEPMEQNDDEDGLPEK-LVKKSPDYHKEREQGPRFAQPGSFEHEYGSRWK 52

This domain is found at the C-terminus of NONA and PSP1 proteins adjacent to 1 or 2 pfam00076 domains. Length = 52

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 79.6 bits (196), Expect = 1e-18
 Identities = 38/70 (54%), Positives = 54/70 (77%)

Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHV 173
           CRL++GN+  DITE D  +LF+ YGE  E+FIN+++ FGFIR++ +  A+ AKA+LDG +
Sbjct: 2   CRLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTI 61

Query: 174 LKGRSLKIRF 183
           LK R L+IRF
Sbjct: 62  LKNRPLRIRF 71

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|240584 cd12949, NOPS_PSPC1, NOPS domain, including C-terminal coiled-coil region, in paraspeckle protein component 1 (PSPC1) and similar proteins

 Score = 76.6 bits (188), Expect = 3e-17
 Identities = 41/93 (44%), Positives = 59/93 (63%), Gaps = 6/93 (6%)

Query: 260 RPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELY 319
           RPVIVEP+E  D+ DGL E+ + +KT +++K+R+  PRFA   +FEFEY SRWK L E+ 
Sbjct: 2   RPVIVEPMEQFDDEDGLPEKLM-QKTQQYHKEREQPPRFAQPGTFEFEYASRWKALDEM- 59

Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQAE 352
               E  ++E   R I   ++K E EM+  + E
Sbjct: 60  ----EKQQREQVDRNIREAKEKLEAEMEAARHE 88

The family contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction NOPS (NONA and PSP1) domain. This model corresponds to the NOPS domain, with a long helical C-terminal extension, of paraspeckle component 1 (PSPC1, also termed PSP1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NONO), which localizes to paraspeckles in an RNA-dependent manner. The NOPS domain specifically binds to the second RNA recognition motif (RRM2) domain of the partner DBHS protein via a substantial interaction surface. Its highly conserved C-terminal residues are critical for functional DBHS dimerization while the highly conserved C-terminal helical extension, forming a right-handed antiparallel heterodimeric coiled-coil, is essential for localization of these proteins to subnuclear bodies. Length = 94

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

 Score = 74.6 bits (183), Expect = 8e-17
 Identities = 35/70 (50%), Positives = 52/70 (74%)

Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHV 173
           CRL++GN+  DITE++  +LF  YGE  E+FINK K FGFI+++ +  A+ AKA+LD   
Sbjct: 2   CRLFVGNLPADITEDEFKKLFAKYGEPGEVFINKGKGFGFIKLESRALAEIAKAELDDTP 61

Query: 174 LKGRSLKIRF 183
           ++GR L++RF
Sbjct: 62  MRGRQLRVRF 71

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

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

 Score = 73.4 bits (180), Expect = 2e-16
 Identities = 33/69 (47%), Positives = 53/69 (76%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
           RL++GN+  DITE ++ +LF+ YG+  E+FI+K+K FGFIR++ +  A+ AKA+LD   L
Sbjct: 3   RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKDKGFGFIRLETRTLAEIAKAELDNMPL 62

Query: 175 KGRSLKIRF 183
           +G+ L++RF
Sbjct: 63  RGKQLRVRF 71

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

>gnl|CDD|240581 cd12946, NOPS_p54nrb_PSF_PSPC1, NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSPC1 family proteins

 Score = 74.0 bits (181), Expect = 2e-16
 Identities = 38/93 (40%), Positives = 56/93 (60%), Gaps = 6/93 (6%)

Query: 260 RPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELY 319
           RPVIVEP+E  D+ DGL E+   +K  +++K+R+  PRFA   +FE+EY  RWK L E+ 
Sbjct: 2   RPVIVEPMEQLDDEDGLPEKLA-QKNQQYHKEREQPPRFAQPGTFEYEYAQRWKALDEM- 59

Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQAE 352
               E  ++E   R I   ++K E EM+  + E
Sbjct: 60  ----EKQQREQVDRNIKEAKEKLESEMEAARHE 88

The family contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction NOPS (NONA and PSP1) domain. This model corresponds to the NOPS domain, with a long helical C-terminal extension, found in the p54nrb/PSF/PSPC1 proteins. The NOPS domain specifically binds to the second RNA recognition motif (RRM2) domain of the partner DBHS protein via a substantial interaction surface. Its highly conserved C-terminal residues are critical for functional DBHS dimerization while the highly conserved C-terminal helical extension, forming a right-handed antiparallel heterodimeric coiled-coil, is essential for localization of these proteins to subnuclear bodies. Members in the family include 54 kDa nuclear RNA- and DNA-binding protein (p54nrb), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and paraspeckle protein component 1 (PSPC1 or PSP1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb, also termed NONO or NMT55, is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF, also termed POMp100, is a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSPC1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSPC1 remains unknown currently. PSF has an additional large N-terminal domain that differentiates it from other family members. Length = 93

>gnl|CDD|240583 cd12948, NOPS_PSF, NOPS domain, including C-terminal coiled-coil region, in polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and similar proteins

 Score = 69.4 bits (169), Expect = 1e-14
 Identities = 41/101 (40%), Positives = 61/101 (60%), Gaps = 10/101 (9%)

Query: 260 RPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELY 319
           RPVIVEPLE  D+ DGL E+ + +K P + K+R+  PRFA   +FE+EY  RWK L E+ 
Sbjct: 2   RPVIVEPLEQLDDEDGLPEK-LAQKNPMYQKERETPPRFAQPGTFEYEYSQRWKSLDEME 60

Query: 320 EHETEMLRKELAQREIDRERQKAEWEMK----ERQAEELKR 356
           + + E + K + +      ++K E EM+    E QA  L++
Sbjct: 61  KQQREQVEKNMKE-----AKEKLESEMEDAYHEHQANLLRQ 96

This model contains the NOPS (NONA and PSP1) domain PSF (also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex), with a long helical C-terminal extension. PSF is a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also single-stranded DNA (ssDNA) as well as double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Additionally, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. As an RNA-binding component of spliceosomes, PSF binds to the insulin-like growth factor response element (IGFRE), and acts as an independent negative regulator of the transcriptional activity of the porcine P-450 cholesterol side-chain cleavage enzyme gene (P450scc) IGFRE. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. In addition, PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NONO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. The NOPS domain specifically binds to the second RNA recognition motif (RRM2) domain of the partner DBHS protein via a substantial interaction surface. Its highly conserved C-terminal residues are critical for functional DBHS dimerization while the highly conserved C-terminal helical extension, forming a right-handed antiparallel heterodimeric coiled-coil, is essential for localization of these proteins to subnuclear bodies. Length = 97

>gnl|CDD|240582 cd12947, NOPS_p54nrb, NOPS domain, including C-terminal coiled-coil region, in 54 kDa nuclear RNA- and DNA-binding protein (p54nrb) and similar proteins

 Score = 69.0 bits (168), Expect = 1e-14
 Identities = 37/93 (39%), Positives = 55/93 (59%), Gaps = 6/93 (6%)

Query: 260 RPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELY 319
           RPV VEP++  D+ +GL E+ + K   +++K+R+  PRFA   SFE+EY  RWK L E+ 
Sbjct: 2   RPVTVEPMDQLDDEEGLPEKLVIK-NQQYHKEREQPPRFAQPGSFEYEYAMRWKALIEM- 59

Query: 320 EHETEMLRKELAQREIDRERQKAEWEMKERQAE 352
               E  ++E   R I   R+K E EM+  + E
Sbjct: 60  ----EKQQQEQVDRNIKEAREKLEMEMEAARHE 88

The family contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction NOPS (NONA and PSP1) domain. This model corresponds to the NOPS domain, with a long helical C-terminal extension, found in p54nrb, also termed non-POU domain-containing octamer-binding protein (NONO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. It is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. p54nrb is ubiquitously expressed and highly conserved in vertebrates. It binds both single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. p54nrb forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner. It also forms a heterodimer with polypyrimidine tract-binding protein-associated-splicing factor (PSF). The NOPS domain specifically binds to the second RNA recognition motif (RRM2) domain of the partner DBHS protein via a substantial interaction surface. Its highly conserved C-terminal residues are critical for functional DBHS dimerization while the highly conserved C-terminal helical extension, forming a right-handed antiparallel heterodimeric coiled-coil, is essential for paraspeckle localization to subnuclear bodies. Length = 94

>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 = 66.5 bits (163), Expect = 5e-14
 Identities = 19/67 (28%), Positives = 38/67 (56%)

Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHV 173
             +Y+GN+   +TE ++   F P+G  +E+ + K+K + F+R D    A  A   ++G  
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKGYAFVRFDTHEAAATAIVAVNGTS 60

Query: 174 LKGRSLK 180
           + G+++K
Sbjct: 61  INGQTVK 67

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

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

 Score = 65.7 bits (161), Expect = 1e-13
 Identities = 23/73 (31%), Positives = 42/73 (57%), Gaps = 6/73 (8%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAK 168
            L++GN+  D TE ++ ELF  +G+ + + + ++K       F F+  + + +A+KA   
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 169 LDGHVLKGRSLKI 181
           L+G  L GR LK+
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 61.9 bits (151), Expect = 3e-12
 Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 5/72 (6%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLD 170
           L++GN+  D TE D+ ELF  +GE + + I ++     K F F+  +   +A+KA   L+
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 171 GHVLKGRSLKIR 182
           G  L GR LK+ 
Sbjct: 61  GKELDGRKLKVS 72

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

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

 Score = 58.8 bits (143), Expect = 3e-11
 Identities = 23/70 (32%), Positives = 39/70 (55%), Gaps = 5/70 (7%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI-----NKEKMFGFIRMDYKHNADKAKAKLD 170
           L++GN+  D TE D+ +LF  +G  + + I      + K F F+  + + +A+KA   L+
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 171 GHVLKGRSLK 180
           G  L GR L+
Sbjct: 61  GKELGGRELR 70

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

>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 56.8 bits (138), Expect = 1e-10
 Identities = 16/56 (28%), Positives = 33/56 (58%), Gaps = 1/56 (1%)

Query: 130 IIELFKPYGETQELFINKEK-MFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA 184
           + +LF P+G  +++ + K+K  F F+    +  A+KA   L+G +  GR L++ ++
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

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

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

 Score = 56.4 bits (137), Expect = 2e-10
 Identities = 22/59 (37%), Positives = 28/59 (47%)

Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRC 248
           + V NL    T E L+  F  FG IE   ++ DE G SK    VEF  +  A +AL   
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEAL 59

(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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 56.4 bits (137), Expect = 2e-10
 Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 4/69 (5%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKM----FGFIRMDYKHNADKAKAKLDG 171
           LY+ N+   +TE D+ E F PYG+ + + + + K     F F+      +A+ A  KL+G
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 172 HVLKGRSLK 180
            VL GR+L+
Sbjct: 61  LVLDGRTLR 69

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

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

 Score = 55.7 bits (135), Expect = 4e-10
 Identities = 25/76 (32%), Positives = 42/76 (55%), Gaps = 6/76 (7%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQ--ELFINKE----KMFGFIRMDYKHNADKAKAK 168
            LY+GN+  ++TE D+ +LF  +GE     +  ++E    + FGF+ M+    A+ A  K
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 169 LDGHVLKGRSLKIRFA 184
           L+G    GR+L +  A
Sbjct: 61  LNGTDFGGRTLTVNEA 76

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

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

 Score = 59.4 bits (144), Expect = 2e-09
 Identities = 42/174 (24%), Positives = 71/174 (40%), Gaps = 36/174 (20%)

Query: 106 KDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFI-----NKEKMFGFIRMDYKH 160
              KF N   LY+ N+   + E+ + ELF  +GE     +      + + F F+  +   
Sbjct: 174 PLKKFTN---LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHE 230

Query: 161 NADKAKAKLDGHVLKG-------------------RSLKIRFAPIN---------AAIKV 192
           +A KA  +++G  +                       L+ +F  +            + V
Sbjct: 231 DAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYV 290

Query: 193 KNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALR 246
           KNL   VT+E L   F   G+I  A V++DE+G S+  G V F+    A +A+ 
Sbjct: 291 KNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVT 344

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

 Score = 51.2 bits (123), Expect = 1e-08
 Identities = 21/59 (35%), Positives = 27/59 (45%)

Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRC 248
           + V NL    T E L   F  FG+IE   ++ D+ G SK    VEF     A +AL   
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEAL 59

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

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 9/79 (11%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKM---------FGFIRMDYKHNADKA 165
           RL++GN+   +TE  +++LF  YG+ ++      K          + F+  + K  A+KA
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 166 KAKLDGHVLKGRSLKIRFA 184
              L+G    G+ L +R+A
Sbjct: 61  LKSLNGKTALGKKLVVRWA 79

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

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

 Score = 50.2 bits (120), Expect = 3e-08
 Identities = 21/64 (32%), Positives = 34/64 (53%)

Query: 117 YLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKG 176
           Y+GNI    T+ D+I LF+ +G   E     ++ F F+++D    A  A  +L G  + G
Sbjct: 4   YVGNIPPYTTQADLIPLFQNFGYILEFRHQPDRGFAFVKLDTHEQAAMAIVQLQGFPVHG 63

Query: 177 RSLK 180
           R L+
Sbjct: 64  RPLR 67

This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 49.9 bits (120), Expect = 3e-08
 Identities = 18/67 (26%), Positives = 37/67 (55%), Gaps = 2/67 (2%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
           +L++GN+    T  ++  LF+ YG   E  + K   +GF+ M+ + +A+ A   L+G+  
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVTECDVVKN--YGFVHMEEEEDAEDAIKALNGYEF 58

Query: 175 KGRSLKI 181
            G+ + +
Sbjct: 59  MGKRINV 65

This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. . Length = 66

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 49.2 bits (118), Expect = 7e-08
 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 6/73 (8%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAK 168
           RL++ N+    TE ++ ELF+ +GE  E+ +       + K F F+   +  +A KA ++
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 169 LDGHVLKGRSLKI 181
           LDG + +GR L +
Sbjct: 61  LDGSIFQGRLLHV 73

This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 74

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

 Score = 49.2 bits (118), Expect = 9e-08
 Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 5/75 (6%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI-----NKEKMFGFIRMDYKHNADKAKAKL 169
           RL + N+    TE D+ +LF P+G   E+ I      K+K F F++   K +A+KA   +
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGV 60

Query: 170 DGHVLKGRSLKIRFA 184
           +G  +KGR + + +A
Sbjct: 61  NGKKIKGRPVAVDWA 75

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

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

 Score = 48.2 bits (115), Expect = 2e-07
 Identities = 23/74 (31%), Positives = 41/74 (55%), Gaps = 4/74 (5%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQ--ELFINKE--KMFGFIRMDYKHNADKAKAKLD 170
           RL++ NI     + D+ ++F  +G     E+  N+   K FGF+      +AD+A+ KL 
Sbjct: 2   RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKLH 61

Query: 171 GHVLKGRSLKIRFA 184
           G V++GR +++  A
Sbjct: 62  GTVVEGRKIEVNNA 75

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

>gnl|CDD|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 = 48.4 bits (116), Expect = 2e-07
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKL 169
           L++  +    TE ++  LF  +G  +E+ + K+        FGF+  +   +AD A   L
Sbjct: 4   LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63

Query: 170 DGHVLKGRSLKI 181
           +G  L+GR +K+
Sbjct: 64  NGKELEGRVIKV 75

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

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 25/72 (34%), Positives = 45/72 (62%), Gaps = 6/72 (8%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKL 169
           LY+GN+  +ITE+D+  +F+P+GE + + + ++      K +GFI+     +A KA  +L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 170 DGHVLKGRSLKI 181
           +G  L GR +K+
Sbjct: 61  NGFELAGRPIKV 72

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

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

 Score = 52.3 bits (124), Expect = 2e-07
 Identities = 26/94 (27%), Positives = 53/94 (56%), Gaps = 6/94 (6%)

Query: 101 SEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFI 154
             P+++      N  L++GN+  D+TE D+ ELFK +G  + + + +++       F F+
Sbjct: 103 ESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFV 162

Query: 155 RMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINA 188
             + + +A+KA  +L+G  L+GR L+++ A   +
Sbjct: 163 EFESEESAEKAIEELNGKELEGRPLRVQKAQPAS 196

Length = 306

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

 Score = 47.4 bits (113), Expect = 4e-07
 Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 6/73 (8%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAK 168
           RL++ N+     E+D+ +LF  +GE  E+ +       K K F ++      +A KA  +
Sbjct: 4   RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 169 LDGHVLKGRSLKI 181
           LDG V +GR + I
Sbjct: 64  LDGKVFQGRLIHI 76

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

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

 Score = 46.4 bits (111), Expect = 6e-07
 Identities = 21/58 (36%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALR 246
           + V NL    T E L   F  FG +E   ++ D E G SK    VEF  +  A +AL 
Sbjct: 2   LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALE 59

Length = 73

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

 Score = 46.1 bits (110), Expect = 9e-07
 Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 3/71 (4%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYK--HNADKAKAKLDGHV 173
           L++ NI  ++ + ++  LF+ +G+ + L+    K  GFI + Y     A +AK  L G  
Sbjct: 4   LFVRNINSNVEDEELRALFEQFGDIRTLY-TACKHRGFIMVSYYDIRAARRAKRALQGTE 62

Query: 174 LKGRSLKIRFA 184
           L GR L I F+
Sbjct: 63  LGGRKLDIHFS 73

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

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

 Score = 46.2 bits (110), Expect = 9e-07
 Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 6/73 (8%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQEL------FINKEKMFGFIRMDYKHNADKAKAK 168
           RL++ N+    TE D+ +LF  YG   E+         K K F F+      +A KA A+
Sbjct: 4   RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63

Query: 169 LDGHVLKGRSLKI 181
           LDG V +GR L +
Sbjct: 64  LDGTVFQGRLLHL 76

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 51.0 bits (122), Expect = 1e-06
 Identities = 40/144 (27%), Positives = 71/144 (49%), Gaps = 14/144 (9%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKL 169
           LY+G++  D+TE  + +LFKP+G    + + ++ +      +G++      +A++A   +
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 170 DGHVLKGRSLKIRF---API-----NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIV 221
           +   L G+ ++I +    P         I VKNL   V N+ L   F  FG+I    V  
Sbjct: 63  NFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVAT 122

Query: 222 DERGNSKCEGIVEFARKPAAAQAL 245
           DE G S+  G V F ++ +A  A+
Sbjct: 123 DENGKSRGYGFVHFEKEESAKAAI 146

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|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 45.6 bits (108), Expect = 1e-06
 Identities = 18/65 (27%), Positives = 37/65 (56%), Gaps = 2/65 (3%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
           ++++GN+  D ++ ++  LF+ YG      + ++  F F+ +  +  AD+A  +L+G  L
Sbjct: 2   KIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ--FAFVHLRGEAAADRAIEELNGREL 59

Query: 175 KGRSL 179
            GR L
Sbjct: 60  HGRKL 64

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

>gnl|CDD|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 = 45.6 bits (109), Expect = 1e-06
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 6/65 (9%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFG------FIRMDYKHNADKAKAK 168
           +L++G +    TE D+  LF+ YG  +E+ I ++K  G      F++   +  A KA   
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 169 LDGHV 173
           L G V
Sbjct: 61  LHGKV 65

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

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 22/55 (40%), Positives = 29/55 (52%)

Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALR 246
           VKNL   + +E L   F  FG I  A V+ DE+G SK  G V F+    A +A+ 
Sbjct: 6   VKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVT 60

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

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

 Score = 45.2 bits (108), Expect = 2e-06
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 7/77 (9%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQEL-FINK-----EKMFGFIRMDYKHNA-DKAKA 167
           RL++G +   +TE+D+ E F  +G   ++  I K     ++ F +I +        K K+
Sbjct: 1   RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKS 60

Query: 168 KLDGHVLKGRSLKIRFA 184
            L+G   KG  LKI  A
Sbjct: 61  TLNGTKWKGSVLKIEEA 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 48.6 bits (116), Expect = 5e-06
 Identities = 30/109 (27%), Positives = 50/109 (45%), Gaps = 11/109 (10%)

Query: 147 KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKI-----RFAPINAAIK------VKNL 195
           K + +GF+  + + +A  A  K++G +L  + + +     +     A +K      VKNL
Sbjct: 127 KSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNL 186

Query: 196 TSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQA 244
              V  + L   F  FG+I  A V+ D  G S+    V F +   AA+A
Sbjct: 187 DPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKA 235

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

 Score = 43.8 bits (104), Expect = 5e-06
 Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 6/68 (8%)

Query: 120 NIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKLDGHV 173
           N+    T +D+  +F+ YGE  +++I +++       F F+R   K +A+ A   +DG  
Sbjct: 5   NLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKE 64

Query: 174 LKGRSLKI 181
           L GR L++
Sbjct: 65  LDGRELRV 72

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

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

 Score = 42.9 bits (101), Expect = 1e-05
 Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 2/67 (2%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
           +L++GN+  + TE +I  LF+ YG+  E  I K   +GF+ MD K  AD+A   L  + L
Sbjct: 2   KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--YGFVHMDDKTAADEAIRNLHHYKL 59

Query: 175 KGRSLKI 181
            G ++ +
Sbjct: 60  HGVAINV 66

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

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

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 5/75 (6%)

Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKM-----FGFIRMDYKHNADKAKAK 168
            RL + N+  D+TE D+ ELF   GE +++ IN ++         +  + + +A++A  +
Sbjct: 1   TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQ 60

Query: 169 LDGHVLKGRSLKIRF 183
            +G +L G+ +++  
Sbjct: 61  FNGVLLDGQPMQVEL 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|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 = 43.1 bits (102), Expect = 1e-05
 Identities = 21/70 (30%), Positives = 41/70 (58%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLK 175
           L++G++   +TE D+  LF+ YGE Q + +   +   ++ M+ + +A +A  KL    L 
Sbjct: 5   LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRGCAYVCMETRQDAHRALQKLRNVKLA 64

Query: 176 GRSLKIRFAP 185
           G+ +K+ +AP
Sbjct: 65  GKKIKVAWAP 74

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

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH- 172
             LY+G +G  +TE D+ + F  +GE + + +   +   F+    +  A+KA  +L    
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQCAFVTFTTREAAEKAAERLFNKL 61

Query: 173 VLKGRSLKIR 182
           ++ GR LK++
Sbjct: 62  IINGRRLKLK 71

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|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 42.7 bits (100), Expect = 1e-05
 Identities = 20/67 (29%), Positives = 35/67 (52%)

Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHV 173
           C +Y G I   +TE  + + F P+G+  E+ +  EK + FIR     +A  A   ++G  
Sbjct: 1   CTVYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPEKGYSFIRFSTHESAAHAIVSVNGTT 60

Query: 174 LKGRSLK 180
           ++G  +K
Sbjct: 61  IEGHVVK 67

This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 73

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

 Score = 42.9 bits (102), Expect = 1e-05
 Identities = 22/53 (41%), Positives = 29/53 (54%)

Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQA 244
           VKNL   + +E L+  FG +G I  A V+ D+ G SK  G V F    AA +A
Sbjct: 6   VKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKA 58

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

>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 25/68 (36%), Positives = 33/68 (48%), Gaps = 8/68 (11%)

Query: 200 TNELLELAFGVFGDIERAIVIVDER-GNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQS 258
           T E L   F  FGDIE   ++ D+  G SK  G V+F +   AA AL  C        +S
Sbjct: 13  TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALENC-------DKS 65

Query: 259 LRPVIVEP 266
            + V+ EP
Sbjct: 66  FKAVLAEP 73

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKL 169
           +++ N+  D  E+ + +LF P+G    + +      NK K +GF+ M     A  A A L
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 170 DGHVLKGRSLKIRF 183
           +G+ L GR L++ F
Sbjct: 64  NGYRLGGRVLQVSF 77

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

>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 20/67 (29%), Positives = 40/67 (59%), Gaps = 2/67 (2%)

Query: 116 LYLGNIGGDITENDIIELFKPYG-ETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
           LY+GN+  D+ E+D+ +LF+ +      + + K   + F+    +  ADKA  KL+G +L
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKGG-YAFVDCPDQSWADKAIEKLNGKIL 59

Query: 175 KGRSLKI 181
           +G+ +++
Sbjct: 60  QGKVIEV 66

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

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

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 117 YLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKLD 170
           ++GNI  D TE  +IE+F   G      +       K K +GF   +    A  A   L+
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 171 GHVLKGRSLKIRFA 184
           G+   GR+L++ FA
Sbjct: 62  GYEFNGRALRVDFA 75

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

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

 Score = 42.0 bits (99), Expect = 3e-05
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 6/74 (8%)

Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQEL------FINKEKMFGFIRMDYKHNADKAKA 167
           CR+Y+G+I  ++ E+ I + F P+G  + +         K K F F+  +    A  A  
Sbjct: 1   CRVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALE 60

Query: 168 KLDGHVLKGRSLKI 181
           +++G +L GR++K+
Sbjct: 61  QMNGVMLGGRNIKV 74

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

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 46.1 bits (109), Expect = 3e-05
 Identities = 37/135 (27%), Positives = 68/135 (50%), Gaps = 13/135 (9%)

Query: 125 ITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKLDGHVLKGRS 178
           +T+ +I  LF   GE +   + ++K+      +GF+      +A+KA   L+G  L+ ++
Sbjct: 15  MTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKT 74

Query: 179 LKIRFA-PINAAIK-----VKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEG 231
           +K+ +A P + +IK     V  L   +T   LE  F  FG I  + ++ D   G SK  G
Sbjct: 75  IKVSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVG 134

Query: 232 IVEFARKPAAAQALR 246
            + F ++  A +A++
Sbjct: 135 FIRFDKRDEADRAIK 149

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

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

 Score = 41.4 bits (98), Expect = 4e-05
 Identities = 22/58 (37%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDER-GNSKCEGIVEFARKPAAAQALR 246
           I V  L    T++ L   F  FG+IE A+VI D + G S+  G V F  K +A +A +
Sbjct: 3   IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 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|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in Saccharomyces cerevisiae protein Nrd1, Schizosaccharomyces pombe Rpb7-binding protein seb1 and similar proteins

 Score = 41.4 bits (97), Expect = 5e-05
 Identities = 14/51 (27%), Positives = 28/51 (54%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAK 166
           L+ G +  ++ E D+   F  +GE Q   +N +K   F++M  + +A+ A+
Sbjct: 6   LFPGGVTFNMIEYDLRSGFGRFGEVQSCILNNDKRHAFVKMYNRRDAENAR 56

This subfamily corresponds to the RRM of Nrd1 and Seb1. Nrd1 is a novel heterogeneous nuclear ribonucleoprotein (hnRNP)-like RNA-binding protein encoded by gene NRD1 (for nuclear pre-mRNA down-regulation) from yeast S. cerevisiae. It is implicated in 3' end formation of small nucleolar and small nuclear RNAs transcribed by polymerase II, and plays a critical role in pre-mRNA metabolism. Nrd1 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a short arginine-, serine-, and glutamate-rich segment similar to the regions rich in RE and RS dipeptides (RE/RS domains) in many metazoan splicing factors, and a proline- and glutamine-rich C-terminal domain (P+Q domain) similar to domains found in several yeast hnRNPs. Disruption of NRD1 gene is lethal to yeast cells. Its N-terminal domain is sufficient for viability, which may facilitate interactions with RNA polymerase II where Nrd1 may function as an auxiliary factor. By contrast, the RRM, RE/RS domains, and P+Q domain are dispensable. Seb1 is an RNA-binding protein encoded by gene seb1 (for seven binding) from fission yeast S. pombe. It is essential for cell viability and bound directly to Rpb7 subunit of RNA polymerase II. Seb1 is involved in processing of polymerase II transcripts. It also contains one RRM motif and a region rich in arginine-serine dipeptides (RS domain). Length = 79

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

 Score = 41.2 bits (97), Expect = 5e-05
 Identities = 16/72 (22%), Positives = 39/72 (54%), Gaps = 4/72 (5%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQEL-FI---NKEKMFGFIRMDYKHNADKAKAKLDG 171
           +++G +  D+T+ ++ E F  +G+  E+  I   N    F FI+ + +  A +A    + 
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESENH 65

Query: 172 HVLKGRSLKIRF 183
            +LK +++ +++
Sbjct: 66  SMLKNKTMHVQY 77

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

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

 Score = 40.9 bits (96), Expect = 6e-05
 Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 2/65 (3%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
           RLY+     D +E+ I E+F PYG  +E+ +     F F+  +   +A +AK  + G VL
Sbjct: 1   RLYVRPFPPDTSESAIREIFSPYGAVKEVKMISN--FAFVEFESLESAIRAKDSVHGKVL 58

Query: 175 KGRSL 179
               L
Sbjct: 59  NNNPL 63

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

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

 Score = 40.7 bits (96), Expect = 8e-05
 Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 6/75 (8%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKL 169
           L++ N+  D T+  + E F   G  +  F+ K+K       FG++    + +A +A  + 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 170 DGHVLKGRSLKIRFA 184
                 GR + + FA
Sbjct: 62  KKTKFGGRKIHVEFA 76

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

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

 Score = 40.5 bits (95), Expect = 9e-05
 Identities = 28/71 (39%), Positives = 39/71 (54%), Gaps = 4/71 (5%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQ-ELFINKE--KMFGFIRMDYKHNADKAKA-KLD 170
            +Y+GN+  DITE+D+ E FK    T   L  +KE  +  GF  +D+        A KLD
Sbjct: 1   TVYIGNLAWDITEDDVREFFKGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALKLD 60

Query: 171 GHVLKGRSLKI 181
           G VL GR ++I
Sbjct: 61  GTVLCGRPIRI 71

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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 44.2 bits (104), Expect = 1e-04
 Identities = 28/102 (27%), Positives = 52/102 (50%), Gaps = 11/102 (10%)

Query: 91  IQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGE--TQELFINK- 147
           +Q  T+ +  + P +  IK AN   LY+  +   +T++++  +F P+G+  T  +  +  
Sbjct: 70  LQNKTIKVSYARPSSDSIKGAN---LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNV 126

Query: 148 ---EKMFGFIRMDYKHNADKAKAKLDGHVLKGRS--LKIRFA 184
               K  GFIR D +  AD+A   L+G    G +  + ++FA
Sbjct: 127 TGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFA 168

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

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

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 14/72 (19%), Positives = 33/72 (45%), Gaps = 10/72 (13%)

Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKA-- 165
            ++++G +    T++ + + F  +GE +E  +       K + +GF+    K +A++A  
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 166 --KAKLDGHVLK 175
                +DG    
Sbjct: 61  DPNPIIDGRKAN 72

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

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 18/73 (24%), Positives = 41/73 (56%), Gaps = 5/73 (6%)

Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKE-KMFGFIRMDYKHNADKAKAKL-DG 171
            ++++G +  D+TE D+ + F  +GE  +++I K  + F F+      + + A++   + 
Sbjct: 1   RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFRAFAFVTFA---DPEVAQSLCGED 57

Query: 172 HVLKGRSLKIRFA 184
           H++KG S+ +  A
Sbjct: 58  HIIKGVSVHVSNA 70

This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 71

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

 Score = 40.2 bits (95), Expect = 1e-04
 Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 6/59 (10%)

Query: 120 NIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKLDGH 172
           N+  D  E+D+ ELF+P+G    +++ K+K       F F+    + +A++A  KL+G 
Sbjct: 6   NLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGF 64

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 17/56 (30%), Positives = 30/56 (53%)

Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRR 247
           V NL   V+++ ++  F  FG +++A V  D  G S     V F R+  A +A+++
Sbjct: 5   VSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQ 60

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, 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. THOC4 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. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 40.4 bits (94), Expect = 1e-04
 Identities = 17/67 (25%), Positives = 36/67 (53%)

Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHV 173
           C +Y G +   +TE  + + F P+G+  E+ +  +K + F+R +   +A  A   ++G  
Sbjct: 1   CTVYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPDKGYSFVRFNSHESAAHAIVSVNGTT 60

Query: 174 LKGRSLK 180
           ++G  +K
Sbjct: 61  IEGHVVK 67

This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

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

 Score = 40.3 bits (94), Expect = 1e-04
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLD 170
           L++GN+   + E  + ELF   G   ++ I K+     K FGF+   +  +   A A L+
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLN 63

Query: 171 GHVLKGRSLKIR 182
           G  L GR +K+ 
Sbjct: 64  GIRLYGRPIKVH 75

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

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

 Score = 40.4 bits (95), Expect = 1e-04
 Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 13/80 (16%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYK------------HNA 162
           R+Y+ N+    +E D+ E  K +     + I  + + GF     +              A
Sbjct: 1   RVYISNLSYSSSEEDLEEFLKDFEPV-SVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59

Query: 163 DKAKAKLDGHVLKGRSLKIR 182
           +K    L+G V K R L ++
Sbjct: 60  EKVVKDLNGKVFKNRKLFVK 79

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

>gnl|CDD|240856 cd12410, RRM2_RRT5, RNA recognition motif 2 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 20/82 (24%), Positives = 32/82 (39%), Gaps = 12/82 (14%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH-- 172
            +Y G +   +T+ D+ E FK Y   QE++I + +      +    +   A   LD    
Sbjct: 4   TVYCGKLPKKVTDEDLREFFKDYN-PQEIWIFRTRKSKRNPLQLHRHFTAALVTLDTEET 62

Query: 173 ------VLKGRSL---KIRFAP 185
                  LK + L   KI   P
Sbjct: 63  LDEIIESLKSKKLNGKKISLKP 84

This subfamily corresponds to the RRM2 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 = 93

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

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 7/74 (9%)

Query: 115 RLYLGNIGGDITENDIIELFKPYG--ETQELFINKE----KMFGFIRMDYKHNADKAKAK 168
           +L++G +  D+TE D+ E F  YG  E+ E+  +KE    + F F+  D     DK   +
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

Query: 169 LDGHVLKGRSLKIR 182
              H + G  ++++
Sbjct: 61  KY-HTINGHRVEVK 73

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

>gnl|CDD|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 = 39.8 bits (94), Expect = 2e-04
 Identities = 27/81 (33%), Positives = 38/81 (46%), Gaps = 16/81 (19%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQEL-----------FINKEKMFGFIRMDYKHNAD 163
           RLY+GN+   ITE ++++ F        L            IN EK F F+        +
Sbjct: 3   RLYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKNFAFVEF---RTVE 59

Query: 164 KAKA--KLDGHVLKGRSLKIR 182
           +A A   LDG + KG+ LKIR
Sbjct: 60  EATAALALDGIIFKGQPLKIR 80

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

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 3/72 (4%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFIN---KEKMFGFIRMDYKHNADKAKAKLDG 171
           R+Y+GN+ GDI E DI +LF  YG  + + +    +   F F+  +   +A+ A    DG
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDG 60

Query: 172 HVLKGRSLKIRF 183
           +   G  L++ F
Sbjct: 61  YDFDGYRLRVEF 72

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

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

 Score = 43.3 bits (102), Expect = 2e-04
 Identities = 22/73 (30%), Positives = 46/73 (63%), Gaps = 6/73 (8%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAK 168
           +LY+GN+  +ITE ++ ++F+P+G+ +++ ++++      K FGFI+      A +A   
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEV 247

Query: 169 LDGHVLKGRSLKI 181
           ++G  L GR +K+
Sbjct: 248 MNGFELAGRPIKV 260

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

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

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 2/69 (2%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLK 175
           LY+ N+    TE  + ELF  YGE +   + K K + F+  + + +A KA  +++G  L+
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVER--VKKIKDYAFVHFEERDDAVKAMEEMNGKELE 61

Query: 176 GRSLKIRFA 184
           G  +++  A
Sbjct: 62  GSPIEVSLA 70

This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Length = 72

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

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 16/71 (22%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI-NKEKMFGFIRMDYKHNADKAKAKLDGHV 173
           ++Y+GN+G   T+ ++ + F+ YG  + +++      F F+  +   +A+ A   LDG  
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRR 60

Query: 174 LKGRSLKIRFA 184
           + G  +++  +
Sbjct: 61  ICGNRVRVELS 71

This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 73

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

 Score = 38.7 bits (91), Expect = 4e-04
 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 5/69 (7%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI-----NKEKMFGFIRMDYKHNADKAKAKLD 170
           +Y+ N+G D+ +  + ELF  YG+     +      K K FGF+  +    A KA  +L+
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELN 63

Query: 171 GHVLKGRSL 179
           G  + G+ L
Sbjct: 64  GKEVNGKKL 72

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

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

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
           R+Y+G +     E D+   FK YG  +E  IN +  FGF+  +   +AD A  +L+G  L
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRIRE--INLKNGFGFVEFEDPRDADDAVYELNGKEL 58

Query: 175 KGRSLKIRFA 184
            G  + +  A
Sbjct: 59  CGERVIVEHA 68

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

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

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 6/76 (7%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKL 169
           L +GN+  + T+    EL  P+G  +  F+       + K +GF+    K +A KAK +L
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 170 DGHVLKGRSLKIRFAP 185
           DG  + GR L++ +A 
Sbjct: 62  DGKQIGGRKLQVDWAD 77

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

>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 8/77 (10%)

Query: 116 LYLGNIGGDITENDIIELFKPYGE---TQELFINK---EKMFGFIRMDYKHNADKAKAKL 169
           LY+  +   +T+ ++  LF PYG    ++ L  N     +  GFIR D +  A++A   L
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 170 DGHVLKGRSLKI--RFA 184
           +G +  G +  I  +FA
Sbjct: 63  NGTIPPGATEPITVKFA 79

This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 79

>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 38.4 bits (90), Expect = 5e-04
 Identities = 21/63 (33%), Positives = 36/63 (57%)

Query: 122 GGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKI 181
           G  +TE  + + F P+G    + + KEK  GF+  +   +AD+A A+L+G  ++G  LK+
Sbjct: 11  GYGLTEEILKKAFSPFGNIINISMEKEKNCGFVTFEKMESADRAIAELNGTTVQGVQLKV 70

Query: 182 RFA 184
             A
Sbjct: 71  SLA 73

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

>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 38.5 bits (90), Expect = 5e-04
 Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 7/76 (9%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKM-----FGFIRMDYKHNADKAKAKLD 170
           LY+ N+   + E D+  + KPYG+     I ++        GF RM+ +   +   +K +
Sbjct: 3   LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKFN 62

Query: 171 GHVLKGRS--LKIRFA 184
           G  LKG    L ++FA
Sbjct: 63  GKYLKGEGEPLLVKFA 78

This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 79

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

 Score = 38.5 bits (90), Expect = 5e-04
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 9/77 (11%)

Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKH--NADKA 165
           +  L++GN+   +TE  + ELF   G  + + I K+     K F F+   +KH  +   A
Sbjct: 1   DRTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFV--TFKHEVSVPYA 58

Query: 166 KAKLDGHVLKGRSLKIR 182
              L+G  L GR L+I+
Sbjct: 59  IQLLNGIRLFGRELRIK 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|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 38.5 bits (90), Expect = 5e-04
 Identities = 18/52 (34%), Positives = 31/52 (59%), Gaps = 6/52 (11%)

Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMD 157
           ++ +L++GN+  DITE+++ E FK +G   E+ IN +        FGF+  D
Sbjct: 2   DSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFD 53

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

>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 38.7 bits (90), Expect = 5e-04
 Identities = 21/78 (26%), Positives = 44/78 (56%), Gaps = 8/78 (10%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKM-----FGFIRMDYKHNADKAKAKL 169
           +L++G +    TE ++ E+F PYG  +++++ +++M       F++   K  A  A   L
Sbjct: 1   KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKAL 60

Query: 170 DG-HVLKG--RSLKIRFA 184
           +G + ++G  + L +RFA
Sbjct: 61  NGVYTMRGCDQPLIVRFA 78

This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

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

 Score = 38.0 bits (89), Expect = 6e-04
 Identities = 20/69 (28%), Positives = 41/69 (59%), Gaps = 3/69 (4%)

Query: 114 CRLYLGNIGGD-ITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH 172
            R+++GN+  D +++ D+ E+F  YG+   + ++K   +GF++ D + +A  A A  +G 
Sbjct: 1   SRVFVGNLNTDKVSKEDLEEIFSKYGKILGISLHKG--YGFVQFDNEEDARAAVAGENGR 58

Query: 173 VLKGRSLKI 181
            + G+ L I
Sbjct: 59  EIAGQKLDI 67

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

>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score = 38.4 bits (90), Expect = 7e-04
 Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 1/46 (2%)

Query: 200 TNELLELAFGVFGDIERAIVIVDER-GNSKCEGIVEFARKPAAAQA 244
           T+E LE+ F  FG I+   VI D++ G+S     +EF  K    +A
Sbjct: 16  TDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

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

 Score = 37.9 bits (89), Expect = 8e-04
 Identities = 22/55 (40%), Positives = 28/55 (50%)

Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQA 244
           I +KNL   + N+ L   F  FG+I    V  DE G SK  G V F  + AA +A
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRA 59

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

>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 37.7 bits (88), Expect = 8e-04
 Identities = 17/72 (23%), Positives = 36/72 (50%), Gaps = 6/72 (8%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKL 169
           +++G++  +I    +   F P+GE  +  +       K K +GF+    K +A+ A   +
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 170 DGHVLKGRSLKI 181
           +G  L GR+++ 
Sbjct: 62  NGQWLGGRAIRT 73

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

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

 Score = 38.0 bits (89), Expect = 9e-04
 Identities = 22/56 (39%), Positives = 31/56 (55%), Gaps = 3/56 (5%)

Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGI--VEFARKPAAAQAL 245
           V+NL    T+E LE  F   G I+R   +V ++G+ KC G   V FA +  A +AL
Sbjct: 4   VRNLPYDTTDEQLEEFFSEVGPIKRC-FVVKDKGSKKCRGFGYVTFALEEDAKRAL 58

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|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 41.4 bits (98), Expect = 9e-04
 Identities = 30/102 (29%), Positives = 53/102 (51%), Gaps = 18/102 (17%)

Query: 313 KQLHELYEHETEMLRKEL---AQREIDRERQKAEWEMKER------------QAEE-LKR 356
           K++ E  + E E L+KE    A+ E+ + R + E E+KER            Q EE L R
Sbjct: 35  KRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNELQRLERRLLQREETLDR 94

Query: 357 RDEELMKK--HAEEMQLRLAQQEEDLRRRQNDNSMFLVEQQQ 396
           + E L KK  + E+ +  L+ +E++L  ++ +    + EQ++
Sbjct: 95  KMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQRE 136

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

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

 Score = 37.1 bits (87), Expect = 0.001
 Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRC 248
           + V+NL   VT E L   F  +G +E  + +V  +   +    VEFA    A  AL++ 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEG-VRLVRNKDRPRGFAFVEFASPEDAEAALKKL 58

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

>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 5/76 (6%)

Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQEL-----FINKEKMFGFIRMDYKHNADKAKAK 168
            +L + N+  + T+ ++ ELF P+G+ + +     F    + F F+    K  A  A   
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60

Query: 169 LDGHVLKGRSLKIRFA 184
           L    L GR L + +A
Sbjct: 61  LKSTHLYGRHLVLEYA 76

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 2/54 (3%)

Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQAL 245
           V NL   VT +LL   F   G I+   +I +   +      VE+    +AA AL
Sbjct: 3   VGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYA--FVEYYDHRSAAAAL 54

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

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 19/56 (33%), Positives = 29/56 (51%)

Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQAL 245
           I V NL   V  + L+  F + G + RA +  D+ G S+  G+V+F     A QA+
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAI 56

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

>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 37.8 bits (87), Expect = 0.001
 Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 6/75 (8%)

Query: 116 LYLGNIGGDITENDIIELFKPYGE------TQELFINKEKMFGFIRMDYKHNADKAKAKL 169
           +++G++  +IT +DI   F P+G        +++   K K +GF+    K +A+ A  ++
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 170 DGHVLKGRSLKIRFA 184
            G  L GR ++  +A
Sbjct: 64  GGQWLGGRQIRTNWA 78

This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 37.5 bits (88), Expect = 0.001
 Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 5/71 (7%)

Query: 114 CRLYLGNIGGDITENDIIELFKPYGET-----QELFINKEKMFGFIRMDYKHNADKAKAK 168
             L++ N      ++DI +LF+ YGE        L  NK + F +++     +A  A A 
Sbjct: 1   STLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVAL 60

Query: 169 LDGHVLKGRSL 179
           L+G + +G  L
Sbjct: 61  LNGKLGEGYKL 71

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 10/75 (13%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI---NKEKM------FGFIRMDYKHNADKAK 166
           +Y+ N+   + E+D+  +F  +GE + + I     EK       F F+      +A+ A 
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA- 61

Query: 167 AKLDGHVLKGRSLKI 181
            +L+G  L GR + +
Sbjct: 62  LQLNGTELGGRKISV 76

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|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 19/74 (25%), Positives = 41/74 (55%), Gaps = 10/74 (13%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH--- 172
           L+L N+  D+TE+D+I L  P+G+   + + + K    + MD   + + AK+ +  +   
Sbjct: 2   LHLRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQALVEMD---SVESAKS-MVDYYLT 57

Query: 173 ---VLKGRSLKIRF 183
              +++GR + I++
Sbjct: 58  VPALIRGRRVYIQY 71

This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM. . Length = 74

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

 Score = 37.6 bits (87), Expect = 0.001
 Identities = 21/77 (27%), Positives = 42/77 (54%), Gaps = 8/77 (10%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFG------FIRMDYKHNADKAKAKL 169
           LY+ N+   +TE+++ ++F+ YG   +  + ++K  G      F+R D +  A  A + L
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 170 DGHVLKGRS--LKIRFA 184
           +G +  G +  L +R+A
Sbjct: 63  NGTIPPGSTMPLSVRYA 79

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

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

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKL 169
           +++ N+G D  E  + ++F P+G    + +      NK K FGF+ M     A  A A L
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 170 DGHVLKGRSLKIRF 183
           +G+ L  + L++ F
Sbjct: 64  NGYRLGDKILQVSF 77

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

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

 Score = 37.8 bits (87), Expect = 0.001
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKL 169
           +++ N+  D  E+ + +LF P+G    + +      NK K FGF+ M     A  A A L
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 170 DGHVLKGRSLKIRF 183
           +G+ L  R L++ F
Sbjct: 66  NGYRLGDRVLQVSF 79

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

>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 6/75 (8%)

Query: 116 LYLGNIGGDITENDIIELFKPYGE------TQELFINKEKMFGFIRMDYKHNADKAKAKL 169
           +++G++  +IT  DI   F P+G+       +++   K K +GF+    K +A+ A   +
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 170 DGHVLKGRSLKIRFA 184
            G  L GR ++  +A
Sbjct: 64  GGQWLGGRQIRTNWA 78

This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

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

 Score = 37.1 bits (86), Expect = 0.001
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEK--MFGFIRMDYKHNADKAKAKLDGH 172
           R+Y+GN+  DI   DI +LF  YG  +++ +   +   F F+  +   +A+ A    DG+
Sbjct: 1   RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPPFAFVEFEDPRDAEDAVYGRDGY 60

Query: 173 VLKGRSLKIRF 183
              G  L++ F
Sbjct: 61  DYDGYRLRVEF 71

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

>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKL 169
           +++ N+  D  E+ + ++F P+G    + +      NK K FGF+ M     A  A A L
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 170 DGHVLKGRSLKIRF 183
           +G+ L  R L++ F
Sbjct: 66  NGYRLGDRVLQVSF 79

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 4/80 (5%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKM----FGFIRMDYKHNADKAKAKLDG 171
           LY+GN+  D+TE  I++LF   G  +   +  E      + F+      +A  A A ++G
Sbjct: 2   LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNG 61

Query: 172 HVLKGRSLKIRFAPINAAIK 191
             + G+ +K+ +A   ++ K
Sbjct: 62  RKILGKEVKVNWATTPSSQK 81

This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 81

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 4/66 (6%)

Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALR--- 246
           ++V NL   VT E LE  FG  G++++  +  D  G S+    V F ++  A +A++   
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFN 62

Query: 247 -RCAEG 251
               +G
Sbjct: 63  GVLLDG 68

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|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 = 19/78 (24%), Positives = 37/78 (47%), Gaps = 9/78 (11%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI---------NKEKMFGFIRMDYKHNADKAK 166
           LY+GN+   +TE  + + F  +G    + I          + +  GF+    + +A++A 
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 167 AKLDGHVLKGRSLKIRFA 184
            +LDG  + G  LK+ + 
Sbjct: 64  DELDGKDVMGYELKLGWG 81

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|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 40.1 bits (94), Expect = 0.002
 Identities = 22/40 (55%), Positives = 22/40 (55%), Gaps = 1/40 (2%)

Query: 41 GGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGG 80
          GG GGGRGGG GG GG  G    GRG      R  G GGG
Sbjct: 4  GGFGGGRGGGRGGGGG-GGRGGGGRGGGRGGGRGRGRGGG 42

Length = 293

>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 1/70 (1%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLK 175
           +Y+GNI   +TE  +   F  YGE + +   +EK   F+      NA KA   +  H L 
Sbjct: 6   VYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREKNCAFVNFTNISNAIKAIDGVKSHPLF 65

Query: 176 GRSLKIRFAP 185
            +  KI +  
Sbjct: 66  -KKFKISYGK 74

This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

>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 = 36.5 bits (85), Expect = 0.002
 Identities = 19/64 (29%), Positives = 36/64 (56%), Gaps = 6/64 (9%)

Query: 124 DITENDIIELFKPYGE--TQELFINKE----KMFGFIRMDYKHNADKAKAKLDGHVLKGR 177
           + T+ D+ +LF P+G   + ++F++K     K FGF+  D   +A  A   ++G  + G+
Sbjct: 9   EFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGK 68

Query: 178 SLKI 181
            LK+
Sbjct: 69  RLKV 72

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

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

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 10/82 (12%)

Query: 113 NCRLYLGNIGGDITENDIIELF----KPYGETQELFI----NKEKMFG--FIRMDYKHNA 162
           + RLY+ N+   +TE D++ +F        E + +F      + +M G  F+    +  A
Sbjct: 1   SKRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIA 60

Query: 163 DKAKAKLDGHVLKGRSLKIRFA 184
            KA   ++G+VLKG+ + I+F 
Sbjct: 61  TKALNLVNGYVLKGKPMVIQFG 82

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

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL- 174
           L++G +G   +  ++   F  +G  + +  +  + + +I  +    A  AK  L G  L 
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGRNYAYIEYESIEAAQAAKEALRGFPLG 60

Query: 175 -KGRSLKIRFA 184
             GR L++ FA
Sbjct: 61  GPGRRLRVDFA 71

This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 72

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 39.5 bits (92), Expect = 0.003
 Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 6/74 (8%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQ------ELFINKEKMFGFIRMDYKHNADKAKAKL 169
           +++ N+  D  E  + +LF P+G  Q      +L  N+ K +GF+ M     A  A   L
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 170 DGHVLKGRSLKIRF 183
           +G+ L  R L++ F
Sbjct: 332 NGYTLGNRVLQVSF 345

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 36.4 bits (84), Expect = 0.003
 Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 7/76 (9%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAK 168
           +L++G + GD+ E D+ E F  +G  ++  +       K++ FGF+      +ADKA A 
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA-AV 59

Query: 169 LDGHVLKGRSLKIRFA 184
           +  H + G  ++++ A
Sbjct: 60  VKFHPINGHRVEVKKA 75

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 36.3 bits (84), Expect = 0.003
 Identities = 14/69 (20%), Positives = 28/69 (40%), Gaps = 2/69 (2%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKM--FGFIRMDYKHNADKAKAKLDGH 172
            +Y G        +D+  LF+  G  +++ +    +    FI  +    A  A   L+G 
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGA 60

Query: 173 VLKGRSLKI 181
            + G  +K+
Sbjct: 61  SVDGNCIKV 69

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

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

 Score = 36.4 bits (85), Expect = 0.003
 Identities = 17/71 (23%), Positives = 38/71 (53%), Gaps = 6/71 (8%)

Query: 120 NIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKLDGHV 173
            +    TE D+ E+F  YG  +++ +       + + FGF+  +   +A +AK +L+G  
Sbjct: 6   GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGME 65

Query: 174 LKGRSLKIRFA 184
           + GR +++ ++
Sbjct: 66  IDGRRIRVDYS 76

This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 78

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

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 6/77 (7%)

Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKA 167
             +Y+ N+   +T ND+ ++F  YG+  ++ I K+K         FI    + +A K   
Sbjct: 2   STVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVK 61

Query: 168 KLDGHVLKGRSLKIRFA 184
            L+   L GR+LK   A
Sbjct: 62  ALNNKELFGRTLKCSIA 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|241131 cd12687, RRM1_PTBPH3, RNA recognition motif 1 in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3)

 Score = 36.1 bits (83), Expect = 0.003
 Identities = 19/74 (25%), Positives = 43/74 (58%), Gaps = 8/74 (10%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHV-- 173
           L++ N+G +I+END+++L +P+G   +L + + K    ++M    +   A + L  +   
Sbjct: 3   LHVRNVGHEISENDLLQLVQPFGVVTKLVMLRAKNQALLQM---QDVSSAISALQYYTTV 59

Query: 174 ---LKGRSLKIRFA 184
              ++GR++ I+F+
Sbjct: 60  QPSVRGRNVYIQFS 73

This subfamily corresponds to the RRM1 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 75

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

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 7/56 (12%)

Query: 192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRR 247
           V+NL    T E L   F  +G++ER   I D          V F  +  A +A+  
Sbjct: 6   VRNLPLSTTEEQLRELFSEYGEVERVKKIKD-------YAFVHFEERDDAVKAMEE 54

This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Length = 72

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 38.9 bits (91), Expect = 0.004
 Identities = 20/40 (50%), Positives = 20/40 (50%)

Query: 41 GGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGG 80
          GG  GG GGG  G GG  G R  GRG        G GGGG
Sbjct: 11 GGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGG 50

Length = 293

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 38.9 bits (91), Expect = 0.004
 Identities = 16/40 (40%), Positives = 16/40 (40%)

Query: 41 GGRGGGRGGGVGGRGGYRGNRPDGRGSDMNESRMGGGGGG 80
          G  GG  GG  GGRGG  G    G G         G G G
Sbjct: 1  GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRG 40

Length = 293

>gnl|CDD|180777 PRK06958, PRK06958, single-stranded DNA-binding protein; Provisional

 Score = 38.2 bits (89), Expect = 0.004
 Identities = 25/42 (59%), Positives = 25/42 (59%), Gaps = 1/42 (2%)

Query: 40  LGGRGGGRGGGVGG-RGGYRGNRPDGRGSDMNESRMGGGGGG 80
           LGGRGG  GGG GG  GGY G    G G    ESR GGGGG 
Sbjct: 108 LGGRGGSGGGGGGGDEGGYGGGGGGGGGGYGGESRSGGGGGR 149

Length = 182

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

 Score = 36.2 bits (83), Expect = 0.004
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 116 LYLGNIGGDITENDIIELFKPYGET------QELFINKEKMFGFIRMDYKHNADKAKAKL 169
           +++ N+  +  E+ + +LF P+G        ++   NK K FGF+ M     A  A A L
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 170 DGHVLKGRSLKIRF 183
           +G+ L  R L++ F
Sbjct: 64  NGYRLGDRVLQVSF 77

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

>gnl|CDD|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3)

 Score = 35.9 bits (83), Expect = 0.004
 Identities = 16/78 (20%), Positives = 33/78 (42%), Gaps = 7/78 (8%)

Query: 113 NCR-----LYLGNIGGDITENDIIELFKPYGETQ--ELFINKEKMFGFIRMDYKHNADKA 165
            C      +++ N+  D+TE D+I     +G     ++F +  K    +    +  A +A
Sbjct: 2   YCCPPTKMIHVSNLPSDVTEEDVINHLAEHGVIVNVKVFESNGKKQALVEFATEEQATEA 61

Query: 166 KAKLDGHVLKGRSLKIRF 183
            A      L G ++++ F
Sbjct: 62  LACKHASSLNGSTIRLAF 79

This subfamily corresponds to the RRM4 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 20/75 (26%), Positives = 42/75 (56%), Gaps = 6/75 (8%)

Query: 114 CRLYLGNIGGDITENDIIELFKPYGE--TQELFINKE----KMFGFIRMDYKHNADKAKA 167
           C L++ ++  + T+ D+ + F P+G   + ++FI+K+    K FGF+  D   +A  A  
Sbjct: 5   CNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQ 64

Query: 168 KLDGHVLKGRSLKIR 182
            ++G  +  + LK++
Sbjct: 65  AMNGFQIGTKRLKVQ 79

This subgroup corresponds to the RRM3 of Bruno protein, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 79

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	503
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.96
KOG0117|consensus	506		99.94
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.94
KOG0144|consensus	510		99.93
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.93
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.93
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.92
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.92
KOG0148|consensus	321		99.91
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.91
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.9
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.9
KOG0131|consensus	203		99.9
KOG0145|consensus	360		99.9
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.89
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.88
KOG0127|consensus	678		99.86
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.86
KOG0117|consensus	506		99.86
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.85
KOG0109|consensus	346		99.85
KOG0123|consensus	369		99.85
KOG0115|consensus	275		99.85
KOG0127|consensus	678		99.84
KOG0145|consensus	360		99.83
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.82
KOG0110|consensus	725		99.8
KOG0124|consensus	544		99.8
KOG0105|consensus	241		99.79
KOG0148|consensus	321		99.76
KOG0146|consensus	371		99.75
KOG0123|consensus	369		99.72
KOG0144|consensus	510		99.67
KOG4205|consensus	311		99.65
KOG0110|consensus	725		99.65
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.63
KOG4661|consensus	940		99.61
KOG0147|consensus	549		99.58
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.58
KOG4206|consensus	221		99.55
KOG4212|consensus	608		99.52
KOG0147|consensus	549		99.52
KOG1548|consensus	382		99.51
KOG0106|consensus	216		99.5
KOG0107|consensus	195		99.5
KOG1457|consensus	284		99.45
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.44
KOG0121|consensus	153		99.44
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.38
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.37
PLN03120	260	nucleic acid binding protein; Provisional	99.35
KOG1456|consensus	494		99.35
KOG4211|consensus	510		99.34
KOG0125|consensus	376		99.34
KOG4661|consensus	940		99.33
KOG1190|consensus	492		99.32
KOG0122|consensus	270		99.31
KOG0114|consensus	124		99.31
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.31
KOG1190|consensus	492		99.27
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.26
KOG0124|consensus	544		99.25
smart00362	72	RRM_2 RNA recognition motif.	99.25
KOG0120|consensus	500		99.25
PLN03213	759	repressor of silencing 3; Provisional	99.24
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.23
PLN03121	243	nucleic acid binding protein; Provisional	99.23
KOG1456|consensus	494		99.22
KOG4212|consensus	608		99.21
KOG0132|consensus	894		99.21
KOG4207|consensus	256		99.19
KOG0130|consensus	170		99.17
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.16
KOG0111|consensus	298		99.15
KOG0149|consensus	247		99.14
KOG0113|consensus	335		99.14
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.13
KOG0122|consensus	270		99.11
KOG0129|consensus	520		99.07
smart00360	71	RRM RNA recognition motif.	99.05
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.05
PLN03120	260	nucleic acid binding protein; Provisional	99.04
KOG0126|consensus	219		99.04
KOG0121|consensus	153		99.0
KOG0109|consensus	346		99.0
KOG0149|consensus	247		98.99
KOG0120|consensus	500		98.98
KOG0125|consensus	376		98.97
KOG0415|consensus	479		98.95
KOG4454|consensus	267		98.94
KOG0108|consensus	435		98.91
PLN03121	243	nucleic acid binding protein; Provisional	98.91
smart00362	72	RRM_2 RNA recognition motif.	98.9
PF08075	52	NOPS: NOPS (NUC059) domain; InterPro: IPR012975 Th	98.88
KOG0107|consensus	195		98.88
KOG0131|consensus	203		98.87
KOG0153|consensus	377		98.87
KOG0126|consensus	219		98.87
KOG4207|consensus	256		98.84
KOG0113|consensus	335		98.83
KOG0146|consensus	371		98.82
KOG0114|consensus	124		98.81
PLN03213	759	repressor of silencing 3; Provisional	98.8
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.79
smart00360	71	RRM RNA recognition motif.	98.78
KOG0130|consensus	170		98.77
KOG0111|consensus	298		98.73
KOG0415|consensus	479		98.72
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.69
KOG0533|consensus	243		98.69
smart00361	70	RRM_1 RNA recognition motif.	98.67
KOG0112|consensus	975		98.66
KOG1365|consensus	508		98.63
KOG0108|consensus	435		98.6
KOG0128|consensus	881		98.59
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.55
smart00361	70	RRM_1 RNA recognition motif.	98.53
KOG4211|consensus	510		98.49
KOG0151|consensus	877		98.48
KOG0226|consensus	290		98.48
KOG0105|consensus	241		98.44
KOG4210|consensus	285		98.43
KOG4208|consensus	214		98.39
KOG4205|consensus	311		98.33
KOG4660|consensus	549		98.3
KOG4206|consensus	221		98.26
KOG2193|consensus	584		98.26
KOG0116|consensus	419		98.24
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.22
KOG2891|consensus	445		98.16
KOG0132|consensus	894		98.16
KOG0153|consensus	377		98.09
KOG4307|consensus	944		98.05
KOG4676|consensus	479		98.04
KOG4208|consensus	214		98.03
KOG2253|consensus	668		98.02
KOG4209|consensus	231		98.0
KOG0533|consensus	243		97.98
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.92
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.87
KOG1548|consensus	382		97.8
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.78
KOG4307|consensus	944		97.77
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.76
KOG0106|consensus	216		97.74
KOG1995|consensus	351		97.72
KOG1457|consensus	284		97.7
KOG0226|consensus	290		97.64
KOG4454|consensus	267		97.62
KOG1365|consensus	508		97.61
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.5
KOG0116|consensus	419		97.49
PTZ00266	1021	NIMA-related protein kinase; Provisional	97.48
KOG4209|consensus	231		97.35
PTZ00266	1021	NIMA-related protein kinase; Provisional	97.34
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.25
KOG0151|consensus	877		97.21
KOG1855|consensus	484		97.14
KOG3152|consensus	278		97.13
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.04
KOG4660|consensus	549		97.0
KOG1029|consensus	1118		96.89
KOG0128|consensus	881		96.8
KOG2314|consensus	698		96.78
KOG0112|consensus	975		96.73
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	96.69
KOG1995|consensus	351		96.62
KOG2314|consensus	698		96.56
KOG2416|consensus	718		96.51
KOG4210|consensus	285		96.46
KOG1029|consensus	1118		96.38
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.24
KOG0163|consensus	1259		95.96
KOG1855|consensus	484		95.85
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.82
KOG2202|consensus	260		95.81
KOG0129|consensus	520		95.73
KOG4849|consensus	498		95.58
KOG2416|consensus	718		95.55
KOG4676|consensus	479		95.52
COG5175	480	MOT2 Transcriptional repressor [Transcription]	95.4
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	95.39
KOG2591|consensus	684		95.08
KOG1996|consensus	378		95.04
KOG2135|consensus	526		94.95
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	94.57
KOG4849|consensus	498		94.55
KOG2068|consensus	327		94.48
KOG1144|consensus	1064		94.39
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	94.07
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	94.0
KOG0163|consensus	1259		93.91
KOG2591|consensus	684		93.87
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	93.62
KOG4285|consensus	350		93.25
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	93.16
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	93.16
KOG2253|consensus	668		93.11
KOG2202|consensus	260		92.91
KOG1996|consensus	378		92.72
KOG3634|consensus	361		92.63
KOG3654|consensus	708		92.62
KOG0115|consensus	275		92.39
KOG4574|consensus	1007		91.77
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	91.46
KOG3152|consensus	278		91.39
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	90.28
KOG2193|consensus	584		90.27
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	90.21
KOG2318|consensus	650		90.12
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	89.67
KOG3634|consensus	361		89.33
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	87.55
KOG2412|consensus	591		87.21
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	86.29
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	86.21
KOG3054|consensus	299		86.17
PTZ00146	293	fibrillarin; Provisional	85.73
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	85.09
KOG3973|consensus	465		83.17
KOG2891|consensus	445		82.55
KOG4364|consensus	811		81.74
KOG2072|consensus	988		81.67
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	80.03

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.96  E-value=1.9e-28  Score=250.61  Aligned_cols=158  Identities=20%  Similarity=0.389  Sum_probs=142.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ...|+|||+|||+++|+++|+++|+.||+|++|+|++      +++||||+|.+.++|.+||..||++.|.+++|+|.++
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a  184 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYA  184 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecc
Confidence            4578999999999999999999999999999999964      3689999999999999999999999999999999998


Q ss_pred             cc------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecC
Q psy93           185 PI------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQ  257 (503)
Q Consensus       185 ~~------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~  257 (503)
                      .+      .++|||.|||..+++++|+++|++||.|+.|.|+.| .++++++||||+|.+.++|.+||..|| ++.+ ..
T Consensus       185 ~p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~ln-g~~~-~g  262 (346)
T TIGR01659       185 RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALN-NVIP-EG  262 (346)
T ss_pred             cccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhC-CCcc-CC
Confidence            54      568999999999999999999999999999999988 488999999999999999999999997 5544 23


Q ss_pred             CCCeEEeecCCcc
Q psy93           258 SLRPVIVEPLELT  270 (503)
Q Consensus       258 ~~rpl~V~~~~~~  270 (503)
                      ..++|.|.+++..
T Consensus       263 ~~~~l~V~~a~~~  275 (346)
T TIGR01659       263 GSQPLTVRLAEEH  275 (346)
T ss_pred             CceeEEEEECCcc
Confidence            4578899887654

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).

>KOG0117|consensus

Probab=99.94  E-value=1.8e-26  Score=231.19  Aligned_cols=223  Identities=19%  Similarity=0.258  Sum_probs=191.3

Q ss_pred             ChhhHHHHHhhcCCCCCC---------CCCCCCccccCcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec----
Q psy93            81 DRYFTEKIMAIQGPTLDL---------PPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINK----  147 (503)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~---------p~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~----  147 (503)
                      ..+...++....+.++++         ||++  +.-......|.|||+.||.++.|++|.-||++.|+|.+++|+.    
T Consensus        44 ~eaal~al~E~tgy~l~ve~gqrk~ggPpP~--weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~s  121 (506)
T KOG0117|consen   44 EEAALKALLERTGYTLVVENGQRKYGGPPPG--WEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFS  121 (506)
T ss_pred             HHHHHHHHHHhcCceEEEeccccccCCCCCc--ccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccC
Confidence            455566777666666655         3333  4555567789999999999999999999999999999999975    


Q ss_pred             --CCCceEEeeCCHHHHHHHHHHhCCcccc-CceEEEEecccccceeccCcccccCHHHHHHHhccCCC-eeeeEEEeC-
Q psy93           148 --EKMFGFIRMDYKHNADKAKAKLDGHVLK-GRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGD-IERAIVIVD-  222 (503)
Q Consensus       148 --~kg~aFV~F~~~e~A~~Ai~~l~g~~l~-g~~l~V~~a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~-V~~~~v~~d-  222 (503)
                        ++|||||+|.+.++|+.||+.||+.+|. |+.|.|+.+..++.|||+|||...++++|.+.|++.++ |+.|.|... 
T Consensus       122 G~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p  201 (506)
T KOG0117|consen  122 GDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSP  201 (506)
T ss_pred             CCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEeeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCc
Confidence              4899999999999999999999999987 89999999999999999999999999999999999985 777777665 


Q ss_pred             -CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCccccccCCcc----cccCCCCchhhhhhccCcc
Q psy93           223 -ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSE----RTINKKTPEFYKQRQVGPR  297 (503)
Q Consensus       223 -~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~~~~~~~~~----k~i~k~~~~~~kere~~~r  297 (503)
                       +..+++|||||+|.+...|..|..+|-.+.+.+  .+..++|+|+++..+.+..+.    -+.+++++...+++.+...
T Consensus       202 ~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~kl--wgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~  279 (506)
T KOG0117|consen  202 DDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKL--WGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKL  279 (506)
T ss_pred             cccccccceEEEEeecchhHHHHHhhccCCceee--cCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHH
Confidence             456789999999999999999999988788776  467899999999887766544    2568899999999999999


Q ss_pred             cCCCCCcchh
Q psy93           298 FATVNSFEFE  307 (503)
Q Consensus       298 f~~~g~~e~e  307 (503)
                      |.+++.++..
T Consensus       280 F~~~G~veRV  289 (506)
T KOG0117|consen  280 FNEFGKVERV  289 (506)
T ss_pred             HHhccceEEe
Confidence            9999988743

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.94  E-value=9.8e-26  Score=232.73  Aligned_cols=154  Identities=25%  Similarity=0.408  Sum_probs=138.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      .++|||+|||+++|+++|+++|+.||+|.+|+|++      ++|||||+|.+.++|.+||..||+..|.|++|.|.|+.+
T Consensus         3 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~   82 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP   82 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecc
Confidence            57899999999999999999999999999999974      358999999999999999999999999999999999864


Q ss_pred             ------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCC
Q psy93           187 ------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSL  259 (503)
Q Consensus       187 ------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~  259 (503)
                            .++|||.|||..+++++|..+|+.||.|..+.++.+. ++.+++||||+|.+.++|..|+..|| +..+ ....
T Consensus        83 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~-g~~~-~g~~  160 (352)
T TIGR01661        83 SSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLN-GTTP-SGCT  160 (352)
T ss_pred             cccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhC-CCcc-CCCc
Confidence                  4589999999999999999999999999999998874 67889999999999999999999998 4443 2344


Q ss_pred             CeEEeecCC
Q psy93           260 RPVIVEPLE  268 (503)
Q Consensus       260 rpl~V~~~~  268 (503)
                      .++.|.++.
T Consensus       161 ~~i~v~~a~  169 (352)
T TIGR01661       161 EPITVKFAN  169 (352)
T ss_pred             eeEEEEECC
Confidence            677777754

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

>KOG0144|consensus

Probab=99.93  E-value=4.2e-26  Score=227.49  Aligned_cols=164  Identities=26%  Similarity=0.427  Sum_probs=150.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCc-cccC--ceEEE
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGH-VLKG--RSLKI  181 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~-~l~g--~~l~V  181 (503)
                      .+..+|||+-||..++|.||+.+|++||.|.+|.|+++      +|||||.|.+.++|.+|+..||.. .|.|  .+|.|
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            34567999999999999999999999999999999876      689999999999999999999988 5555  78999


Q ss_pred             Eeccc-------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeee
Q psy93           182 RFAPI-------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFF  254 (503)
Q Consensus       182 ~~a~~-------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~  254 (503)
                      ++++.       ..+|||+-|+..+++.+|+++|++||.|++|.|++|+.+.++|+|||+|.+++.|..||+.|| +.+.
T Consensus       112 k~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~n-g~~t  190 (510)
T KOG0144|consen  112 KYADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALN-GTQT  190 (510)
T ss_pred             cccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhc-ccee
Confidence            99864       568999999999999999999999999999999999999999999999999999999999997 7777


Q ss_pred             ecCCCCeEEeecCCccccccC
Q psy93           255 LTQSLRPVIVEPLELTDEIDG  275 (503)
Q Consensus       255 ~~~~~rpl~V~~~~~~~~~~~  275 (503)
                      +..+..|++|+|++..++.+.
T Consensus       191 meGcs~PLVVkFADtqkdk~~  211 (510)
T KOG0144|consen  191 MEGCSQPLVVKFADTQKDKDG  211 (510)
T ss_pred             eccCCCceEEEecccCCCchH
Confidence            788999999999999876543

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

Probab=99.93  E-value=9.7e-26  Score=247.04  Aligned_cols=187  Identities=25%  Similarity=0.408  Sum_probs=161.2

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc--
Q psy93           115 RLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI--  186 (503)
Q Consensus       115 ~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~--  186 (503)
                      +|||+|||+++|+++|+++|+.||+|.+|+|.+      ++|||||+|.+.++|.+||+.|++..|.|++|+|.|+..  
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~   81 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDP   81 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccc
Confidence            699999999999999999999999999999964      368999999999999999999999999999999999852  


Q ss_pred             ------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCC
Q psy93           187 ------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLR  260 (503)
Q Consensus       187 ------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~r  260 (503)
                            ..+|||+|||.++++++|+++|+.||.|.+|+|+.+.++++++||||+|.+.++|.+|+..|| +..+   .++
T Consensus        82 ~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~ln-g~~~---~~~  157 (562)
T TIGR01628        82 SLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVN-GMLL---NDK  157 (562)
T ss_pred             cccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhc-ccEe---cCc
Confidence                  357999999999999999999999999999999999999999999999999999999999997 6665   577


Q ss_pred             eEEeecCCcccccc----CCcccccCCCCchhhhhhccCcccCCCCCcc
Q psy93           261 PVIVEPLELTDEID----GLSERTINKKTPEFYKQRQVGPRFATVNSFE  305 (503)
Q Consensus       261 pl~V~~~~~~~~~~----~~~~k~i~k~~~~~~kere~~~rf~~~g~~e  305 (503)
                      .+.|.......+..    .....+++++++...++.++...|..+|.+.
T Consensus       158 ~i~v~~~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~  206 (562)
T TIGR01628       158 EVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEIT  206 (562)
T ss_pred             eEEEeccccccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEE
Confidence            88887655443321    1223455667777778888888888877654

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

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

Probab=99.93  E-value=7.5e-25  Score=235.67  Aligned_cols=155  Identities=21%  Similarity=0.338  Sum_probs=139.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ...|+|||+|||+++++++|+++|+.||+|.+|.|+.      ++|||||+|.+.++|.+||..||+..|.|+.|+|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            4568999999999999999999999999999999863      5899999999999999999999999999999999765


Q ss_pred             c-----------------cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHH
Q psy93           185 P-----------------INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALR  246 (503)
Q Consensus       185 ~-----------------~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~  246 (503)
                      .                 ..++|||+|||+++++++|+++|+.||.|.+|.|.+|. ++.++|||||+|.+.++|.+|+.
T Consensus       185 ~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~  264 (612)
T TIGR01645       185 SNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIA  264 (612)
T ss_pred             ccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHH
Confidence            3                 13589999999999999999999999999999999984 67899999999999999999999


Q ss_pred             HhhCCeeeecCCCCeEEeecCCc
Q psy93           247 RCAEGCFFLTQSLRPVIVEPLEL  269 (503)
Q Consensus       247 ~ln~g~~~~~~~~rpl~V~~~~~  269 (503)
                      .|| +..+   .++.|.|.++..
T Consensus       265 amN-g~el---gGr~LrV~kAi~  283 (612)
T TIGR01645       265 SMN-LFDL---GGQYLRVGKCVT  283 (612)
T ss_pred             HhC-CCee---CCeEEEEEecCC
Confidence            998 5555   688888876553

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.

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

Probab=99.92  E-value=1.3e-24  Score=233.40  Aligned_cols=226  Identities=19%  Similarity=0.237  Sum_probs=179.5

Q ss_pred             CChhhHHHHHhhcCCCCCCCCCCC-------CccccCcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec-----
Q psy93            80 GDRYFTEKIMAIQGPTLDLPPSEP-------QNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINK-----  147 (503)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~p~~~~-------~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~-----  147 (503)
                      ++.....++....+.++...+...       .+........|+|||+|||.++++++|+++|++||+|.+|+|++     
T Consensus        18 ~~~~a~~a~~~~~gy~~~~~~g~r~~g~Pp~~~~~~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~   97 (578)
T TIGR01648        18 PDEAALKALLERTGYTLVQENGQRKYGGPPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQ   97 (578)
T ss_pred             ccHHHHHHHHHhhCccccccCCcccCCCCCCcccCCCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCC
Confidence            566667777777776665521110       12223344569999999999999999999999999999999863     


Q ss_pred             CCCceEEeeCCHHHHHHHHHHhCCcccc-CceEEEEecccccceeccCcccccCHHHHHHHhccCCC-eeeeEEEeC--C
Q psy93           148 EKMFGFIRMDYKHNADKAKAKLDGHVLK-GRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGD-IERAIVIVD--E  223 (503)
Q Consensus       148 ~kg~aFV~F~~~e~A~~Ai~~l~g~~l~-g~~l~V~~a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~-V~~~~v~~d--~  223 (503)
                      +++||||+|.+.++|++||+.||+..|. ++.|.|.++...++|||.|||.++++++|.+.|++++. |+.+.++..  .
T Consensus        98 sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~  177 (578)
T TIGR01648        98 NRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAAD  177 (578)
T ss_pred             ccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccccccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccc
Confidence            5899999999999999999999999886 89999999999999999999999999999999999974 444444332  3


Q ss_pred             CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCccccccC----CcccccCCCCchhhhhhccCcccC
Q psy93           224 RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDG----LSERTINKKTPEFYKQRQVGPRFA  299 (503)
Q Consensus       224 ~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~~~~~~----~~~k~i~k~~~~~~kere~~~rf~  299 (503)
                      .+++++||||+|.+.++|.+|+..|+.+.+.+  .++.|.|.|+.+..+.+.    ....+++.+++...+++++...|.
T Consensus       178 kgKnRGFAFVeF~s~edAa~AirkL~~gki~l--~Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~  255 (578)
T TIGR01648       178 KKKNRGFAFVEYESHRAAAMARRKLMPGRIQL--WGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFS  255 (578)
T ss_pred             cCccCceEEEEcCCHHHHHHHHHHhhccceEe--cCceEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHH
Confidence            56789999999999999999999987555433  578899999887654322    123466778888888899999999


Q ss_pred             CC--CCcchh
Q psy93           300 TV--NSFEFE  307 (503)
Q Consensus       300 ~~--g~~e~e  307 (503)
                      .+  +.++..
T Consensus       256 ~f~~G~I~rV  265 (578)
T TIGR01648       256 EFKPGKVERV  265 (578)
T ss_pred             hcCCCceEEE
Confidence            98  777643

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.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.92  E-value=4.9e-24  Score=220.06  Aligned_cols=156  Identities=26%  Similarity=0.386  Sum_probs=139.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccC--ceEEEEe
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKG--RSLKIRF  183 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g--~~l~V~~  183 (503)
                      ..++|||+|||.++++++|+.+|+.||.|..+.+..      +++||||+|.+.++|..||+.||+..+.+  .+|.|.|
T Consensus        88 ~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~  167 (352)
T TIGR01661        88 KGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKF  167 (352)
T ss_pred             ccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            457899999999999999999999999999988853      37899999999999999999999998887  5678877


Q ss_pred             cccc----------------------------------------------------------------------------
Q psy93           184 APIN----------------------------------------------------------------------------  187 (503)
Q Consensus       184 a~~~----------------------------------------------------------------------------  187 (503)
                      +...                                                                            
T Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (352)
T TIGR01661       168 ANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPP  247 (352)
T ss_pred             CCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCc
Confidence            5210                                                                            


Q ss_pred             ----------------------cceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHH
Q psy93           188 ----------------------AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQA  244 (503)
Q Consensus       188 ----------------------~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kA  244 (503)
                                            .+|||.|||.++++++|+++|++||.|.+|+|+.|. ++.++|||||+|.+.++|.+|
T Consensus       248 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~A  327 (352)
T TIGR01661       248 ATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMA  327 (352)
T ss_pred             cccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHH
Confidence                                  149999999999999999999999999999999995 999999999999999999999


Q ss_pred             HHHhhCCeeeecCCCCeEEeecCCccc
Q psy93           245 LRRCAEGCFFLTQSLRPVIVEPLELTD  271 (503)
Q Consensus       245 l~~ln~g~~~~~~~~rpl~V~~~~~~~  271 (503)
                      |..|| +..+   .+++|.|.+...+.
T Consensus       328 i~~ln-G~~~---~gr~i~V~~~~~~~  350 (352)
T TIGR01661       328 ILSLN-GYTL---GNRVLQVSFKTNKA  350 (352)
T ss_pred             HHHhC-CCEE---CCeEEEEEEccCCC
Confidence            99997 6666   79999999987653

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

>KOG0148|consensus

Probab=99.91  E-value=1.3e-23  Score=198.83  Aligned_cols=151  Identities=25%  Similarity=0.432  Sum_probs=139.4

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc-
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP-  185 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~-  185 (503)
                      .-.|||+.|.+.|+.++|++.|.+||+|.+++|++      +|||+||.|.+.++|++||..|||.-|.+|.|+-.|+. 
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            44699999999999999999999999999999974      58999999999999999999999999999999999994 


Q ss_pred             ---------------------cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHH
Q psy93           186 ---------------------INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQA  244 (503)
Q Consensus       186 ---------------------~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kA  244 (503)
                                           .+++|||+|++..+++++|++.|+.||.|.+|+|.++     ++|+||.|+++++|.+|
T Consensus       142 Kp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~-----qGYaFVrF~tkEaAahA  216 (321)
T KOG0148|consen  142 KPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD-----QGYAFVRFETKEAAAHA  216 (321)
T ss_pred             CccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc-----cceEEEEecchhhHHHH
Confidence                                 2578999999999999999999999999999999999     89999999999999999


Q ss_pred             HHHhhCCeeeecCCCCeEEeecCCcccc
Q psy93           245 LRRCAEGCFFLTQSLRPVIVEPLELTDE  272 (503)
Q Consensus       245 l~~ln~g~~~~~~~~rpl~V~~~~~~~~  272 (503)
                      |..+| +..+   .+.+|.+.|-+..++
T Consensus       217 Iv~mN-ntei---~G~~VkCsWGKe~~~  240 (321)
T KOG0148|consen  217 IVQMN-NTEI---GGQLVRCSWGKEGDD  240 (321)
T ss_pred             HHHhc-Ccee---CceEEEEeccccCCC
Confidence            99998 5545   688999999776644

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

Probab=99.91  E-value=1.5e-23  Score=229.77  Aligned_cols=193  Identities=19%  Similarity=0.308  Sum_probs=162.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec-----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc-
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP-  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~-  185 (503)
                      ..++|||+|||.++++++|+++|+.||.|.+|+|..     +++||||+|.+.++|.+||+.||+..+.++.|.|.... 
T Consensus        87 ~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~  166 (562)
T TIGR01628        87 GVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIK  166 (562)
T ss_pred             CCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEecccc
Confidence            456899999999999999999999999999999864     57999999999999999999999999999999996542 


Q ss_pred             ----------cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeee-
Q psy93           186 ----------INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFF-  254 (503)
Q Consensus       186 ----------~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~-  254 (503)
                                ..++|||+|||.++|+++|+++|+.||.|.++.++.+.++.+++||||+|.+.++|.+|+..|+ +..+ 
T Consensus       167 ~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~-g~~i~  245 (562)
T TIGR01628       167 KHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMN-GKKIG  245 (562)
T ss_pred             ccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhC-CcEec
Confidence                      2357999999999999999999999999999999999889999999999999999999999997 4444 


Q ss_pred             ecCCCCeEEeecCCccccc-----------------cCCcccccCCCCchhhhhhccCcccCCCCCcc
Q psy93           255 LTQSLRPVIVEPLELTDEI-----------------DGLSERTINKKTPEFYKQRQVGPRFATVNSFE  305 (503)
Q Consensus       255 ~~~~~rpl~V~~~~~~~~~-----------------~~~~~k~i~k~~~~~~kere~~~rf~~~g~~e  305 (503)
                      ....++.+.|.++....+.                 ......+++++++...++.++...|..+|.+.
T Consensus       246 ~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~  313 (562)
T TIGR01628       246 LAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEIT  313 (562)
T ss_pred             ccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeE
Confidence            2233677888776554332                 11222355667777778888888898888764

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

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

Probab=99.90  E-value=3.4e-23  Score=221.34  Aligned_cols=152  Identities=26%  Similarity=0.342  Sum_probs=138.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||.++++++|+++|+.||+|..|.|++      ++|||||+|.+.++|.+||. |++..|.|++|.|.++.
T Consensus        88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~~  166 (457)
T TIGR01622        88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQ  166 (457)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeecc
Confidence            467899999999999999999999999999999975      37899999999999999996 89999999999998753


Q ss_pred             ------------------cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHH
Q psy93           186 ------------------INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALR  246 (503)
Q Consensus       186 ------------------~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~  246 (503)
                                        ...+|||.|||..+++++|.++|+.||.|..|.++.+. ++.+++||||+|.+.++|.+|+.
T Consensus       167 ~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~  246 (457)
T TIGR01622       167 AEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALE  246 (457)
T ss_pred             hhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHH
Confidence                              13689999999999999999999999999999999885 56899999999999999999999


Q ss_pred             HhhCCeeeecCCCCeEEeecCC
Q psy93           247 RCAEGCFFLTQSLRPVIVEPLE  268 (503)
Q Consensus       247 ~ln~g~~~~~~~~rpl~V~~~~  268 (503)
                      .|| +..+   .+++|.|.++.
T Consensus       247 ~l~-g~~i---~g~~i~v~~a~  264 (457)
T TIGR01622       247 VMN-GFEL---AGRPIKVGYAQ  264 (457)
T ss_pred             hcC-CcEE---CCEEEEEEEcc
Confidence            997 5555   68999999976

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.

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

Probab=99.90  E-value=6.4e-23  Score=220.33  Aligned_cols=152  Identities=16%  Similarity=0.237  Sum_probs=132.4

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHh--CCccccCceEEEEecccc---
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL--DGHVLKGRSLKIRFAPIN---  187 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l--~g~~l~g~~l~V~~a~~~---  187 (503)
                      +.+|||+|||+++|+++|+++|+.||+|.+|.|+++|+||||+|.+.++|.+||..|  ++..|.|++|.|.|+...   
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~~~   81 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEIK   81 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCcccc
Confidence            568999999999999999999999999999999999999999999999999999874  678999999999997421   


Q ss_pred             ---------------cceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCe
Q psy93           188 ---------------AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGC  252 (503)
Q Consensus       188 ---------------~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~  252 (503)
                                     .+|+|.||+..+++++|+++|+.||.|.+|.|+++.   .+++|||+|.+.++|.+|+..|| +.
T Consensus        82 ~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~---~~~~afVef~~~~~A~~A~~~Ln-g~  157 (481)
T TIGR01649        82 RDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKN---NVFQALVEFESVNSAQHAKAALN-GA  157 (481)
T ss_pred             cCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecC---CceEEEEEECCHHHHHHHHHHhc-CC
Confidence                           268999999999999999999999999999998763   24689999999999999999998 54


Q ss_pred             eeecCCCCeEEeecCCc
Q psy93           253 FFLTQSLRPVIVEPLEL  269 (503)
Q Consensus       253 ~~~~~~~rpl~V~~~~~  269 (503)
                      .+.. ..+.+.|.+++.
T Consensus       158 ~i~~-~~~~l~v~~sk~  173 (481)
T TIGR01649       158 DIYN-GCCTLKIEYAKP  173 (481)
T ss_pred             cccC-CceEEEEEEecC
Confidence            4422 235677777654

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).

>KOG0131|consensus

Probab=99.90  E-value=1.5e-23  Score=188.15  Aligned_cols=157  Identities=29%  Similarity=0.439  Sum_probs=141.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ...||||+||+..++++.|++||-++|+|..+.|+++      +|||||+|.+.++|+-||+.||...|.|++|+|..+.
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            4568999999999999999999999999999999754      7999999999999999999999999999999999885


Q ss_pred             -------cccceeccCcccccCHHHHHHHhccCCCeeee-EEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeec
Q psy93           186 -------INAAIKVKNLTSCVTNELLELAFGVFGDIERA-IVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLT  256 (503)
Q Consensus       186 -------~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~-~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~  256 (503)
                             .+.+|||+||.+.+++..|.+.|+.||.+... +|+++ .++.+++|+||.|++.+.+.+|+..+| +.++  
T Consensus        88 ~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~n-gq~l--  164 (203)
T KOG0131|consen   88 AHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMN-GQYL--  164 (203)
T ss_pred             cccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhc-cchh--
Confidence                   25789999999999999999999999998763 67777 468899999999999999999999997 7766  


Q ss_pred             CCCCeEEeecCCcccc
Q psy93           257 QSLRPVIVEPLELTDE  272 (503)
Q Consensus       257 ~~~rpl~V~~~~~~~~  272 (503)
                       +.++++|..+..++.
T Consensus       165 -~nr~itv~ya~k~~~  179 (203)
T KOG0131|consen  165 -CNRPITVSYAFKKDT  179 (203)
T ss_pred             -cCCceEEEEEEecCC
Confidence             789999988766543

>KOG0145|consensus

Probab=99.90  E-value=2.4e-23  Score=195.75  Aligned_cols=157  Identities=24%  Similarity=0.410  Sum_probs=143.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCC------CceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEK------MFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~k------g~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..|+|+|.-||.++|+++|+.||...|+|++|+++++|      ||+||.|-+++||++||..|||..|..++|+|.++.
T Consensus        40 skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyAR  119 (360)
T KOG0145|consen   40 SKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYAR  119 (360)
T ss_pred             ccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEecc
Confidence            35689999999999999999999999999999998775      799999999999999999999999999999999998


Q ss_pred             c------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCC
Q psy93           186 I------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQS  258 (503)
Q Consensus       186 ~------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~  258 (503)
                      |      ..+|||.+||..+|..+|..+|+.||.|...+|+.| -++.++|.+||.|+...+|..||..|| +... ..+
T Consensus       120 PSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lN-G~~P-~g~  197 (360)
T KOG0145|consen  120 PSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLN-GQKP-SGC  197 (360)
T ss_pred             CChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhcc-CCCC-CCC
Confidence            7      468999999999999999999999999999888888 589999999999999999999999998 5443 345


Q ss_pred             CCeEEeecCCcc
Q psy93           259 LRPVIVEPLELT  270 (503)
Q Consensus       259 ~rpl~V~~~~~~  270 (503)
                      ..||+|+++...
T Consensus       198 tepItVKFannP  209 (360)
T KOG0145|consen  198 TEPITVKFANNP  209 (360)
T ss_pred             CCCeEEEecCCc
Confidence            678999987544

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

Probab=99.89  E-value=1.5e-22  Score=219.31  Aligned_cols=155  Identities=24%  Similarity=0.305  Sum_probs=136.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccC------------CCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCce
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPY------------GETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRS  178 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~------------G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~  178 (503)
                      ...++|||+|||+++|+++|.++|..|            +.|..+.+.++++||||+|.+.++|..|| .|+++.|.|++
T Consensus       173 ~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~~~g~~  251 (509)
T TIGR01642       173 RQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAM-ALDSIIYSNVF  251 (509)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCCCCEEEEEeCCHHHHhhhh-cCCCeEeeCce
Confidence            346789999999999999999999864            46778888889999999999999999999 59999999999


Q ss_pred             EEEEecc-----------------------------------cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-
Q psy93           179 LKIRFAP-----------------------------------INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-  222 (503)
Q Consensus       179 l~V~~a~-----------------------------------~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-  222 (503)
                      |+|....                                   ...+|||+|||..+++++|.++|+.||.|..+.|+.+ 
T Consensus       252 l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~  331 (509)
T TIGR01642       252 LKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDI  331 (509)
T ss_pred             eEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC
Confidence            9996321                                   1357999999999999999999999999999999988 


Q ss_pred             CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCcc
Q psy93           223 ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELT  270 (503)
Q Consensus       223 ~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~  270 (503)
                      .++.++|||||+|.+.++|..|+..|| +..+   .++.|.|.++...
T Consensus       332 ~~g~~~g~afv~f~~~~~a~~A~~~l~-g~~~---~~~~l~v~~a~~~  375 (509)
T TIGR01642       332 ATGLSKGYAFCEYKDPSVTDVAIAALN-GKDT---GDNKLHVQRACVG  375 (509)
T ss_pred             CCCCcCeEEEEEECCHHHHHHHHHHcC-CCEE---CCeEEEEEECccC
Confidence            578899999999999999999999997 6665   5778888887543

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

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

Probab=99.88  E-value=6.1e-22  Score=212.77  Aligned_cols=142  Identities=20%  Similarity=0.263  Sum_probs=126.5

Q ss_pred             CCCcEEEEcCCCC-CCCHHHHHHhhccCCCeEEEEEecC-CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc---
Q psy93           111 ANNCRLYLGNIGG-DITENDIIELFKPYGETQELFINKE-KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP---  185 (503)
Q Consensus       111 ~~~~~l~V~nLp~-~~te~~L~~~F~~~G~V~~v~i~~~-kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~---  185 (503)
                      .++++|||+|||+ .+|+++|+++|+.||.|.+|+|+++ ++||||+|.+.++|..||..||+..|.|++|.|.+++   
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~  352 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQN  352 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccccc
Confidence            3568999999997 6999999999999999999999875 6899999999999999999999999999999998762   


Q ss_pred             ----------------------------------------cccceeccCcccccCHHHHHHHhccCCC--eeeeEEEeCC
Q psy93           186 ----------------------------------------INAAIKVKNLTSCVTNELLELAFGVFGD--IERAIVIVDE  223 (503)
Q Consensus       186 ----------------------------------------~~~~L~V~nLp~~~tee~L~~~Fs~~G~--V~~~~v~~d~  223 (503)
                                                              ++.+|||.|||..+++++|+++|+.||.  |..+++....
T Consensus       353 ~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~  432 (481)
T TIGR01649       353 VQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKD  432 (481)
T ss_pred             ccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCC
Confidence                                                    1247999999999999999999999998  8888876554


Q ss_pred             CCCceeEEEEEeCCHHHHHHHHHHhhCCeee
Q psy93           224 RGNSKCEGIVEFARKPAAAQALRRCAEGCFF  254 (503)
Q Consensus       224 ~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~  254 (503)
                      +. .+++|||+|.+.++|.+||..|| +..+
T Consensus       433 ~~-~~~~gfVeF~~~e~A~~Al~~ln-~~~l  461 (481)
T TIGR01649       433 NE-RSKMGLLEWESVEDAVEALIALN-HHQL  461 (481)
T ss_pred             CC-cceeEEEEcCCHHHHHHHHHHhc-CCcc
Confidence            33 47899999999999999999997 5554

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

Probab=99.86  E-value=1.5e-21  Score=199.72  Aligned_cols=154  Identities=21%  Similarity=0.294  Sum_probs=141.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc-
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI-  186 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~-  186 (503)
                      .||||++||++++.++|.++|+.+|+|..|.++.+      +||+||+|+-.+|+++|+..++++.|.|+.|.|.++.+ 
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R   85 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKR   85 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccccc
Confidence            68999999999999999999999999999999753      68999999999999999999999999999999988731 


Q ss_pred             -------------------------------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEe
Q psy93           187 -------------------------------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEF  235 (503)
Q Consensus       187 -------------------------------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F  235 (503)
                                                     ...|.|.|||+.+...+|+.+|+.||.|..|.|++...++--|||||.|
T Consensus        86 ~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~f  165 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQF  165 (678)
T ss_pred             ccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEE
Confidence                                           4579999999999999999999999999999999887777779999999


Q ss_pred             CCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCccc
Q psy93           236 ARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTD  271 (503)
Q Consensus       236 ~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~~  271 (503)
                      ....+|.+|++.+| +..+   .+|||.|.|+..++
T Consensus       166 k~~~dA~~Al~~~N-~~~i---~gR~VAVDWAV~Kd  197 (678)
T KOG0127|consen  166 KEKKDAEKALEFFN-GNKI---DGRPVAVDWAVDKD  197 (678)
T ss_pred             eeHHHHHHHHHhcc-Ccee---cCceeEEeeecccc
Confidence            99999999999998 5555   69999999987653

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

Probab=99.86  E-value=6.9e-21  Score=204.82  Aligned_cols=151  Identities=26%  Similarity=0.421  Sum_probs=130.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCC-eEEEEEe-------cCCCceEEeeCCHHHHHHHHHHhCC--ccccCceEE
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGE-TQELFIN-------KEKMFGFIRMDYKHNADKAKAKLDG--HVLKGRSLK  180 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~-V~~v~i~-------~~kg~aFV~F~~~e~A~~Ai~~l~g--~~l~g~~l~  180 (503)
                      ...++|||+|||.++|+++|.++|++++. |+++.+.       ++++||||+|.+.++|..|+..|+.  ..+.++.|.
T Consensus       136 ~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~  215 (578)
T TIGR01648       136 VDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIA  215 (578)
T ss_pred             ccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEE
Confidence            34689999999999999999999999974 4444442       3579999999999999999998864  367899999


Q ss_pred             EEeccc-----------ccceeccCcccccCHHHHHHHhccC--CCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHH
Q psy93           181 IRFAPI-----------NAAIKVKNLTSCVTNELLELAFGVF--GDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRR  247 (503)
Q Consensus       181 V~~a~~-----------~~~L~V~nLp~~~tee~L~~~Fs~~--G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~  247 (503)
                      |.|+.+           .++|||+||+.++++++|+++|+.|  |.|++|.++++       ||||+|.+.++|.+|+..
T Consensus       216 VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~rg-------fAFVeF~s~e~A~kAi~~  288 (578)
T TIGR01648       216 VDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD-------YAFVHFEDREDAVKAMDE  288 (578)
T ss_pred             EEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeecC-------eEEEEeCCHHHHHHHHHH
Confidence            999864           3579999999999999999999999  99999987654       999999999999999999


Q ss_pred             hhCCeeeecCCCCeEEeecCCcccc
Q psy93           248 CAEGCFFLTQSLRPVIVEPLELTDE  272 (503)
Q Consensus       248 ln~g~~~~~~~~rpl~V~~~~~~~~  272 (503)
                      || +..+   .++.|.|.++.+.+.
T Consensus       289 ln-G~~i---~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       289 LN-GKEL---EGSEIEVTLAKPVDK  309 (578)
T ss_pred             hC-CCEE---CCEEEEEEEccCCCc
Confidence            97 6666   689999999977644

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.

>KOG0117|consensus

Probab=99.86  E-value=4.4e-21  Score=192.63  Aligned_cols=153  Identities=27%  Similarity=0.415  Sum_probs=134.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCC-eEEEEEe-------cCCCceEEeeCCHHHHHHHHHHhCCc--cccCceEEE
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGE-TQELFIN-------KEKMFGFIRMDYKHNADKAKAKLDGH--VLKGRSLKI  181 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~-V~~v~i~-------~~kg~aFV~F~~~e~A~~Ai~~l~g~--~l~g~~l~V  181 (503)
                      .+|+|||+|||.+.++++|.+-|++.++ |+.|.|.       +++|||||+|.+...|..|...|-.-  .|.|..+.|
T Consensus       163 an~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tV  242 (506)
T KOG0117|consen  163 ANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITV  242 (506)
T ss_pred             ecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCccee
Confidence            4789999999999999999999999985 6666663       56899999999999999888776443  677999999


Q ss_pred             Eeccc-----------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhC
Q psy93           182 RFAPI-----------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAE  250 (503)
Q Consensus       182 ~~a~~-----------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~  250 (503)
                      .||.+           -..|||+||+.++|++.|+++|+.||.|+.|+.++|       ||||.|.+.++|.+||+.+| 
T Consensus       243 dWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-------YaFVHf~eR~davkAm~~~n-  314 (506)
T KOG0117|consen  243 DWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-------YAFVHFAEREDAVKAMKETN-  314 (506)
T ss_pred             eccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc-------eeEEeecchHHHHHHHHHhc-
Confidence            99976           257999999999999999999999999999999877       99999999999999999997 


Q ss_pred             CeeeecCCCCeEEeecCCccccccC
Q psy93           251 GCFFLTQSLRPVIVEPLELTDEIDG  275 (503)
Q Consensus       251 g~~~~~~~~rpl~V~~~~~~~~~~~  275 (503)
                      +..+   .+.+|-|..+++.++...
T Consensus       315 gkel---dG~~iEvtLAKP~~k~k~  336 (506)
T KOG0117|consen  315 GKEL---DGSPIEVTLAKPVDKKKK  336 (506)
T ss_pred             Ccee---cCceEEEEecCChhhhcc
Confidence            6666   688999999988876443

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

Probab=99.85  E-value=1.2e-20  Score=204.31  Aligned_cols=155  Identities=21%  Similarity=0.291  Sum_probs=131.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||..+|+++|+++|+.||.|..|.|++      ++|||||+|.+.++|..||..||+..|.++.|.|.++.
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~  373 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRAC  373 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECc
Confidence            357899999999999999999999999999998864      47999999999999999999999999999999998862


Q ss_pred             ----------------------------------cccceeccCcccc--c--------CHHHHHHHhccCCCeeeeEEEe
Q psy93           186 ----------------------------------INAAIKVKNLTSC--V--------TNELLELAFGVFGDIERAIVIV  221 (503)
Q Consensus       186 ----------------------------------~~~~L~V~nLp~~--~--------tee~L~~~Fs~~G~V~~~~v~~  221 (503)
                                                        ++.+|+|.||...  +        ..++|+++|++||.|..|.|++
T Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~  453 (509)
T TIGR01642       374 VGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPR  453 (509)
T ss_pred             cCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeec
Confidence                                              2345777787531  1        1267899999999999999987


Q ss_pred             CC----CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCcc
Q psy93           222 DE----RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELT  270 (503)
Q Consensus       222 d~----~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~  270 (503)
                      +.    ++...|++||+|.+.++|.+|+..|| +..+   .++.|.|.+++..
T Consensus       454 ~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~ln-Gr~~---~gr~v~~~~~~~~  502 (509)
T TIGR01642       454 PNGDRNSTPGVGKVFLEYADVRSAEKAMEGMN-GRKF---NDRVVVAAFYGED  502 (509)
T ss_pred             cCcCCCcCCCcceEEEEECCHHHHHHHHHHcC-CCEE---CCeEEEEEEeCHH
Confidence            52    34557899999999999999999998 6666   6899999887654

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

>KOG0109|consensus

Probab=99.85  E-value=2e-21  Score=185.62  Aligned_cols=141  Identities=26%  Similarity=0.448  Sum_probs=130.3

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc----ccce
Q psy93           115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI----NAAI  190 (503)
Q Consensus       115 ~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~----~~~L  190 (503)
                      +|||+|||..+++.+|+.||.+||+|++|.|+  |.|+||..++...|..||..||+..|+|..|.|+.+++    +++|
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDIv--KNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKsk~stkl   81 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDIV--KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKSKASTKL   81 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeeee--cccceEEeecccccHHHHhhcccceecceEEEEEeccccCCCcccc
Confidence            59999999999999999999999999999998  56999999999999999999999999999999998864    5789


Q ss_pred             eccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCC
Q psy93           191 KVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLE  268 (503)
Q Consensus       191 ~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~  268 (503)
                      +|.||.+..+.++|+..|.+||.|.+|+|++|       |+||.|+..++|..|+..|| +..+   .+++++|....
T Consensus        82 ~vgNis~tctn~ElRa~fe~ygpviecdivkd-------y~fvh~d~~eda~~air~l~-~~~~---~gk~m~vq~st  148 (346)
T KOG0109|consen   82 HVGNISPTCTNQELRAKFEKYGPVIECDIVKD-------YAFVHFDRAEDAVEAIRGLD-NTEF---QGKRMHVQLST  148 (346)
T ss_pred             ccCCCCccccCHHHhhhhcccCCceeeeeecc-------eeEEEEeeccchHHHHhccc-cccc---ccceeeeeeec
Confidence            99999999999999999999999999999977       99999999999999999998 5545   58888876543

>KOG0123|consensus

Probab=99.85  E-value=1.1e-20  Score=194.64  Aligned_cols=183  Identities=23%  Similarity=0.389  Sum_probs=151.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC---CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc-ccc
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKE---KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI-NAA  189 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~---kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~-~~~  189 (503)
                      ..|||+   +++|+..|.++|+++|+|++|++.++   -|||||.|.++++|.+||+.||...|.|++|+|.|+.. ...
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~tslgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~~~   78 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDATSLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDPSL   78 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecCCccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCCce
Confidence            359999   89999999999999999999998654   58999999999999999999999999999999999964 345


Q ss_pred             eeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCc
Q psy93           190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLEL  269 (503)
Q Consensus       190 L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~  269 (503)
                      |||.||+++++..+|.++|+.||.|.+|+|.++.+| +++| ||+|++.++|.+|+..+| +.++   .++.+.|-+...
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-~kg~-FV~f~~e~~a~~ai~~~n-g~ll---~~kki~vg~~~~  152 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-SKGY-FVQFESEESAKKAIEKLN-GMLL---NGKKIYVGLFER  152 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-ceee-EEEeCCHHHHHHHHHHhc-Cccc---CCCeeEEeeccc
Confidence            999999999999999999999999999999999888 8999 999999999999999997 7766   688888877666


Q ss_pred             cccccCCc-------ccccCCCCchhhhhhccCcccCCCCCcc
Q psy93           270 TDEIDGLS-------ERTINKKTPEFYKQRQVGPRFATVNSFE  305 (503)
Q Consensus       270 ~~~~~~~~-------~k~i~k~~~~~~kere~~~rf~~~g~~e  305 (503)
                      ..+.....       ...+.++.........+.+.|..++++.
T Consensus       153 ~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~  195 (369)
T KOG0123|consen  153 KEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSIT  195 (369)
T ss_pred             hhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcce
Confidence            54432211       1123333443344445556666666543

>KOG0115|consensus

Probab=99.85  E-value=1.6e-21  Score=183.83  Aligned_cols=204  Identities=45%  Similarity=0.619  Sum_probs=177.0

Q ss_pred             HHHHHHHHHhCCccccCceEEEEecccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHH
Q psy93           160 HNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKP  239 (503)
Q Consensus       160 e~A~~Ai~~l~g~~l~g~~l~V~~a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e  239 (503)
                      .-|..|...|+++...++.|.|.|+.. ..|+|.||+..++.+.|...|+.||.|....++.|..+++.+.++|.|....
T Consensus         5 t~ae~ak~eLd~~~~~~~~lr~rfa~~-a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~   83 (275)
T KOG0115|consen    5 TLAEIAKRELDGRFPKGRSLRVRFAMH-AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKP   83 (275)
T ss_pred             cHHHHHHHhcCCCCCCCCceEEEeecc-ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcch
Confidence            356677778999999999999999999 9999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhCCeeeecCCCCeEEeecCCccccccCCcccccCCCCchhhhhhccCcccCCCCCcchhhhhhhHHHHHHH
Q psy93           240 AAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELY  319 (503)
Q Consensus       240 ~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~~~~~~~~~k~i~k~~~~~~kere~~~rf~~~g~~e~e~~~r~k~l~e~e  319 (503)
                      .|.+|+..|+++.+.++..++|+.|.|....++.++.+.+ ...+.+.+.+++..+++|+.+++|+++|+++|+.+.+++
T Consensus        84 ~a~~a~rr~~~~g~~~~~~~~p~~VeP~eq~~d~~G~~~k-~~~~~~~~~~e~~~p~r~a~~g~fe~e~~~~~k~l~~me  162 (275)
T KOG0115|consen   84 NARKAARRCREGGFGGTTGGRPVGVEPMEQPDDNDGGPEK-GGGGGPSGPKEREQPPRFAQQGSFEVEYGSRWKMLGGME  162 (275)
T ss_pred             hHHHHHHHhccCccccCCCCCccCCChhhccCCCCcchhh-cCCCCCCCCccccCCchhccccccccccCcccccccccc
Confidence            9999999999999999999999999999999999999999 566788999999999999999999999999999999988


Q ss_pred             ----------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q psy93           320 ----------------------------EHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKH  365 (503)
Q Consensus       320 ----------------------------e~e~e~~Ree~~~rE~~rEr~r~E~E~~eRq~ee~r~reeE~~r~r  365 (503)
                                                  +.+..+.++.+++++.+..|..+.|.++.+...+-..++++...++
T Consensus       163 kq~qd~v~~n~kea~~klE~~me~arghe~q~~l~rq~lmrrqeelrrme~l~nqe~qkr~~~~~~eee~r~r~  236 (275)
T KOG0115|consen  163 KQGQDQVDRNIKEAQDKLEAPMEKARGHECQLMLGRQPLMRREEELRRMEELHNQEAKKRKEINLREEEERLRR  236 (275)
T ss_pred             ccCCcccccccchhhhccccccccccCccceeeecCCCcccccHHHHHHHHHhhHHHHHhhhhhhhHHHHHHHH
Confidence                                        3334566777777777666666667776655555555555444433

>KOG0127|consensus

Probab=99.84  E-value=3.1e-20  Score=190.21  Aligned_cols=162  Identities=26%  Similarity=0.427  Sum_probs=143.8

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc-
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI-  186 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~-  186 (503)
                      .-+|+|.|||+.+...+|+.+|+.||.|..|.|++.     .|||||.|....+|.+|++.+|+..|.|++|-|.||.+ 
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~K  196 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDK  196 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccc
Confidence            457999999999999999999999999999999854     48999999999999999999999999999999999810 


Q ss_pred             --------------------------------------------------------------------------------
Q psy93           187 --------------------------------------------------------------------------------  186 (503)
Q Consensus       187 --------------------------------------------------------------------------------  186 (503)
                                                                                                      
T Consensus       197 d~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~  276 (678)
T KOG0127|consen  197 DTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKES  276 (678)
T ss_pred             ccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccCcc
Confidence                                                                                            


Q ss_pred             ---------------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhh-
Q psy93           187 ---------------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCA-  249 (503)
Q Consensus       187 ---------------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln-  249 (503)
                                     ..+|||.|||.++++++|...|++||.|.++.|+.+ .++.++|.|||.|.+..+|..||...+ 
T Consensus       277 ~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Asp  356 (678)
T KOG0127|consen  277 DKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASP  356 (678)
T ss_pred             cchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCc
Confidence                           147999999999999999999999999999999888 689999999999999999999999873 


Q ss_pred             ---CCeeeecCCCCeEEeecCCccccccCC
Q psy93           250 ---EGCFFLTQSLRPVIVEPLELTDEIDGL  276 (503)
Q Consensus       250 ---~g~~~~~~~~rpl~V~~~~~~~~~~~~  276 (503)
                         .+.+++  .+|.|.|.++...++....
T Consensus       357 a~e~g~~ll--~GR~Lkv~~Av~RkeA~dm  384 (678)
T KOG0127|consen  357 ASEDGSVLL--DGRLLKVTLAVTRKEAADM  384 (678)
T ss_pred             cCCCceEEE--eccEEeeeeccchHHHHHH
Confidence               343443  7999999998877654333

>KOG0145|consensus

Probab=99.83  E-value=6.1e-20  Score=172.84  Aligned_cols=154  Identities=26%  Similarity=0.366  Sum_probs=136.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe------cCCCceEEeeCCHHHHHHHHHHhCCccccC--ceEEEEe
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFIN------KEKMFGFIRMDYKHNADKAKAKLDGHVLKG--RSLKIRF  183 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~------~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g--~~l~V~~  183 (503)
                      ...+|||++||..+|..+|..+|++||.|..-+|.      -++|.+||.|+...+|+.||..|||..-.|  .+|.|+|
T Consensus       126 k~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKF  205 (360)
T KOG0145|consen  126 KDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKF  205 (360)
T ss_pred             cccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEe
Confidence            45689999999999999999999999988655543      358999999999999999999999997776  5899998


Q ss_pred             ccc---------------------------------------------------------------------ccceeccC
Q psy93           184 API---------------------------------------------------------------------NAAIKVKN  194 (503)
Q Consensus       184 a~~---------------------------------------------------------------------~~~L~V~n  194 (503)
                      +..                                                                     ..+|||-|
T Consensus       206 annPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciFvYN  285 (360)
T KOG0145|consen  206 ANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCIFVYN  285 (360)
T ss_pred             cCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCeeEEEEEe
Confidence            830                                                                     35899999


Q ss_pred             cccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCc
Q psy93           195 LTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLEL  269 (503)
Q Consensus       195 Lp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~  269 (503)
                      |.++.++..|..+|..||.|.+++|++|. +.+.|||+||++.+.++|..||..|| +.-+   ..|.+.|.+...
T Consensus       286 Lspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLN-Gy~l---g~rvLQVsFKtn  357 (360)
T KOG0145|consen  286 LSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLN-GYRL---GDRVLQVSFKTN  357 (360)
T ss_pred             cCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhc-Cccc---cceEEEEEEecC
Confidence            99999999999999999999999999994 68999999999999999999999997 7665   688888887543

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

Probab=99.82  E-value=2.1e-19  Score=192.17  Aligned_cols=151  Identities=23%  Similarity=0.411  Sum_probs=127.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe------cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc-
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFIN------KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP-  185 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~------~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~-  185 (503)
                      .++|||+|||+++|+++|+++|+.||.|..|.|+      ++++||||+|.+.++|.+|+..||+..|.|++|.|.|+. 
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            5899999999999999999999999999999987      347899999999999999999999999999999999931 


Q ss_pred             --------------------------------------------------------------------------------
Q psy93           186 --------------------------------------------------------------------------------  185 (503)
Q Consensus       186 --------------------------------------------------------------------------------  185 (503)
                                                                                                      
T Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  345 (457)
T TIGR01622       266 STYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALA  345 (457)
T ss_pred             CCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhccccccccccccccccccccccc
Confidence                                                                                            


Q ss_pred             ---------------cccceeccCcccccC----------HHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHH
Q psy93           186 ---------------INAAIKVKNLTSCVT----------NELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPA  240 (503)
Q Consensus       186 ---------------~~~~L~V~nLp~~~t----------ee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~  240 (503)
                                     ++.+|+|.||....+          .++|++.|++||.|+.|.|...   .+.|++||+|.+.++
T Consensus       346 ~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~---~~~G~~fV~F~~~e~  422 (457)
T TIGR01622       346 IMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTK---NSAGKIYLKFSSVDA  422 (457)
T ss_pred             cccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCC---CCceeEEEEECCHHH
Confidence                           012455566533222          3679999999999999988643   347899999999999


Q ss_pred             HHHHHHHhhCCeeeecCCCCeEEeecCCcc
Q psy93           241 AAQALRRCAEGCFFLTQSLRPVIVEPLELT  270 (503)
Q Consensus       241 A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~  270 (503)
                      |.+|+..|| +.++   .+++|.+.++...
T Consensus       423 A~~A~~~ln-Gr~f---~gr~i~~~~~~~~  448 (457)
T TIGR01622       423 ALAAFQALN-GRYF---GGKMITAAFVVND  448 (457)
T ss_pred             HHHHHHHhc-Cccc---CCeEEEEEEEcHH
Confidence            999999997 6666   7999999887544

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

Probab=99.80  E-value=1.8e-19  Score=190.17  Aligned_cols=155  Identities=23%  Similarity=0.363  Sum_probs=139.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC---------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKE---------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~---------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      .|+|||.||++++|.++|..+|..+|.|.+|.|.+.         .|||||+|.++++|+.|+..|+|+.|+|+.|.|.+
T Consensus       515 ~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~  594 (725)
T KOG0110|consen  515 ETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKI  594 (725)
T ss_pred             chhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEe
Confidence            345999999999999999999999999999988643         39999999999999999999999999999999999


Q ss_pred             ccc---------------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHH
Q psy93           184 API---------------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRR  247 (503)
Q Consensus       184 a~~---------------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~  247 (503)
                      ++.               .++|+|.|||...+-.+|+.+|..||.|.+|.|+.. ..+.++|||||+|-++.+|..|+.+
T Consensus       595 S~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~a  674 (725)
T KOG0110|consen  595 SENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDA  674 (725)
T ss_pred             ccCccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHh
Confidence            871               358999999999999999999999999999999877 4566799999999999999999999


Q ss_pred             hhCCeeeecCCCCeEEeecCCccc
Q psy93           248 CAEGCFFLTQSLRPVIVEPLELTD  271 (503)
Q Consensus       248 ln~g~~~~~~~~rpl~V~~~~~~~  271 (503)
                      |. .+.+   -+|.++++|++...
T Consensus       675 l~-STHl---yGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  675 LG-STHL---YGRRLVLEWAKSDN  694 (725)
T ss_pred             hc-ccce---echhhheehhccch
Confidence            97 5555   38999999986653

>KOG0124|consensus

Probab=99.80  E-value=1.6e-19  Score=176.90  Aligned_cols=138  Identities=22%  Similarity=0.429  Sum_probs=127.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEE------ecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i------~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      -.|+|||+.|.+.+.++.|+..|.+||+|++|.+      .++|+||||+|+-++.|+.|++.||+..+.|+.|+|....
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCC
Confidence            3589999999999999999999999999999998      3679999999999999999999999999999999997653


Q ss_pred             c-----------------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCC-CCceeEEEEEeCCHHHHHHHHHH
Q psy93           186 I-----------------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDER-GNSKCEGIVEFARKPAAAQALRR  247 (503)
Q Consensus       186 ~-----------------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~-g~skg~gfV~F~s~e~A~kAl~~  247 (503)
                      +                 -+.|||..+.++++++||+.+|+.||+|.+|.+.++++ +.++||+||+|.+..+...|+..
T Consensus       192 NmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAias  271 (544)
T KOG0124|consen  192 NMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS  271 (544)
T ss_pred             CCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhh
Confidence            2                 35899999999999999999999999999999999864 46799999999999999999988


Q ss_pred             hh
Q psy93           248 CA  249 (503)
Q Consensus       248 ln  249 (503)
                      ||
T Consensus       272 MN  273 (544)
T KOG0124|consen  272 MN  273 (544)
T ss_pred             cc
Confidence            87

>KOG0105|consensus

Probab=99.79  E-value=1e-18  Score=157.23  Aligned_cols=137  Identities=29%  Similarity=0.421  Sum_probs=124.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC---CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc--
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE---KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI--  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~---kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~--  186 (503)
                      .+++|||+|||.+|.+.+|.+||.+||.|..|.+...   .+||||+|+++-+|+.||..-+|..++|+.|+|+++..  
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprggr   84 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGGR   84 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCCC
Confidence            4689999999999999999999999999999988533   57999999999999999999999999999999999841  


Q ss_pred             ------------------------------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeC
Q psy93           187 ------------------------------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFA  236 (503)
Q Consensus       187 ------------------------------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~  236 (503)
                                                    ...|.|..||++-++++|++...+-|.|..+.|.+|      ++++|+|.
T Consensus        85 ~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD------g~GvV~~~  158 (241)
T KOG0105|consen   85 SSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD------GVGVVEYL  158 (241)
T ss_pred             cccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc------cceeeeee
Confidence                                          347999999999999999999999999999999887      48999999


Q ss_pred             CHHHHHHHHHHhhCCeee
Q psy93           237 RKPAAAQALRRCAEGCFF  254 (503)
Q Consensus       237 s~e~A~kAl~~ln~g~~~  254 (503)
                      ..++.+-|+.+|++.++.
T Consensus       159 r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  159 RKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             ehhhHHHHHHhhcccccc
Confidence            999999999999865544

>KOG0148|consensus

Probab=99.76  E-value=1.7e-18  Score=164.34  Aligned_cols=160  Identities=24%  Similarity=0.326  Sum_probs=129.4

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc-------
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP-------  185 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~-------  185 (503)
                      -.||||+||+.+|||+.|..||+++|+|++++|+.+                             .|+|.|+.       
T Consensus         6 prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~-----------------------------e~~v~wa~~p~nQsk   56 (321)
T KOG0148|consen    6 PRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD-----------------------------ELKVNWATAPGNQSK   56 (321)
T ss_pred             CceEEeeccChhhHHHHHHHHHHhccccccceeehh-----------------------------hhccccccCcccCCC
Confidence            358999999999999999999999999999998744                             23333331       


Q ss_pred             c----ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCC
Q psy93           186 I----NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLR  260 (503)
Q Consensus       186 ~----~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~r  260 (503)
                      +    .-.+||..|...++.++|++.|.+||+|.+++|++| .++++|||+||.|.++++|+.||..|| +.++   ..|
T Consensus        57 ~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~Mn-GqWl---G~R  132 (321)
T KOG0148|consen   57 PTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMN-GQWL---GRR  132 (321)
T ss_pred             CccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhC-Ceee---ccc
Confidence            1    125899999999999999999999999999999999 699999999999999999999999997 8877   688


Q ss_pred             eEEeecCCccccccC---------------CcccccCCCCchhhhhhccCcccCCCCCcc
Q psy93           261 PVIVEPLELTDEIDG---------------LSERTINKKTPEFYKQRQVGPRFATVNSFE  305 (503)
Q Consensus       261 pl~V~~~~~~~~~~~---------------~~~k~i~k~~~~~~kere~~~rf~~~g~~e  305 (503)
                      .|...|+..+....+               .+......++.....+.++...|+++|++-
T Consensus       133 ~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~  192 (321)
T KOG0148|consen  133 TIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQ  192 (321)
T ss_pred             eeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcce
Confidence            899988876542211               112233445555667888888999988873

>KOG0146|consensus

Probab=99.75  E-value=9.3e-18  Score=158.75  Aligned_cols=170  Identities=24%  Similarity=0.421  Sum_probs=140.5

Q ss_pred             CCCCCCCCCCCccccCcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec-----CCCceEEeeCCHHHHHHHHHH
Q psy93            94 PTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINK-----EKMFGFIRMDYKHNADKAKAK  168 (503)
Q Consensus        94 ~~~~~p~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~  168 (503)
                      .++.+.|.+++   ..-....+|||+-|...-+|+|++.+|..||.|.+|.+.+     +||||||.|.+..+|..||..
T Consensus         3 rpiqvkpadse---srg~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~a   79 (371)
T KOG0146|consen    3 RPIQVKPADSE---SRGGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINA   79 (371)
T ss_pred             CCccccccccc---cCCccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHH
Confidence            34555555542   1122456899999999999999999999999999999964     599999999999999999999


Q ss_pred             hCCc-cccC--ceEEEEecc------------------------------------------------------------
Q psy93           169 LDGH-VLKG--RSLKIRFAP------------------------------------------------------------  185 (503)
Q Consensus       169 l~g~-~l~g--~~l~V~~a~------------------------------------------------------------  185 (503)
                      |++. .+.|  ..|.|++++                                                            
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            9998 5554  678888872                                                            


Q ss_pred             --------------------------------------------------------------------------------
Q psy93           186 --------------------------------------------------------------------------------  185 (503)
Q Consensus       186 --------------------------------------------------------------------------------  185 (503)
                                                                                                      
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                                                                                            


Q ss_pred             --------------------------------------------cccceeccCcccccCHHHHHHHhccCCCeeeeEEEe
Q psy93           186 --------------------------------------------INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIV  221 (503)
Q Consensus       186 --------------------------------------------~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~  221 (503)
                                                                  ..|+|||-.||....+.+|..+|-.||.|++.+|..
T Consensus       240 a~~lq~a~~g~~~Y~Aaypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFv  319 (371)
T KOG0146|consen  240 ADPLQQAYAGVQQYAAAYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFV  319 (371)
T ss_pred             cchhhhhhhhHHHHhhhcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeee
Confidence                                                        037899999999999999999999999999999999


Q ss_pred             C-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCcc
Q psy93           222 D-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELT  270 (503)
Q Consensus       222 d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~  270 (503)
                      | .++.||+|+||.|+++.+|..||..|| +..+   .-+.+.|....++
T Consensus       320 DRATNQSKCFGFVSfDNp~SaQaAIqAMN-GFQI---GMKRLKVQLKRPk  365 (371)
T KOG0146|consen  320 DRATNQSKCFGFVSFDNPASAQAAIQAMN-GFQI---GMKRLKVQLKRPK  365 (371)
T ss_pred             hhccccccceeeEecCCchhHHHHHHHhc-chhh---hhhhhhhhhcCcc
Confidence            9 689999999999999999999999998 5544   2334455444444

>KOG0123|consensus

Probab=99.72  E-value=5.5e-17  Score=167.32  Aligned_cols=149  Identities=25%  Similarity=0.412  Sum_probs=133.5

Q ss_pred             EEEcCCCCCCCHHHHHHhhccCCCeEEEEEec----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc-----
Q psy93           116 LYLGNIGGDITENDIIELFKPYGETQELFINK----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI-----  186 (503)
Q Consensus       116 l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~-----  186 (503)
                      |||.||+++++..+|.++|+.||+|++|++..    +++| ||+|++.+.|.+||+.|||..+.++.|.|.....     
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~  157 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEERE  157 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhhc
Confidence            99999999999999999999999999999975    4789 9999999999999999999999999999966532     


Q ss_pred             ---------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecC
Q psy93           187 ---------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQ  257 (503)
Q Consensus       187 ---------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~  257 (503)
                               -+.++|.|++.+++++.|.++|+.||.|.++.++.+..+.+++|+||.|++.++|.+|+..|+ +...   
T Consensus       158 ~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~-~~~~---  233 (369)
T KOG0123|consen  158 APLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLN-GKIF---  233 (369)
T ss_pred             ccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhcc-CCcC---
Confidence                     357899999999999999999999999999999999988899999999999999999999997 5444   


Q ss_pred             CCCeEEeecCCc
Q psy93           258 SLRPVIVEPLEL  269 (503)
Q Consensus       258 ~~rpl~V~~~~~  269 (503)
                      ....+.|..+..
T Consensus       234 ~~~~~~V~~aqk  245 (369)
T KOG0123|consen  234 GDKELYVGRAQK  245 (369)
T ss_pred             Cccceeeccccc
Confidence            345566655544

>KOG0144|consensus

Probab=99.67  E-value=1.5e-16  Score=159.45  Aligned_cols=74  Identities=26%  Similarity=0.556  Sum_probs=68.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec-----CCCceEEeeCCHHHHHHHHHHhCCc-cccC--ceEEEE
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINK-----EKMFGFIRMDYKHNADKAKAKLDGH-VLKG--RSLKIR  182 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~-~l~g--~~l~V~  182 (503)
                      ....+|||+-|+..+||.+|+++|++||.|++|.|.+     ++|||||+|.+.+.|..||+.||++ .+.|  .+|.|+
T Consensus       122 ~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVk  201 (510)
T KOG0144|consen  122 VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVK  201 (510)
T ss_pred             ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEE
Confidence            4467899999999999999999999999999999975     5899999999999999999999999 6665  689999


Q ss_pred             ec
Q psy93           183 FA  184 (503)
Q Consensus       183 ~a  184 (503)
                      |+
T Consensus       202 FA  203 (510)
T KOG0144|consen  202 FA  203 (510)
T ss_pred             ec
Confidence            98

>KOG4205|consensus

Probab=99.65  E-value=3.7e-16  Score=156.19  Aligned_cols=156  Identities=21%  Similarity=0.308  Sum_probs=134.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..|+|||++|+.+++++.|++.|..||+|..|.+++      +++|+||+|++++.+..++.. .-..|+++.|.+..+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceecc
Confidence            568999999999999999999999999999999975      478999999999998888753 4557889999888775


Q ss_pred             c------------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCe
Q psy93           186 I------------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGC  252 (503)
Q Consensus       186 ~------------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~  252 (503)
                      +            ..+|||+.||.+++++++++.|.+||.|..+.++.| .+..+++|+||.|.+.+++.+++..-  -+
T Consensus        84 ~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~~--f~  161 (311)
T KOG4205|consen   84 SREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQK--FH  161 (311)
T ss_pred             CcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecccc--ee
Confidence            4            348999999999999999999999999999999888 57889999999999999999987642  33


Q ss_pred             eeecCCCCeEEeecCCccccc
Q psy93           253 FFLTQSLRPVIVEPLELTDEI  273 (503)
Q Consensus       253 ~~~~~~~rpl~V~~~~~~~~~  273 (503)
                      .   .+++.|.|.-+.+++..
T Consensus       162 ~---~~gk~vevkrA~pk~~~  179 (311)
T KOG4205|consen  162 D---FNGKKVEVKRAIPKEVM  179 (311)
T ss_pred             e---ecCceeeEeeccchhhc
Confidence            3   37889999888877653

>KOG0110|consensus

Probab=99.65  E-value=8.4e-16  Score=162.72  Aligned_cols=190  Identities=21%  Similarity=0.219  Sum_probs=159.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc-----
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI-----  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~-----  186 (503)
                      ..+.|+|+|||..+..++|..+|..||+|..|.|++.-.-|+|.|.++.+|.+|+..|..+.+...+|.+.|++.     
T Consensus       384 s~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~~G~~aiv~fl~p~eAr~Afrklaysr~k~~plyle~aP~dvf~~  463 (725)
T KOG0110|consen  384 SDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPPGGTGAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWAPEDVFTE  463 (725)
T ss_pred             hcceeeeccCccccccHHHHHHhhcccccceeecCcccceeeeeecCccchHHHHHHhchhhhccCccccccChhhhccC
Confidence            457899999999999999999999999999997774444699999999999999999999999999998888730     


Q ss_pred             ---------------------------------------------------ccceeccCcccccCHHHHHHHhccCCCee
Q psy93           187 ---------------------------------------------------NAAIKVKNLTSCVTNELLELAFGVFGDIE  215 (503)
Q Consensus       187 ---------------------------------------------------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~  215 (503)
                                                                         .++|||+||+.+++.++|..+|..+|.|.
T Consensus       464 ~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~F~k~G~Vl  543 (725)
T KOG0110|consen  464 DPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLEDLFSKQGTVL  543 (725)
T ss_pred             CccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHHHHHhcCeEE
Confidence                                                               13499999999999999999999999999


Q ss_pred             eeEEEeCCCC----CceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCC--------ccccccCCcccccCC
Q psy93           216 RAIVIVDERG----NSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLE--------LTDEIDGLSERTINK  283 (503)
Q Consensus       216 ~~~v~~d~~g----~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~--------~~~~~~~~~~k~i~k  283 (503)
                      ++.|....+.    .|.|||||+|.+.++|..|+..|+ ++.+   .++.|.|....        .....+....+++++
T Consensus       544 S~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lq-gtvl---dGH~l~lk~S~~k~~~~~gK~~~~kk~~tKIlVR  619 (725)
T KOG0110|consen  544 SIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQ-GTVL---DGHKLELKISENKPASTVGKKKSKKKKGTKILVR  619 (725)
T ss_pred             EEEEeccccccccccccceeEEEecCHHHHHHHHHHhc-Ccee---cCceEEEEeccCccccccccccccccccceeeee
Confidence            9988766433    356999999999999999999997 7777   78888887766        222222334578888


Q ss_pred             CCchhhhhhccCcccCCCCCcc
Q psy93           284 KTPEFYKQRQVGPRFATVNSFE  305 (503)
Q Consensus       284 ~~~~~~kere~~~rf~~~g~~e  305 (503)
                      ++|-....++....|..+|.+-
T Consensus       620 NipFeAt~rEVr~LF~aFGqlk  641 (725)
T KOG0110|consen  620 NIPFEATKREVRKLFTAFGQLK  641 (725)
T ss_pred             ccchHHHHHHHHHHHhccccee
Confidence            8998888888888888887664

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

Probab=99.63  E-value=7.1e-15  Score=158.90  Aligned_cols=73  Identities=25%  Similarity=0.462  Sum_probs=68.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ..++|||+|||+++++++|+++|+.||.|.+|.|.+      ++|||||+|.+.++|.+||..||+..|.|+.|+|.++
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kA  281 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC  281 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEec
Confidence            346899999999999999999999999999999964      4789999999999999999999999999999999775

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.

>KOG4661|consensus

Probab=99.61  E-value=4.4e-14  Score=145.53  Aligned_cols=77  Identities=21%  Similarity=0.364  Sum_probs=70.9

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       110 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      .+...+|||.+|+..+...+|+.||++||+|+-.+|+.+      +||+||+|.+.++|.+||..|+.++|+|+.|.|+.
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            455678999999999999999999999999999998754      68999999999999999999999999999999998


Q ss_pred             ccc
Q psy93           184 API  186 (503)
Q Consensus       184 a~~  186 (503)
                      ++.
T Consensus       482 aKN  484 (940)
T KOG4661|consen  482 AKN  484 (940)
T ss_pred             ccc
Confidence            864

>KOG0147|consensus

Probab=99.58  E-value=2e-15  Score=156.06  Aligned_cols=151  Identities=23%  Similarity=0.313  Sum_probs=133.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ...+||+--|+..++..+|.+||+.+|+|..|.|+.      +||.|||+|.+.+.+..|| .|.|..+.|.+|.|....
T Consensus       178 d~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq~sE  256 (549)
T KOG0147|consen  178 DQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQLSE  256 (549)
T ss_pred             hHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEecccH
Confidence            456899999999999999999999999999999974      4899999999999999999 599999999999997652


Q ss_pred             --------------------cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHH
Q psy93           186 --------------------INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQA  244 (503)
Q Consensus       186 --------------------~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kA  244 (503)
                                          +-..|||+||..+++++.|+.+|+.||.|..|.+..|. +|.++||+||+|.+.++|.+|
T Consensus       257 aeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a  336 (549)
T KOG0147|consen  257 AEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKA  336 (549)
T ss_pred             HHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHH
Confidence                                11238999999999999999999999999999999995 999999999999999999999


Q ss_pred             HHHhhCCeeeecCCCCeEEeecC
Q psy93           245 LRRCAEGCFFLTQSLRPVIVEPL  267 (503)
Q Consensus       245 l~~ln~g~~~~~~~~rpl~V~~~  267 (503)
                      +..|| +..+   -++++.|...
T Consensus       337 ~e~ln-gfel---AGr~ikV~~v  355 (549)
T KOG0147|consen  337 LEQLN-GFEL---AGRLIKVSVV  355 (549)
T ss_pred             HHHhc-ccee---cCceEEEEEe
Confidence            99998 5444   6777777553

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

Probab=99.58  E-value=1.4e-14  Score=130.64  Aligned_cols=76  Identities=20%  Similarity=0.428  Sum_probs=70.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ..+++|||+|||+++|+++|+++|++||.|.+|.|+.      +++||||+|.+.++|++||+.||+..|.+++|+|.|+
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a  111 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPA  111 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeC
Confidence            3467899999999999999999999999999999974      4799999999999999999999999999999999998


Q ss_pred             cc
Q psy93           185 PI  186 (503)
Q Consensus       185 ~~  186 (503)
                      ..
T Consensus       112 ~~  113 (144)
T PLN03134        112 ND  113 (144)
T ss_pred             Cc
Confidence            64

>KOG4206|consensus

Probab=99.55  E-value=8.2e-14  Score=130.35  Aligned_cols=148  Identities=22%  Similarity=0.319  Sum_probs=125.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHH----hhccCCCeEEEEEe---cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           113 NCRLYLGNIGGDITENDIIE----LFKPYGETQELFIN---KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~----~F~~~G~V~~v~i~---~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +.||||.||+..+..++|+.    ||+.||.|..|...   +.+|-|||.|.+.+.|..|+..|+|..+.|++++|.+|+
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~   88 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAK   88 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheeccc
Confidence            34899999999999999888    99999999999875   458999999999999999999999999999999998883


Q ss_pred             c--------------------------------------------------------ccceeccCcccccCHHHHHHHhc
Q psy93           186 I--------------------------------------------------------NAAIKVKNLTSCVTNELLELAFG  209 (503)
Q Consensus       186 ~--------------------------------------------------------~~~L~V~nLp~~~tee~L~~~Fs  209 (503)
                      .                                                        ...||+.|||..++.+.|..+|.
T Consensus        89 s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~lf~  168 (221)
T KOG4206|consen   89 SDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSDLFE  168 (221)
T ss_pred             CccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHHHHHh
Confidence            1                                                        23588999999999999999999


Q ss_pred             cCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecC
Q psy93           210 VFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPL  267 (503)
Q Consensus       210 ~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~  267 (503)
                      +|.-...+.++...    ++.|||+|.+...|..|...+. +..+ + +..++.+.++
T Consensus       169 qf~g~keir~i~~~----~~iAfve~~~d~~a~~a~~~lq-~~~i-t-~~~~m~i~~a  219 (221)
T KOG4206|consen  169 QFPGFKEIRLIPPR----SGIAFVEFLSDRQASAAQQALQ-GFKI-T-KKNTMQITFA  219 (221)
T ss_pred             hCcccceeEeccCC----CceeEEecchhhhhHHHhhhhc-ccee-c-cCceEEeccc
Confidence            99988888887653    5699999999999999999986 4333 2 2455555544

>KOG4212|consensus

Probab=99.52  E-value=2.5e-13  Score=136.48  Aligned_cols=149  Identities=24%  Similarity=0.317  Sum_probs=130.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhc-cCCCeEEEEEe-----cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc-
Q psy93           114 CRLYLGNIGGDITENDIIELFK-PYGETQELFIN-----KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI-  186 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~-~~G~V~~v~i~-----~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~-  186 (503)
                      ..|||+|||+++.+.+|++||. +.|+|+.|.+.     +.++||.|+|+++|.+++|++.||...+.|++|.|+-.+. 
T Consensus        45 R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d~  124 (608)
T KOG4212|consen   45 RSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHDE  124 (608)
T ss_pred             ceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCch
Confidence            4599999999999999999996 66899999885     5689999999999999999999999999999999965410 


Q ss_pred             --------------------------------------------------------------------------------
Q psy93           187 --------------------------------------------------------------------------------  186 (503)
Q Consensus       187 --------------------------------------------------------------------------------  186 (503)
                                                                                                      
T Consensus       125 q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~Fl  204 (608)
T KOG4212|consen  125 QRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSASFL  204 (608)
T ss_pred             hhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchhhhh
Confidence                                                                                            


Q ss_pred             ----------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeec
Q psy93           187 ----------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLT  256 (503)
Q Consensus       187 ----------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~  256 (503)
                                ..++||.||...+..+.|++.|.-.|+|..+.+-.|+.+.+++|+.|+|+.+-.|..||..|+.+..+  
T Consensus       205 r~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~~g~~--  282 (608)
T KOG4212|consen  205 RSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDRQGLF--  282 (608)
T ss_pred             hhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhccCCCc--
Confidence                      13688999999999999999999999999999999999999999999999999999999999743322  


Q ss_pred             CCCCeEEeec
Q psy93           257 QSLRPVIVEP  266 (503)
Q Consensus       257 ~~~rpl~V~~  266 (503)
                        .++.++..
T Consensus       283 --~~~~~~Rl  290 (608)
T KOG4212|consen  283 --DRRMTVRL  290 (608)
T ss_pred             --cccceeec
Confidence              55655554

>KOG0147|consensus

Probab=99.52  E-value=6.7e-14  Score=144.88  Aligned_cols=148  Identities=29%  Similarity=0.413  Sum_probs=120.7

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc---
Q psy93           115 RLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP---  185 (503)
Q Consensus       115 ~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~---  185 (503)
                      +|||+||.+++++++|+.+|++||.|..|.+.+      +|||+||+|.+.++|.+|+..|||.+|.|+.|+|..-.   
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~  359 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERV  359 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeec
Confidence            399999999999999999999999999998864      48999999999999999999999999999999985431   


Q ss_pred             --------------------------------------------------------------------------------
Q psy93           186 --------------------------------------------------------------------------------  185 (503)
Q Consensus       186 --------------------------------------------------------------------------------  185 (503)
                                                                                                      
T Consensus       360 ~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~  439 (549)
T KOG0147|consen  360 DTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASPAF  439 (549)
T ss_pred             ccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCcccccccc
Confidence                                                                                            


Q ss_pred             --cccceeccCccc--ccC--------HHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCee
Q psy93           186 --INAAIKVKNLTS--CVT--------NELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCF  253 (503)
Q Consensus       186 --~~~~L~V~nLp~--~~t--------ee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~  253 (503)
                        ++.|+.++|+=.  ..|        .++|.+.+.+||+|..|.|.++    +-|+.||.|.+.+.|..|+..|+ +.+
T Consensus       440 ~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~n----s~g~VYvrc~s~~~A~~a~~alh-grW  514 (549)
T KOG0147|consen  440 DIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKN----SAGCVYVRCPSAEAAGTAVKALH-GRW  514 (549)
T ss_pred             CCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccC----CCceEEEecCcHHHHHHHHHHHh-hhh
Confidence              012444555421  111        1678888999999998877654    24899999999999999999997 776


Q ss_pred             eecCCCCeEEeecCCcc
Q psy93           254 FLTQSLRPVIVEPLELT  270 (503)
Q Consensus       254 ~~~~~~rpl~V~~~~~~  270 (503)
                      |   .++.|+..++...
T Consensus       515 F---~gr~Ita~~~~~~  528 (549)
T KOG0147|consen  515 F---AGRMITAKYLPLE  528 (549)
T ss_pred             h---ccceeEEEEeehh
Confidence            6   6888888776544

>KOG1548|consensus

Probab=99.51  E-value=4.4e-13  Score=131.67  Aligned_cols=154  Identities=19%  Similarity=0.246  Sum_probs=126.2

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHhhccCCCeE--------EEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccccC
Q psy93           110 FANNCRLYLGNIGGDITENDIIELFKPYGETQ--------ELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVLKG  176 (503)
Q Consensus       110 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~--------~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g  176 (503)
                      ...++.|||+|||.++|.+++.++|++||.|.        .|+|.++     ||-|+|.|-..+++..||..|++..|.|
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            44578899999999999999999999999886        3566433     7899999999999999999999999999


Q ss_pred             ceEEEEecc--------------------------------------------cccceeccCccc----ccC-------H
Q psy93           177 RSLKIRFAP--------------------------------------------INAAIKVKNLTS----CVT-------N  201 (503)
Q Consensus       177 ~~l~V~~a~--------------------------------------------~~~~L~V~nLp~----~~t-------e  201 (503)
                      +.|+|..|.                                            ..++|.|+|+-.    ..+       .
T Consensus       211 ~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlk  290 (382)
T KOG1548|consen  211 KKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLK  290 (382)
T ss_pred             cEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHH
Confidence            999998873                                            135788888631    122       2


Q ss_pred             HHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCcc
Q psy93           202 ELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELT  270 (503)
Q Consensus       202 e~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~  270 (503)
                      ++|.+-+++||.|.+|.|.-.   .+.|.+.|.|.+.+.|..||..|+ |.++   .+|.|+....+-.
T Consensus       291 edl~eec~K~G~v~~vvv~d~---hPdGvvtV~f~n~eeA~~ciq~m~-GR~f---dgRql~A~i~DG~  352 (382)
T KOG1548|consen  291 EDLTEECEKFGQVRKVVVYDR---HPDGVVTVSFRNNEEADQCIQTMD-GRWF---DGRQLTASIWDGK  352 (382)
T ss_pred             HHHHHHHHHhCCcceEEEecc---CCCceeEEEeCChHHHHHHHHHhc-Ceee---cceEEEEEEeCCc
Confidence            567778999999999877643   347899999999999999999997 7777   6888888765433

>KOG0106|consensus

Probab=99.50  E-value=2.6e-14  Score=134.91  Aligned_cols=138  Identities=27%  Similarity=0.367  Sum_probs=120.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc-------
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI-------  186 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~-------  186 (503)
                      ..|||++||+.+.+.+|..||..||.|..|.+.  .+|+||+|.+.-+|..||..||+.+|.+-.+.|+|+..       
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~~~g~   79 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRRGRGR   79 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--cccceeccCchhhhhcccchhcCceecceeeeeecccccccccCC
Confidence            369999999999999999999999999999884  68999999999999999999999999998899988751       


Q ss_pred             -------------------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHH
Q psy93           187 -------------------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRR  247 (503)
Q Consensus       187 -------------------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~  247 (503)
                                         .+.|+|.+++..+.+.+|.+.|..+|.+....+.       .+++||+|++.++|.+|+..
T Consensus        80 ~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~~-------~~~~~v~Fs~~~da~ra~~~  152 (216)
T KOG0106|consen   80 PRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDAR-------RNFAFVEFSEQEDAKRALEK  152 (216)
T ss_pred             CCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhhh-------ccccceeehhhhhhhhcchh
Confidence                               2468889999999999999999999999655442       55999999999999999999


Q ss_pred             hhCCeeeecCCCCeEEe
Q psy93           248 CAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       248 ln~g~~~~~~~~rpl~V  264 (503)
                      |++ ..+   .++.|.+
T Consensus       153 l~~-~~~---~~~~l~~  165 (216)
T KOG0106|consen  153 LDG-KKL---NGRRISV  165 (216)
T ss_pred             ccc-hhh---cCceeee
Confidence            974 433   4777777

>KOG0107|consensus

Probab=99.50  E-value=4.5e-14  Score=126.65  Aligned_cols=75  Identities=23%  Similarity=0.550  Sum_probs=70.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ..|+|||+||+..+++.||..+|..||+|.+|+|..+ .+||||+|+++-||..|+..|||+.|.|..|+|+++.-
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            4689999999999999999999999999999999754 68999999999999999999999999999999998853

>KOG1457|consensus

Probab=99.45  E-value=7.8e-13  Score=122.78  Aligned_cols=138  Identities=17%  Similarity=0.278  Sum_probs=114.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe-cC------CCceEEeeCCHHHHHHHHHHhCCcccc---CceEEEE
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFIN-KE------KMFGFIRMDYKHNADKAKAKLDGHVLK---GRSLKIR  182 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~-~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~---g~~l~V~  182 (503)
                      -+||||.+||.++...+|..||..|--...+.|. .+      +.+|||+|.+..+|..|+..|||..|+   +..|+|+
T Consensus        34 VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiE  113 (284)
T KOG1457|consen   34 VRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIE  113 (284)
T ss_pred             cceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEee
Confidence            5789999999999999999999999766666553 22      369999999999999999999999887   6889998


Q ss_pred             eccc----------------------------------------------------------------------------
Q psy93           183 FAPI----------------------------------------------------------------------------  186 (503)
Q Consensus       183 ~a~~----------------------------------------------------------------------------  186 (503)
                      +++.                                                                            
T Consensus       114 lAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P~a  193 (284)
T KOG1457|consen  114 LAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAPSA  193 (284)
T ss_pred             ehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCCcc
Confidence            8730                                                                            


Q ss_pred             ----------------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhC
Q psy93           187 ----------------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAE  250 (503)
Q Consensus       187 ----------------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~  250 (503)
                                      ..+|||.||.+++++++|+.+|+.|--....+|... .|  .+.+||+|++.+.|..|+..|. 
T Consensus       194 ~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~-~g--~~vaf~~~~~~~~at~am~~lq-  269 (284)
T KOG1457|consen  194 NAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR-GG--MPVAFADFEEIEQATDAMNHLQ-  269 (284)
T ss_pred             cchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC-CC--cceEeecHHHHHHHHHHHHHhh-
Confidence                            137999999999999999999999987666655432 22  5689999999999999999996 


Q ss_pred             Ceee
Q psy93           251 GCFF  254 (503)
Q Consensus       251 g~~~  254 (503)
                      +..+
T Consensus       270 g~~~  273 (284)
T KOG1457|consen  270 GNLL  273 (284)
T ss_pred             ccee
Confidence            5443

>PF00076 RRM_1: RNA recognition motif

Probab=99.44  E-value=1.7e-13  Score=107.03  Aligned_cols=65  Identities=28%  Similarity=0.694  Sum_probs=61.6

Q ss_pred             EEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccccCceEE
Q psy93           116 LYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLK  180 (503)
Q Consensus       116 l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~  180 (503)
                      |||+|||+++|+++|+++|+.||.|..+.+..+     ++||||+|.+.++|++|++.|++..+.+++|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999763     68999999999999999999999999999885

(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 ....

>KOG0121|consensus

Probab=99.44  E-value=1.3e-13  Score=117.58  Aligned_cols=77  Identities=25%  Similarity=0.503  Sum_probs=70.4

Q ss_pred             CcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEE
Q psy93           109 KFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIR  182 (503)
Q Consensus       109 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~  182 (503)
                      ....+|||||+||++.++|+.|.+||+++|+|..|.|.-+      -|||||+|-+.++|..|++.++++.|+.++|+|.
T Consensus        32 a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D  111 (153)
T KOG0121|consen   32 ALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRID  111 (153)
T ss_pred             HHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeee
Confidence            3446799999999999999999999999999999998533      4799999999999999999999999999999999


Q ss_pred             ecc
Q psy93           183 FAP  185 (503)
Q Consensus       183 ~a~  185 (503)
                      |..
T Consensus       112 ~D~  114 (153)
T KOG0121|consen  112 WDA  114 (153)
T ss_pred             ccc
Confidence            864

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

Probab=99.38  E-value=2e-12  Score=116.62  Aligned_cols=82  Identities=30%  Similarity=0.381  Sum_probs=74.0

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      ..+++|||.|||..+++++|+++|++||.|.+|.|+.| .++.+++||||+|.+.++|.+|++.|| +..+   .+++|.
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~ln-g~~i---~Gr~l~  107 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMD-GKEL---NGRHIR  107 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcC-CCEE---CCEEEE
Confidence            34678999999999999999999999999999999988 588999999999999999999999997 6655   689999


Q ss_pred             eecCCcc
Q psy93           264 VEPLELT  270 (503)
Q Consensus       264 V~~~~~~  270 (503)
                      |.++...
T Consensus       108 V~~a~~~  114 (144)
T PLN03134        108 VNPANDR  114 (144)
T ss_pred             EEeCCcC
Confidence            9987654

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.37  E-value=9.2e-13  Score=135.31  Aligned_cols=116  Identities=16%  Similarity=0.165  Sum_probs=98.9

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ..++|||.|||.++++++|+++|+.||.|++|+|+.| .++++++||||+|.+.++|.+||..|| +..+   .+++|.|
T Consensus       106 ~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~Ln-G~~l---~gr~i~V  181 (346)
T TIGR01659       106 SGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLN-GITV---RNKRLKV  181 (346)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcC-CCcc---CCceeee
Confidence            4679999999999999999999999999999999998 588999999999999999999999997 5555   5889999


Q ss_pred             ecCCccccccCCcccccCCCCchhhhhhccCcccCCCCCcch
Q psy93           265 EPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEF  306 (503)
Q Consensus       265 ~~~~~~~~~~~~~~k~i~k~~~~~~kere~~~rf~~~g~~e~  306 (503)
                      .++.+.... ....++++.+++...+++++...|..++.+..
T Consensus       182 ~~a~p~~~~-~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~  222 (346)
T TIGR01659       182 SYARPGGES-IKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQ  222 (346)
T ss_pred             ecccccccc-cccceeEEeCCCCcccHHHHHHHHHhcCCEEE
Confidence            887654322 22346777888888899999999999987753

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).

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.35  E-value=2.8e-12  Score=124.25  Aligned_cols=72  Identities=22%  Similarity=0.301  Sum_probs=67.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC---CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKE---KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~---kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      .++|||+|||+.+|+++|+++|+.||+|.+|.|+.+   ++||||+|.++++|..||. |++..|.|+.|.|.++.
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~   78 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAE   78 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEecc
Confidence            468999999999999999999999999999999764   6899999999999999995 99999999999999885

>KOG1456|consensus

Probab=99.35  E-value=9.3e-11  Score=116.21  Aligned_cols=154  Identities=18%  Similarity=0.184  Sum_probs=126.3

Q ss_pred             CCcEEEEcCCCC-CCCHHHHHHhhccCCCeEEEEEecCC-CceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc----
Q psy93           112 NNCRLYLGNIGG-DITENDIIELFKPYGETQELFINKEK-MFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP----  185 (503)
Q Consensus       112 ~~~~l~V~nLp~-~~te~~L~~~F~~~G~V~~v~i~~~k-g~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~----  185 (503)
                      +.+.+.|.+|.. .++.+.|..+|..||.|..|++++.| +.|+|++.+..+.++|+..||+..+.|.+|.|.+++    
T Consensus       286 ~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~~v  365 (494)
T KOG1456|consen  286 PGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQNFV  365 (494)
T ss_pred             CCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccceeEEEcCcHHHHHHHHHHhccCccccceEEEeecccccc
Confidence            567899999975 47889999999999999999998875 799999999999999999999999999999998873    


Q ss_pred             ---------------------------------------cccceeccCcccccCHHHHHHHhccCCC-eeeeEEEeCCCC
Q psy93           186 ---------------------------------------INAAIKVKNLTSCVTNELLELAFGVFGD-IERAIVIVDERG  225 (503)
Q Consensus       186 ---------------------------------------~~~~L~V~nLp~~~tee~L~~~Fs~~G~-V~~~~v~~d~~g  225 (503)
                                                             |++.|+.-|.|..+|++.|.++|..... .++++|..-.+-
T Consensus       366 ~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~svkvFp~kse  445 (494)
T KOG1456|consen  366 SPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSVKVFPLKSE  445 (494)
T ss_pred             ccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcceEEeeccccc
Confidence                                                   3567888999999999999999987764 344555544332


Q ss_pred             CceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           226 NSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       226 ~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      + ...++++|++.++|..||..||+-.+......-|.++++
T Consensus       446 r-SssGllEfe~~s~Aveal~~~NH~pi~~p~gs~PfilKl  485 (494)
T KOG1456|consen  446 R-SSSGLLEFENKSDAVEALMKLNHYPIEGPNGSFPFILKL  485 (494)
T ss_pred             c-cccceeeeehHHHHHHHHHHhccccccCCCCCCCeeeee
Confidence            3 347899999999999999999966555444455666555

>KOG4211|consensus

Probab=99.34  E-value=1.5e-11  Score=126.03  Aligned_cols=134  Identities=19%  Similarity=0.283  Sum_probs=113.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc----
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINK----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP----  185 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~----  185 (503)
                      --|-+.+||+++|++||.+||+.| .|.++.+.+    ..|-|||+|.+.+++++|++ .|...+..+-|.|-.+.    
T Consensus        11 ~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~~e~   88 (510)
T KOG4211|consen   11 FEVRLRGLPWSATEKEILDFFSNC-GIENLEIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGGAEA   88 (510)
T ss_pred             eEEEecCCCccccHHHHHHHHhcC-ceeEEEEeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCCccc
Confidence            357889999999999999999999 466666653    46899999999999999997 58888888888886552    


Q ss_pred             -------------cccceeccCcccccCHHHHHHHhccCCCeee-eEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhh
Q psy93           186 -------------INAAIKVKNLTSCVTNELLELAFGVFGDIER-AIVIVDERGNSKCEGIVEFARKPAAAQALRRCA  249 (503)
Q Consensus       186 -------------~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~-~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln  249 (503)
                                   +...|.+..||..+|+++|.++|+..-.|.. +.++.+..+++.+.|||.|++.+.|++||....
T Consensus        89 d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~rhr  166 (510)
T KOG4211|consen   89 DWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGRHR  166 (510)
T ss_pred             cccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHHHH
Confidence                         1346888999999999999999998877766 446677888999999999999999999998743

>KOG0125|consensus

Probab=99.34  E-value=2.9e-12  Score=125.14  Aligned_cols=75  Identities=31%  Similarity=0.520  Sum_probs=70.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ..++|+|+|||+...+-||+.+|.+||+|.+|.|+-    +|||+||+|++++||++|-.+|||+.|.|++|.|+.+..
T Consensus        95 ~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATa  173 (376)
T KOG0125|consen   95 TPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATA  173 (376)
T ss_pred             CCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccch
Confidence            346899999999999999999999999999999973    599999999999999999999999999999999998864

>KOG4661|consensus

Probab=99.33  E-value=1.1e-10  Score=120.84  Aligned_cols=79  Identities=19%  Similarity=0.271  Sum_probs=69.2

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ..+|||.+|+..+...+|+.+|++||+|+-++|+++. +.-.++|+||++.+.++|.+||..|+ .+.|   .++.|.|+
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLH-rTEL---HGrmISVE  480 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLH-RTEL---HGRMISVE  480 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhh-hhhh---cceeeeee
Confidence            3589999999999999999999999999999999983 45568999999999999999999996 7666   68888887


Q ss_pred             cCCc
Q psy93           266 PLEL  269 (503)
Q Consensus       266 ~~~~  269 (503)
                      .++.
T Consensus       481 kaKN  484 (940)
T KOG4661|consen  481 KAKN  484 (940)
T ss_pred             eccc
Confidence            6543

>KOG1190|consensus

Probab=99.32  E-value=1.7e-11  Score=122.75  Aligned_cols=149  Identities=23%  Similarity=0.300  Sum_probs=123.6

Q ss_pred             CcEEEEcCCC-CCCCHHHHHHhhccCCCeEEEEEecC-CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc-----
Q psy93           113 NCRLYLGNIG-GDITENDIIELFKPYGETQELFINKE-KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP-----  185 (503)
Q Consensus       113 ~~~l~V~nLp-~~~te~~L~~~F~~~G~V~~v~i~~~-kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~-----  185 (503)
                      ++.|.|.||. ..||.+-|..+|+-||.|..|+|..+ +--|+|.|.+...|.-|+..|+|..|+|++|+|.+++     
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vq  376 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQ  376 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCcccc
Confidence            5789999995 56899999999999999999999765 4589999999999999999999999999999998884     


Q ss_pred             ------------------------------------cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCcee
Q psy93           186 ------------------------------------INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKC  229 (503)
Q Consensus       186 ------------------------------------~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg  229 (503)
                                                          ++.+|++.|+|.++++++|+.+|..-|-.........   +.+.
T Consensus       377 lp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~---kd~k  453 (492)
T KOG1190|consen  377 LPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQ---KDRK  453 (492)
T ss_pred             CCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecC---CCcc
Confidence                                                2457899999999999999999999997766544332   2256


Q ss_pred             EEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecC
Q psy93           230 EGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPL  267 (503)
Q Consensus       230 ~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~  267 (503)
                      ++++.+.+.+.|..|+-.++ .+.+.  ....+.|.+.
T Consensus       454 mal~q~~sveeA~~ali~~h-nh~lg--en~hlRvSFS  488 (492)
T KOG1190|consen  454 MALPQLESVEEAIQALIDLH-NHYLG--ENHHLRVSFS  488 (492)
T ss_pred             eeecccCChhHhhhhccccc-cccCC--CCceEEEEee
Confidence            99999999999999998885 44332  2334566554

>KOG0122|consensus

Probab=99.31  E-value=4.2e-12  Score=119.62  Aligned_cols=76  Identities=24%  Similarity=0.563  Sum_probs=71.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|-|.|||.++++++|.+||.+||.|..|.|.++      ||||||.|.+.++|.+||..|||.-++.-.|+|+|++
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            4678999999999999999999999999999999754      7999999999999999999999999999999999998


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      |.
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            75

>KOG0114|consensus

Probab=99.31  E-value=8.5e-12  Score=102.74  Aligned_cols=98  Identities=26%  Similarity=0.372  Sum_probs=78.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec---CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINK---EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAA  189 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~---~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~~~  189 (503)
                      +.-|||.|||+++|.+++.++|.+||+|..|.|.-   .+|.|||.|++..+|.+|++.|+|..+.++.|.|-+..+...
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~~~   97 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPEDA   97 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHHHH
Confidence            45799999999999999999999999999999963   479999999999999999999999999999999988766432


Q ss_pred             eeccCcccccCHHHHHHHhccCC
Q psy93           190 IKVKNLTSCVTNELLELAFGVFG  212 (503)
Q Consensus       190 L~V~nLp~~~tee~L~~~Fs~~G  212 (503)
                      ..+  .......++|..+-.+||
T Consensus        98 ~~~--~~~~k~~~~l~~~~~ky~  118 (124)
T KOG0114|consen   98 FKL--MDSRKAREELSILKEKYG  118 (124)
T ss_pred             HHH--HHhHHhhhHHHHHHHHhc
Confidence            211  122333444555544554

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.31  E-value=4.6e-12  Score=99.48  Aligned_cols=65  Identities=26%  Similarity=0.575  Sum_probs=59.4

Q ss_pred             EEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccccCceEE
Q psy93           116 LYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLK  180 (503)
Q Consensus       116 l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~  180 (503)
                      |||+|||+++++++|.++|+.||.|..+.+..+     +++|||+|.+.++|.+|+..+++..|.|+.|.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            799999999999999999999999999999876     58999999999999999999999999999874

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG1190|consensus

Probab=99.27  E-value=9.5e-11  Score=117.48  Aligned_cols=150  Identities=23%  Similarity=0.359  Sum_probs=125.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEE-ecCCCc-eEEeeCCHHHHHHHHHHhCCccccC--ceEEEEecc----
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFI-NKEKMF-GFIRMDYKHNADKAKAKLDGHVLKG--RSLKIRFAP----  185 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i-~~~kg~-aFV~F~~~e~A~~Ai~~l~g~~l~g--~~l~V~~a~----  185 (503)
                      -+++|.|+-+.||-+-|..+|++||.|..|.. -++.+| |+|.|.+++.|..|...|+|..|..  |.|+|.+++    
T Consensus       151 Lr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~L  230 (492)
T KOG1190|consen  151 LRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTKNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDL  230 (492)
T ss_pred             EEEEeccceeeeEHHHHHHHHhhcceeEEEEEEecccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccc
Confidence            46889999999999999999999999987754 456564 9999999999999999999997773  788887762    


Q ss_pred             ---------------------------------------------------------------c--ccceeccCcc-ccc
Q psy93           186 ---------------------------------------------------------------I--NAAIKVKNLT-SCV  199 (503)
Q Consensus       186 ---------------------------------------------------------------~--~~~L~V~nLp-~~~  199 (503)
                                                                                     +  +..|.|.||. ..+
T Consensus       231 nvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln~~~V  310 (492)
T KOG1190|consen  231 NVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLNEEAV  310 (492)
T ss_pred             eeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecCchhcc
Confidence                                                                           0  1457788886 469


Q ss_pred             CHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCccc
Q psy93           200 TNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTD  271 (503)
Q Consensus       200 tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~~  271 (503)
                      |.+.|..+|..||.|.+|+|+.++    +-.|+|.|.+...|.-|+.+|+ +..+   .+++|.|.+.++.+
T Consensus       311 T~d~LftlFgvYGdVqRVkil~nk----kd~ALIQmsd~~qAqLA~~hL~-g~~l---~gk~lrvt~SKH~~  374 (492)
T KOG1190|consen  311 TPDVLFTLFGVYGDVQRVKILYNK----KDNALIQMSDGQQAQLAMEHLE-GHKL---YGKKLRVTLSKHTN  374 (492)
T ss_pred             chhHHHHHHhhhcceEEEEeeecC----CcceeeeecchhHHHHHHHHhh-ccee---cCceEEEeeccCcc
Confidence            999999999999999999999874    3479999999999999999997 5555   36889998876653

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

Probab=99.26  E-value=4.1e-11  Score=116.95  Aligned_cols=110  Identities=33%  Similarity=0.514  Sum_probs=97.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc-
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP-  185 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~-  185 (503)
                      .++|||+|||.++|+++|.++|..||.|..|.|..+      ++||||+|.+.++|..|+..+++..|.+++|.|.++. 
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            589999999999999999999999999998888643      6999999999999999999999999999999999842 


Q ss_pred             -----------------------------cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC
Q psy93           186 -----------------------------INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD  222 (503)
Q Consensus       186 -----------------------------~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d  222 (503)
                                                   ....+++.+++..++...+...|..++.+..+.+...
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  260 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPS  260 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCC
Confidence                                         1245778889999999999999999999966655544

>KOG0124|consensus

Probab=99.25  E-value=6.2e-11  Score=117.04  Aligned_cols=72  Identities=25%  Similarity=0.447  Sum_probs=66.2

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe------cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFIN------KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~------~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      -++|||..+.++.+++||+..|+.||+|++|.+.      .+|||+||+|.+..+-..||..||-..|.|+.|+|-.+
T Consensus       210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~  287 (544)
T KOG0124|consen  210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC  287 (544)
T ss_pred             hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccc
Confidence            3589999999999999999999999999999995      35899999999999999999999999999999998544

>smart00362 RRM_2 RNA recognition motif

Probab=99.25  E-value=2.3e-11  Score=94.11  Aligned_cols=67  Identities=36%  Similarity=0.693  Sum_probs=63.2

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCC----CceEEeeCCHHHHHHHHHHhCCccccCceEEE
Q psy93           115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEK----MFGFIRMDYKHNADKAKAKLDGHVLKGRSLKI  181 (503)
Q Consensus       115 ~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~k----g~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V  181 (503)
                      +|||+|||.+++.++|+++|..||+|..+.+..++    ++|||+|.+.++|.+|+..+++..+.++.|.|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            48999999999999999999999999999998765    99999999999999999999999999999887

>KOG0120|consensus

Probab=99.25  E-value=1.9e-11  Score=128.22  Aligned_cols=156  Identities=20%  Similarity=0.280  Sum_probs=124.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ...+.|||++||..+++..+.++...||++....+++      +|+|||.+|.++.....||..|||+.+.++.|.|..+
T Consensus       287 ~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A  366 (500)
T KOG0120|consen  287 DSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRA  366 (500)
T ss_pred             cccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehh
Confidence            3457899999999999999999999999998877754      4899999999999999999999999999999999877


Q ss_pred             cc------------------------------ccceeccCc--ccc-cCH-------HHHHHHhccCCCeeeeEEEeC-C
Q psy93           185 PI------------------------------NAAIKVKNL--TSC-VTN-------ELLELAFGVFGDIERAIVIVD-E  223 (503)
Q Consensus       185 ~~------------------------------~~~L~V~nL--p~~-~te-------e~L~~~Fs~~G~V~~~~v~~d-~  223 (503)
                      -.                              +..|++.|+  |.. .++       ++|+..|++||.|..|.|.++ .
T Consensus       367 ~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~  446 (500)
T KOG0120|consen  367 IVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYP  446 (500)
T ss_pred             hccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCC
Confidence            32                              122333332  111 111       456777899999999999877 3


Q ss_pred             C---CCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCcc
Q psy93           224 R---GNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELT  270 (503)
Q Consensus       224 ~---g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~  270 (503)
                      +   ....|..||+|.+.+++++|+..|+ |..+   .+|.|+...++..
T Consensus       447 ~~~~~~G~GkVFVefas~ed~qrA~~~L~-GrKF---~nRtVvtsYydeD  492 (500)
T KOG0120|consen  447 DENPVPGTGKVFVEFADTEDSQRAMEELT-GRKF---ANRTVVASYYDED  492 (500)
T ss_pred             CCCcCCCcccEEEEecChHHHHHHHHHcc-Ccee---CCcEEEEEecCHH
Confidence            2   2345678999999999999999997 7666   6888888887654

>PLN03213 repressor of silencing 3; Provisional

Probab=99.24  E-value=1.6e-11  Score=125.14  Aligned_cols=75  Identities=23%  Similarity=0.478  Sum_probs=69.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC--CCceEEeeCCH--HHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE--KMFGFIRMDYK--HNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~--kg~aFV~F~~~--e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ...+||||||+++|++++|..+|+.||.|..|.|++.  +|||||+|.+.  .++.+||..|||..+.|+.|+|..|.+
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP   87 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKE   87 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccH
Confidence            3478999999999999999999999999999999864  78999999987  789999999999999999999999975

>PF00076 RRM_1: RNA recognition motif

Probab=99.23  E-value=4.9e-11  Score=92.98  Aligned_cols=64  Identities=36%  Similarity=0.413  Sum_probs=60.1

Q ss_pred             eeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeee
Q psy93           190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFF  254 (503)
Q Consensus       190 L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~  254 (503)
                      |||+|||..+++++|+++|+.||.|..+.+..+.++.++++|||+|.+.++|.+|+..|+ +..+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~-g~~~   64 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELN-GKKI   64 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHT-TEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcC-CCEE
Confidence            799999999999999999999999999999998888899999999999999999999997 5655

(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 ....

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.23  E-value=3.3e-11  Score=115.10  Aligned_cols=73  Identities=15%  Similarity=0.208  Sum_probs=67.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC---CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE---KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~---kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ...+|||+||++.+|+++|++||+.||+|.+|.|+++   ++||||+|.++++|..|+ .|+|..|.+++|.|..+.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCc
Confidence            3468999999999999999999999999999999865   579999999999999999 599999999999998754

>KOG1456|consensus

Probab=99.22  E-value=2.9e-10  Score=112.79  Aligned_cols=152  Identities=14%  Similarity=0.172  Sum_probs=120.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhC--CccccCceEEEEecc-----
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLD--GHVLKGRSLKIRFAP-----  185 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~--g~~l~g~~l~V~~a~-----  185 (503)
                      +-.|.|.+|-..+++.+|.+.++.||+|..|.++..+..|+|+|++.+.|+.|+..-.  ...+.|+.-.+.++.     
T Consensus        31 spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~NyStsq~i~  110 (494)
T KOG1456|consen   31 SPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHKRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNYSTSQCIE  110 (494)
T ss_pred             CceEEEeccccccchhHHHHHHhcCCceEEEEeccccceeeeeeccccchhhheehhccCcccccCchhhcccchhhhhc
Confidence            3469999999999999999999999999999999999999999999999999886433  335567777777663     


Q ss_pred             --------cccceecc--CcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeee
Q psy93           186 --------INAAIKVK--NLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFL  255 (503)
Q Consensus       186 --------~~~~L~V~--nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~  255 (503)
                              ++..|.++  |--..+|-+-|..++...|+|..|.|++. ++   -.|.|+|++.+.|++|...||.-.+..
T Consensus       111 R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk-ng---VQAmVEFdsv~~AqrAk~alNGADIYs  186 (494)
T KOG1456|consen  111 RPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK-NG---VQAMVEFDSVEVAQRAKAALNGADIYS  186 (494)
T ss_pred             cCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec-cc---eeeEEeechhHHHHHHHhhcccccccc
Confidence                    23344444  43457899999999999999999988876 33   379999999999999999998443331


Q ss_pred             cCCCCeEEeecCCcc
Q psy93           256 TQSLRPVIVEPLELT  270 (503)
Q Consensus       256 ~~~~rpl~V~~~~~~  270 (503)
                        .-+.+.++.+++.
T Consensus       187 --GCCTLKIeyAkP~  199 (494)
T KOG1456|consen  187 --GCCTLKIEYAKPT  199 (494)
T ss_pred             --cceeEEEEecCcc
Confidence              2345666666553

>KOG4212|consensus

Probab=99.21  E-value=3.1e-10  Score=114.50  Aligned_cols=71  Identities=25%  Similarity=0.259  Sum_probs=61.4

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      ++|+|+|||.+.|++.|++.|..||.|.++.|+.  .+++++  +|.|.++++|+.|+..|+ ++.+   +++-|.|..
T Consensus       537 ~qIiirNlP~dfTWqmlrDKfre~G~v~yadime--~GkskG--VVrF~s~edAEra~a~Mn-gs~l---~Gr~I~V~y  607 (608)
T KOG4212|consen  537 CQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME--NGKSKG--VVRFFSPEDAERACALMN-GSRL---DGRNIKVTY  607 (608)
T ss_pred             cEEEEecCCccccHHHHHHHHHhccceehhhhhc--cCCccc--eEEecCHHHHHHHHHHhc-cCcc---cCceeeeee
Confidence            5799999999999999999999999999998843  455655  999999999999999997 6666   678787764

>KOG0132|consensus

Probab=99.21  E-value=8.8e-11  Score=125.75  Aligned_cols=101  Identities=25%  Similarity=0.357  Sum_probs=84.5

Q ss_pred             CcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc--
Q psy93           109 KFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI--  186 (503)
Q Consensus       109 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~--  186 (503)
                      ....++||||+.|+..+++.||..+|+.||.|.+|.++.+++||||++....+|.+|+..|....+..+.|+|.|+-.  
T Consensus       417 isV~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G  496 (894)
T KOG0132|consen  417 ISVCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKG  496 (894)
T ss_pred             eeEeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCC
Confidence            344678999999999999999999999999999999999999999999999999999999999999999999999953  


Q ss_pred             ---------ccceeccCcccccCHHHHHHHhc
Q psy93           187 ---------NAAIKVKNLTSCVTNELLELAFG  209 (503)
Q Consensus       187 ---------~~~L~V~nLp~~~tee~L~~~Fs  209 (503)
                               ...|=|..||...-.++|..++.
T Consensus       497 ~kse~k~~wD~~lGVt~IP~~kLt~dl~~~~e  528 (894)
T KOG0132|consen  497 PKSEYKDYWDVELGVTYIPWEKLTDDLEAWCE  528 (894)
T ss_pred             cchhhhhhhhcccCeeEeehHhcCHHHHHhhh
Confidence                     12234666776533333554443

>KOG4207|consensus

Probab=99.19  E-value=2.1e-11  Score=112.18  Aligned_cols=74  Identities=28%  Similarity=0.590  Sum_probs=69.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|.|-||.+-|+.++|+.+|++||.|.+|.|+.+      +|||||.|....+|+.|++.|+|.+|+|+.|.|.+|.
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            4678999999999999999999999999999999754      7999999999999999999999999999999999884

>KOG0130|consensus

Probab=99.17  E-value=5.9e-11  Score=102.25  Aligned_cols=74  Identities=22%  Similarity=0.463  Sum_probs=68.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ...-.|||.++...+|+++|.+.|..||+|+.|.+.-+      ||||+|+|++.+.|++||..||+..|.+++|.|.|+
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~  149 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWC  149 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEE
Confidence            34567999999999999999999999999999998643      799999999999999999999999999999999997

>PF13893 RRM_5: RNA recognition motif

Probab=99.16  E-value=1.2e-10  Score=87.64  Aligned_cols=55  Identities=35%  Similarity=0.648  Sum_probs=51.7

Q ss_pred             HHHhhccCCCeEEEEEecCC-CceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           130 IIELFKPYGETQELFINKEK-MFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       130 L~~~F~~~G~V~~v~i~~~k-g~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      |.++|++||+|..|.+.+++ ++|||+|.+.++|.+|+..||+..+.|++|+|.|+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68999999999999999887 99999999999999999999999999999999986

(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 ....

>KOG0111|consensus

Probab=99.15  E-value=3.4e-11  Score=111.61  Aligned_cols=76  Identities=25%  Similarity=0.553  Sum_probs=71.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe------cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFIN------KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~------~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||++|...|++.-|...|-+||.|+.|.|+      ++++||||+|.-.+||..||+.||+.+|.|+.|+|+++.
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            34689999999999999999999999999999996      458999999999999999999999999999999999998


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      |.
T Consensus        89 P~   90 (298)
T KOG0111|consen   89 PE   90 (298)
T ss_pred             Cc
Confidence            74

>KOG0149|consensus

Probab=99.14  E-value=5.4e-11  Score=111.88  Aligned_cols=73  Identities=18%  Similarity=0.419  Sum_probs=64.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe------cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFIN------KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~------~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      .-|+|||++|++.++.++|+.+|++||+|+++.|+      ++|||+||+|.+.++|.+||+. ..-.|+||+-.|+++-
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLAS   89 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhh
Confidence            45789999999999999999999999999998886      5689999999999999999975 3457899988887763

>KOG0113|consensus

Probab=99.14  E-value=2.2e-10  Score=110.93  Aligned_cols=74  Identities=19%  Similarity=0.383  Sum_probs=69.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      .+-+||||+-|+++++|..|+..|+.||+|+.|.|++      ++|||||+|++.-+...|.+..+|+.|+|+.|.|.+-
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            3568999999999999999999999999999999974      4899999999999999999999999999999999864

>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=99.13  E-value=2.2e-10  Score=88.98  Aligned_cols=69  Identities=36%  Similarity=0.724  Sum_probs=64.3

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           115 RLYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       115 ~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      +|+|+|||+++++++|+++|..||.|..+.+..+     +++|||+|.+.++|..|+..+++..+.++.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999999764     68999999999999999999999999999998864

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).

>KOG0122|consensus

Probab=99.11  E-value=1.7e-10  Score=108.97  Aligned_cols=81  Identities=30%  Similarity=0.315  Sum_probs=72.4

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ..++|.|.||+.++++++|.++|..||.|..+.|.+| .+|.++|||||.|.+.++|.+||..|| +.-+   +.-.|.|
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~Ln-G~gy---d~LILrv  263 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLN-GYGY---DNLILRV  263 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHcc-Cccc---ceEEEEE
Confidence            3568999999999999999999999999999999999 699999999999999999999999998 5332   4567889


Q ss_pred             ecCCcc
Q psy93           265 EPLELT  270 (503)
Q Consensus       265 ~~~~~~  270 (503)
                      +|..+.
T Consensus       264 EwskP~  269 (270)
T KOG0122|consen  264 EWSKPS  269 (270)
T ss_pred             EecCCC
Confidence            998764

>KOG0129|consensus

Probab=99.07  E-value=1.9e-09  Score=111.57  Aligned_cols=160  Identities=19%  Similarity=0.200  Sum_probs=118.2

Q ss_pred             cCcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEE-EE--E-----ecCCC---ceEEeeCCHHHHHHHHHHhCCc----
Q psy93           108 IKFANNCRLYLGNIGGDITENDIIELFKPYGETQE-LF--I-----NKEKM---FGFIRMDYKHNADKAKAKLDGH----  172 (503)
Q Consensus       108 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~-v~--i-----~~~kg---~aFV~F~~~e~A~~Ai~~l~g~----  172 (503)
                      ....-++.||||+||.+++|+.|...|..||.|.- +-  .     ...+|   |+|+.|++..++..-|..+.-.    
T Consensus       254 ~~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~  333 (520)
T KOG0129|consen  254 RSPRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGNY  333 (520)
T ss_pred             CccccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccce
Confidence            33445688999999999999999999999998742 11  1     12367   9999999988887766554321    


Q ss_pred             -------cccCceEEEEec---------------ccccceeccCcccccCHHHHHHHhc-cCCCeeeeEEEeC-CCCCce
Q psy93           173 -------VLKGRSLKIRFA---------------PINAAIKVKNLTSCVTNELLELAFG-VFGDIERAIVIVD-ERGNSK  228 (503)
Q Consensus       173 -------~l~g~~l~V~~a---------------~~~~~L~V~nLp~~~tee~L~~~Fs-~~G~V~~~~v~~d-~~g~sk  228 (503)
                             .+..+.+.|...               ++..+|||+.||-.++.++|..+|+ -||.|..+-|-+| +-..++
T Consensus       334 yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPk  413 (520)
T KOG0129|consen  334 YFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPK  413 (520)
T ss_pred             EEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCC
Confidence                   112222333221               3578999999999999999999999 8999999999998 677889


Q ss_pred             eEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCC
Q psy93           229 CEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLE  268 (503)
Q Consensus       229 g~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~  268 (503)
                      |-|-|+|.+..+-.+||.+-- -.+-.+...+.|.|+|+.
T Consensus       414 GaGRVtFsnqqsYi~AIsarF-vql~h~d~~KRVEIkPYv  452 (520)
T KOG0129|consen  414 GAGRVTFSNQQAYIKAISARF-VQLDHTDIDKRVEIKPYV  452 (520)
T ss_pred             CcceeeecccHHHHHHHhhhe-EEEeccccceeeeeccee
Confidence            999999999999999998721 011112234556666665

>smart00360 RRM RNA recognition motif

Probab=99.05  E-value=5.1e-10  Score=86.07  Aligned_cols=65  Identities=34%  Similarity=0.695  Sum_probs=59.8

Q ss_pred             EcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEE
Q psy93           118 LGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIR  182 (503)
Q Consensus       118 V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~  182 (503)
                      |+|||..+++++|+.+|..||.|..+.+..+      ++||||+|.+.++|..|+..|++..+.++.|.|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            6899999999999999999999999998754      5799999999999999999999999999998873

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.05  E-value=1.2e-09  Score=85.74  Aligned_cols=64  Identities=30%  Similarity=0.405  Sum_probs=57.7

Q ss_pred             eeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeee
Q psy93           190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFF  254 (503)
Q Consensus       190 L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~  254 (503)
                      |+|+|||+.+++++|.++|+.||.|..+.+..+.++.++++|||+|.+.++|..|+..++ +..+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~-~~~~   64 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLN-GKEI   64 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHT-TEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCC-CcEE
Confidence            689999999999999999999999999999998668899999999999999999999985 6666

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=99.04  E-value=7.5e-10  Score=107.50  Aligned_cols=79  Identities=23%  Similarity=0.219  Sum_probs=68.9

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      .++|||+|||+.+++++|+++|+.||+|.+|.|+.+..  +++||||+|.+.++|..||. || +..+   .+++|.|.+
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~--~~GfAFVtF~d~eaAe~All-Ln-G~~l---~gr~V~Vt~   76 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE--RSQIAYVTFKDPQGAETALL-LS-GATI---VDQSVTITP   76 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC--CCCEEEEEeCcHHHHHHHHH-hc-CCee---CCceEEEEe
Confidence            46899999999999999999999999999999998853  47899999999999999995 76 6655   599999999


Q ss_pred             CCcccc
Q psy93           267 LELTDE  272 (503)
Q Consensus       267 ~~~~~~  272 (503)
                      ....+.
T Consensus        77 a~~~~~   82 (260)
T PLN03120         77 AEDYQL   82 (260)
T ss_pred             ccCCCC
Confidence            765543

>KOG0126|consensus

Probab=99.04  E-value=3.8e-11  Score=108.48  Aligned_cols=75  Identities=24%  Similarity=0.525  Sum_probs=70.2

Q ss_pred             cCcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEE
Q psy93           108 IKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKI  181 (503)
Q Consensus       108 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V  181 (503)
                      ..+.++.-|||+|||+++|+.||.-+|++||+|+.|.+++      ++||||+.|++.-+...|+..|||..|.|+.|+|
T Consensus        30 ~~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirV  109 (219)
T KOG0126|consen   30 QEYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRV  109 (219)
T ss_pred             hhcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEe
Confidence            4566788999999999999999999999999999999975      4799999999999999999999999999999999


Q ss_pred             E
Q psy93           182 R  182 (503)
Q Consensus       182 ~  182 (503)
                      .
T Consensus       110 D  110 (219)
T KOG0126|consen  110 D  110 (219)
T ss_pred             e
Confidence            7

>KOG0121|consensus

Probab=99.00  E-value=6.6e-10  Score=95.10  Aligned_cols=80  Identities=26%  Similarity=0.280  Sum_probs=69.9

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      +++|||+||+..++++.|.++|+++|+|..|.+-.|. +..+=|||||+|.+.++|..|+..+| +..+   ..++|.+.
T Consensus        36 S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~Alryis-gtrL---ddr~ir~D  111 (153)
T KOG0121|consen   36 SCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYIS-GTRL---DDRPIRID  111 (153)
T ss_pred             cceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhc-cCcc---cccceeee
Confidence            6899999999999999999999999999998876663 45567899999999999999999997 6666   78999998


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      |---.
T Consensus       112 ~D~GF  116 (153)
T KOG0121|consen  112 WDAGF  116 (153)
T ss_pred             ccccc
Confidence            85443

>KOG0109|consensus

Probab=99.00  E-value=3.4e-10  Score=109.20  Aligned_cols=97  Identities=24%  Similarity=0.348  Sum_probs=78.7

Q ss_pred             HHhhcCCCCCCCCCCCCccccCcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHH
Q psy93            88 IMAIQGPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKA  167 (503)
Q Consensus        88 ~~~~~~~~~~~p~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~  167 (503)
                      +..+.+.++.--....+.+..+.+.+++|+|+||.+.++..+|+..|.+||+|.+|+|+  |.|+||.|+-.++|..||+
T Consensus        53 irNLhgYtLhg~nInVeaSksKsk~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv--kdy~fvh~d~~eda~~air  130 (346)
T KOG0109|consen   53 IRNLHGYTLHGVNINVEASKSKSKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV--KDYAFVHFDRAEDAVEAIR  130 (346)
T ss_pred             HhhcccceecceEEEEEeccccCCCccccccCCCCccccCHHHhhhhcccCCceeeeee--cceeEEEEeeccchHHHHh
Confidence            33344444443322222233345567899999999999999999999999999999997  6799999999999999999


Q ss_pred             HhCCccccCceEEEEeccc
Q psy93           168 KLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       168 ~l~g~~l~g~~l~V~~a~~  186 (503)
                      .||++++.|++|+|.++..
T Consensus       131 ~l~~~~~~gk~m~vq~sts  149 (346)
T KOG0109|consen  131 GLDNTEFQGKRMHVQLSTS  149 (346)
T ss_pred             cccccccccceeeeeeecc
Confidence            9999999999999998753

>KOG0149|consensus

Probab=98.99  E-value=5.6e-10  Score=105.08  Aligned_cols=62  Identities=35%  Similarity=0.415  Sum_probs=58.8

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhh
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCA  249 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln  249 (503)
                      ++|||++|++.+..+.|++.|++||+|+++.|+.| .+++||||+||+|.+.++|.+|+..-|
T Consensus        13 TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~   75 (247)
T KOG0149|consen   13 TKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN   75 (247)
T ss_pred             EEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC
Confidence            68999999999999999999999999999999999 699999999999999999999998754

>KOG0120|consensus

Probab=98.98  E-value=9.5e-10  Score=115.64  Aligned_cols=153  Identities=28%  Similarity=0.399  Sum_probs=130.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccC-----------C-CeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceE
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPY-----------G-ETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSL  179 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~-----------G-~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l  179 (503)
                      ....+||+++|+.++++.+..+|..-           | .|..|.+...+.||||+|.+.++|..|+. +++..+.|.++
T Consensus       174 q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~~nfa~ie~~s~~~at~~~~-~~~~~f~g~~~  252 (500)
T KOG0120|consen  174 QARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLEKNFAFIEFRSISEATEAMA-LDGIIFEGRPL  252 (500)
T ss_pred             hhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecccccceeEEecCCCchhhhhc-ccchhhCCCCc
Confidence            45679999999999999999998654           3 58889999999999999999999998875 78888888888


Q ss_pred             EEEecc-----------------------------cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCcee
Q psy93           180 KIRFAP-----------------------------INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKC  229 (503)
Q Consensus       180 ~V~~a~-----------------------------~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg  229 (503)
                      ++....                             ....++|++||..++++.+.++...||.+....++.| .++.+++
T Consensus       253 ~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg  332 (500)
T KOG0120|consen  253 KIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKG  332 (500)
T ss_pred             eecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccc
Confidence            774321                             1357999999999999999999999999999999988 5789999


Q ss_pred             EEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCc
Q psy93           230 EGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLEL  269 (503)
Q Consensus       230 ~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~  269 (503)
                      |||++|-+......|+..|| ++.+   ..+.++|..+-.
T Consensus       333 ~af~ey~dpsvtd~A~agLn-Gm~l---gd~~lvvq~A~~  368 (500)
T KOG0120|consen  333 FAFCEYCDPSVTDQAIAGLN-GMQL---GDKKLVVQRAIV  368 (500)
T ss_pred             eeeeeeeCCcchhhhhcccc-hhhh---cCceeEeehhhc
Confidence            99999999999999999997 6655   356777766543

>KOG0125|consensus

Probab=98.97  E-value=9.8e-10  Score=107.68  Aligned_cols=97  Identities=22%  Similarity=0.281  Sum_probs=81.9

Q ss_pred             hCCccccCceEEEEecc------cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHH
Q psy93           169 LDGHVLKGRSLKIRFAP------INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAA  242 (503)
Q Consensus       169 l~g~~l~g~~l~V~~a~------~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~  242 (503)
                      -++....|.++.+..+.      ..+.|+|+|||....+-||+.+|.+||+|.+|.|+.++.| ||||+||+|++.++|.
T Consensus        72 ~~~~~t~g~~~~~~~st~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERG-SKGFGFVTmen~~dad  150 (376)
T KOG0125|consen   72 SNGAPTDGQPIQTQPSTNSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERG-SKGFGFVTMENPADAD  150 (376)
T ss_pred             cCCCCCCCCccccCCCCcCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCC-CCccceEEecChhhHH
Confidence            34556667777665543      2568999999999999999999999999999999999766 5999999999999999


Q ss_pred             HHHHHhhCCeeeecCCCCeEEeecCCcc
Q psy93           243 QALRRCAEGCFFLTQSLRPVIVEPLELT  270 (503)
Q Consensus       243 kAl~~ln~g~~~~~~~~rpl~V~~~~~~  270 (503)
                      +|..+|+ +..+   .+|.|.|..+...
T Consensus       151 RARa~LH-gt~V---EGRkIEVn~ATar  174 (376)
T KOG0125|consen  151 RARAELH-GTVV---EGRKIEVNNATAR  174 (376)
T ss_pred             HHHHHhh-ccee---eceEEEEeccchh
Confidence            9999997 6666   5899999877654

>KOG0415|consensus

Probab=98.95  E-value=4.2e-09  Score=103.99  Aligned_cols=87  Identities=26%  Similarity=0.332  Sum_probs=77.1

Q ss_pred             EEEecccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCC
Q psy93           180 KIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQS  258 (503)
Q Consensus       180 ~V~~a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~  258 (503)
                      ....++|.+.|||-.|.+-+++++|.-+|+.||+|.+|.|++| .+|.+-.||||+|++.+++.+|.-+|+ ..++   .
T Consensus       232 dAd~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMd-NvLI---D  307 (479)
T KOG0415|consen  232 DADVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMD-NVLI---D  307 (479)
T ss_pred             ccccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhc-ceee---c
Confidence            3456688999999999999999999999999999999999999 799999999999999999999999996 5555   6


Q ss_pred             CCeEEeecCCcc
Q psy93           259 LRPVIVEPLELT  270 (503)
Q Consensus       259 ~rpl~V~~~~~~  270 (503)
                      .+-|+|.+....
T Consensus       308 DrRIHVDFSQSV  319 (479)
T KOG0415|consen  308 DRRIHVDFSQSV  319 (479)
T ss_pred             cceEEeehhhhh
Confidence            888888775443

>KOG4454|consensus

Probab=98.94  E-value=1.9e-10  Score=106.86  Aligned_cols=133  Identities=23%  Similarity=0.250  Sum_probs=113.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKE----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINA  188 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~~  188 (503)
                      ..||||.||...|+++.|.++|-+.|+|..|.|.+.    ..||||.|.+..++.-|++.+||..+.+.+|.|.+-.-+.
T Consensus         9 drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~G~s   88 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCGNS   88 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchhccchhhcccccCCC
Confidence            357999999999999999999999999999999753    2399999999999999999999999999999886532211


Q ss_pred             ceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHh
Q psy93           189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRC  248 (503)
Q Consensus       189 ~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~l  248 (503)
                      .   .-|...++.+.+...|+.-+.+..+.+.++.++.++.++||++-...+.-.++...
T Consensus        89 h---apld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y  145 (267)
T KOG4454|consen   89 H---APLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLY  145 (267)
T ss_pred             c---chhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhhh
Confidence            0   11667789999999999999999999999888888999999987777766676654

>KOG0108|consensus

Probab=98.91  E-value=2.3e-09  Score=112.14  Aligned_cols=73  Identities=25%  Similarity=0.482  Sum_probs=69.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      +.|||+|||+++++++|..+|+..|.|.+++++-      .+|||||+|.+.++|.+|++.||+.++.|++|+|.|+..
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~   97 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASN   97 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeecccc
Confidence            6899999999999999999999999999999963      489999999999999999999999999999999999864

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.91  E-value=4.9e-09  Score=100.32  Aligned_cols=77  Identities=22%  Similarity=0.224  Sum_probs=66.2

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      ..+|+|+||++.+|+++|+++|+.||+|.+|.|+.|  +..++||||+|.+.++|..|+ .|+ +..+   .+++|.|.+
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D--~et~gfAfVtF~d~~aaetAl-lLn-Ga~l---~d~~I~It~   77 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS--GEYACTAYVTFKDAYALETAV-LLS-GATI---VDQRVCITR   77 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC--CCcceEEEEEECCHHHHHHHH-hcC-CCee---CCceEEEEe
Confidence            468999999999999999999999999999999988  345689999999999999999 576 6555   477888887


Q ss_pred             CCcc
Q psy93           267 LELT  270 (503)
Q Consensus       267 ~~~~  270 (503)
                      ....
T Consensus        78 ~~~y   81 (243)
T PLN03121         78 WGQY   81 (243)
T ss_pred             Cccc
Confidence            6643

>smart00362 RRM_2 RNA recognition motif

Probab=98.90  E-value=7.5e-09  Score=79.78  Aligned_cols=71  Identities=35%  Similarity=0.415  Sum_probs=61.7

Q ss_pred             ceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       189 ~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +|+|.|||..++.++|.++|..||.|..+.+..+. +.++++|||+|.+.++|..|+..++ +..+   .++++.|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~-~~~~~~~~v~f~~~~~a~~a~~~~~-~~~~---~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT-GKSKGFAFVEFESEEDAEKAIEALN-GTKL---GGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-CCCCceEEEEeCCHHHHHHHHHHhC-CcEE---CCEEEee
Confidence            58999999999999999999999999999988776 6778999999999999999999987 4444   4566554

>PF08075 NOPS: NOPS (NUC059) domain; InterPro: IPR012975 This domain is found C-terminal to 1 or 2 IPR000504 from INTERPRO domains [] in NONA and PSP1 proteins

Probab=98.88  E-value=6.9e-10  Score=79.99  Aligned_cols=52  Identities=62%  Similarity=1.117  Sum_probs=38.0

Q ss_pred             eEEeecCCccccccCCcccccCCCCchhhhhhccCcccCCCCCcchhhhhhhH
Q psy93           261 PVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWK  313 (503)
Q Consensus       261 pl~V~~~~~~~~~~~~~~k~i~k~~~~~~kere~~~rf~~~g~~e~e~~~r~k  313 (503)
                      ||+|++++..++.|+++++ +.+++++|.++++.+|||+++++||++|++|||
T Consensus         1 PvvVEp~e~~DdedGlpEk-l~~k~~~y~kERe~~PRFA~pgsfE~eyg~RWK   52 (52)
T PF08075_consen    1 PVVVEPLEQLDDEDGLPEK-LIKKNPQYHKEREQGPRFAQPGSFEFEYGMRWK   52 (52)
T ss_dssp             B-EEEE---EESSS---GG-GS--SHHHHHHCTS-SEE--TTSHHHHHHHHHH
T ss_pred             CceeccCccccccccchHH-HHHHhHHHHHhhhcCCCcCCCCCcchhhccccC
Confidence            6899999999999999999 556899999999999999999999999999997

; PDB: 3SDE_B.

>KOG0107|consensus

Probab=98.88  E-value=3e-09  Score=95.87  Aligned_cols=77  Identities=27%  Similarity=0.208  Sum_probs=66.5

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ..++|||+||+..+++.+|..+|..||.|..|.|...+    .+||||+|+++.+|..|+..|+ +..+   ++.-+.|+
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP----PGfAFVEFed~RDA~DAvr~LD-G~~~---cG~r~rVE   80 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP----PGFAFVEFEDPRDAEDAVRYLD-GKDI---CGSRIRVE   80 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC----CCceEEeccCcccHHHHHhhcC-Cccc---cCceEEEE
Confidence            36789999999999999999999999999999887753    6799999999999999999997 5544   57778887


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      ...-.
T Consensus        81 ~S~G~   85 (195)
T KOG0107|consen   81 LSTGR   85 (195)
T ss_pred             eecCC
Confidence            75443

>KOG0131|consensus

Probab=98.87  E-value=1.9e-09  Score=97.73  Aligned_cols=116  Identities=17%  Similarity=0.131  Sum_probs=90.6

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      +...+|||+||++.++++.|+++|-+.|.|.++.+.+| -+....|||||+|.+.++|.-|++.|| ...+   -++||.
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln-~VkL---YgrpIr   82 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILN-MVKL---YGRPIR   82 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHH-HHHh---cCceeE
Confidence            34679999999999999999999999999999999998 466789999999999999999999998 5444   699999


Q ss_pred             eecCCccccccCCcccccCCCCchhhhhhccCcccCCCCCc
Q psy93           264 VEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSF  304 (503)
Q Consensus       264 V~~~~~~~~~~~~~~k~i~k~~~~~~kere~~~rf~~~g~~  304 (503)
                      |..+...........++.++++.....+..+-..|+.+|.+
T Consensus        83 v~kas~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l  123 (203)
T KOG0131|consen   83 VNKASAHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVL  123 (203)
T ss_pred             EEecccccccccccccccccccCcchhHHHHHHHHHhcccc
Confidence            98887443333344455566665555555555555555443

>KOG0153|consensus

Probab=98.87  E-value=9.1e-09  Score=101.73  Aligned_cols=75  Identities=29%  Similarity=0.496  Sum_probs=68.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHH-hCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAK-LDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~-l~g~~l~g~~l~V~~a~~  186 (503)
                      ..++|||++|-..+++.+|+++|.+||+|.+|.+...+++|||+|.+.++|+.|... ++...|.|+.|+|.|..+
T Consensus       227 ~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  227 SIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             ceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            467899999988999999999999999999999999999999999999999997765 455588999999999977

>KOG0126|consensus

Probab=98.87  E-value=3.1e-10  Score=102.66  Aligned_cols=99  Identities=23%  Similarity=0.248  Sum_probs=79.9

Q ss_pred             HHHHHhCCcccc-CceEEEEec---ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCH
Q psy93           164 KAKAKLDGHVLK-GRSLKIRFA---PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARK  238 (503)
Q Consensus       164 ~Ai~~l~g~~l~-g~~l~V~~a---~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~  238 (503)
                      +-|..||..++. |-.-.+.|.   +.+.-|||++||..+|+.+|.-+|++||+|+.|.+++| .||+|+||||+.|++.
T Consensus         8 k~i~~lne~Elq~g~~~~~SWH~~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQ   87 (219)
T KOG0126|consen    8 KNIQKLNERELQLGIADKKSWHQEYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQ   87 (219)
T ss_pred             HHHHHhhHHhhccccccccchhhhcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCc
Confidence            345556655544 222244444   34678999999999999999999999999999999999 6999999999999999


Q ss_pred             HHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           239 PAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       239 e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      .+..-|+..|| +..++   +|.|.|..
T Consensus        88 RSTILAVDN~N-Giki~---gRtirVDH  111 (219)
T KOG0126|consen   88 RSTILAVDNLN-GIKIL---GRTIRVDH  111 (219)
T ss_pred             cceEEEEeccC-Cceec---ceeEEeee
Confidence            99999999997 76663   66666654

>KOG4207|consensus

Probab=98.84  E-value=3.2e-09  Score=97.97  Aligned_cols=80  Identities=24%  Similarity=0.268  Sum_probs=71.8

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ...|.|.||..-++.++|..+|++||.|.+|.|..| -+..+++||||.|.+..+|+.|+++|+ +.++   +++.|.|.
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damD-G~~l---dgRelrVq   88 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMD-GAVL---DGRELRVQ   88 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhc-ceee---ccceeeeh
Confidence            357899999999999999999999999999999999 588899999999999999999999996 7777   68888887


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      .+..-
T Consensus        89 ~aryg   93 (256)
T KOG4207|consen   89 MARYG   93 (256)
T ss_pred             hhhcC
Confidence            76543

>KOG0113|consensus

Probab=98.83  E-value=1e-08  Score=99.55  Aligned_cols=79  Identities=20%  Similarity=0.273  Sum_probs=72.0

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      +|-++|||.-|+.++++..|+..|+.||.|..|.|+.| .+++++|||||+|++..+...|.+..+ +..+   +++-|+
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~ad-G~~I---dgrri~  174 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDAD-GIKI---DGRRIL  174 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhcc-Ccee---cCcEEE
Confidence            45689999999999999999999999999999999999 699999999999999999999999986 6666   688888


Q ss_pred             eecC
Q psy93           264 VEPL  267 (503)
Q Consensus       264 V~~~  267 (503)
                      |..-
T Consensus       175 VDvE  178 (335)
T KOG0113|consen  175 VDVE  178 (335)
T ss_pred             EEec
Confidence            8763

>KOG0146|consensus

Probab=98.82  E-value=5.6e-09  Score=99.67  Aligned_cols=96  Identities=22%  Similarity=0.306  Sum_probs=83.4

Q ss_pred             CceEEEEeccc------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhh
Q psy93           176 GRSLKIRFAPI------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCA  249 (503)
Q Consensus       176 g~~l~V~~a~~------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln  249 (503)
                      .++|.|+.++.      .++|||+-|...-+|++++.+|..||.|.+|.+++..++.+||++||.|.+..+|..||..|+
T Consensus         2 nrpiqvkpadsesrg~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLH   81 (371)
T KOG0146|consen    2 NRPIQVKPADSESRGGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALH   81 (371)
T ss_pred             CCCccccccccccCCccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhc
Confidence            46788877753      578999999999999999999999999999999999999999999999999999999999996


Q ss_pred             CCeeeecCCCCeEEeecCCcccc
Q psy93           250 EGCFFLTQSLRPVIVEPLELTDE  272 (503)
Q Consensus       250 ~g~~~~~~~~rpl~V~~~~~~~~  272 (503)
                       +...+..-...++|++++..++
T Consensus        82 -gSqTmpGASSSLVVK~ADTdkE  103 (371)
T KOG0146|consen   82 -GSQTMPGASSSLVVKFADTDKE  103 (371)
T ss_pred             -ccccCCCCccceEEEeccchHH
Confidence             6555555566788888776654

>KOG0114|consensus

Probab=98.81  E-value=1.4e-08  Score=84.00  Aligned_cols=79  Identities=20%  Similarity=0.233  Sum_probs=66.9

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      +..|||.|||.++|.+++.++|.+||.|..+.|-..+  ..+|.|||.|++..+|.+|+.+|+ +..+   +++.+.|-.
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k--~TrGTAFVVYedi~dAk~A~dhls-g~n~---~~ryl~vly   91 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK--ETRGTAFVVYEDIFDAKKACDHLS-GYNV---DNRYLVVLY   91 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecCcc--CcCceEEEEehHhhhHHHHHHHhc-cccc---CCceEEEEe
Confidence            5679999999999999999999999999999886552  348899999999999999999997 6555   688888866


Q ss_pred             CCccc
Q psy93           267 LELTD  271 (503)
Q Consensus       267 ~~~~~  271 (503)
                      ..+.+
T Consensus        92 yq~~~   96 (124)
T KOG0114|consen   92 YQPED   96 (124)
T ss_pred             cCHHH
Confidence            55443

>PLN03213 repressor of silencing 3; Provisional

Probab=98.80  E-value=1.2e-08  Score=104.60  Aligned_cols=76  Identities=14%  Similarity=0.288  Sum_probs=67.5

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCH--HHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARK--PAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~--e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ..+|||+||++.+++++|..+|+.||.|..|.|++. +|  +|||||+|.+.  .++.+||..|| ++.+   .++.|.|
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE-TG--RGFAFVEMssdddaEeeKAISaLN-GAEW---KGR~LKV   82 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT-KG--RSFAYIDFSPSSTNSLTKLFSTYN-GCVW---KGGRLRL   82 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc-cC--CceEEEEecCCcHHHHHHHHHHhc-CCee---cCceeEE
Confidence            467999999999999999999999999999999944 55  89999999987  78999999997 7766   6899999


Q ss_pred             ecCCc
Q psy93           265 EPLEL  269 (503)
Q Consensus       265 ~~~~~  269 (503)
                      ..+.+
T Consensus        83 NKAKP   87 (759)
T PLN03213         83 EKAKE   87 (759)
T ss_pred             eeccH
Confidence            87655

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

Probab=98.79  E-value=4e-08  Score=76.06  Aligned_cols=73  Identities=34%  Similarity=0.402  Sum_probs=63.8

Q ss_pred             ceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       189 ~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      +|+|.+||..+++++|.++|..||.|..+.+..+....++++|||+|.+.++|..|+..++ +..+   .++.+.|.
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~-~~~~---~~~~~~v~   73 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALN-GKEL---GGRPLRVE   73 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhC-CCeE---CCeEEEEe
Confidence            4789999999999999999999999999999988666778999999999999999999987 5444   46666664

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>smart00360 RRM RNA recognition motif

Probab=98.78  E-value=3.4e-08  Score=75.74  Aligned_cols=69  Identities=38%  Similarity=0.451  Sum_probs=59.7

Q ss_pred             ccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           192 VKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       192 V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      |.|||..+++++|+++|+.||.|..+.+..+. ++.++++|||+|.+.++|..|+..++ +..+   .++.+.|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~-~~~~---~~~~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALN-GKEL---DGRPLKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcC-CCee---CCcEEEe
Confidence            67999999999999999999999999998875 57889999999999999999999997 5544   4555554

>KOG0130|consensus

Probab=98.77  E-value=8.4e-09  Score=89.09  Aligned_cols=77  Identities=23%  Similarity=0.239  Sum_probs=69.1

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ...|||+++.+..++++|.+.|..||+|.++.+..| .+|-.+||++|+|++.+.|++|+..+| +..++   +..|.|.
T Consensus        72 GwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~N-g~~ll---~q~v~VD  147 (170)
T KOG0130|consen   72 GWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALN-GAELL---GQNVSVD  147 (170)
T ss_pred             eEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhcc-chhhh---CCceeEE
Confidence            567999999999999999999999999999999888 689999999999999999999999998 55553   6677777


Q ss_pred             cC
Q psy93           266 PL  267 (503)
Q Consensus       266 ~~  267 (503)
                      |.
T Consensus       148 w~  149 (170)
T KOG0130|consen  148 WC  149 (170)
T ss_pred             EE
Confidence            74

>KOG0111|consensus

Probab=98.73  E-value=8.7e-09  Score=95.84  Aligned_cols=84  Identities=27%  Similarity=0.297  Sum_probs=75.4

Q ss_pred             cccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeE
Q psy93           184 APINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPV  262 (503)
Q Consensus       184 a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl  262 (503)
                      +..+++|||++|...+++..|...|-.||.|..|.++.| ++.++++|+||+|.-.++|..||..|| ...+   .+|.|
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMn-esEL---~Grti   82 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMN-ESEL---FGRTI   82 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCc-hhhh---cceeE
Confidence            455789999999999999999999999999999999998 788999999999999999999999998 4444   49999


Q ss_pred             EeecCCccc
Q psy93           263 IVEPLELTD  271 (503)
Q Consensus       263 ~V~~~~~~~  271 (503)
                      .|..+.+..
T Consensus        83 rVN~AkP~k   91 (298)
T KOG0111|consen   83 RVNLAKPEK   91 (298)
T ss_pred             EEeecCCcc
Confidence            999876653

>KOG0415|consensus

Probab=98.72  E-value=1.6e-08  Score=99.96  Aligned_cols=79  Identities=16%  Similarity=0.386  Sum_probs=71.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCC------CceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEK------MFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~k------g~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ++.+.|||..|.+-+|.++|.-+|+.||+|.+|.|++++      .||||+|++.+++++|.-.|++..|+.+.|.|.|+
T Consensus       237 PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFS  316 (479)
T KOG0415|consen  237 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFS  316 (479)
T ss_pred             CCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehh
Confidence            355689999999999999999999999999999998763      59999999999999999999999999999999998


Q ss_pred             ccccc
Q psy93           185 PINAA  189 (503)
Q Consensus       185 ~~~~~  189 (503)
                      .+-.+
T Consensus       317 QSVsk  321 (479)
T KOG0415|consen  317 QSVSK  321 (479)
T ss_pred             hhhhh
Confidence            76444

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

Probab=98.69  E-value=5.4e-08  Score=94.80  Aligned_cols=78  Identities=32%  Similarity=0.413  Sum_probs=71.9

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ..+|||+|||..+++++|.++|..||.|..+.+..+ .++.+++||||+|.+.++|..|+..++ +..+   .++++.|.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~-~~~~---~~~~~~v~  190 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELN-GKEL---EGRPLRVQ  190 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcC-CCeE---CCceeEee
Confidence            489999999999999999999999999999999998 589999999999999999999999997 5555   68999998


Q ss_pred             cCC
Q psy93           266 PLE  268 (503)
Q Consensus       266 ~~~  268 (503)
                      +..
T Consensus       191 ~~~  193 (306)
T COG0724         191 KAQ  193 (306)
T ss_pred             ccc
Confidence            864

>KOG0533|consensus

Probab=98.69  E-value=2.2e-07  Score=90.05  Aligned_cols=76  Identities=21%  Similarity=0.423  Sum_probs=67.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe-----cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFIN-----KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~-----~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +..++|+|.|||+.|+++||++||..||.+..+.|.     ++.|.|-|.|...+||..||+.++++.++|++|.+....
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIIS  160 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEec
Confidence            345789999999999999999999999988888774     346899999999999999999999999999999988765


Q ss_pred             c
Q psy93           186 I  186 (503)
Q Consensus       186 ~  186 (503)
                      +
T Consensus       161 ~  161 (243)
T KOG0533|consen  161 S  161 (243)
T ss_pred             C
Confidence            4

>smart00361 RRM_1 RNA recognition motif

Probab=98.67  E-value=4.9e-08  Score=76.90  Aligned_cols=55  Identities=24%  Similarity=0.430  Sum_probs=48.6

Q ss_pred             HHHHHHhhc----cCCCeEEEE-E-e-------cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEE
Q psy93           127 ENDIIELFK----PYGETQELF-I-N-------KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKI  181 (503)
Q Consensus       127 e~~L~~~F~----~~G~V~~v~-i-~-------~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V  181 (503)
                      +++|+++|+    .||.|.+|. | +       .++|||||+|.+.++|.+|+..|||..+.|+.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578889998    999999885 3 2       23789999999999999999999999999999986

>KOG0112|consensus

Probab=98.66  E-value=1.3e-08  Score=111.04  Aligned_cols=153  Identities=20%  Similarity=0.275  Sum_probs=126.0

Q ss_pred             cCcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEE
Q psy93           108 IKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIR  182 (503)
Q Consensus       108 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~  182 (503)
                      .....+.+||++||+..+++.+|+..|..+|.|.+|.|...     ..||||.|.+...+-.|+..+.+..|..-.+++.
T Consensus       367 DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~g  446 (975)
T KOG0112|consen  367 DDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIG  446 (975)
T ss_pred             cchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccccc
Confidence            34445789999999999999999999999999999988543     3599999999999999999999988875555555


Q ss_pred             ec----ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCC
Q psy93           183 FA----PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQS  258 (503)
Q Consensus       183 ~a----~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~  258 (503)
                      +.    .+++.++|+.|...+....|...|..||.|..|.+-..     ..|++|.|++...|+.|+..|. +.. ++..
T Consensus       447 lG~~kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg-----q~yayi~yes~~~aq~a~~~~r-gap-~G~P  519 (975)
T KOG0112|consen  447 LGQPKSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG-----QPYAYIQYESPPAAQAATHDMR-GAP-LGGP  519 (975)
T ss_pred             ccccccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC-----CcceeeecccCccchhhHHHHh-cCc-CCCC
Confidence            44    46788999999999999999999999999998766443     4599999999999999999985 333 3445


Q ss_pred             CCeEEeecC
Q psy93           259 LRPVIVEPL  267 (503)
Q Consensus       259 ~rpl~V~~~  267 (503)
                      .+.+.|.++
T Consensus       520 ~~r~rvdla  528 (975)
T KOG0112|consen  520 PRRLRVDLA  528 (975)
T ss_pred             Ccccccccc
Confidence            555666554

>KOG1365|consensus

Probab=98.63  E-value=5.5e-08  Score=97.14  Aligned_cols=150  Identities=17%  Similarity=0.220  Sum_probs=108.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCC----CeEEEEEe-----cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEE---
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYG----ETQELFIN-----KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKI---  181 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G----~V~~v~i~-----~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V---  181 (503)
                      -.|-+.+||+++++.++.+||..-=    -+..|.++     +..|-|||.|+.+++|+.|+.. |...|.-+-|.+   
T Consensus       162 vivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElFRS  240 (508)
T KOG1365|consen  162 VIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELFRS  240 (508)
T ss_pred             eEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHHHH
Confidence            3577889999999999999996322    22333332     2368999999999999999874 222222222211   


Q ss_pred             ----------------------------------EecccccceeccCcccccCHHHHHHHhccCCCe-ee--eEEEeCCC
Q psy93           182 ----------------------------------RFAPINAAIKVKNLTSCVTNELLELAFGVFGDI-ER--AIVIVDER  224 (503)
Q Consensus       182 ----------------------------------~~a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V-~~--~~v~~d~~  224 (503)
                                                        -...++.+|.+.+||...+.++|.++|..|-.- ..  +.++.+..
T Consensus       241 TaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~q  320 (508)
T KOG1365|consen  241 TAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQ  320 (508)
T ss_pred             hHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCC
Confidence                                              111235689999999999999999999999753 33  67778888


Q ss_pred             CCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCC
Q psy93           225 GNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLE  268 (503)
Q Consensus       225 g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~  268 (503)
                      |.+.|.|||+|.+.+.|..|..+++ +++.   ..|-|.|-+..
T Consensus       321 GrPSGeAFIqm~nae~a~aaaqk~h-k~~m---k~RYiEvfp~S  360 (508)
T KOG1365|consen  321 GRPSGEAFIQMRNAERARAAAQKCH-KKLM---KSRYIEVFPCS  360 (508)
T ss_pred             CCcChhhhhhhhhhHHHHHHHHHHH-Hhhc---ccceEEEeecc
Confidence            9999999999999999999999986 4433   35555555543

>KOG0108|consensus

Probab=98.60  E-value=7.7e-08  Score=100.81  Aligned_cols=81  Identities=25%  Similarity=0.284  Sum_probs=74.9

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      ..|||+|+|.++++++|.++|+..|.|.+++++.| ++|+++||+||+|.+.++|..|+..|| +..+   .++++.|.+
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lN-g~~~---~gr~l~v~~   94 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLN-GAEF---NGRKLRVNY   94 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcC-Cccc---CCceEEeec
Confidence            78999999999999999999999999999999999 699999999999999999999999998 5555   699999999


Q ss_pred             CCcccc
Q psy93           267 LELTDE  272 (503)
Q Consensus       267 ~~~~~~  272 (503)
                      +...+.
T Consensus        95 ~~~~~~  100 (435)
T KOG0108|consen   95 ASNRKN  100 (435)
T ss_pred             ccccch
Confidence            877654

>KOG0128|consensus

Probab=98.59  E-value=6e-09  Score=113.28  Aligned_cols=127  Identities=16%  Similarity=0.235  Sum_probs=112.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe------cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFIN------KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~------~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..+++||+||++.+.+.+|...|..++.|..+.+.      +-+|+|||.|..+++|.+||...+.+.+.          
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g----------  735 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG----------  735 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh----------
Confidence            45789999999999999999999999988776653      23799999999999999999865555444          


Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhh
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCA  249 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln  249 (503)
                       +..|+|.|+|+.-|.+.|+.+|+.+|.+.+..++....|+++|.++|.|.+..++..++...+
T Consensus       736 -K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d  798 (881)
T KOG0128|consen  736 -KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVD  798 (881)
T ss_pred             -hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccch
Confidence             457899999999999999999999999999998888899999999999999999999988765

>PF13893 RRM_5: RNA recognition motif

Probab=98.55  E-value=2.3e-07  Score=69.50  Aligned_cols=56  Identities=27%  Similarity=0.393  Sum_probs=47.5

Q ss_pred             HHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecC
Q psy93           204 LELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPL  267 (503)
Q Consensus       204 L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~  267 (503)
                      |.++|++||+|..+.+..+.    +++|||+|.+.++|.+|+..|| +..+   .+++|.|.++
T Consensus         1 L~~~f~~fG~V~~i~~~~~~----~~~a~V~f~~~~~A~~a~~~l~-~~~~---~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK----RGFAFVEFASVEDAQKAIEQLN-GRQF---NGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS----TTEEEEEESSHHHHHHHHHHHT-TSEE---TTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhC-CCEE---CCcEEEEEEC
Confidence            67899999999999887763    4799999999999999999997 6655   6889998763

(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 ....

>smart00361 RRM_1 RNA recognition motif

Probab=98.53  E-value=3.4e-07  Score=72.06  Aligned_cols=60  Identities=25%  Similarity=0.423  Sum_probs=49.2

Q ss_pred             HHHHHHHhc----cCCCeeeeE-EEeC-CC--CCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           201 NELLELAFG----VFGDIERAI-VIVD-ER--GNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       201 ee~L~~~Fs----~~G~V~~~~-v~~d-~~--g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +++|.++|+    .||.|.++. |+.+ .+  +.++||+||+|.+.++|.+|+..|| +..+   .+++|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~-g~~~---~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLN-GRYF---DGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhC-CCEE---CCEEEEe
Confidence            567888888    999999995 5555 34  7899999999999999999999998 5555   4777655

>KOG4211|consensus

Probab=98.49  E-value=7.8e-07  Score=91.94  Aligned_cols=134  Identities=18%  Similarity=0.247  Sum_probs=105.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEE-EEEe-----cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQE-LFIN-----KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~-v~i~-----~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +...|-+.+||+.||++||.+||+..-.|.. |.++     +..+-|||+|++.++|++|+.. |...|.-+-|.|-.+.
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRSS  180 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehhH
Confidence            3457999999999999999999998866555 3333     3467899999999999999874 4444544544442210


Q ss_pred             --------------------------------------------------------------------------------
Q psy93           186 --------------------------------------------------------------------------------  185 (503)
Q Consensus       186 --------------------------------------------------------------------------------  185 (503)
                                                                                                      
T Consensus       181 ~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~gs~~~~~~~~~~  260 (510)
T KOG4211|consen  181 RAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFGSYGGGRDPNYP  260 (510)
T ss_pred             HHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCccccccccccccccccccccC
Confidence                                                                                            


Q ss_pred             ------------------c-ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHH
Q psy93           186 ------------------I-NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALR  246 (503)
Q Consensus       186 ------------------~-~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~  246 (503)
                                        + ...++...||...++.+|..+|+..-.+ .+.|...++++.++.|+|+|.|.++|..|+.
T Consensus       261 ~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~-~v~i~ig~dGr~TGEAdveF~t~edav~Ams  339 (510)
T KOG4211|consen  261 VSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPY-RVHIEIGPDGRATGEADVEFATGEDAVGAMG  339 (510)
T ss_pred             CCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCce-eEEEEeCCCCccCCcceeecccchhhHhhhc
Confidence                              0 1356677899999999999999887655 7788888899999999999999999999997


Q ss_pred             H
Q psy93           247 R  247 (503)
Q Consensus       247 ~  247 (503)
                      +
T Consensus       340 k  340 (510)
T KOG4211|consen  340 K  340 (510)
T ss_pred             c
Confidence            6

>KOG0151|consensus

Probab=98.48  E-value=2.2e-07  Score=99.24  Aligned_cols=74  Identities=23%  Similarity=0.483  Sum_probs=68.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe---------cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEE
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFIN---------KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIR  182 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~---------~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~  182 (503)
                      .+|+|||+||++.++++.|...|..||+|.+|+|+         +.+.|+||-|-+..||++|++.|++..+....|++-
T Consensus       173 ~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~g  252 (877)
T KOG0151|consen  173 QTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLG  252 (877)
T ss_pred             cccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeec
Confidence            46789999999999999999999999999999996         236799999999999999999999999999999999


Q ss_pred             ecc
Q psy93           183 FAP  185 (503)
Q Consensus       183 ~a~  185 (503)
                      |++
T Consensus       253 Wgk  255 (877)
T KOG0151|consen  253 WGK  255 (877)
T ss_pred             ccc
Confidence            983

>KOG0226|consensus

Probab=98.48  E-value=7.8e-08  Score=91.55  Aligned_cols=152  Identities=20%  Similarity=0.312  Sum_probs=117.3

Q ss_pred             EEEEcCCCCCCCHHH-H--HHhhccCCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccccCceEEE-----
Q psy93           115 RLYLGNIGGDITEND-I--IELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKI-----  181 (503)
Q Consensus       115 ~l~V~nLp~~~te~~-L--~~~F~~~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V-----  181 (503)
                      ..+++++-.++..+- |  ...|+.|-.+...++.++     .+++|+.|.....-.++-..-+++.+.-.+|++     
T Consensus        98 ~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gts  177 (290)
T KOG0226|consen   98 RPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTS  177 (290)
T ss_pred             cccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeeccccc
Confidence            356777766665544 3  567777766655555433     579999999877777776665666666665554     


Q ss_pred             -------EecccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCee
Q psy93           182 -------RFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCF  253 (503)
Q Consensus       182 -------~~a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~  253 (503)
                             +|......||.+.|...++++.|...|.+|-.....++++| .++++++|+||.|.+..++..|+..|+ +.+
T Consensus       178 wedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~-gky  256 (290)
T KOG0226|consen  178 WEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMN-GKY  256 (290)
T ss_pred             cCCcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhc-ccc
Confidence                   34445678999999999999999999999999999999998 599999999999999999999999997 777


Q ss_pred             eecCCCCeEEeecCCcc
Q psy93           254 FLTQSLRPVIVEPLELT  270 (503)
Q Consensus       254 ~~~~~~rpl~V~~~~~~  270 (503)
                      +   ..+||.+.-..++
T Consensus       257 V---gsrpiklRkS~wk  270 (290)
T KOG0226|consen  257 V---GSRPIKLRKSEWK  270 (290)
T ss_pred             c---ccchhHhhhhhHH
Confidence            6   5777766555444

>KOG0105|consensus

Probab=98.44  E-value=2.5e-07  Score=84.19  Aligned_cols=78  Identities=21%  Similarity=0.114  Sum_probs=64.8

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ..+.|||.|||.++.+.+|.++|.+||.|..|.+....  ...+||||+|+++.+|..||..-+ +.-+   .++.|.|+
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~--g~ppfafVeFEd~RDAeDAiygRd-GYdy---dg~rLRVE   78 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP--GPPPFAFVEFEDPRDAEDAIYGRD-GYDY---DGCRLRVE   78 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC--CCCCeeEEEecCccchhhhhhccc-cccc---CcceEEEE
Confidence            35789999999999999999999999999998775432  235699999999999999998875 5444   67888888


Q ss_pred             cCCc
Q psy93           266 PLEL  269 (503)
Q Consensus       266 ~~~~  269 (503)
                      ++-.
T Consensus        79 fprg   82 (241)
T KOG0105|consen   79 FPRG   82 (241)
T ss_pred             eccC
Confidence            7644

>KOG4210|consensus

Probab=98.43  E-value=1.6e-07  Score=93.92  Aligned_cols=154  Identities=20%  Similarity=0.177  Sum_probs=118.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe------cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFIN------KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~------~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..+++||+++...+.+.++..+|..+|.+..+.+.      .++++++|.|+..+.+..|+...-...+.+..+...+..
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            46789999999999999999999999977666553      458999999999999999987533334444433222211


Q ss_pred             ----------------ccccee-ccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHH
Q psy93           186 ----------------INAAIK-VKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRR  247 (503)
Q Consensus       186 ----------------~~~~L~-V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~  247 (503)
                                      +..+++ |.+|+..++.++|+..|..+|.|..+.+..+ .++.+++|++|.|.+...+..++..
T Consensus       167 ~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~  246 (285)
T KOG4210|consen  167 RRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND  246 (285)
T ss_pred             cccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc
Confidence                            123444 9999999999999999999999999999887 6889999999999999999999885


Q ss_pred             hhCCeeeecCCCCeEEeecCCcc
Q psy93           248 CAEGCFFLTQSLRPVIVEPLELT  270 (503)
Q Consensus       248 ln~g~~~~~~~~rpl~V~~~~~~  270 (503)
                       .... +   .++++.+...+..
T Consensus       247 -~~~~-~---~~~~~~~~~~~~~  264 (285)
T KOG4210|consen  247 -QTRS-I---GGRPLRLEEDEPR  264 (285)
T ss_pred             -ccCc-c---cCcccccccCCCC
Confidence             4222 2   3666666655444

>KOG4208|consensus

Probab=98.39  E-value=7e-07  Score=82.93  Aligned_cols=75  Identities=17%  Similarity=0.387  Sum_probs=67.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccC-CCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPY-GETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~-G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..-+||..||..+.+..|..+|.+| |.|..+.+.+      +||||||+|++++.|.-|.+.||+..|.++.|.|.+-+
T Consensus        49 ~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmp  128 (214)
T KOG4208|consen   49 EGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMP  128 (214)
T ss_pred             ccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeC
Confidence            4569999999999999999999999 6777777743      58999999999999999999999999999999999887


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus       129 pe  130 (214)
T KOG4208|consen  129 PE  130 (214)
T ss_pred             ch
Confidence            76

>KOG4205|consensus

Probab=98.33  E-value=3.6e-07  Score=91.88  Aligned_cols=115  Identities=17%  Similarity=0.213  Sum_probs=91.9

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ..++|||++|++.++++.|++.|++||+|..|.+++| .++.+++|+||+|++.+....+|..-.  +.+   .++.|-+
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~--h~~---dgr~ve~   79 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNART--HKL---DGRSVEP   79 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccc--ccc---CCccccc
Confidence            4578999999999999999999999999999999999 578999999999999999988887643  222   5777777


Q ss_pred             ecCCccccccCC-----cccccCCCCchhhhhhccCcccCCCCCcc
Q psy93           265 EPLELTDEIDGL-----SERTINKKTPEFYKQRQVGPRFATVNSFE  305 (503)
Q Consensus       265 ~~~~~~~~~~~~-----~~k~i~k~~~~~~kere~~~rf~~~g~~e  305 (503)
                      +.+.+..+....     ..++.+..++....+.++...|.+++.+.
T Consensus        80 k~av~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~  125 (311)
T KOG4205|consen   80 KRAVSREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVA  125 (311)
T ss_pred             eeccCcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeE
Confidence            666665543222     33666777888888888889998888543

>KOG4660|consensus

Probab=98.30  E-value=4.7e-07  Score=94.89  Aligned_cols=131  Identities=20%  Similarity=0.205  Sum_probs=94.4

Q ss_pred             cCcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc-
Q psy93           108 IKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP-  185 (503)
Q Consensus       108 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~-  185 (503)
                      ...++..+|+|-|||.+|++++|..+|+.||+|..|..-.+ .+.+||+|-+.-+|++|++.|++..|.++.|+..... 
T Consensus        70 ~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~~~~~  149 (549)
T KOG4660|consen   70 EKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIKRPGGAR  149 (549)
T ss_pred             cccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCCCccc
Confidence            33456778999999999999999999999999999877544 6899999999999999999999999999888732110 


Q ss_pred             -----------------------c----ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCH
Q psy93           186 -----------------------I----NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARK  238 (503)
Q Consensus       186 -----------------------~----~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~  238 (503)
                                             +    ...+++ .|++..+...+...|+.+|.+.. ...    +.-...-|+.|.+.
T Consensus       150 ~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g-~l~P~~s~~~~~~~~~~~~~~~~-~~~----~~~~hq~~~~~~~~  223 (549)
T KOG4660|consen  150 RAMGLQSGTSFLNHFGSPLANSPPGGWPRGQLFG-MLSPTRSSILLEHISSVDGSSPG-RET----PLLNHQRFVEFADN  223 (549)
T ss_pred             ccchhcccchhhhhccchhhcCCCCCCcCCccee-eeccchhhhhhhcchhccCcccc-ccc----cchhhhhhhhhccc
Confidence                                   0    112222 27888888777777887777654 211    11112445566665


Q ss_pred             HHHHHH
Q psy93           239 PAAAQA  244 (503)
Q Consensus       239 e~A~kA  244 (503)
                      .++..+
T Consensus       224 ~s~a~~  229 (549)
T KOG4660|consen  224 RSYAFS  229 (549)
T ss_pred             cchhhc
Confidence            555333

>KOG4206|consensus

Probab=98.26  E-value=2.1e-06  Score=80.94  Aligned_cols=81  Identities=22%  Similarity=0.311  Sum_probs=67.5

Q ss_pred             cccceeccCcccccCHHHHHH----HhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCe
Q psy93           186 INAAIKVKNLTSCVTNELLEL----AFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRP  261 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~----~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rp  261 (503)
                      +..+|||.||++.+..++|+.    +|++||+|..|....  +.+.+|.|||.|.+.+.|..|+..|+ +..+   -+++
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k--t~KmRGQA~VvFk~~~~As~A~r~l~-gfpF---ygK~   81 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK--TPKMRGQAFVVFKETEAASAALRALQ-GFPF---YGKP   81 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC--CCCccCceEEEecChhHHHHHHHHhc-CCcc---cCch
Confidence            344999999999999999887    999999999876664  45779999999999999999999998 5444   3888


Q ss_pred             EEeecCCcccc
Q psy93           262 VIVEPLELTDE  272 (503)
Q Consensus       262 l~V~~~~~~~~  272 (503)
                      +.+.++....+
T Consensus        82 mriqyA~s~sd   92 (221)
T KOG4206|consen   82 MRIQYAKSDSD   92 (221)
T ss_pred             hheecccCccc
Confidence            88888766544

>KOG2193|consensus

Probab=98.26  E-value=2.6e-07  Score=93.44  Aligned_cols=134  Identities=18%  Similarity=0.306  Sum_probs=109.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCc-cccCceEEEEeccc----cc
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH-VLKGRSLKIRFAPI----NA  188 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~-~l~g~~l~V~~a~~----~~  188 (503)
                      +.||++||.+.++.++|..+|...-.-.+-.+.-..+|+||.+.+...|.+|++.++++ .+.|+++.|..+-+    ++
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkqrsr   81 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQRSR   81 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeeecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHHHhh
Confidence            35899999999999999999987632222222234689999999999999999999998 88899999988754    56


Q ss_pred             ceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhh
Q psy93           189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCA  249 (503)
Q Consensus       189 ~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln  249 (503)
                      .+-|.|+|+...++-|..+...||.|..|..+...+  ..-..-|+|.+.+.+..||.+|+
T Consensus        82 k~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~--etavvnvty~~~~~~~~ai~kl~  140 (584)
T KOG2193|consen   82 KIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDS--ETAVVNVTYSAQQQHRQAIHKLN  140 (584)
T ss_pred             hhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccch--HHHHHHHHHHHHHHHHHHHHhhc
Confidence            799999999999999999999999999997643311  12233467889999999999997

>KOG0116|consensus

Probab=98.24  E-value=1.4e-06  Score=91.00  Aligned_cols=71  Identities=23%  Similarity=0.384  Sum_probs=61.2

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ..+|||.|||++++.++|+++|..||+|+...|..      ..+||||+|.+.++++.||.+ +-..|.++.|.|+--
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek  364 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEK  364 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEec
Confidence            45699999999999999999999999999877642      238999999999999999986 566788999999754

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.22  E-value=5.2e-06  Score=66.47  Aligned_cols=70  Identities=19%  Similarity=0.384  Sum_probs=50.1

Q ss_pred             cEEEEcCCCCCCCHHH----HHHhhccCC-CeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           114 CRLYLGNIGGDITEND----IIELFKPYG-ETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~----L~~~F~~~G-~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      +.|||.|||.+.+...    |+.|+..|| .|..|    ..+.|+|.|.+.+.|.+|.+.|++..+.|..|.|.+.+..
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v----~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~~   77 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV----SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPKN   77 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--S
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE----eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCCc
Confidence            4699999999988665    566777887 78777    3689999999999999999999999999999999988654

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

>KOG2891|consensus

Probab=98.16  E-value=1e-05  Score=78.14  Aligned_cols=52  Identities=25%  Similarity=0.323  Sum_probs=34.6

Q ss_pred             ccCHHHHHHHhccCCCeeeeEEEe-CC-----CCCce-----eE---------EEEEeCCHHHHHHHHHHhh
Q psy93           198 CVTNELLELAFGVFGDIERAIVIV-DE-----RGNSK-----CE---------GIVEFARKPAAAQALRRCA  249 (503)
Q Consensus       198 ~~tee~L~~~Fs~~G~V~~~~v~~-d~-----~g~sk-----g~---------gfV~F~s~e~A~kAl~~ln  249 (503)
                      ..+++.|...|..||.|..|.|+. |+     +++..     +|         |||.|........|+..|.
T Consensus       172 lpse~rlr~a~eafg~ir~vdipicdplr~~mn~kisgiq~~gfg~g~dlffeayvqfmeykgfa~amdalr  243 (445)
T KOG2891|consen  172 LPSEDRLRKAFEAFGEIRNVDIPICDPLREEMNGKISGIQFHGFGFGGDLFFEAYVQFMEYKGFAQAMDALR  243 (445)
T ss_pred             CChHHHHHHHHHHhccceecCCcccchhHHHhcCccccceeeccccCcchhHHHHHHHHHHHhHHHHHHHHh
Confidence            357788999999999999988753 32     34332     23         3455555555666676665

>KOG0132|consensus

Probab=98.16  E-value=4.4e-06  Score=90.47  Aligned_cols=75  Identities=19%  Similarity=0.240  Sum_probs=67.0

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      +++|||+.|+..+++.+|..+|+.||.|.+|+++..     +++|||++....+|.+|+.+|++-. +   ..+.|.+.|
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~-----R~cAfI~M~~RqdA~kalqkl~n~k-v---~~k~Iki~W  491 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP-----RGCAFIKMVRRQDAEKALQKLSNVK-V---ADKTIKIAW  491 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC-----CceeEEEEeehhHHHHHHHHHhccc-c---cceeeEEee
Confidence            689999999999999999999999999999999876     8899999999999999999998333 3   478888899


Q ss_pred             CCcc
Q psy93           267 LELT  270 (503)
Q Consensus       267 ~~~~  270 (503)
                      +..+
T Consensus       492 a~g~  495 (894)
T KOG0132|consen  492 AVGK  495 (894)
T ss_pred             eccC
Confidence            7655

>KOG0153|consensus

Probab=98.09  E-value=6.5e-06  Score=81.84  Aligned_cols=75  Identities=15%  Similarity=0.126  Sum_probs=66.6

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      -.+|||++|.+.+++.+|++.|.+||.|.++.++..     +++|||+|.+..+|++|..++.+..++   ++.-|.|.|
T Consensus       228 I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-----~~CAFv~ftTR~aAE~Aae~~~n~lvI---~G~Rl~i~W  299 (377)
T KOG0153|consen  228 IKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-----KGCAFVTFTTREAAEKAAEKSFNKLVI---NGFRLKIKW  299 (377)
T ss_pred             eeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-----cccceeeehhhHHHHHHHHhhcceeee---cceEEEEEe
Confidence            468999999999999999999999999999999876     679999999999999999998764444   788899989


Q ss_pred             CCc
Q psy93           267 LEL  269 (503)
Q Consensus       267 ~~~  269 (503)
                      ..+
T Consensus       300 g~~  302 (377)
T KOG0153|consen  300 GRP  302 (377)
T ss_pred             CCC
Confidence            877

>KOG4307|consensus

Probab=98.05  E-value=5.4e-06  Score=88.60  Aligned_cols=150  Identities=11%  Similarity=-0.040  Sum_probs=113.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEE-----ecC-CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFI-----NKE-KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i-----~~~-kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +.|.|-+.+++++++..|++++|... .|.++.|     ..+ .|.++|.|....++++|+.. |.+.+-.+.+.|..+.
T Consensus       310 d~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~r-n~~~~~~R~~q~~P~g  387 (944)
T KOG4307|consen  310 DKYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTR-NPSDDVNRPFQTGPPG  387 (944)
T ss_pred             hhheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhc-CchhhhhcceeecCCC
Confidence            45667788999999999999999643 2322222     233 68999999999999999864 6666667777774331


Q ss_pred             ---------------------------------------------cccceeccCcccccCHHHHHHHhccCCCeee-eEE
Q psy93           186 ---------------------------------------------INAAIKVKNLTSCVTNELLELAFGVFGDIER-AIV  219 (503)
Q Consensus       186 ---------------------------------------------~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~-~~v  219 (503)
                                                                   ...+|||..||..+++..+.++|...-.|++ |.|
T Consensus       388 ~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~l  467 (944)
T KOG4307|consen  388 NLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIEL  467 (944)
T ss_pred             ccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEe
Confidence                                                         1358999999999999999999998888887 555


Q ss_pred             EeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecC
Q psy93           220 IVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPL  267 (503)
Q Consensus       220 ~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~  267 (503)
                      ..-++++-++.|||.|...+++.+|+..- ++.+.   ..+.|.|.+.
T Consensus       468 t~~P~~~~~~~afv~F~~~~a~~~a~~~~-~k~y~---G~r~irv~si  511 (944)
T KOG4307|consen  468 TRLPTDLLRPAAFVAFIHPTAPLTASSVK-TKFYP---GHRIIRVDSI  511 (944)
T ss_pred             ccCCcccccchhhheeccccccchhhhcc-ccccc---CceEEEeech
Confidence            55578888999999999988888887643 34444   3566666553

>KOG4676|consensus

Probab=98.04  E-value=2.5e-06  Score=85.73  Aligned_cols=130  Identities=18%  Similarity=0.211  Sum_probs=105.4

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC---------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           115 RLYLGNIGGDITENDIIELFKPYGETQELFINKE---------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       115 ~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~---------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      .|-|.||.+.+|.+.+..||...|+|..+.|..+         ...|||.|.+...+..| ++|..+++-++.|.|....
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~va-QhLtntvfvdraliv~p~~   87 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVA-QHLTNTVFVDRALIVRPYG   87 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHH-hhhccceeeeeeEEEEecC
Confidence            4899999999999999999999999999988643         35899999999888877 5688888888888775441


Q ss_pred             c--------------------------------------------------------------ccceeccCcccccCHHH
Q psy93           186 I--------------------------------------------------------------NAAIKVKNLTSCVTNEL  203 (503)
Q Consensus       186 ~--------------------------------------------------------------~~~L~V~nLp~~~tee~  203 (503)
                      .                                                              ..+++|.+|+..+...+
T Consensus        88 ~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~e  167 (479)
T KOG4676|consen   88 DEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAILPE  167 (479)
T ss_pred             CCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcchh
Confidence            0                                                              13577888888888899


Q ss_pred             HHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHh
Q psy93           204 LELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRC  248 (503)
Q Consensus       204 L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~l  248 (503)
                      +.++|..+|.|....+...   ....+|.|.|....+...|+...
T Consensus       168 ~~e~f~r~Gev~ya~~ask---~~s~~c~~sf~~qts~~halr~~  209 (479)
T KOG4676|consen  168 SGESFERKGEVSYAHTASK---SRSSSCSHSFRKQTSSKHALRSH  209 (479)
T ss_pred             hhhhhhhcchhhhhhhhcc---CCCcchhhhHhhhhhHHHHHHhc
Confidence            9999999999988766543   23457889999888888888874

>KOG4208|consensus

Probab=98.03  E-value=1.1e-05  Score=75.04  Aligned_cols=80  Identities=18%  Similarity=0.184  Sum_probs=65.0

Q ss_pred             ccceeccCcccccCHHHHHHHhccC-CCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVF-GDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~-G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ...++|..+|..+.+..+..+|.+| |.|..+.+.++ .||.|++||||+|++.+.|..|-+.|| ..++   ..+.+.|
T Consensus        49 ~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMN-NYLl---~e~lL~c  124 (214)
T KOG4208|consen   49 EGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMN-NYLL---MEHLLEC  124 (214)
T ss_pred             ccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhh-hhhh---hhheeee
Confidence            4567899999999999999999999 77777777677 699999999999999999999999998 5444   3555555


Q ss_pred             ecCCcc
Q psy93           265 EPLELT  270 (503)
Q Consensus       265 ~~~~~~  270 (503)
                      ..+.+.
T Consensus       125 ~vmppe  130 (214)
T KOG4208|consen  125 HVMPPE  130 (214)
T ss_pred             EEeCch
Confidence            554443

>KOG2253|consensus

Probab=98.02  E-value=5.1e-06  Score=88.84  Aligned_cols=69  Identities=16%  Similarity=0.148  Sum_probs=62.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      ..-+|||+||...+..+-++.+...||.|.+++..+   |+|+.|..+..+..|+..|+-..+.++.|.+..
T Consensus        39 ~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   39 PRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---FGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             CCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---hcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            455799999999999999999999999999998765   999999999999999999999999998887765

>KOG4209|consensus

Probab=98.00  E-value=8e-06  Score=79.29  Aligned_cols=77  Identities=19%  Similarity=0.315  Sum_probs=68.0

Q ss_pred             cCcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEE
Q psy93           108 IKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKI  181 (503)
Q Consensus       108 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V  181 (503)
                      +.....+.|||+|+.+.+|.++|...|+.||.|..|.|..      .|+||||+|.+.+.+..|+. ||+..|.++.|.|
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~v  174 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEV  174 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccccccccee
Confidence            4455667899999999999999999999999998777753      47899999999999999998 9999999999999


Q ss_pred             Eecc
Q psy93           182 RFAP  185 (503)
Q Consensus       182 ~~a~  185 (503)
                      .+..
T Consensus       175 t~~r  178 (231)
T KOG4209|consen  175 TLKR  178 (231)
T ss_pred             eeee
Confidence            7653

>KOG0533|consensus

Probab=97.98  E-value=1.7e-05  Score=77.00  Aligned_cols=81  Identities=27%  Similarity=0.401  Sum_probs=70.7

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ...+|+|.|||..+++++|+++|..|+.+..+.|..++.|.+.+.|-|.|...++|..|+..++ +..+   +++++.+.
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~-gv~l---dG~~mk~~  157 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYN-GVAL---DGRPMKIE  157 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhc-Cccc---CCceeeeE
Confidence            3467899999999999999999999999999999999999999999999999999999999997 5444   67777666


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      .....
T Consensus       158 ~i~~~  162 (243)
T KOG0533|consen  158 IISSP  162 (243)
T ss_pred             EecCc
Confidence            55443

>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=97.92  E-value=2.2e-05  Score=66.86  Aligned_cols=59  Identities=27%  Similarity=0.461  Sum_probs=41.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCc
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH  172 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~  172 (503)
                      +.|.|.+++..++-++|+++|+.||.|..|.+.+.-..|||.|.++++|++|+..+...
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhc
Confidence            57899999999999999999999999999999887789999999999999999876544

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

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

Probab=97.87  E-value=6e-05  Score=63.02  Aligned_cols=72  Identities=14%  Similarity=0.270  Sum_probs=56.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccC--CCeEEEEEe------cCCCceEEeeCCHHHHHHHHHHhCCcccc----CceEEE
Q psy93           114 CRLYLGNIGGDITENDIIELFKPY--GETQELFIN------KEKMFGFIRMDYKHNADKAKAKLDGHVLK----GRSLKI  181 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~--G~V~~v~i~------~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~----g~~l~V  181 (503)
                      |||.|.|||...|.++|.+++...  |...-+.++      .+.|||||.|.++++|.+..+.++|..+.    .+...|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            789999999999999999888654  444444443      24799999999999999999999999775    355566


Q ss_pred             Eecc
Q psy93           182 RFAP  185 (503)
Q Consensus       182 ~~a~  185 (503)
                      .||.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            6663

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

>KOG1548|consensus

Probab=97.80  E-value=5.8e-05  Score=75.19  Aligned_cols=80  Identities=16%  Similarity=0.194  Sum_probs=70.3

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeee--------eEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCC
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIER--------AIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQS  258 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~--------~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~  258 (503)
                      ++.|||.|||.++|.+++.++|++||.|..        |++.++..|..+|=|+|.|-..+++.-|+..|+ ...+   .
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilD-e~~~---r  209 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILD-EDEL---R  209 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhC-cccc---c
Confidence            567999999999999999999999998754        688999899999999999999999999999997 5555   4


Q ss_pred             CCeEEeecCCcc
Q psy93           259 LRPVIVEPLELT  270 (503)
Q Consensus       259 ~rpl~V~~~~~~  270 (503)
                      ++.+.|+.+.-.
T Consensus       210 g~~~rVerAkfq  221 (382)
T KOG1548|consen  210 GKKLRVERAKFQ  221 (382)
T ss_pred             CcEEEEehhhhh
Confidence            888999887654

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.78  E-value=3.6e-05  Score=76.15  Aligned_cols=74  Identities=26%  Similarity=0.512  Sum_probs=62.5

Q ss_pred             CcEEEEcCCCCCCCHHHH------HHhhccCCCeEEEEEecCC-------Cc--eEEeeCCHHHHHHHHHHhCCccccCc
Q psy93           113 NCRLYLGNIGGDITENDI------IELFKPYGETQELFINKEK-------MF--GFIRMDYKHNADKAKAKLDGHVLKGR  177 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L------~~~F~~~G~V~~v~i~~~k-------g~--aFV~F~~~e~A~~Ai~~l~g~~l~g~  177 (503)
                      .+-|||-+||+.+..+++      .++|.+||.|..|.|.+..       +.  .||+|.+.++|.+||...+|..++|+
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            345899999998877763      5799999999999996531       23  39999999999999999999999999


Q ss_pred             eEEEEeccc
Q psy93           178 SLKIRFAPI  186 (503)
Q Consensus       178 ~l~V~~a~~  186 (503)
                      .|+..+...
T Consensus       194 ~lkatYGTT  202 (480)
T COG5175         194 VLKATYGTT  202 (480)
T ss_pred             eEeeecCch
Confidence            999988754

>KOG4307|consensus

Probab=97.77  E-value=0.00044  Score=74.42  Aligned_cols=70  Identities=24%  Similarity=0.397  Sum_probs=59.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCe-EEEEEec-----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGET-QELFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V-~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      +.|-+.|+|++++-+||.+||..|-.+ .+|.+..     ..|-|.|-|++.++|..|...|++..|..++|+|.+
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            368899999999999999999999755 3444432     257899999999999999999999999999998864

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

Probab=97.76  E-value=0.00015  Score=60.65  Aligned_cols=82  Identities=13%  Similarity=0.129  Sum_probs=66.4

Q ss_pred             cceeccCcccccCHHHHHHHhccC--CCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVF--GDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~--G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ++|.|+|||...|.+.|.+++...  |....+.++.| .+..+.|||||.|.+++.|.+-...+++..+-...+.+++.|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            689999999999999998887654  55666677777 577889999999999999999999998665554556777777


Q ss_pred             ecCCc
Q psy93           265 EPLEL  269 (503)
Q Consensus       265 ~~~~~  269 (503)
                      .++.-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            77643

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

>KOG0106|consensus

Probab=97.74  E-value=2.1e-05  Score=74.85  Aligned_cols=69  Identities=28%  Similarity=0.514  Sum_probs=63.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEE
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIR  182 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~  182 (503)
                      ..+.|+|-||+..+.+.+|.+.|..+|.+....+  ..+++||+|.+.++|.+|+..|++..+.++.|++.
T Consensus        98 s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~  166 (216)
T KOG0106|consen   98 THFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVE  166 (216)
T ss_pred             ccceeeeccchhhhhHHHHhhhhcccCCCchhhh--hccccceeehhhhhhhhcchhccchhhcCceeeec
Confidence            3678999999999999999999999999955544  67899999999999999999999999999999993

>KOG1995|consensus

Probab=97.72  E-value=0.00012  Score=73.53  Aligned_cols=79  Identities=18%  Similarity=0.216  Sum_probs=67.0

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEE--------EEEe------cCCCceEEeeCCHHHHHHHHHHhCCcccc
Q psy93           110 FANNCRLYLGNIGGDITENDIIELFKPYGETQE--------LFIN------KEKMFGFIRMDYKHNADKAKAKLDGHVLK  175 (503)
Q Consensus       110 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~--------v~i~------~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~  175 (503)
                      .+...+|||-+||..+++++|.++|.+||.|..        |+|.      +.|+-|.|.|.++..|+.||.-+++..+.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            345567999999999999999999999998852        3332      34789999999999999999999999999


Q ss_pred             CceEEEEeccccc
Q psy93           176 GRSLKIRFAPINA  188 (503)
Q Consensus       176 g~~l~V~~a~~~~  188 (503)
                      +.+|+|.++...+
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999998775544

>KOG1457|consensus

Probab=97.70  E-value=0.00018  Score=67.71  Aligned_cols=83  Identities=16%  Similarity=0.110  Sum_probs=69.2

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC--CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE--RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~--~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      -++|||.+||.++...+|+.+|..|---+.+.+....  ....+.+|||+|.+..+|..|++.|| |+.|-......+.+
T Consensus        34 VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLN-GvrFDpE~~stLhi  112 (284)
T KOG1457|consen   34 VRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALN-GVRFDPETGSTLHI  112 (284)
T ss_pred             cceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhc-CeeeccccCceeEe
Confidence            4689999999999999999999999777776664432  22446799999999999999999997 88887778888888


Q ss_pred             ecCCcc
Q psy93           265 EPLELT  270 (503)
Q Consensus       265 ~~~~~~  270 (503)
                      +.++..
T Consensus       113 ElAKSN  118 (284)
T KOG1457|consen  113 ELAKSN  118 (284)
T ss_pred             eehhcC
Confidence            887654

>KOG0226|consensus

Probab=97.64  E-value=4.9e-05  Score=72.79  Aligned_cols=73  Identities=21%  Similarity=0.482  Sum_probs=63.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe------cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFIN------KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~------~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      +..+||.+.|..+++.+.|...|.+|-.....+++      +++||+||.|.++.++..|+..|+|..+..++|++..+
T Consensus       189 ~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  189 DDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             ccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            45679999999999999999999999765555554      56899999999999999999999999999999988754

>KOG4454|consensus

Probab=97.62  E-value=3.4e-05  Score=72.36  Aligned_cols=77  Identities=18%  Similarity=0.090  Sum_probs=66.2

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ...+|||.|+...++++.|.++|-+-|.|..+.|..+.++..+ ||||.|.+.-+..-|++.+| +..+   -.+++.+.
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~n-g~~l---~~~e~q~~   82 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLEN-GDDL---EEDEEQRT   82 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcc-cchh---ccchhhcc
Confidence            3578999999999999999999999999999999888888877 99999999999999999997 5444   35555555


Q ss_pred             cC
Q psy93           266 PL  267 (503)
Q Consensus       266 ~~  267 (503)
                      +.
T Consensus        83 ~r   84 (267)
T KOG4454|consen   83 LR   84 (267)
T ss_pred             cc
Confidence            53

>KOG1365|consensus

Probab=97.61  E-value=0.0005  Score=69.37  Aligned_cols=134  Identities=18%  Similarity=0.178  Sum_probs=101.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCe----EEEEE--ecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGET----QELFI--NKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V----~~v~i--~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ++.|-..+||...++.+|..||...-..    .-|..  .+..+.+.|.|.+++.-+-|++. +...+.++.|.|-.+..
T Consensus        60 ~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkR-hkhh~g~ryievYka~g  138 (508)
T KOG1365|consen   60 NVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKR-HKHHMGTRYIEVYKATG  138 (508)
T ss_pred             ceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHh-hhhhccCCceeeeccCc
Confidence            4456678999999999999999754221    11211  23467999999999988888874 66677788888865532


Q ss_pred             ----------------------ccceeccCcccccCHHHHHHHhccCC----CeeeeEEEeCCCCCceeEEEEEeCCHHH
Q psy93           187 ----------------------NAAIKVKNLTSCVTNELLELAFGVFG----DIERAIVIVDERGNSKCEGIVEFARKPA  240 (503)
Q Consensus       187 ----------------------~~~L~V~nLp~~~tee~L~~~Fs~~G----~V~~~~v~~d~~g~skg~gfV~F~s~e~  240 (503)
                                            .-.|...+||.+.++.++.++|..-.    .++.+-+++.++|+.+|-|||.|...++
T Consensus       139 e~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~  218 (508)
T KOG1365|consen  139 EEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEED  218 (508)
T ss_pred             hhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHH
Confidence                                  12356679999999999999997433    3445666677789999999999999999


Q ss_pred             HHHHHHH
Q psy93           241 AAQALRR  247 (503)
Q Consensus       241 A~kAl~~  247 (503)
                      |..|+.+
T Consensus       219 aq~aL~k  225 (508)
T KOG1365|consen  219 AQFALRK  225 (508)
T ss_pred             HHHHHHH
Confidence            9999987

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.50  E-value=0.00017  Score=53.55  Aligned_cols=52  Identities=17%  Similarity=0.481  Sum_probs=44.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHH
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAK  166 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai  166 (503)
                      +.|-|.+.|++..+. |..+|..||+|..+.+.....+.||.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCCCCcEEEEEECCHHHHHhhC
Confidence            568899999776654 5558889999999999877899999999999999985

>KOG0116|consensus

Probab=97.49  E-value=0.00014  Score=76.15  Aligned_cols=74  Identities=32%  Similarity=0.361  Sum_probs=59.0

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      ..|||.|||.+++..+|+++|..||.|....|.... .++..+||||+|.+.+++..||.+-  ...   ...+.+.|+-
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As--p~~---ig~~kl~Vee  363 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS--PLE---IGGRKLNVEE  363 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC--ccc---cCCeeEEEEe
Confidence            359999999999999999999999999998886542 3444599999999999999999873  222   2556666653

>PTZ00266 NIMA-related protein kinase; Provisional

Probab=97.48  E-value=0.002  Score=74.54  Aligned_cols=22  Identities=14%  Similarity=0.099  Sum_probs=11.0

Q ss_pred             ccccccccCCCCCCcccCCCCC
Q psy93           429 VVGNVTGVDNKGSAMDFDQGGR  450 (503)
Q Consensus       429 ~~~~~~~~~~~~~~~~~~~~~~  450 (503)
                      +++..-.+.+-+++|..+..-+
T Consensus       560 ~~~~~~~~~~~~~~~~~~~~~~  581 (1021)
T PTZ00266        560 SDGRNHSGVRSGIHCSIQSSAR  581 (1021)
T ss_pred             ccCCCccccccccccccccccc
Confidence            3344444555566666554433

>KOG4209|consensus

Probab=97.35  E-value=0.00023  Score=69.12  Aligned_cols=80  Identities=26%  Similarity=0.243  Sum_probs=67.6

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .....+||+|+...++.+++...|+.||.|..+.|.+|. .+.+++|+||+|.+.+.+.+|+. |+ +..+   .++++.
T Consensus        99 ~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~-gs~i---~~~~i~  173 (231)
T KOG4209|consen   99 VDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LD-GSEI---PGPAIE  173 (231)
T ss_pred             cCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cC-Cccc---ccccce
Confidence            346789999999999999999999999999999999884 55789999999999999999999 86 4444   477777


Q ss_pred             eecCCc
Q psy93           264 VEPLEL  269 (503)
Q Consensus       264 V~~~~~  269 (503)
                      |.+...
T Consensus       174 vt~~r~  179 (231)
T KOG4209|consen  174 VTLKRT  179 (231)
T ss_pred             eeeeee
Confidence            766443

>PTZ00266 NIMA-related protein kinase; Provisional

Probab=97.34  E-value=0.0028  Score=73.34  Aligned_cols=15  Identities=20%  Similarity=0.003  Sum_probs=6.4

Q ss_pred             cccccccccCCCCCC
Q psy93           428 AVVGNVTGVDNKGSA  442 (503)
Q Consensus       428 ~~~~~~~~~~~~~~~  442 (503)
                      .++.--+.++..+++
T Consensus       566 ~~~~~~~~~~~~~~~  580 (1021)
T PTZ00266        566 SGVRSGIHCSIQSSA  580 (1021)
T ss_pred             ccccccccccccccc
Confidence            334444444444444

>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=97.25  E-value=0.00049  Score=58.65  Aligned_cols=57  Identities=26%  Similarity=0.351  Sum_probs=38.9

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhh
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCA  249 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln  249 (503)
                      +.|+|.+++..++-++|+++|+.||.|..|.+...     ...|||.|.+.+.|.+|+..+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G-----~~~g~VRf~~~~~A~~a~~~~~   58 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG-----DTEGYVRFKTPEAAQKALEKLK   58 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT------SEEEEEESS---HHHHHHHHH
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC-----CCEEEEEECCcchHHHHHHHHH
Confidence            45788899999999999999999999999888765     3489999999999999999986

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0151|consensus

Probab=97.21  E-value=0.00053  Score=74.05  Aligned_cols=68  Identities=25%  Similarity=0.429  Sum_probs=59.2

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC----CCCCceeEEEEEeCCHHHHHHHHHHhhCCeee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD----ERGNSKCEGIVEFARKPAAAQALRRCAEGCFF  254 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d----~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~  254 (503)
                      .+++|||.||+++++++.|...|..||+|..++|+..    +.-....++||.|-+..+|..|+..|+ +.++
T Consensus       173 ~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lq-g~iv  244 (877)
T KOG0151|consen  173 QTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQ-GIIV  244 (877)
T ss_pred             cccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhc-ceee
Confidence            4789999999999999999999999999999999765    233456799999999999999999997 5444

>KOG1855|consensus

Probab=97.14  E-value=0.00044  Score=70.81  Aligned_cols=62  Identities=18%  Similarity=0.224  Sum_probs=54.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-------------------CCceEEeeCCHHHHHHHHHHhCC
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-------------------KMFGFIRMDYKHNADKAKAKLDG  171 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-------------------kg~aFV~F~~~e~A~~Ai~~l~g  171 (503)
                      .++.+|.+.|||.+-.-+.|.+||+.||.|+.|.|.+.                   +-+|||+|+..+.|.+|.+.|+.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            35789999999999999999999999999999999532                   34899999999999999987754


Q ss_pred             c
Q psy93           172 H  172 (503)
Q Consensus       172 ~  172 (503)
                      .
T Consensus       309 e  309 (484)
T KOG1855|consen  309 E  309 (484)
T ss_pred             h
Confidence            3

>KOG3152|consensus

Probab=97.13  E-value=0.00033  Score=67.34  Aligned_cols=67  Identities=21%  Similarity=0.381  Sum_probs=58.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCC------------------CceEEeeCCHHHHHHHHHHhCCcc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEK------------------MFGFIRMDYKHNADKAKAKLDGHV  173 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~k------------------g~aFV~F~~~e~A~~Ai~~l~g~~  173 (503)
                      ..-.||+++||+.+...-|+++|+.||.|-.|.+-+..                  .-+.|+|.+...|..+...||++.
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            34579999999999999999999999999999984321                  138899999999999999999999


Q ss_pred             ccCce
Q psy93           174 LKGRS  178 (503)
Q Consensus       174 l~g~~  178 (503)
                      |.|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99865

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.04  E-value=0.0017  Score=54.67  Aligned_cols=71  Identities=17%  Similarity=0.271  Sum_probs=53.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEE-------------EecCCCceEEeeCCHHHHHHHHHHhCCccccCce-
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELF-------------INKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRS-  178 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~-------------i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~-  178 (503)
                      .+.|.|-+.|+. ....|...|++||.|.+..             +........|+|+++.+|.+|+. .||..|.|.. 
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEE
Confidence            456899999977 6677888999999998885             45567899999999999999997 5999998754 


Q ss_pred             EEEEecc
Q psy93           179 LKIRFAP  185 (503)
Q Consensus       179 l~V~~a~  185 (503)
                      +-|.+++
T Consensus        84 vGV~~~~   90 (100)
T PF05172_consen   84 VGVKPCD   90 (100)
T ss_dssp             EEEEE-H
T ss_pred             EEEEEcH
Confidence            4566654

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.

>KOG4660|consensus

Probab=97.00  E-value=0.0006  Score=72.04  Aligned_cols=61  Identities=26%  Similarity=0.310  Sum_probs=53.9

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhh
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCA  249 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln  249 (503)
                      .+..+|+|-|||..+++++|..+|+.||+|..+..-..    ..+..||+|-+..+|+.|++.|+
T Consensus        73 ~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~----~~~~~~v~FyDvR~A~~Alk~l~  133 (549)
T KOG4660|consen   73 MNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN----KRGIVFVEFYDVRDAERALKALN  133 (549)
T ss_pred             CccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc----cCceEEEEEeehHhHHHHHHHHH
Confidence            45678999999999999999999999999998654333    36799999999999999999998

>KOG1029|consensus

Probab=96.89  E-value=0.026  Score=61.99  Aligned_cols=18  Identities=17%  Similarity=0.222  Sum_probs=10.9

Q ss_pred             HHHHhhhccccCCCCCCC
Q psy93            14 QLYQARLRSYTGHFKIPE   31 (503)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~   31 (503)
                      +..--|++++.-+-..|-
T Consensus        76 kLi~lkLqG~~lP~~LPP   93 (1118)
T KOG1029|consen   76 KLIKLKLQGIQLPPVLPP   93 (1118)
T ss_pred             HHHHHHhcCCcCCCCCCh
Confidence            455667777766555443

>KOG0128|consensus

Probab=96.80  E-value=0.00018  Score=79.18  Aligned_cols=139  Identities=22%  Similarity=0.189  Sum_probs=112.2

Q ss_pred             cEEEEcCCCCCCCHH-HHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           114 CRLYLGNIGGDITEN-DIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       114 ~~l~V~nLp~~~te~-~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ...++.|+.+..... .++..|..++.|..|.++..      ..+.++.+....+++.|.. ..+.-+.++.+.|..+++
T Consensus       572 ~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~-pa~~~~a~~~~av~~ad~  650 (881)
T KOG0128|consen  572 REKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATV-PAGGALANRSAAVGLADA  650 (881)
T ss_pred             hhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhccc-ccccccCCccccCCCCCc
Confidence            346777887666555 67889999999999999751      2389999999999998865 577778888888877653


Q ss_pred             ----------------ccceeccCcccccCHHHHHHHhccCCCeeeeEEE-eCCCCCceeEEEEEeCCHHHHHHHHHHhh
Q psy93           187 ----------------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVI-VDERGNSKCEGIVEFARKPAAAQALRRCA  249 (503)
Q Consensus       187 ----------------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~-~d~~g~skg~gfV~F~s~e~A~kAl~~ln  249 (503)
                                      -.++||+||+..+.+.+|...|+.++.+..+.+. ...++..+|+|||.|...+.+.+|+....
T Consensus       651 ~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d  730 (881)
T KOG0128|consen  651 EEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRD  730 (881)
T ss_pred             hhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhh
Confidence                            2478999999999999999999999988877665 33467779999999999999999998764


Q ss_pred             CCeee
Q psy93           250 EGCFF  254 (503)
Q Consensus       250 ~g~~~  254 (503)
                       ++++
T Consensus       731 -~~~~  734 (881)
T KOG0128|consen  731 -SCFF  734 (881)
T ss_pred             -hhhh
Confidence             6655

>KOG2314|consensus

Probab=96.78  E-value=0.0027  Score=67.11  Aligned_cols=81  Identities=20%  Similarity=0.206  Sum_probs=62.0

Q ss_pred             cceeccCcccc------cCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCe
Q psy93           188 AAIKVKNLTSC------VTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRP  261 (503)
Q Consensus       188 ~~L~V~nLp~~------~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rp  261 (503)
                      .+|+|.|+|--      .-...|.++|+++|+|....++.++.+.++||.|++|.+..+|..|++.|| |..+.  ....
T Consensus        59 ~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~-G~~ld--knHt  135 (698)
T KOG2314|consen   59 SVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLN-GKRLD--KNHT  135 (698)
T ss_pred             eEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcc-cceec--ccce
Confidence            46677777632      222457789999999999999989888899999999999999999999998 44442  4556


Q ss_pred             EEeecCCccc
Q psy93           262 VIVEPLELTD  271 (503)
Q Consensus       262 l~V~~~~~~~  271 (503)
                      ..|..+...+
T Consensus       136 f~v~~f~d~e  145 (698)
T KOG2314|consen  136 FFVRLFKDFE  145 (698)
T ss_pred             EEeehhhhHH
Confidence            6666654443

>KOG0112|consensus

Probab=96.73  E-value=0.0021  Score=71.32  Aligned_cols=78  Identities=21%  Similarity=0.318  Sum_probs=71.4

Q ss_pred             CcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccC--ceEEEEeccc
Q psy93           109 KFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKG--RSLKIRFAPI  186 (503)
Q Consensus       109 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g--~~l~V~~a~~  186 (503)
                      ..+.++.|||++|++++....|...|..||+|..|.+-....||||.|++...|+.|+..|-+..|.+  +.|.|.++.+
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~  530 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASP  530 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccCCcceeeecccCccchhhHHHHhcCcCCCCCcccccccccC
Confidence            55667899999999999999999999999999999998778899999999999999999999999985  7899988853

>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=96.69  E-value=0.0057  Score=49.31  Aligned_cols=70  Identities=19%  Similarity=0.136  Sum_probs=44.6

Q ss_pred             cceeccCcccccCHHH----HHHHhccCC-CeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeE
Q psy93           188 AAIKVKNLTSCVTNEL----LELAFGVFG-DIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPV  262 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~----L~~~Fs~~G-~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl  262 (503)
                      ..|+|.|||.+.+...    |+.++..|| +|..+         +.+.|+|.|.+.+.|..|.+.|++...+    +..|
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v---------~~~tAilrF~~~~~A~RA~KRmegEdVf----G~kI   69 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV---------SGGTAILRFPNQEFAERAQKRMEGEDVF----GNKI   69 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-----------TT-EEEEESSHHHHHHHHHHHTT--SS----SS--
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE---------eCCEEEEEeCCHHHHHHHHHhhcccccc----cceE
Confidence            4689999999887765    556777886 55544         1358999999999999999999744433    7778


Q ss_pred             EeecCCcc
Q psy93           263 IVEPLELT  270 (503)
Q Consensus       263 ~V~~~~~~  270 (503)
                      .|.+....
T Consensus        70 ~v~~~~~~   77 (90)
T PF11608_consen   70 SVSFSPKN   77 (90)
T ss_dssp             EEESS--S
T ss_pred             EEEEcCCc
Confidence            88776443

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

>KOG1995|consensus

Probab=96.62  E-value=0.0016  Score=65.52  Aligned_cols=79  Identities=27%  Similarity=0.215  Sum_probs=64.1

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeee--------eEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCC
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIER--------AIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQS  258 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~--------~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~  258 (503)
                      .+|||.+||..++..+|.++|.+|+.|..        |.|.+| +|+.+|+-|.|+|+++..|+.|+.-++... +   +
T Consensus        67 ~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkd-f---~  142 (351)
T KOG1995|consen   67 ETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKD-F---C  142 (351)
T ss_pred             ccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccc-c---c
Confidence            57899999999999999999999998753        345555 688999999999999999999999997443 3   3


Q ss_pred             CCeEEeecCCcc
Q psy93           259 LRPVIVEPLELT  270 (503)
Q Consensus       259 ~rpl~V~~~~~~  270 (503)
                      +.+|.|..+...
T Consensus       143 gn~ikvs~a~~r  154 (351)
T KOG1995|consen  143 GNTIKVSLAERR  154 (351)
T ss_pred             CCCchhhhhhhc
Confidence            466666665544

>KOG2314|consensus

Probab=96.56  E-value=0.0051  Score=65.15  Aligned_cols=72  Identities=15%  Similarity=0.231  Sum_probs=58.4

Q ss_pred             CCcEEEEcCCCCCC--C----HHHHHHhhccCCCeEEEEEec-----CCCceEEeeCCHHHHHHHHHHhCCcccc-CceE
Q psy93           112 NNCRLYLGNIGGDI--T----ENDIIELFKPYGETQELFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLK-GRSL  179 (503)
Q Consensus       112 ~~~~l~V~nLp~~~--t----e~~L~~~F~~~G~V~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~-g~~l  179 (503)
                      -.+.|+|.|+|.--  .    ..-|.++|+++|+|+.+.++.     .+||.|++|++..+|+.|++.|||+.|+ .+++
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            34679999998421  1    234577899999999999863     4899999999999999999999999877 6788


Q ss_pred             EEEe
Q psy93           180 KIRF  183 (503)
Q Consensus       180 ~V~~  183 (503)
                      .|..
T Consensus       137 ~v~~  140 (698)
T KOG2314|consen  137 FVRL  140 (698)
T ss_pred             Eeeh
Confidence            7753

>KOG2416|consensus

Probab=96.51  E-value=0.0019  Score=68.63  Aligned_cols=74  Identities=18%  Similarity=0.234  Sum_probs=62.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhc-cCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCcccc---CceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFK-PYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLK---GRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~-~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~---g~~l~V~~a~  185 (503)
                      .++.|||.||--.+|.-.|+.|+. .+|.|.+.+|.+-|..|||.|.+.++|...+..||+..+.   .+.|.|.|..
T Consensus       443 ~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf~~  520 (718)
T KOG2416|consen  443 PSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADFVR  520 (718)
T ss_pred             ccceEeeecccccchHHHHHHHHhhccCchHHHHHHHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeeecc
Confidence            467899999999999999999998 6778888888777889999999999999999999998554   4566666543

>KOG4210|consensus

Probab=96.46  E-value=0.0021  Score=64.61  Aligned_cols=72  Identities=18%  Similarity=0.331  Sum_probs=63.8

Q ss_pred             cEEE-EcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           114 CRLY-LGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       114 ~~l~-V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      .++| |++|+.+++.++|+.+|..+|.|..+.++.      .++||||.|.+...+..++.. +...+.++++.|....+
T Consensus       185 ~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~  263 (285)
T KOG4210|consen  185 DTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEP  263 (285)
T ss_pred             ccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCC
Confidence            3455 999999999999999999999999999964      378999999999999999876 77789999999988765

>KOG1029|consensus

Probab=96.38  E-value=0.038  Score=60.77  Aligned_cols=11  Identities=9%  Similarity=-0.097  Sum_probs=5.0

Q ss_pred             HHHHHHHHHHh
Q psy93           238 KPAAAQALRRC  248 (503)
Q Consensus       238 ~e~A~kAl~~l  248 (503)
                      .+...-|+..+
T Consensus       248 ~dEfilam~li  258 (1118)
T KOG1029|consen  248 ADEFILAMHLI  258 (1118)
T ss_pred             HHHHHHHHHHH
Confidence            44444454443

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.24  E-value=0.0064  Score=45.04  Aligned_cols=52  Identities=19%  Similarity=0.208  Sum_probs=40.7

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHH
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQAL  245 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl  245 (503)
                      +.|.|.+.++...+ .|...|..||+|..+.+...     ..+.+|+|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~~-----~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPES-----TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCCC-----CcEEEEEECCHHHHHhhC
Confidence            45677787776554 45568999999999877622     558999999999999985

>KOG0163|consensus

Probab=95.96  E-value=0.069  Score=58.66  Aligned_cols=36  Identities=33%  Similarity=0.451  Sum_probs=17.8

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhhHHH
Q psy93           344 WEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEED  379 (503)
Q Consensus       344 ~E~~eRq~ee~r~reeE~~r~rqee~~~~~~r~eEe  379 (503)
                      +|.+++++|+++.+.+|..++-+.+.++++.++.|+
T Consensus       960 ~e~kRK~eEeqr~~qee~e~~l~~e~q~qla~e~ee  995 (1259)
T KOG0163|consen  960 METKRKAEEEQRKAQEEEERRLALELQEQLAKEAEE  995 (1259)
T ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence            333444455555555555455555555555554444

>KOG1855|consensus

Probab=95.85  E-value=0.016  Score=59.70  Aligned_cols=64  Identities=27%  Similarity=0.251  Sum_probs=54.4

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC---C---CCCc--------eeEEEEEeCCHHHHHHHHHHhh
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD---E---RGNS--------KCEGIVEFARKPAAAQALRRCA  249 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d---~---~g~s--------kg~gfV~F~s~e~A~kAl~~ln  249 (503)
                      +..+|.+.|||.+..-+.|.++|+.+|.|..|.|...   +   .+.+        +-+|+|+|+..+.|.+|.+.++
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            4678999999999999999999999999999998765   2   2222        4468999999999999999986

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=95.82  E-value=0.04  Score=44.46  Aligned_cols=54  Identities=20%  Similarity=0.374  Sum_probs=42.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhC
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLD  170 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~  170 (503)
                      ...+|+ .|..+...||.++|+.||.|.--.|  +-..|||.....+.|..|+..++
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi--~dTSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWI--NDTSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEEEEEE--CTTEEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEEEEEE--cCCcEEEEeecHHHHHHHHHHhc
Confidence            346666 9999999999999999999876666  45689999999999999988875

; 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

Probab=95.81  E-value=0.0051  Score=59.45  Aligned_cols=57  Identities=21%  Similarity=0.432  Sum_probs=48.3

Q ss_pred             HHHHhhc-cCCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           129 DIIELFK-PYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       129 ~L~~~F~-~~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +|...|+ +||+|.+++|-.+     .|-+||.|...++|++|+..||+..+.|++|...+.+
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            4444445 9999999987554     5789999999999999999999999999999998764

>KOG0129|consensus

Probab=95.73  E-value=0.036  Score=58.49  Aligned_cols=93  Identities=15%  Similarity=0.265  Sum_probs=69.7

Q ss_pred             cccCcCCCcEEEEcCCCCCCCHHHHHHhhc-cCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCce
Q psy93           106 KDIKFANNCRLYLGNIGGDITENDIIELFK-PYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRS  178 (503)
Q Consensus       106 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~-~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~  178 (503)
                      ......+..|||||+||-.++.++|..+|. -||.|..+-|..+      ||-|=|+|.+..+-.+||..        +-
T Consensus       363 ~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa--------rF  434 (520)
T KOG0129|consen  363 HNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA--------RF  434 (520)
T ss_pred             cCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh--------he
Confidence            344555678999999999999999999999 8999999988654      78899999999999999875        34


Q ss_pred             EEEEecccccceeccCcccccCHHHHHHHhc
Q psy93           179 LKIRFAPINAAIKVKNLTSCVTNELLELAFG  209 (503)
Q Consensus       179 l~V~~a~~~~~L~V~nLp~~~tee~L~~~Fs  209 (503)
                      |.|.-.+-.+.|-|+   +.+-++.+.+.++
T Consensus       435 vql~h~d~~KRVEIk---PYv~eDq~CdeC~  462 (520)
T KOG0129|consen  435 VQLDHTDIDKRVEIK---PYVMEDQLCDECG  462 (520)
T ss_pred             EEEeccccceeeeec---ceeccccchhhhc
Confidence            455444444444443   4454555555554

>KOG4849|consensus

Probab=95.58  E-value=0.0089  Score=59.85  Aligned_cols=70  Identities=14%  Similarity=0.258  Sum_probs=58.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCC--CeEEEEEe------cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYG--ETQELFIN------KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G--~V~~v~i~------~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      -++||+||-+.+|++||.+.+...|  .|.++++.      .+||||+|...+..+.++.++.|-.+.|+|+.-.|..
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~  158 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLS  158 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeec
Confidence            3699999999999999999887776  45555553      4689999999999999999999999999998766643

>KOG2416|consensus

Probab=95.55  E-value=0.026  Score=60.32  Aligned_cols=78  Identities=17%  Similarity=0.196  Sum_probs=63.0

Q ss_pred             ccceeccCcccccCHHHHHHHhc-cCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFG-VFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs-~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ++.|+|.||-..+|.-+|+.++. .+|.|+..  +.|   +-+..|||.|.+.++|...+.+|+ +..|-..+++.|.+.
T Consensus       444 SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~--WmD---kIKShCyV~yss~eEA~atr~Alh-nV~WP~sNPK~L~ad  517 (718)
T KOG2416|consen  444 SNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF--WMD---KIKSHCYVSYSSVEEAAATREALH-NVQWPPSNPKHLIAD  517 (718)
T ss_pred             cceEeeecccccchHHHHHHHHhhccCchHHH--HHH---HhhcceeEecccHHHHHHHHHHHh-ccccCCCCCceeEee
Confidence            57899999999999999999999 56667666  333   226689999999999999999997 666666778888887


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      +....
T Consensus       518 f~~~d  522 (718)
T KOG2416|consen  518 FVRAD  522 (718)
T ss_pred             ecchh
Confidence            76543

>KOG4676|consensus

Probab=95.52  E-value=0.016  Score=58.92  Aligned_cols=76  Identities=21%  Similarity=0.267  Sum_probs=60.6

Q ss_pred             ceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC----CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE----RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       189 ~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~----~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .|.|.||.+.++.+.++.+|...|+|..+.|+.+.    -......|||.|.+...+..|-..- +-.|+    +++++|
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLt-ntvfv----draliv   83 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLT-NTVFV----DRALIV   83 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhc-cceee----eeeEEE
Confidence            67899999999999999999999999999988752    2234568999999999988886544 35555    777777


Q ss_pred             ecCCc
Q psy93           265 EPLEL  269 (503)
Q Consensus       265 ~~~~~  269 (503)
                      .|+..
T Consensus        84 ~p~~~   88 (479)
T KOG4676|consen   84 RPYGD   88 (479)
T ss_pred             EecCC
Confidence            76543

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=95.40  E-value=0.057  Score=54.07  Aligned_cols=76  Identities=20%  Similarity=0.284  Sum_probs=55.7

Q ss_pred             ccceeccCcccccCHHHH------HHHhccCCCeeeeEEEeCC-CCCc-ee-E-EEEEeCCHHHHHHHHHHhhCCeeeec
Q psy93           187 NAAIKVKNLTSCVTNELL------ELAFGVFGDIERAIVIVDE-RGNS-KC-E-GIVEFARKPAAAQALRRCAEGCFFLT  256 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L------~~~Fs~~G~V~~~~v~~d~-~g~s-kg-~-gfV~F~s~e~A~kAl~~ln~g~~~~~  256 (503)
                      ++-+||-+||+.+..+++      .++|.+||+|..|.|.+.. .-.+ .+ + .||+|.+.++|..||...+ +.++  
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vD-gs~~--  190 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVD-GSLL--  190 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhc-cccc--
Confidence            467899999988877762      4789999999998886652 1111 11 2 2999999999999999986 6665  


Q ss_pred             CCCCeEEeec
Q psy93           257 QSLRPVIVEP  266 (503)
Q Consensus       257 ~~~rpl~V~~  266 (503)
                       ++|.+....
T Consensus       191 -DGr~lkatY  199 (480)
T COG5175         191 -DGRVLKATY  199 (480)
T ss_pred             -cCceEeeec
Confidence             566655543

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=95.39  E-value=0.054  Score=48.53  Aligned_cols=71  Identities=21%  Similarity=0.328  Sum_probs=51.7

Q ss_pred             cEEEEcCCC------CCCCH---HHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           114 CRLYLGNIG------GDITE---NDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       114 ~~l~V~nLp------~~~te---~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      .||.|.=+.      ....+   .+|.+.|..||.|.-|++..  +.-+|+|.+..+|.+|+. ++|+.+.|+.|+|..-
T Consensus        28 aTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~--~~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LK  104 (146)
T PF08952_consen   28 ATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG--DTMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLK  104 (146)
T ss_dssp             -EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET--TCEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE-
T ss_pred             ceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC--CeEEEEECccHHHHHHHc-cCCcEECCEEEEEEeC
Confidence            367776554      12232   36778899999999888875  478999999999999996 8999999999999876


Q ss_pred             ccc
Q psy93           185 PIN  187 (503)
Q Consensus       185 ~~~  187 (503)
                      .+.
T Consensus       105 tpd  107 (146)
T PF08952_consen  105 TPD  107 (146)
T ss_dssp             ---
T ss_pred             Ccc
Confidence            554

; PDB: 1UFW_A 2DNR_A.

>KOG2591|consensus

Probab=95.08  E-value=0.038  Score=58.63  Aligned_cols=86  Identities=10%  Similarity=0.082  Sum_probs=72.5

Q ss_pred             HHHHHHHHHHhCCccccCceEEEEecccccceeccCcccccCHHHHHHHhcc--CCCeeeeEEEeCCCCCceeEEEEEeC
Q psy93           159 KHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGV--FGDIERAIVIVDERGNSKCEGIVEFA  236 (503)
Q Consensus       159 ~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~~~L~V~nLp~~~tee~L~~~Fs~--~G~V~~~~v~~d~~g~skg~gfV~F~  236 (503)
                      .+-...+++...+..++.+-++|......+.|++..||..+..|+|+.+|+.  |-++++|.+..+.      --||+|+
T Consensus       147 vdLI~Evlresp~VqvDekgekVrp~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~------nWyITfe  220 (684)
T KOG2591|consen  147 VDLIVEVLRESPNVQVDEKGEKVRPNHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND------NWYITFE  220 (684)
T ss_pred             hHHHHHHHhcCCCceeccCccccccCcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC------ceEEEee
Confidence            4445567777778888999999998888888999999999999999999985  7788899886653      3599999


Q ss_pred             CHHHHHHHHHHhhC
Q psy93           237 RKPAAAQALRRCAE  250 (503)
Q Consensus       237 s~e~A~kAl~~ln~  250 (503)
                      +..+|+.|...|.+
T Consensus       221 sd~DAQqAykylre  234 (684)
T KOG2591|consen  221 SDTDAQQAYKYLRE  234 (684)
T ss_pred             cchhHHHHHHHHHH
Confidence            99999999998863

>KOG1996|consensus

Probab=95.04  E-value=0.046  Score=53.79  Aligned_cols=58  Identities=24%  Similarity=0.349  Sum_probs=49.4

Q ss_pred             HHHHHHhhccCCCeEEEEEecC-------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           127 ENDIIELFKPYGETQELFINKE-------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       127 e~~L~~~F~~~G~V~~v~i~~~-------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ++++++-+.+||.|..|.|...       .--.||+|...++|.+|+-.|||..|.|+.++..|.
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fy  364 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFY  364 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheec
Confidence            4567888999999999888532       235899999999999999999999999999988765

>KOG2135|consensus

Probab=94.95  E-value=0.014  Score=60.81  Aligned_cols=82  Identities=21%  Similarity=0.316  Sum_probs=66.0

Q ss_pred             CcEEEEcCCCCCC-CHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccccccee
Q psy93           113 NCRLYLGNIGGDI-TENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIK  191 (503)
Q Consensus       113 ~~~l~V~nLp~~~-te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~~~L~  191 (503)
                      .|.|-+.-.|+.. |.++|...|.+||.|..|.|.-+.-.|.|+|.+..+|-.|.. .++..|+++.|+|.|.+++.   
T Consensus       372 hs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps~---  447 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPSP---  447 (526)
T ss_pred             cchhhhhccCCCCchHhhhhhhhhhcCccccccccCchhhheeeeeccccccchhc-cccceecCceeEEEEecCCc---
Confidence            3445566666554 578999999999999999997666689999999999977764 68999999999999998765   


Q ss_pred             ccCcccc
Q psy93           192 VKNLTSC  198 (503)
Q Consensus       192 V~nLp~~  198 (503)
                      +.|+|..
T Consensus       448 ~tn~pav  454 (526)
T KOG2135|consen  448 VTNIPAV  454 (526)
T ss_pred             ccCcccC
Confidence            5666543

>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=94.57  E-value=0.087  Score=44.41  Aligned_cols=77  Identities=18%  Similarity=0.192  Sum_probs=48.1

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEE-EeC-------CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCC
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIV-IVD-------ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQS  258 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v-~~d-------~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~  258 (503)
                      .+.|.|-+.|+. ....|.+.|++||+|.+..- ..+       +......+-.|+|+++.+|.+||..  +|.++   .
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~--NG~i~---~   79 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK--NGTIF---S   79 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT--TTEEE---T
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh--CCeEE---c
Confidence            345677788887 44567789999999987741 110       0011245889999999999999986  68887   3


Q ss_pred             C-CeEEeecCCc
Q psy93           259 L-RPVIVEPLEL  269 (503)
Q Consensus       259 ~-rpl~V~~~~~  269 (503)
                      + -.+-|.|.+.
T Consensus        80 g~~mvGV~~~~~   91 (100)
T PF05172_consen   80 GSLMVGVKPCDP   91 (100)
T ss_dssp             TCEEEEEEE-HH
T ss_pred             CcEEEEEEEcHH
Confidence            4 3455666543

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.

>KOG4849|consensus

Probab=94.55  E-value=0.032  Score=55.96  Aligned_cols=67  Identities=18%  Similarity=0.084  Sum_probs=54.5

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCC--eeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGD--IERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFF  254 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~--V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~  254 (503)
                      ..++||+||-+.+|+++|.+.+...|.  +.++++..+ .+|.+||||+|...+..+.++.++.|- ...+
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP-~k~i  149 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILP-TKTI  149 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcc-ccee
Confidence            357899999999999999999887773  455555555 578999999999999999999999885 4444

>KOG2068|consensus

Probab=94.48  E-value=0.017  Score=57.97  Aligned_cols=73  Identities=25%  Similarity=0.471  Sum_probs=60.5

Q ss_pred             cEEEEcCCCCCCCHHHHH---HhhccCCCeEEEEEecCC---------CceEEeeCCHHHHHHHHHHhCCccccCceEEE
Q psy93           114 CRLYLGNIGGDITENDII---ELFKPYGETQELFINKEK---------MFGFIRMDYKHNADKAKAKLDGHVLKGRSLKI  181 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~---~~F~~~G~V~~v~i~~~k---------g~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V  181 (503)
                      .-+||-+|+..+..+++.   +.|.+||.|.+|.+.+..         .-++|+|...++|..||...++..++++.|+.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            458899999887666553   589999999999886532         35899999999999999999999999999888


Q ss_pred             Eeccc
Q psy93           182 RFAPI  186 (503)
Q Consensus       182 ~~a~~  186 (503)
                      .+...
T Consensus       158 ~~gtt  162 (327)
T KOG2068|consen  158 SLGTT  162 (327)
T ss_pred             hhCCC
Confidence            77654

>KOG1144|consensus

Probab=94.39  E-value=0.19  Score=55.62  Aligned_cols=11  Identities=18%  Similarity=0.371  Sum_probs=5.0

Q ss_pred             HHHHHhccCCC
Q psy93           203 LLELAFGVFGD  213 (503)
Q Consensus       203 ~L~~~Fs~~G~  213 (503)
                      ++..+...+|.
T Consensus       111 d~dkllas~~e  121 (1064)
T KOG1144|consen  111 DLDKLLASLGE  121 (1064)
T ss_pred             chHHHhhhcCC
Confidence            34444444443

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=94.07  E-value=0.2  Score=44.45  Aligned_cols=73  Identities=10%  Similarity=0.149  Sum_probs=55.8

Q ss_pred             CCCcEEEEcCCCCCCC----HHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           111 ANNCRLYLGNIGGDIT----ENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~t----e~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ++-.||.|.=|..++.    -..|...++.||+|.+|.+. .+-.|.|.|.+..+|-+|+.++.. ...|..+.+.|-.
T Consensus        84 pPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWqq  160 (166)
T PF15023_consen   84 PPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-GRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQQ  160 (166)
T ss_pred             CCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-CCceEEEEehhhHHHHHHHHhhcC-CCCCceEEeeccc
Confidence            3456788877766553    33455668999999999875 355799999999999999998765 6677788887753

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=94.00  E-value=0.22  Score=38.04  Aligned_cols=53  Identities=15%  Similarity=0.229  Sum_probs=41.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccC----CCeEEEEEecCCCceEEeeCCHHHHHHHHHHh
Q psy93           114 CRLYLGNIGGDITENDIIELFKPY----GETQELFINKEKMFGFIRMDYKHNADKAKAKL  169 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~----G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l  169 (503)
                      ..|+|.++. +++.++|+.+|..|    ++. .|..+ +-..|-|.|.+.+.|.+|+..|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~-~IEWI-dDtScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPF-RIEWI-DDTSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCc-eEEEe-cCCcEEEEECCHHHHHHHHHcC
Confidence            369999996 69999999999999    543 34333 3346899999999999998764

>KOG0163|consensus

Probab=93.91  E-value=0.6  Score=51.69  Aligned_cols=14  Identities=0%  Similarity=0.062  Sum_probs=6.7

Q ss_pred             CCHHHHHHHHHHhh
Q psy93           236 ARKPAAAQALRRCA  249 (503)
Q Consensus       236 ~s~e~A~kAl~~ln  249 (503)
                      .+++....-+.+.|
T Consensus       771 sDPe~m~~lv~kVn  784 (1259)
T KOG0163|consen  771 SDPETMLELVAKVN  784 (1259)
T ss_pred             cCHHHHHHHHHHHH
Confidence            34555555555443

>KOG2591|consensus

Probab=93.87  E-value=0.082  Score=56.24  Aligned_cols=73  Identities=16%  Similarity=0.218  Sum_probs=58.7

Q ss_pred             CcCCCcEEEEcCCCCCCCHHHHHHhhcc--CCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCc--cccCceEEEE
Q psy93           109 KFANNCRLYLGNIGGDITENDIIELFKP--YGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH--VLKGRSLKIR  182 (503)
Q Consensus       109 ~~~~~~~l~V~nLp~~~te~~L~~~F~~--~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~--~l~g~~l~V~  182 (503)
                      .....|.|++.-||.++..++|+.||+.  |-++.+|.+.-+.+ =||+|++..||+.|.+.|...  +|.|++|..+
T Consensus       171 p~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n-WyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  171 PNHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN-WYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             cCcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc-eEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            3345688999999999999999999975  77888998865444 599999999999999887543  6677776544

>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=93.62  E-value=0.045  Score=51.10  Aligned_cols=74  Identities=16%  Similarity=0.300  Sum_probs=48.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhcc-CCCe---EEEEE-ecC-------CCceEEeeCCHHHHHHHHHHhCCccccCc--
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKP-YGET---QELFI-NKE-------KMFGFIRMDYKHNADKAKAKLDGHVLKGR--  177 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~-~G~V---~~v~i-~~~-------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~--  177 (503)
                      ..+.|.|.+||+++|++++.+.++. ++..   ..+.- ...       -.-|||.|.+.+++...+..++|..+.+.  
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            4568999999999999999998887 6655   22221 111       23699999999999999999999866532  


Q ss_pred             ---eEEEEecc
Q psy93           178 ---SLKIRFAP  185 (503)
Q Consensus       178 ---~l~V~~a~  185 (503)
                         +-.|++|+
T Consensus        86 ~~~~~~VE~Ap   96 (176)
T PF03467_consen   86 NEYPAVVEFAP   96 (176)
T ss_dssp             -EEEEEEEE-S
T ss_pred             CCcceeEEEcc
Confidence               33455554

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

Probab=93.25  E-value=0.22  Score=49.45  Aligned_cols=69  Identities=17%  Similarity=0.275  Sum_probs=55.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCce-EEEEe
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRS-LKIRF  183 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~-l~V~~  183 (503)
                      .+-|-|-++|+. .-..|..+|++||.|++.....+-.+-+|.|.+.-+|.+||.. ||+.|.+.. |-|..
T Consensus       197 D~WVTVfGFppg-~~s~vL~~F~~cG~Vvkhv~~~ngNwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkp  266 (350)
T KOG4285|consen  197 DTWVTVFGFPPG-QVSIVLNLFSRCGEVVKHVTPSNGNWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKP  266 (350)
T ss_pred             cceEEEeccCcc-chhHHHHHHHhhCeeeeeecCCCCceEEEEecchhHHHHhhhh-cCeeeccceEEeeee
Confidence            456777788764 4456778999999999998887778999999999999999974 898888744 34443

>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=93.16  E-value=0.17  Score=47.45  Aligned_cols=61  Identities=20%  Similarity=0.281  Sum_probs=48.6

Q ss_pred             CHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhC--CccccCceEEEEeccc
Q psy93           126 TENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLD--GHVLKGRSLKIRFAPI  186 (503)
Q Consensus       126 te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~--g~~l~g~~l~V~~a~~  186 (503)
                      ..+.|+++|..|+.+..+.+.++=+-..|.|.+.++|.+|...|+  +..+.|..|+|.++..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            457899999999999999988887889999999999999999999  8999999999988844

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.

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=93.16  E-value=0.092  Score=43.09  Aligned_cols=56  Identities=14%  Similarity=0.244  Sum_probs=42.2

Q ss_pred             eEEeeCCHHHHHHHHHHhCCc--cccCceEEEEec---------------ccccceeccCcccccCHHHHHHHh
Q psy93           152 GFIRMDYKHNADKAKAKLDGH--VLKGRSLKIRFA---------------PINAAIKVKNLTSCVTNELLELAF  208 (503)
Q Consensus       152 aFV~F~~~e~A~~Ai~~l~g~--~l~g~~l~V~~a---------------~~~~~L~V~nLp~~~tee~L~~~F  208 (503)
                      |+|+|.++.-|++.++. ...  .+.++.+.|...               .+..+|.|+|||..+++++|.+.+
T Consensus         1 AlITF~e~~VA~~i~~~-~~~~v~l~~~~~~V~v~P~~~~~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~L   73 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKK-KKHPVPLEDCCVRVKVSPVTLGHLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKL   73 (88)
T ss_pred             CEEEeCcHHHHHHHHhC-CEEEEEECCEEEEEEEEeEecCCceEEEEEEcccCCEEEEeCCCCCCChhhheeeE
Confidence            78999999999998864 222  444555555444               357889999999999999998765

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG2253|consensus

Probab=93.11  E-value=0.49  Score=51.65  Aligned_cols=58  Identities=19%  Similarity=0.149  Sum_probs=51.6

Q ss_pred             cccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhh
Q psy93           184 APINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCA  249 (503)
Q Consensus       184 a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln  249 (503)
                      .++..++||+|+...++.+-++.+...||.|.++..+.        |+|+.|.....+..|+..|+
T Consensus        37 ~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~--------fgf~~f~~~~~~~ra~r~~t   94 (668)
T KOG2253|consen   37 LPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK--------FGFCEFLKHIGDLRASRLLT   94 (668)
T ss_pred             CCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh--------hcccchhhHHHHHHHHHHhc
Confidence            34578999999999999999999999999998876643        99999999999999999876

>KOG2202|consensus

Probab=92.91  E-value=0.056  Score=52.43  Aligned_cols=66  Identities=23%  Similarity=0.238  Sum_probs=49.5

Q ss_pred             HHHHHHhc-cCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCccc
Q psy93           202 ELLELAFG-VFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTD  271 (503)
Q Consensus       202 e~L~~~Fs-~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~~  271 (503)
                      ++|...|+ +||+|++++|-.+-.-.-.|-++|.|...++|++|+..|| +.++   .++||..+...-.+
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~ln-nRw~---~G~pi~ae~~pvT~  149 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLN-NRWY---NGRPIHAELSPVTD  149 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHc-Cccc---cCCcceeeecCcCc
Confidence            34444555 9999999877665333447789999999999999999998 4444   68999888755443

>KOG1996|consensus

Probab=92.72  E-value=0.28  Score=48.49  Aligned_cols=64  Identities=19%  Similarity=0.200  Sum_probs=49.6

Q ss_pred             HHHHHHHhccCCCeeeeEEEeCCCCC--ceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCC
Q psy93           201 NELLELAFGVFGDIERAIVIVDERGN--SKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLE  268 (503)
Q Consensus       201 ee~L~~~Fs~~G~V~~~~v~~d~~g~--skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~  268 (503)
                      ++++++.+.+||+|..|.|..++.-.  ..---||+|...++|.+|+-.|| |.+|   .++.+..-++.
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~Vdln-GRyF---GGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLN-GRYF---GGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcC-Ccee---cceeeeheecc
Confidence            45688899999999999888764221  12246999999999999999997 7777   57777766654

>KOG3634|consensus

Probab=92.63  E-value=0.96  Score=45.49  Aligned_cols=56  Identities=27%  Similarity=0.353  Sum_probs=25.9

Q ss_pred             hhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHH
Q psy93           306 FEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEEL  361 (503)
Q Consensus       306 ~e~~~r~k~l~e~ee~e~e~~Ree~~~rE~~rEr~r~E~E~~eRq~ee~r~reeE~  361 (503)
                      .+|...++...+..+.+...+++.+..+.+.++....+...+.|+.+++|..++++
T Consensus        86 ~ey~~~~~~~rer~E~eL~eLkekq~~r~~eR~~eE~e~~~rkr~~e~RR~~~aee  141 (361)
T KOG3634|consen   86 GEYEDFDRIEREREEKELKELKEKQEKRKLEREEEEEELAERKRRIEERRREEAEE  141 (361)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcHHHHHHHHhhHHhhhhchHHH
Confidence            34445555555555666666665555554443333332333333333333333333

>KOG3654|consensus

Probab=92.62  E-value=0.85  Score=48.20  Aligned_cols=71  Identities=25%  Similarity=0.347  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhhHHHHHHhH
Q psy93           313 KQLHELYEHETEMLR-KELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQ  384 (503)
Q Consensus       313 k~l~e~ee~e~e~~R-ee~~~rE~~rEr~r~E~E~~eRq~ee~r~reeE~~r~rqee~~~~~~r~eEelrRrq  384 (503)
                      |.-++|......++. ++.+.+|.++.+|.+|-|++.+++|-+|.-+||+.+.++|.-+.++-|| |-+||.|
T Consensus       384 kaedema~kraallekqqrraeear~rkqqleae~e~kreearrkaeeer~~keee~arrefirq-ey~rrkq  455 (708)
T KOG3654|consen  384 KAEDEMAQKRAALLEKQQRRAEEARRRKQQLEAEKEQKREEARRKAEEERAPKEEEVARREFIRQ-EYERRKQ  455 (708)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhhhcchhhhhhHHHHHHH-HHHHHHH
Confidence            334444443333333 3333345566677788888888877777777766554444333333343 3344444

>KOG0115|consensus

Probab=92.39  E-value=0.17  Score=49.21  Aligned_cols=62  Identities=23%  Similarity=0.339  Sum_probs=51.6

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe-----cCCCceEEeeCCHHHHHHHHHHhCC
Q psy93           110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFIN-----KEKMFGFIRMDYKHNADKAKAKLDG  171 (503)
Q Consensus       110 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~-----~~kg~aFV~F~~~e~A~~Ai~~l~g  171 (503)
                      +.....|||.||+..++.+.|...|+.||+|....++     +..+-++|.|...-.|.+|+..+.-
T Consensus        28 fa~~a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~   94 (275)
T KOG0115|consen   28 FAMHAELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCRE   94 (275)
T ss_pred             eeccceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhcc
Confidence            3334679999999999999999999999999876553     2356899999999999999988743

>KOG4574|consensus

Probab=91.77  E-value=0.11  Score=57.85  Aligned_cols=70  Identities=19%  Similarity=0.286  Sum_probs=61.0

Q ss_pred             EEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCcccc--CceEEEEecc
Q psy93           116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLK--GRSLKIRFAP  185 (503)
Q Consensus       116 l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~--g~~l~V~~a~  185 (503)
                      .++-|.+-..+...|..+|+.||.|.+++..++-..|.|.|.+.+.|..|++.|+|+++.  |-+.+|.+++
T Consensus       301 ~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak  372 (1007)
T KOG4574|consen  301 QSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAK  372 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhcchhhheecccccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecc
Confidence            445555556788899999999999999999988899999999999999999999999654  7888888885

>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=91.46  E-value=1.9  Score=42.86  Aligned_cols=136  Identities=15%  Similarity=0.215  Sum_probs=89.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCC-------------CceEEeeCCHHHHHHHHH----HhCC--cc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEK-------------MFGFIRMDYKHNADKAKA----KLDG--HV  173 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~k-------------g~aFV~F~~~e~A~~Ai~----~l~g--~~  173 (503)
                      ++.|.+.|+..+++-..+...|-+||+|++|.++.+.             ....+.|-+.+.+.....    .|..  +.
T Consensus        15 TRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEfK~~   94 (309)
T PF10567_consen   15 TRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEFKTK   94 (309)
T ss_pred             eHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHHHHh
Confidence            4568899999999999999999999999999997654             688999999988654332    2221  24


Q ss_pred             ccCceEEEEecc--------------------------------cccceeccCccccc-CHHHHHHHh---ccCC----C
Q psy93           174 LKGRSLKIRFAP--------------------------------INAAIKVKNLTSCV-TNELLELAF---GVFG----D  213 (503)
Q Consensus       174 l~g~~l~V~~a~--------------------------------~~~~L~V~nLp~~~-tee~L~~~F---s~~G----~  213 (503)
                      +....|+|.+..                                .++.|.|.= ...+ +++.+.+.+   ..-+    .
T Consensus        95 L~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~IeF-~~~~~~~dl~~~kL~fL~~~~n~RYV  173 (309)
T PF10567_consen   95 LKSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIEF-KDPVDKDDLIEKKLPFLKNSNNKRYV  173 (309)
T ss_pred             cCCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEEe-cCccchhHHHHHhhhhhccCCCceEE
Confidence            555666665542                                012233321 1222 233333322   2222    2


Q ss_pred             eeeeEEEeCC---CCCceeEEEEEeCCHHHHHHHHHHhh
Q psy93           214 IERAIVIVDE---RGNSKCEGIVEFARKPAAAQALRRCA  249 (503)
Q Consensus       214 V~~~~v~~d~---~g~skg~gfV~F~s~e~A~kAl~~ln  249 (503)
                      |+++.++...   ..-++.||+++|-+...|...+..|.
T Consensus       174 lEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk  212 (309)
T PF10567_consen  174 LESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLK  212 (309)
T ss_pred             EEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHH
Confidence            5566666432   33457799999999999999998876

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.

>KOG3152|consensus

Probab=91.39  E-value=1.3  Score=43.14  Aligned_cols=65  Identities=18%  Similarity=0.311  Sum_probs=53.4

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-C--------CCc----eeEEEEEeCCHHHHHHHHHHhhCC
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-R--------GNS----KCEGIVEFARKPAAAQALRRCAEG  251 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~--------g~s----kg~gfV~F~s~e~A~kAl~~ln~g  251 (503)
                      ...||+++||+.+.-.-|+++|+.||.|-.|.+.... .        +.+    -..|.|+|.+...|..+...||+.
T Consensus        74 ~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~  151 (278)
T KOG3152|consen   74 TGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNT  151 (278)
T ss_pred             ceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCC
Confidence            4678999999999999999999999999999886542 1        111    234789999999999999999833

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=90.28  E-value=0.91  Score=34.72  Aligned_cols=54  Identities=20%  Similarity=0.218  Sum_probs=41.6

Q ss_pred             cceeccCcccccCHHHHHHHhccC---CCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHh
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVF---GDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRC  248 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~---G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~l  248 (503)
                      ..|+|.++. .++.++|+.+|..|   .....+..+-|.      .|-|.|.+.+.|.+||.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC------cEEEEECCHHHHHHHHHcC
Confidence            568888875 47888999999998   124456666652      5889999999999999764

>KOG2193|consensus

Probab=90.27  E-value=0.21  Score=51.59  Aligned_cols=75  Identities=19%  Similarity=0.088  Sum_probs=56.6

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecC
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPL  267 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~  267 (503)
                      +.||+.||.+.++..+|..+|...-.-.+-.++..     .+|+||.+.+...|.+|++.++.+..+   .++.+.++..
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k-----~gyafvd~pdq~wa~kaie~~sgk~el---qGkr~e~~~s   73 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK-----SGYAFVDCPDQQWANKAIETLSGKVEL---QGKRQEVEHS   73 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee-----cceeeccCCchhhhhhhHHhhchhhhh---cCceeeccch
Confidence            46899999999999999999976532222233333     679999999999999999999855544   6777777665


Q ss_pred             Ccc
Q psy93           268 ELT  270 (503)
Q Consensus       268 ~~~  270 (503)
                      .++
T Consensus        74 v~k   76 (584)
T KOG2193|consen   74 VPK   76 (584)
T ss_pred             hhH
Confidence            444

>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=90.21  E-value=1.6  Score=37.42  Aligned_cols=63  Identities=11%  Similarity=0.175  Sum_probs=47.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCC-CeEEEEEecC----CCceEEeeCCHHHHHHHHHHhCCccccC
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYG-ETQELFINKE----KMFGFIRMDYKHNADKAKAKLDGHVLKG  176 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G-~V~~v~i~~~----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g  176 (503)
                      +.+.+...|..++.++|..+.+.+- .|..++|+++    +-.+++.|.+.++|......+||+.+..
T Consensus        14 ~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   14 TLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             eEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            3445555566666777777777665 5667777754    4479999999999999999999997764

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2318|consensus

Probab=90.12  E-value=1.3  Score=47.65  Aligned_cols=74  Identities=24%  Similarity=0.426  Sum_probs=59.3

Q ss_pred             CCcEEEEcCCCCC-CCHHHHHHhhccC----CCeEEEEEecC--------------------------------------
Q psy93           112 NNCRLYLGNIGGD-ITENDIIELFKPY----GETQELFINKE--------------------------------------  148 (503)
Q Consensus       112 ~~~~l~V~nLp~~-~te~~L~~~F~~~----G~V~~v~i~~~--------------------------------------  148 (503)
                      .+.+|-|.||.++ +...+|..+|+.|    |.|.+|.|.++                                      
T Consensus       173 ~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~~~  252 (650)
T KOG2318|consen  173 ETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEEED  252 (650)
T ss_pred             ccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhhhh
Confidence            4578999999975 7889999998866    58999998311                                      


Q ss_pred             --------------C-CceEEeeCCHHHHHHHHHHhCCcccc--CceEEEEecc
Q psy93           149 --------------K-MFGFIRMDYKHNADKAKAKLDGHVLK--GRSLKIRFAP  185 (503)
Q Consensus       149 --------------k-g~aFV~F~~~e~A~~Ai~~l~g~~l~--g~~l~V~~a~  185 (503)
                                    + -||.|+|.+.+.|.+....|+|+.|.  +..|-++|.+
T Consensus       253 ~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFIP  306 (650)
T KOG2318|consen  253 VDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFIP  306 (650)
T ss_pred             HHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeeecC
Confidence                          0 27999999999999999999999887  4556666654

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=89.67  E-value=0.94  Score=40.69  Aligned_cols=56  Identities=20%  Similarity=0.182  Sum_probs=41.6

Q ss_pred             HHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCcc
Q psy93           203 LLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELT  270 (503)
Q Consensus       203 ~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~  270 (503)
                      +|.+.|..||.|.-++++-+       .-+|+|.+..+|.+|+..  ++..+   +++.+.|....+.
T Consensus        52 ~ll~~~~~~GevvLvRfv~~-------~mwVTF~dg~sALaals~--dg~~v---~g~~l~i~LKtpd  107 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD-------TMWVTFRDGQSALAALSL--DGIQV---NGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT-------CEEEEESSCHHHHHHHHG--CCSEE---TTEEEEEEE----
T ss_pred             HHHHHHHhCCceEEEEEeCC-------eEEEEECccHHHHHHHcc--CCcEE---CCEEEEEEeCCcc
Confidence            67788999999887777654       579999999999999986  46666   6888888765544

; PDB: 1UFW_A 2DNR_A.

>KOG3634|consensus

Probab=89.33  E-value=4.5  Score=40.86  Aligned_cols=70  Identities=34%  Similarity=0.376  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhhHHHHHHhHhhhhH
Q psy93           320 EHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQLRLAQQEEDLRRRQNDNSM  389 (503)
Q Consensus       320 e~e~e~~Ree~~~rE~~rEr~r~E~E~~eRq~ee~r~reeE~~r~rqee~~~~~~r~eEelrRrq~E~~~  389 (503)
                      ..+++.+.++|..-...++..+++++..+++..+++++.+++.+++.++++.+-.+.+++..|..+|+.+
T Consensus        93 ~~~rer~E~eL~eLkekq~~r~~eR~~eE~e~~~rkr~~e~RR~~~aeerk~r~~k~de~r~r~~Eek~R  162 (361)
T KOG3634|consen   93 RIEREREEKELKELKEKQEKRKLEREEEEEELAERKRRIEERRREEAEERKIREAKEDERRIRLEEEKSR  162 (361)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhcHHHHHHHHhhHHhhhhchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444444333444455555555555555555555443322222222223333334444444443

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=87.55  E-value=0.8  Score=36.22  Aligned_cols=66  Identities=23%  Similarity=0.405  Sum_probs=39.6

Q ss_pred             EEEEcCC--CCCCCHHHHHHhhccCCCe-----EEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           115 RLYLGNI--GGDITENDIIELFKPYGET-----QELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       115 ~l~V~nL--p~~~te~~L~~~F~~~G~V-----~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      +|||. +  -..++..+|..++...+.|     -.|.|.  ..|+||+-... .|..++..|++..+.|++|.|+.|
T Consensus         2 rl~in-~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~--~~~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen    2 RLFIN-VGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIF--DNFSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             EEEES--SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE---SS-EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             EEEEE-cccccCCCHHHHHHHHHhccCCCHHhEEEEEEe--eeEEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            45663 3  2468899999998877554     455553  56899998874 788899999999999999999864

; PDB: 2G0C_A 3MOJ_B.

>KOG2412|consensus

Probab=87.21  E-value=4.5  Score=43.54  Aligned_cols=16  Identities=6%  Similarity=0.001  Sum_probs=9.0

Q ss_pred             CCCCCCHHHHHHhhcc
Q psy93           121 IGGDITENDIIELFKP  136 (503)
Q Consensus       121 Lp~~~te~~L~~~F~~  136 (503)
                      .+++++-.||...|+.
T Consensus        20 ~epn~~fpdl~a~~as   35 (591)
T KOG2412|consen   20 PEPNWNFPDLVAEIAS   35 (591)
T ss_pred             CCCCCCchhHHHHhhh
Confidence            3455666666666544

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=86.29  E-value=2.2  Score=38.13  Aligned_cols=72  Identities=14%  Similarity=0.098  Sum_probs=50.3

Q ss_pred             ccceeccC----cccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeE
Q psy93           187 NAAIKVKN----LTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPV  262 (503)
Q Consensus       187 ~~~L~V~n----Lp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl  262 (503)
                      -.+|.|.-    +.+.-+-..|...++.||+|.++.+.-      +-.|+|.|.+..+|-+|+.++...     ..+..+
T Consensus        86 MsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG------rqsavVvF~d~~SAC~Av~Af~s~-----~pgtm~  154 (166)
T PF15023_consen   86 MSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG------RQSAVVVFKDITSACKAVSAFQSR-----APGTMF  154 (166)
T ss_pred             ceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC------CceEEEEehhhHHHHHHHHhhcCC-----CCCceE
Confidence            34555544    444444456777889999999987643      447999999999999999998622     235556


Q ss_pred             EeecCCc
Q psy93           263 IVEPLEL  269 (503)
Q Consensus       263 ~V~~~~~  269 (503)
                      .+.|...
T Consensus       155 qCsWqqr  161 (166)
T PF15023_consen  155 QCSWQQR  161 (166)
T ss_pred             Eeecccc
Confidence            6666543

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=86.21  E-value=2.2  Score=34.59  Aligned_cols=53  Identities=15%  Similarity=0.174  Sum_probs=39.1

Q ss_pred             ceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhh
Q psy93           189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCA  249 (503)
Q Consensus       189 ~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln  249 (503)
                      ..+|. .|......||.++|+.||.|. |..+.|      ..|||.....+.|..|+..++
T Consensus        11 VFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d------TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   11 VFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND------TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             EEEEE---TT--HHHHHHHCCCCCCEE-EEEECT------TEEEEEECCCHHHHHHHHHHT
T ss_pred             EEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC------CcEEEEeecHHHHHHHHHHhc
Confidence            34444 889999999999999999975 333433      279999999999999999886

; 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.

>KOG3054|consensus

Probab=86.17  E-value=7.6  Score=37.65  Aligned_cols=17  Identities=12%  Similarity=0.388  Sum_probs=8.4

Q ss_pred             hhHHHHHHhHhhhhHHH
Q psy93           375 QQEEDLRRRQNDNSMFL  391 (503)
Q Consensus       375 r~eEelrRrq~E~~~~~  391 (503)
                      ..+||..|+..|.++.|
T Consensus       163 kakEE~arkeheEylkm  179 (299)
T KOG3054|consen  163 KAKEEEARKEHEEYLKM  179 (299)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            33344445555555555

>PTZ00146 fibrillarin; Provisional

Probab=85.73  E-value=1.4  Score=44.45  Aligned_cols=15  Identities=13%  Similarity=0.000  Sum_probs=7.2

Q ss_pred             EEEEEeCCHHHHHHH
Q psy93           230 EGIVEFARKPAAAQA  244 (503)
Q Consensus       230 ~gfV~F~s~e~A~kA  244 (503)
                      +.|+....+..+..+
T Consensus       205 vV~~Dva~pdq~~il  219 (293)
T PTZ00146        205 VIFADVAQPDQARIV  219 (293)
T ss_pred             EEEEeCCCcchHHHH
Confidence            455555555444333

>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=85.09  E-value=2.6  Score=39.36  Aligned_cols=80  Identities=14%  Similarity=0.118  Sum_probs=48.0

Q ss_pred             ccceeccCcccccCHHHHHHHhcc-CCCee---eeEEEeC--C-CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCC
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGV-FGDIE---RAIVIVD--E-RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSL  259 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~-~G~V~---~~~v~~d--~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~  259 (503)
                      ..+|.|.+||+.+|++++.+.++. ++...   .+.-...  . ......-|||.|.+.+++..-+..++ ++.+....+
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~-g~~F~D~kg   85 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFD-GHVFVDSKG   85 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCT-TEEEE-TTS
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcC-CcEEECCCC
Confidence            458999999999999999987776 66552   2221122  1 11224569999999999999999986 665654444


Q ss_pred             C--eEEeecC
Q psy93           260 R--PVIVEPL  267 (503)
Q Consensus       260 r--pl~V~~~  267 (503)
                      .  +..|+.+
T Consensus        86 ~~~~~~VE~A   95 (176)
T PF03467_consen   86 NEYPAVVEFA   95 (176)
T ss_dssp             -EEEEEEEE-
T ss_pred             CCcceeEEEc
Confidence            3  3444443

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.

>KOG3973|consensus

Probab=83.17  E-value=2  Score=43.58  Aligned_cols=57  Identities=35%  Similarity=0.572  Sum_probs=30.0

Q ss_pred             ccCCCCCCCCCCCCCCCcCCccchhccCCCCccCCCCCcCCCCC----CCCCCCCCCCCCC
Q psy93           444 DFDQGGRSGGGGGRRNDSASSGWSRREGGAGRWGPSVDHGSRRG----GSGGGGPTDYQPK  500 (503)
Q Consensus       444 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~  500 (503)
                      .||++|+-|||-|.--++.|-.----|++.+|-|-+++||.|+|    +++|||+.-+||.
T Consensus       328 ~~~~~ggrgggkg~f~~~~~~~~~~~eqgg~Rgg~Gg~~gGrGgGRGggG~GGGggyqqp~  388 (465)
T KOG3973|consen  328 TFDRQGGRGGGKGTFDRPKTHEEQVLEQGGSRGGSGGNWGGRGGGRGGGGRGGGGGYQQPQ  388 (465)
T ss_pred             CCCCCCCcCCCCCCCcCccccccchhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCch
Confidence            35655555555444444445444444566666666666654433    3344555555663

>KOG2891|consensus

Probab=82.55  E-value=21  Score=35.26  Aligned_cols=20  Identities=25%  Similarity=0.572  Sum_probs=11.6

Q ss_pred             CHHHHHHhhccCCCeEEEEE
Q psy93           126 TENDIIELFKPYGETQELFI  145 (503)
Q Consensus       126 te~~L~~~F~~~G~V~~v~i  145 (503)
                      +++-|+..|..||.|..|.|
T Consensus       174 se~rlr~a~eafg~ir~vdi  193 (445)
T KOG2891|consen  174 SEDRLRKAFEAFGEIRNVDI  193 (445)
T ss_pred             hHHHHHHHHHHhccceecCC
Confidence            34556666666666655555

>KOG4364|consensus

Probab=81.74  E-value=18  Score=39.96  Aligned_cols=12  Identities=0%  Similarity=-0.155  Sum_probs=5.5

Q ss_pred             CCCCCCCCccCC
Q psy93           402 GGYGSPGQAYGN  413 (503)
Q Consensus       402 ~~~~~~~~~~~~  413 (503)
                      ++--+....|-|
T Consensus       390 ~~a~~s~~~f~p  401 (811)
T KOG4364|consen  390 CEATVSDIRFEP  401 (811)
T ss_pred             cccccccccccc
Confidence            444444444444

>KOG2072|consensus

Probab=81.67  E-value=21  Score=40.60  Aligned_cols=15  Identities=7%  Similarity=-0.082  Sum_probs=7.4

Q ss_pred             eEEeeCCHHHHHHHH
Q psy93           152 GFIRMDYKHNADKAK  166 (503)
Q Consensus       152 aFV~F~~~e~A~~Ai  166 (503)
                      -+|.|-+.-+.++++
T Consensus       455 ~La~F~~~~~lEk~~  469 (988)
T KOG2072|consen  455 KLAPFFSAFELEKLL  469 (988)
T ss_pred             HHHhhcCHHHHHHHH
Confidence            344555555555443

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=80.03  E-value=6.5  Score=30.47  Aligned_cols=55  Identities=13%  Similarity=0.213  Sum_probs=43.1

Q ss_pred             CCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEE
Q psy93           124 DITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKI  181 (503)
Q Consensus       124 ~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V  181 (503)
                      .++.++|+..+..|.-. .|.  .++.=-||.|.+..+|++|....+++.+....|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~~-~I~--~d~tGfYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRWD-RIR--DDRTGFYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCcc-eEE--ecCCEEEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            47889999999999642 233  34444689999999999999999999887766654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	503
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-61
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		9e-56
2cpj_A	99	Solution Structure Of The N-Terminal Rna Recognitio		1e-13
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		8e-10
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		8e-10
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		8e-10
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		5e-09
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		2e-08
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		1e-04
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		1e-04
1x4g_A	109	Solution Structure Of Rrm Domain In Nucleolysin Tia		1e-04
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		2e-04
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		2e-04
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		3e-04
1x4a_A	109	Solution Structure Of Rrm Domain In Splicing Factor		4e-04
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		5e-04
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		8e-04
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		9e-04

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score =  233 bits (594), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 122/253 (48%), Positives = 169/253 (66%), Gaps = 12/253 (4%)
Query: 110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL 169
           +   CRL++GN+  DITE D   LF+ YGE  E+FIN+++ FGFIR++ +  A+ AKA+L
Sbjct: 19  YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAEL 78
Query: 170 DGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKC 229
           DG +LK R L+IRFA   AA+ VKNL+  V+NELLE AF  FG +E+A+V+VD+RG +  
Sbjct: 79  DGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATG 138
Query: 230 EGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFY 289
           +G VEFA KP A +AL RC +G F LT + RPVIVEP+E  D+ DGL E+ + +KT +++
Sbjct: 139 KGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEK-LMQKTQQYH 197
Query: 290 KQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKER 349
           K+R+  PRFA   +FEFEY SRWK L E+     E  ++E   R I   ++K E EM   
Sbjct: 198 KEREQPPRFAQPGTFEFEYASRWKALDEM-----EKQQREQVDRNIREAKEKLEAEM--- 249
Query: 350 QAEELKRRDEELM 362
              E  R + +LM
Sbjct: 250 ---EAARHEHQLM 259

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score =  214 bits (545), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 117/257 (45%), Positives = 170/257 (66%), Gaps = 9/257 (3%)
Query: 91  IQGPTLDLPP-SEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEK 149
           ++G T+DL    +P  K   F    RL++GN+  DITE ++ +LF+ YG+  E+FI+K+K
Sbjct: 1   MEGLTIDLKNFRKPGEKT--FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK 58
Query: 150 MFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFG 209
            FGFIR++ +  A+ AK +LD   L+G+ L++RFA  +A++ V+NL   V+NELLE AF 
Sbjct: 59  GFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTVRNLPQYVSNELLEEAFS 118
Query: 210 VFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLEL 269
           VFG +ERA+VIVD+RG    +GIVEF+ KPAA +AL RC+EG F LT   RPV VEP++ 
Sbjct: 119 VFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCSEGSFLLTTFPRPVTVEPMDQ 178
Query: 270 TDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEMLRKE 329
            D+ +GL E+ + K   +F+K+R+  PRFA   SFE+EY  RWK L E+ + + + +   
Sbjct: 179 LDDEEGLPEKLVIKNQ-QFHKEREQPPRFAQPGSFEYEYAMRWKALIEMEKQQQDQV--- 234
Query: 330 LAQREIDRERQKAEWEM 346
              R I   R+K E EM
Sbjct: 235 --DRNIKEAREKLEMEM 249

>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif Of Nono Length = 99

Iteration: 1
 Score = 74.7 bits (182), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 35/81 (43%), Positives = 58/81 (71%)
Query: 110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL 169
           F    RL++GN+  DITE ++ +LF+ YG+  E+FI+K+K FGFIR++ +  A+ AK +L
Sbjct: 12  FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVEL 71
Query: 170 DGHVLKGRSLKIRFAPINAAI 190
           D   L+G+ L++RFA  +A++
Sbjct: 72  DNMPLRGKQLRVRFACHSASL 92

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 62.0 bits (149), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 39/137 (28%), Positives = 68/137 (49%), Gaps = 2/137 (1%)
Query: 109 KFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAK 168
           +F N  ++ +  + GD+T  ++ +L   Y E +  F++K K   F+ +     A+ A   
Sbjct: 18  QFRNRRKILIRGLPGDVTNQEVHDLLSDY-ELKYCFVDKYKGTAFVTLLNGEQAEAAINA 76
Query: 169 LDGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDER-GNS 227
                L+ R L ++  P +A + V NL   +T +  E     FG +ER  ++  ER G S
Sbjct: 77  FHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQS 136
Query: 228 KCEGIVEFARKPAAAQA 244
           K  G  E+ +K +AA+A
Sbjct: 137 KGYGFAEYMKKDSAARA 153

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 62.0 bits (149), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 39/137 (28%), Positives = 68/137 (49%), Gaps = 2/137 (1%)
Query: 109 KFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAK 168
           +F N  ++ +  + GD+T  ++ +L   Y E +  F++K K   F+ +     A+ A   
Sbjct: 18  QFRNRRKILIRGLPGDVTNQEVHDLLSDY-ELKYCFVDKYKGTAFVTLLNGEQAEAAINA 76
Query: 169 LDGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDER-GNS 227
                L+ R L ++  P +A + V NL   +T +  E     FG +ER  ++  ER G S
Sbjct: 77  FHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQS 136
Query: 228 KCEGIVEFARKPAAAQA 244
           K  G  E+ +K +AA+A
Sbjct: 137 KGYGFAEYMKKDSAARA 153

>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With Human Vinculin Tail Domain Vt Length = 283

Iteration: 1
 Score = 62.0 bits (149), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 39/137 (28%), Positives = 68/137 (49%), Gaps = 2/137 (1%)
Query: 109 KFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAK 168
           +F N  ++ +  + GD+T  ++ +L   Y E +  F++K K   F+ +     A+ A   
Sbjct: 16  QFRNRRKILIRGLPGDVTNQEVHDLLSDY-ELKYCFVDKYKGTAFVTLLNGEQAEAAINA 74
Query: 169 LDGHVLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDER-GNS 227
                L+ R L ++  P +A + V NL   +T +  E     FG +ER  ++  ER G S
Sbjct: 75  FHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQS 134
Query: 228 KCEGIVEFARKPAAAQA 244
           K  G  E+ +K +AA+A
Sbjct: 135 KGYGFAEYMKKDSAARA 151

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 59.3 bits (142), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 44/169 (26%), Positives = 82/169 (48%), Gaps = 21/169 (12%)
Query: 93  GPTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKM-- 150
           GP   + PS P            LY+G++  D+TE  + E F P G    + + ++ +  
Sbjct: 1   GPLGSMNPSAPSYP------MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITR 54
Query: 151 --FGFIRMDYKHNADKAKA--KLDGHVLKGRSLKIRFAPINAAIK--------VKNLTSC 198
              G+  ++++  AD  +A   ++  V+KG+ ++I ++  + +++        +KNL   
Sbjct: 55  RSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKS 114
Query: 199 VTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRR 247
           + N+ L   F  FG+I    V+ DE G SK  G V F  + AA +A+ +
Sbjct: 115 IDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEK 162

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 39/146 (26%), Positives = 76/146 (52%), Gaps = 15/146 (10%)
Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKM----FGFIRMDYKHNADKAKA--KL 169
           LY+G++  D+TE  + E F P G    + + ++ +     G+  ++++  AD  +A   +
Sbjct: 13  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 170 DGHVLKGRSLKIRFAPINAAIK--------VKNLTSCVTNELLELAFGVFGDIERAIVIV 221
           +  V+KG+ ++I ++  + +++        +KNL   + N+ L   F  FG+I    V+ 
Sbjct: 73  NFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC 132
Query: 222 DERGNSKCEGIVEFARKPAAAQALRR 247
           DE G SK  G V F  + AA +A+ +
Sbjct: 133 DENG-SKGYGFVHFETQEAAERAIEK 157

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 35/136 (25%), Positives = 72/136 (52%), Gaps = 13/136 (9%)
Query: 124 DITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKLDGHVLKGR 177
           ++T+ +   LF   GE +   + ++K+      +GF+      +A+KA   L+G  L+ +
Sbjct: 13  NMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTK 72
Query: 178 SLKIRFA-PINAAIK-----VKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCE 230
           ++K+ +A P +A+I+     V  L   +T + LE  F  +G I  + ++VD+  G S+  
Sbjct: 73  TIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGV 132
Query: 231 GIVEFARKPAAAQALR 246
           G + F ++  A +A++
Sbjct: 133 GFIRFDKRIEAEEAIK 148

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 32/136 (23%), Positives = 74/136 (54%), Gaps = 13/136 (9%)
Query: 124 DITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKLDGHVLKGR 177
           ++T+++   LF   G+ +   + ++K+      +GF+     ++ADKA   L+G  L+ +
Sbjct: 15  NMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTK 74
Query: 178 SLKIRFA-PINAAIK-----VKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCE 230
           ++K+ +A P +A+I+     V  L   ++ + +E  F  +G I  + +++D+  G S+  
Sbjct: 75  TIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGV 134
Query: 231 GIVEFARKPAAAQALR 246
           G + F ++  A +A++
Sbjct: 135 GFIRFDKRIEAEEAIK 150

>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar Length = 109

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/68 (27%), Positives = 36/68 (52%)
Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH 172
           NC +Y G I   +T+  + + F P+G+  E+ +  EK + F+R     +A  A   ++G 
Sbjct: 25  NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGT 84
Query: 173 VLKGRSLK 180
            ++G  +K
Sbjct: 85  TIEGHVVK 92

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 36/148 (24%), Positives = 71/148 (47%), Gaps = 13/148 (8%)
Query: 111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE----KMFGFIRMDYKHNADKAK 166
           A+N  L +  +  D T+ ++  LF+  G      I ++      FG+  +D+    D  +
Sbjct: 12  ASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQR 71
Query: 167 A--KLDGHVLKGRSLKIRFA-PINAAIK-----VKNLTSCVTNELLELAFGVFGDIERAI 218
           A   L+G  ++ + LK+ +A P   +IK     V NL   +T++ L+  FG +G I +  
Sbjct: 72  AIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKN 131
Query: 219 VIVDE-RGNSKCEGIVEFARKPAAAQAL 245
           ++ D+  G  +    V + ++  A +A+
Sbjct: 132 ILRDKLTGRPRGVAFVRYNKREEAQEAI 159

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 6/73 (8%)
Query: 115 RLYLGNIGGDITENDIIELFKPYGETQEL------FINKEKMFGFIRMDYKHNADKAKAK 168
           RL++ N+    +E D+ +LF  YG   EL         K K F F+   +  +A KA A+
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 169 LDGHVLKGRSLKI 181
           +DG V +GR L +
Sbjct: 70  VDGQVFQGRMLHV 82

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 25/90 (27%), Positives = 46/90 (51%), Gaps = 8/90 (8%)
Query: 101 SEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGE------TQELFINKEKMFGFI 154
           S  Q KD   +N+  +++G++  +IT  DI   F P+G+       +++   K K +GF+
Sbjct: 5   SSGQKKDT--SNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFV 62
Query: 155 RMDYKHNADKAKAKLDGHVLKGRSLKIRFA 184
               K +A+ A   + G  L GR ++  +A
Sbjct: 63  SFYNKLDAENAIVHMGGQWLGGRQIRTNWA 92

>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2 Length = 109

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEK---MFGFIRMDYKHNADKAKAK 168
           N+CR+Y+GN+  DI   DI ++F  YG  +++ +   +    F F+  +   +A+ A   
Sbjct: 21  NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYG 80
Query: 169 LDGHVLKGRSLKIRF 183
            DG+   G  L++ F
Sbjct: 81  RDGYDYDGYRLRVEF 95

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 45/77 (58%), Gaps = 6/77 (7%)
Query: 111 ANNCRLYLGNIGGDITENDIIELFKPYG--ETQELFINKE----KMFGFIRMDYKHNADK 164
           A   RLY+G++  +ITE+ +  +F+P+G  E+ +L ++ E    K +GFI       A K
Sbjct: 24  AGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKK 83
Query: 165 AKAKLDGHVLKGRSLKI 181
           A  +L+G  L GR +K+
Sbjct: 84  ALEQLNGFELAGRPMKV 100

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 35/148 (23%), Positives = 72/148 (48%), Gaps = 13/148 (8%)
Query: 111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE----KMFGFIRMDYKHNADKAK 166
           A+N  L +  +  D+T+ ++  LF+  G      I ++      +G+  +D+    D  +
Sbjct: 1   ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 167 A--KLDGHVLKGRSLKIRFA-PINAAIK-----VKNLTSCVTNELLELAFGVFGDIERAI 218
           A   L+G  ++ + LK+ +A P   +IK     V NL   +T++ L+  FG +G I +  
Sbjct: 61  AIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKN 120
Query: 219 VIVDE-RGNSKCEGIVEFARKPAAAQAL 245
           ++ D+  G  +    V + ++  A +A+
Sbjct: 121 ILRDKLTGRPRGVAFVRYNKREEAQEAI 148

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 25/90 (27%), Positives = 46/90 (51%), Gaps = 8/90 (8%)
Query: 101 SEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGE------TQELFINKEKMFGFI 154
           S  Q KD   +N+  +++G++  +IT  DI   F P+G        +++   K K +GF+
Sbjct: 5   SSGQKKDT--SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFV 62
Query: 155 RMDYKHNADKAKAKLDGHVLKGRSLKIRFA 184
               K +A+ A  ++ G  L GR ++  +A
Sbjct: 63  SFFNKWDAENAIQQMGGQWLGGRQIRTNWA 92

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	503
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.96
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.96
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.96
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.96
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.96
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.96
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.96
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.96
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.95
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.95
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.95
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.95
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.94
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.94
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.94
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.94
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.93
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.93
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.93
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.8
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.74
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.73
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.73
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.72
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.72
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.7
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.7
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.7
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.7
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.69
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.68
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.67
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.67
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.67
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.67
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.67
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.66
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.66
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.66
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.66
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.65
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.65
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.65
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.65
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.64
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.64
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.64
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.64
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.64
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.64
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.64
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.64
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.64
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.64
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.63
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.63
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.63
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.63
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.63
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.63
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.63
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.63
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.63
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.63
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.62
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.62
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.62
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.62
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.62
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.62
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.62
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.62
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.62
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.62
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.62
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.62
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.62
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.61
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.61
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.61
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.61
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.61
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.61
1x5p_A	97	Negative elongation factor E; structure genomics,	99.61
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.61
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.61
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.61
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.61
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.61
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.61
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.61
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.61
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.61
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.61
2div_A	99	TRNA selenocysteine associated protein; structural	99.6
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.6
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.6
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.6
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.6
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.6
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.6
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.6
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.59
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.59
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.59
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.59
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.59
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.58
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.58
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.58
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.58
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.58
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.58
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.58
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.58
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.58
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.58
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.58
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.58
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.58
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.57
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.57
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.57
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.57
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.57
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.57
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.57
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.57
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.56
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.56
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.56
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.56
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.56
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.56
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.56
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.55
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.55
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.55
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.55
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.55
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.55
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.55
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.54
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.54
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.54
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.54
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.54
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.54
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.54
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.53
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.53
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.53
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.53
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.53
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.53
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.53
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.52
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.52
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.52
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.52
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.51
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.51
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.51
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.51
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.5
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.5
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.5
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.5
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.5
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.49
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.49
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.49
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.49
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.49
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.49
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.48
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.48
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.22
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.48
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.48
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.47
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.47
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.47
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.47
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.46
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.46
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.46
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.46
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.45
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.45
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.45
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.45
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.45
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.45
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.44
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.44
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.44
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.44
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.44
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.44
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.44
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.44
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.44
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.43
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.43
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.43
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.43
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.43
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.43
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.43
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.43
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.43
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.42
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.42
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.42
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.42
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.42
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.42
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.42
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.42
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.41
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.41
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.41
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.41
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.41
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.4
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.4
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.4
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.4
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.4
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.4
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.4
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.4
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.4
2div_A	99	TRNA selenocysteine associated protein; structural	99.39
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.39
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.39
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.39
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.39
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.38
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.38
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.38
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.38
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.38
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.38
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.38
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.38
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.38
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.38
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.38
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.38
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.37
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.37
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.37
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.37
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.37
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.37
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.36
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.36
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.36
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.36
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.36
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.36
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.36
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.36
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.36
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.36
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.35
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.35
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.35
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.35
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.35
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.35
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.34
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.34
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.34
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.34
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.34
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.34
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.34
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.34
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.34
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.34
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.34
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.34
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.34
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.33
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.33
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.33
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.33
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.32
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.32
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.32
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.32
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.32
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.32
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.32
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.32
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.31
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.31
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.31
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.31
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.3
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.3
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.3
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.3
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.29
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.29
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.29
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.29
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.28
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.28
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.28
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.28
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.28
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.28
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.27
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.27
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.27
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.26
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.26
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.26
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.26
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.26
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.25
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.25
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.25
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.25
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.24
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.24
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.24
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.24
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.23
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.23
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.23
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.23
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.22
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.22
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.22
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.21
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.21
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.21
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.21
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	98.84
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.2
1x5p_A	97	Negative elongation factor E; structure genomics,	99.2
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.2
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.19
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.19
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.19
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.19
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.17
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.17
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.16
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.15
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.14
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.13
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.13
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.12
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.11
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.1
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.1
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.08
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.07
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.05
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.02
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.0
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.0
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.94
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.92
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.9
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.89
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.69
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.67
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.66
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.4
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.3
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.28
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.2
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.19
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.08
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.75
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.22
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.13
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.93
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.85
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.61
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.24
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.12
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	95.99
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.95
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	95.69
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.45
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	95.2
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	95.16
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	93.77
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	92.41
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	91.58
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	89.61
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	85.63

>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=100.00  E-value=4.4e-39  Score=317.60  Aligned_cols=230  Identities=49%  Similarity=0.854  Sum_probs=209.1

Q ss_pred             CCCCCCCCCCCccccCcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCcc
Q psy93            94 PTLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHV  173 (503)
Q Consensus        94 ~~~~~p~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~  173 (503)
                      .++++++... +.....+..++|||+|||+++|+++|+++|+.||.|..|.|.+++|||||+|.+.++|.+|+..||+..
T Consensus         4 ~~~~~~~~~~-p~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~A~~A~~~l~g~~   82 (261)
T 3sde_A            4 FTIDIKSFLK-PGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTI   82 (261)
T ss_dssp             ---CCCCCCC-TTCCSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCE
T ss_pred             cccCccccCC-CCCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCCCcEEEEEECCHHHHHHHHHHcCCcE
Confidence            4455544443 355667788999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCceEEEEecccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCee
Q psy93           174 LKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCF  253 (503)
Q Consensus       174 l~g~~l~V~~a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~  253 (503)
                      |.|++|.|.++.+.++|||.|||..+|+++|+++|+.||.|..|.|+.+.++.+++||||+|.+.++|.+|+..||++.+
T Consensus        83 i~g~~l~v~~a~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~  162 (261)
T 3sde_A           83 LKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAF  162 (261)
T ss_dssp             ETTEECEEEECCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCE
T ss_pred             ECCceeEeeecccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999988999


Q ss_pred             eecCCCCeEEeecCCccccccCCcccccCCCCchhhhhhccCcccCCCCCcchhhhhhhHHHHHHHHHHHHH
Q psy93           254 FLTQSLRPVIVEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEFEYGSRWKQLHELYEHETEM  325 (503)
Q Consensus       254 ~~~~~~rpl~V~~~~~~~~~~~~~~k~i~k~~~~~~kere~~~rf~~~g~~e~e~~~r~k~l~e~ee~e~e~  325 (503)
                      ++...+++|.|.++...++.+..+.+.+. +.+.+.+++..+++|+.+++++++++++|+.+.++++.+.+.
T Consensus       163 ~~~~~~r~i~v~~~~~~~~~~~~~~~~~~-~~~~~~~~r~~~p~~~~pgs~~~~~~~~~~~~~~~~~~~~~~  233 (261)
T 3sde_A          163 LLTTTPRPVIVEPMEQFDDEDGLPEKLMQ-KTQQYHKEREQPPRFAQPGTFEFEYASRWKALDEMEKQQREQ  233 (261)
T ss_dssp             ESSSSCCBCEEEECCCEESSSCCCGGGSC-CCHHHHHHHTSCSEECCTTSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EecCCCceEEEeeccccCccCCCcchhhh-cchhhhhhccCCCCCCCCCcccccccchHHHHHHHHHHHHHH
Confidence            88888999999999999888888888776 567889999999999999999999999999998887655443

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.96  E-value=1.7e-29  Score=241.35  Aligned_cols=156  Identities=27%  Similarity=0.458  Sum_probs=142.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +.++|||+|||+++|+++|+++|++||+|.+|+|+++      +|||||+|.+.++|.+||..|++..+.|+.|+|.++.
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~   93 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   93 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccc
Confidence            4678999999999999999999999999999999753      5799999999999999999999999999999999986


Q ss_pred             c--------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecC
Q psy93           186 I--------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQ  257 (503)
Q Consensus       186 ~--------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~  257 (503)
                      .        ..+|||.|||..+++++|+++|+.||.|..|.|+.|. +.+++||||+|.+.++|.+|+..|| +..+   
T Consensus        94 ~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~-~~~~g~~fV~f~~~~~a~~Ai~~ln-g~~~---  168 (213)
T 4f02_A           94 RDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMN-GMLL---  168 (213)
T ss_dssp             CCTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TEEEEEEEEEESSHHHHHHHHHHHT-TCEE---
T ss_pred             ccccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC-CCCceEEEEEeCCHHHHHHHHHHhC-CCEE---
Confidence            3        4689999999999999999999999999999999885 3479999999999999999999997 6666   


Q ss_pred             CCCeEEeecCCcccc
Q psy93           258 SLRPVIVEPLELTDE  272 (503)
Q Consensus       258 ~~rpl~V~~~~~~~~  272 (503)
                      .+++|.|.++.+..+
T Consensus       169 ~g~~i~V~~a~~~~~  183 (213)
T 4f02_A          169 NDRKVFVGRFKSRKE  183 (213)
T ss_dssp             TTEECEEEECCCHHH
T ss_pred             CCEEEEEEEcCCCcc
Confidence            689999999876543

>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=3.1e-29  Score=230.04  Aligned_cols=156  Identities=19%  Similarity=0.323  Sum_probs=141.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe--------cCCCceEEeeCCHHHHHHHHHHhCCcccc---CceEE
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFIN--------KEKMFGFIRMDYKHNADKAKAKLDGHVLK---GRSLK  180 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~--------~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~---g~~l~  180 (503)
                      ++++|||+|||+++|+++|+++|++||+|.+|.|+        ++++||||+|.+.++|.+|+..|++..+.   +++|.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            46899999999999999999999999999999986        35689999999999999999999998776   68888


Q ss_pred             EEecc-------cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCee
Q psy93           181 IRFAP-------INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCF  253 (503)
Q Consensus       181 V~~a~-------~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~  253 (503)
                      |.++.       ..++|||+|||..+++++|+++|+.||.|..+.++.+.++.+++||||+|.+.++|.+|+..|| +..
T Consensus        82 ~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~-g~~  160 (175)
T 3nmr_A           82 MKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH-QAQ  160 (175)
T ss_dssp             EEECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHT-TSC
T ss_pred             EccccccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhc-CCc
Confidence            88875       4578999999999999999999999999999999999889999999999999999999999998 544


Q ss_pred             eecCCCCeEEeecCC
Q psy93           254 FLTQSLRPVIVEPLE  268 (503)
Q Consensus       254 ~~~~~~rpl~V~~~~  268 (503)
                      +...++++|.|.+++
T Consensus       161 ~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          161 TMEGCSSPMVVKFAD  175 (175)
T ss_dssp             CCTTCSSCCEEEECC
T ss_pred             ccCCCCCCeEEEecC
Confidence            444446999999874

>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=99.96  E-value=2.5e-28  Score=242.65  Aligned_cols=192  Identities=22%  Similarity=0.336  Sum_probs=170.6

Q ss_pred             CcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccccc
Q psy93           109 KFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINA  188 (503)
Q Consensus       109 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~~  188 (503)
                      ...++++|||+|||+++|+++|+++|+.|| |.+|.+.+++|||||+|.+.++|.+|+..||+..|.|++|.|.++++.+
T Consensus        18 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~~~~   96 (284)
T 3smz_A           18 QFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDA   96 (284)
T ss_dssp             HHHCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCSC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEEecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecCCCC
Confidence            345678999999999999999999999999 9999999999999999999999999999999999999999999999999


Q ss_pred             ceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecC
Q psy93           189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPL  267 (503)
Q Consensus       189 ~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~  267 (503)
                      +|||+|||..+++++|.++|+.||.|..+.++.+ .++.+++||||+|.+.++|.+|+..|+ +..+   .+++|.|.++
T Consensus        97 ~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~-~~~~---~g~~i~v~~a  172 (284)
T 3smz_A           97 LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLL-GKPL---GPRTLYVHWT  172 (284)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT-TCEE---TTEECEEEEC
T ss_pred             EEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhC-CCEe---CCcEEEEEEC
Confidence            9999999999999999999999999999999988 588999999999999999999999997 6655   6899999998


Q ss_pred             CccccccC--CcccccCCCCchhh-hhhccCcccCCCCCcc
Q psy93           268 ELTDEIDG--LSERTINKKTPEFY-KQRQVGPRFATVNSFE  305 (503)
Q Consensus       268 ~~~~~~~~--~~~k~i~k~~~~~~-kere~~~rf~~~g~~e  305 (503)
                      ........  ....++..+++... ++..+...|..+|.+.
T Consensus       173 ~~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~  213 (284)
T 3smz_A          173 DAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPT  213 (284)
T ss_dssp             CGGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCS
T ss_pred             CCCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeE
Confidence            77653322  23345666777763 7788888898888764

>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=99.96  E-value=2.8e-28  Score=222.38  Aligned_cols=154  Identities=20%  Similarity=0.408  Sum_probs=139.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ++++|||+|||+++|+++|+++|+.||+|.+|.++++      +|||||+|.+.++|.+|+..|++..+.|++|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            4679999999999999999999999999999998643      5899999999999999999999999999999999986


Q ss_pred             c------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCC
Q psy93           186 I------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQS  258 (503)
Q Consensus       186 ~------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~  258 (503)
                      +      .++|+|.|||..+++++|+++|+.||.|..+.++.+. ++.+++||||+|.+.++|.+|+..|| +..+ ...
T Consensus        82 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~-~g~  159 (168)
T 1b7f_A           82 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN-NVIP-EGG  159 (168)
T ss_dssp             CCSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT-TCCC-TTC
T ss_pred             CCcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhc-CCEe-cCC
Confidence            4      5789999999999999999999999999999999985 88999999999999999999999997 5544 223


Q ss_pred             CCeEEeecC
Q psy93           259 LRPVIVEPL  267 (503)
Q Consensus       259 ~rpl~V~~~  267 (503)
                      .++|.|.++
T Consensus       160 ~~~l~V~~A  168 (168)
T 1b7f_A          160 SQPLSVRLA  168 (168)
T ss_dssp             SSCCEEEEC
T ss_pred             CeEEEEEeC
Confidence            488888764

>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=99.96  E-value=2e-28  Score=233.03  Aligned_cols=154  Identities=14%  Similarity=0.173  Sum_probs=135.1

Q ss_pred             CCcEEEEcCCC-CCCCHHHHHHhhccCCCeEEEEEecC-CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc---
Q psy93           112 NNCRLYLGNIG-GDITENDIIELFKPYGETQELFINKE-KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI---  186 (503)
Q Consensus       112 ~~~~l~V~nLp-~~~te~~L~~~F~~~G~V~~v~i~~~-kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~---  186 (503)
                      ++++|||+||| ..+|+++|+++|+.||.|.+|+|+++ +|||||+|.+.++|.+||+.||+..|.|++|.|.++..   
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~~   82 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAI   82 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSCC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCcc
Confidence            46799999999 79999999999999999999999875 79999999999999999999999999999999998731   


Q ss_pred             ----------------------------------------ccceeccCcccccCHHHHHHHhccCCCe--eeeEEEeCCC
Q psy93           187 ----------------------------------------NAAIKVKNLTSCVTNELLELAFGVFGDI--ERAIVIVDER  224 (503)
Q Consensus       187 ----------------------------------------~~~L~V~nLp~~~tee~L~~~Fs~~G~V--~~~~v~~d~~  224 (503)
                                                              ..+|||.|||+.+++++|+++|+.||.|  ..++++.+. 
T Consensus        83 ~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~-  161 (205)
T 3tyt_A           83 MPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK-  161 (205)
T ss_dssp             CCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC-
T ss_pred             CCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC-
Confidence                                                    2359999999999999999999999999  888888775 


Q ss_pred             CCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           225 GNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       225 g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      +.++++|||+|.+.++|.+||..||+..+-......|++|++
T Consensus       162 ~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~  203 (205)
T 3tyt_A          162 SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKL  203 (205)
T ss_dssp             SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEE
T ss_pred             CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEe
Confidence            455799999999999999999999844443334456787765

>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=99.96  E-value=2.1e-28  Score=224.27  Aligned_cols=151  Identities=25%  Similarity=0.397  Sum_probs=141.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccC----C-------CeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEE
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPY----G-------ETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLK  180 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~----G-------~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~  180 (503)
                      ++++|||+|||+++|+++|+++|+.|    |       .|.++.+.++++||||+|.+.++|.+|+ .||+..|.|++|.
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~   81 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   81 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETTTTEEEEEESSHHHHHHHG-GGTTCEETTEECE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCCCCEEEEEeCCHHHHHHHH-HhCCcEecCceee
Confidence            46899999999999999999999999    7       8999999999999999999999999999 8999999999999


Q ss_pred             EEeccc------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCee
Q psy93           181 IRFAPI------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCF  253 (503)
Q Consensus       181 V~~a~~------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~  253 (503)
                      |.++.+      .++|||+|||..+++++|+++|+.||.|..+.++.+ .++.+++||||+|.+.++|.+|+..|| +..
T Consensus        82 v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~-g~~  160 (172)
T 2g4b_A           82 IRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN-GMQ  160 (172)
T ss_dssp             EECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHT-TCE
T ss_pred             ecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcC-CCE
Confidence            999865      478999999999999999999999999999999999 489999999999999999999999997 666


Q ss_pred             eecCCCCeEEeecC
Q psy93           254 FLTQSLRPVIVEPL  267 (503)
Q Consensus       254 ~~~~~~rpl~V~~~  267 (503)
                      +   .+++|.|.++
T Consensus       161 ~---~g~~l~V~~A  171 (172)
T 2g4b_A          161 L---GDKKLLVQRA  171 (172)
T ss_dssp             E---TTEECEEEEC
T ss_pred             E---CCeEEEEEeC
Confidence            6   6899999876

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.96  E-value=3.6e-28  Score=220.75  Aligned_cols=151  Identities=26%  Similarity=0.351  Sum_probs=140.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc--
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI--  186 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~--  186 (503)
                      ++|||+|||+++|+++|+++|+.||+|.+|.|..+     ++||||+|.+.++|.+|+..|++..+.|++|.|.++.+  
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            47999999999999999999999999999999644     58999999999999999999999999999999999853  


Q ss_pred             ------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCC
Q psy93           187 ------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSL  259 (503)
Q Consensus       187 ------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~  259 (503)
                            ..+|||.|||..+++++|.++|+.||.|..+.++.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+
T Consensus        81 ~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~---~g  156 (166)
T 3md3_A           81 QSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQ-GQDL---NG  156 (166)
T ss_dssp             CCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHT-TCEE---TT
T ss_pred             CCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhC-CCcc---CC
Confidence                  568999999999999999999999999999999988 688999999999999999999999997 6655   68


Q ss_pred             CeEEeecCC
Q psy93           260 RPVIVEPLE  268 (503)
Q Consensus       260 rpl~V~~~~  268 (503)
                      ++|.|.++.
T Consensus       157 ~~i~v~~a~  165 (166)
T 3md3_A          157 RPLRINWAA  165 (166)
T ss_dssp             EECEEEESC
T ss_pred             cEEEEEecC
Confidence            999999875

>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=99.96  E-value=4.8e-28  Score=220.15  Aligned_cols=153  Identities=24%  Similarity=0.416  Sum_probs=137.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCC------CceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEK------MFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~k------g~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      +++|||+|||+++|+++|+++|+.||+|.+|.+++++      +||||+|.+.++|.+|+..|++..+.|++|.|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            5789999999999999999999999999999997654      8999999999999999999999999999999999864


Q ss_pred             ------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCC
Q psy93           187 ------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSL  259 (503)
Q Consensus       187 ------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~  259 (503)
                            ..+|||.|||..+++++|+++|+.||.|..+.++.+. ++.+++||||+|.+.++|.+|+..|| +..+ ....
T Consensus        82 ~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~-g~~~-~g~~  159 (167)
T 1fxl_A           82 SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN-GQKP-SGAT  159 (167)
T ss_dssp             CCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT-TCCC-TTCS
T ss_pred             CcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhc-CCcc-CCCc
Confidence                  4679999999999999999999999999999999884 88899999999999999999999997 5544 1222


Q ss_pred             CeEEeecC
Q psy93           260 RPVIVEPL  267 (503)
Q Consensus       260 rpl~V~~~  267 (503)
                      .+|.|.++
T Consensus       160 ~~i~v~~A  167 (167)
T 1fxl_A          160 EPITVKFA  167 (167)
T ss_dssp             SCCEEEEC
T ss_pred             cceEEEeC
Confidence            45777764

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.95  E-value=1.3e-27  Score=227.07  Aligned_cols=154  Identities=21%  Similarity=0.333  Sum_probs=141.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      .++|||+|||+++|+++|+++|+.||+|.+|.|++      +++||||+|.+.++|.+|+..|++..|.|+.|.|.++..
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN  107 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCC
Confidence            46899999999999999999999999999999964      478999999999999999999999999999999988743


Q ss_pred             -----------------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHh
Q psy93           187 -----------------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRC  248 (503)
Q Consensus       187 -----------------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~l  248 (503)
                                       .++|||.|||..+++++|+++|+.||.|..+.|+.+ .++.+++||||+|.+.++|.+|+..|
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l  187 (216)
T 2qfj_A          108 IGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM  187 (216)
T ss_dssp             CGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             ccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHc
Confidence                             368999999999999999999999999999999998 58899999999999999999999999


Q ss_pred             hCCeeeecCCCCeEEeecCCcc
Q psy93           249 AEGCFFLTQSLRPVIVEPLELT  270 (503)
Q Consensus       249 n~g~~~~~~~~rpl~V~~~~~~  270 (503)
                      | +..+   .+++|.|.++...
T Consensus       188 ~-g~~~---~g~~i~V~~a~~~  205 (216)
T 2qfj_A          188 N-LFDL---GGQYLRVGKAVTP  205 (216)
T ss_dssp             T-TCBC---SSSBCEEEECSSC
T ss_pred             c-CCEe---CCcEEEEEEecCC
Confidence            7 5555   6899999998665

>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=99.95  E-value=1e-27  Score=224.33  Aligned_cols=156  Identities=17%  Similarity=0.252  Sum_probs=138.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ...++|||+|||+++|+++|+++|+.||+|.+|.|+.+      +|||||+|.+.++|.+||.. ++..|.|+.|.|.++
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~   89 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRA   89 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecc
Confidence            35679999999999999999999999999999999753      57999999999999999975 899999999999998


Q ss_pred             cc------------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCC
Q psy93           185 PI------------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEG  251 (503)
Q Consensus       185 ~~------------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g  251 (503)
                      .+            .++|||.|||..+++++|+++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+|+.. + +
T Consensus        90 ~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~-~  167 (196)
T 1l3k_A           90 VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-K-Y  167 (196)
T ss_dssp             CC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-S-C
T ss_pred             cCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-C-C
Confidence            53            378999999999999999999999999999999998 4889999999999999999999986 4 6


Q ss_pred             eeeecCCCCeEEeecCCcccc
Q psy93           252 CFFLTQSLRPVIVEPLELTDE  272 (503)
Q Consensus       252 ~~~~~~~~rpl~V~~~~~~~~  272 (503)
                      ..+   .+++|.|.++.+..+
T Consensus       168 ~~~---~G~~i~v~~a~~k~~  185 (196)
T 1l3k_A          168 HTV---NGHNCEVRKALSKQE  185 (196)
T ss_dssp             CEE---TTEECEEEECC----
T ss_pred             cEE---CCEEEEEEecCChhH
Confidence            655   689999999877654

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.95  E-value=1.5e-27  Score=223.70  Aligned_cols=154  Identities=24%  Similarity=0.385  Sum_probs=142.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccC----C-------CeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEE
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPY----G-------ETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLK  180 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~----G-------~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~  180 (503)
                      .+++|||+|||+++|+++|+++|+.|    |       .|.++.+.++++||||+|.+.++|.+|+ .||+..|.|++|.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i~   81 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   81 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETTTTEEEEEESCSHHHHHHG-GGTTEEETTEEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceEE
Confidence            35799999999999999999999999    6       8899999999999999999999999999 8999999999999


Q ss_pred             EEeccc--------------------------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEE
Q psy93           181 IRFAPI--------------------------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIV  233 (503)
Q Consensus       181 V~~a~~--------------------------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV  233 (503)
                      |.++.+                          .++|||.|||..+++++|+++|+.||.|..+.++.+. ++.+++||||
T Consensus        82 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV  161 (198)
T 2yh0_A           82 IRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC  161 (198)
T ss_dssp             EECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEE
T ss_pred             EeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEE
Confidence            998742                          3789999999999999999999999999999999984 8899999999


Q ss_pred             EeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCcc
Q psy93           234 EFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELT  270 (503)
Q Consensus       234 ~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~  270 (503)
                      +|.+.++|.+|+..|| +..+   .+++|.|.++.+.
T Consensus       162 ~f~~~~~a~~A~~~l~-g~~~---~g~~l~v~~a~~~  194 (198)
T 2yh0_A          162 EYVDINVTDQAIAGLN-GMQL---GDKKLLVQRASVG  194 (198)
T ss_dssp             EESSSSHHHHHHHHHT-TCEE---TTEECEEEESCCC
T ss_pred             EECCHHHHHHHHHHcC-CCEE---CCEEEEEEECCCC
Confidence            9999999999999997 6666   6899999998665

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.95  E-value=2.2e-27  Score=216.45  Aligned_cols=152  Identities=24%  Similarity=0.411  Sum_probs=137.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ++++|||+|||+++|+++|+++|+.||+|.+|.|+++      +|||||+|.+.++|.+|+..  +..+.|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            3579999999999999999999999999999999754      68999999999999999984  578999999999986


Q ss_pred             c------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCC
Q psy93           186 I------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQS  258 (503)
Q Consensus       186 ~------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~  258 (503)
                      +      ..+|||.|||..+++++|+++|+.||.|..+.++.+ .++.++|||||+|.+.++|.+|+. ++ +..+   .
T Consensus        80 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~-~~~~---~  154 (167)
T 2cjk_A           80 PRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NK-FIDF---K  154 (167)
T ss_dssp             CHHHHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CS-EECS---S
T ss_pred             chhhccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CC-CEEe---C
Confidence            4      568999999999999999999999999999999988 578999999999999999999998 64 6655   6


Q ss_pred             CCeEEeecCCcc
Q psy93           259 LRPVIVEPLELT  270 (503)
Q Consensus       259 ~rpl~V~~~~~~  270 (503)
                      +++|.|.++.+.
T Consensus       155 g~~i~V~~a~pk  166 (167)
T 2cjk_A          155 DRKIEIKRAEPR  166 (167)
T ss_dssp             SSCEEEEECCCC
T ss_pred             CeEEEEeecCCC
Confidence            899999998764

>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=99.94  E-value=1.6e-27  Score=237.79  Aligned_cols=192  Identities=10%  Similarity=0.062  Sum_probs=155.0

Q ss_pred             CcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           109 KFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINK----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       109 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      .....++|||+|||+++|+++|+++|+.||+|.+|.|++    +++||||+|.+.++|.+|+. |++..|.|++|.|.++
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~~~  115 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL  115 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEEEC
Confidence            344678999999999999999999999999999999986    47999999999999999995 9999999999999987


Q ss_pred             ccccceeccCcccccCHHHHHHHhccCC-CeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFG-DIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G-~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                       ..++|||+|||..+++++|.++|+.|| .|..|.++.+..+.+++||||+|.+.++|.+|+..|+ +..+   .+++|.
T Consensus       116 -~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~  190 (292)
T 2ghp_A          116 -TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLN-GLKI---EGYTLV  190 (292)
T ss_dssp             -CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHT-TCEE---TTEECE
T ss_pred             -CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhC-CCEe---CCcEEE
Confidence             467899999999999999999999999 9999999998778899999999999999999999997 6666   689999


Q ss_pred             eecCCccccccC------CcccccCCCCchh-hhhhccCcccCCCCCcch
Q psy93           264 VEPLELTDEIDG------LSERTINKKTPEF-YKQRQVGPRFATVNSFEF  306 (503)
Q Consensus       264 V~~~~~~~~~~~------~~~k~i~k~~~~~-~kere~~~rf~~~g~~e~  306 (503)
                      |.++.+......      ....++..+++.. .++..+...|..+|.+..
T Consensus       191 v~~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~  240 (292)
T 2ghp_A          191 TKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEK  240 (292)
T ss_dssp             EEECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEE
T ss_pred             EEECCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeE
Confidence            998876543321      1234555566666 677777788888777643

>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=99.94  E-value=2.2e-26  Score=211.73  Aligned_cols=151  Identities=19%  Similarity=0.252  Sum_probs=134.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCe-----EEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGET-----QELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V-----~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ...++|||+|||+++|+++|+++|+.||.|     ......++++||||+|.+.++|.+|+ .||+..|.|++|.|.++.
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~~~   89 (175)
T 1fje_B           11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPK   89 (175)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEecCC
Confidence            357899999999999999999999999854     34444567999999999999999999 599999999999999986


Q ss_pred             c--------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecC
Q psy93           186 I--------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQ  257 (503)
Q Consensus       186 ~--------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~  257 (503)
                      +        .++|||.|||..+++++|+++|+.||.|..+    ..++.+++||||+|.+.++|.+|+..|| +..+   
T Consensus        90 ~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~---  161 (175)
T 1fje_B           90 GRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQ-GAEI---  161 (175)
T ss_dssp             CSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CSSSSCCSEEEEECSSHHHHHHHHHHHT-EEEE---
T ss_pred             CccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cCCCCCceEEEEEECCHHHHHHHHHHhC-CCEE---
Confidence            3        5789999999999999999999999988765    6678889999999999999999999997 6666   


Q ss_pred             CCCeEEeecCCcc
Q psy93           258 SLRPVIVEPLELT  270 (503)
Q Consensus       258 ~~rpl~V~~~~~~  270 (503)
                      .+++|.|.++.++
T Consensus       162 ~g~~i~v~~a~~k  174 (175)
T 1fje_B          162 DGRSVSLYYTGEK  174 (175)
T ss_dssp             TTEEEEEEECSSC
T ss_pred             CCeEEEEEecCCC
Confidence            6899999998653

>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=4.5e-26  Score=220.01  Aligned_cols=152  Identities=22%  Similarity=0.299  Sum_probs=137.0

Q ss_pred             CCCcEEEEcCCCC-CCCHHHHHHhhccCCCeEEEEEecC-CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc--
Q psy93           111 ANNCRLYLGNIGG-DITENDIIELFKPYGETQELFINKE-KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI--  186 (503)
Q Consensus       111 ~~~~~l~V~nLp~-~~te~~L~~~F~~~G~V~~v~i~~~-kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~--  186 (503)
                      .++++|||+|||+ ++++++|+++|+.||.|.+|.|+++ ++||||+|.+.++|.+|++.|++..|.|++|.|.++.+  
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  111 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN  111 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCcc
Confidence            3568999999999 9999999999999999999999877 59999999999999999999999999999999998752  


Q ss_pred             ---------------------------------------ccceeccCcccccCHHHHHHHhccCC-CeeeeEEEeCCCCC
Q psy93           187 ---------------------------------------NAAIKVKNLTSCVTNELLELAFGVFG-DIERAIVIVDERGN  226 (503)
Q Consensus       187 ---------------------------------------~~~L~V~nLp~~~tee~L~~~Fs~~G-~V~~~~v~~d~~g~  226 (503)
                                                             .++|||.|||..+++++|+++|+.|| .|..+.++.+    
T Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~----  187 (229)
T 2adc_A          112 VQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----  187 (229)
T ss_dssp             CCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS----
T ss_pred             ccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC----
Confidence                                                   36799999999999999999999999 9999998664    


Q ss_pred             ceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCc
Q psy93           227 SKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLEL  269 (503)
Q Consensus       227 skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~  269 (503)
                      +++||||+|.+.++|.+|+..|| +..+  ..+++|.|.++.+
T Consensus       188 ~~g~afV~f~~~~~A~~Ai~~l~-g~~~--~~g~~l~v~~a~~  227 (229)
T 2adc_A          188 DRKMALIQMGSVEEAVQALIDLH-NHDL--GENHHLRVSFSKS  227 (229)
T ss_dssp             STTCEEEEESSHHHHHHHHHHHT-TCBS--SSSCBCEEEECSS
T ss_pred             CCcEEEEEECCHHHHHHHHHHHC-CCcc--CCCCeEEEEEecC
Confidence            26899999999999999999997 5555  1388999998764

>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=99.94  E-value=1.1e-25  Score=223.36  Aligned_cols=151  Identities=16%  Similarity=0.311  Sum_probs=135.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHH----HhhccCCCeEEEEEec---CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           111 ANNCRLYLGNIGGDITENDII----ELFKPYGETQELFINK---EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~----~~F~~~G~V~~v~i~~---~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      .++++|||+|||+++|+++|+    ++|+.||.|.+|.|.+   ++|||||+|.+.++|.+||+.||+..|.|+.|+|.|
T Consensus         7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   86 (282)
T 3pgw_A            7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   86 (282)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEE
Confidence            357899999999999999966    8999999999999875   579999999999999999999999999999999998


Q ss_pred             ccc-----------------------------------------------------------------------------
Q psy93           184 API-----------------------------------------------------------------------------  186 (503)
Q Consensus       184 a~~-----------------------------------------------------------------------------  186 (503)
                      +..                                                                             
T Consensus        87 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~  166 (282)
T 3pgw_A           87 AKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPP  166 (282)
T ss_pred             eccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCCCCC
Confidence            742                                                                             


Q ss_pred             ----------------------------------------ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCC
Q psy93           187 ----------------------------------------NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGN  226 (503)
Q Consensus       187 ----------------------------------------~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~  226 (503)
                                                              .++|||.|||..+++++|+++|+.||.|.+|.|+.+.   
T Consensus       167 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~---  243 (282)
T 3pgw_A          167 PGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR---  243 (282)
T ss_pred             CCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC---
Confidence                                                    2459999999999999999999999999999998763   


Q ss_pred             ceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCC
Q psy93           227 SKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLE  268 (503)
Q Consensus       227 skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~  268 (503)
                       ++||||+|.+.++|.+|+..|| +..+.  .+++|.|.|++
T Consensus       244 -~g~afV~f~~~~~A~~A~~~l~-g~~~~--~g~~l~v~~ak  281 (282)
T 3pgw_A          244 -HDIAFVEFDNEVQAGAARDALQ-GFKIT--QNNAMKISFAK  281 (282)
T ss_pred             -CcEEEEEeCCHHHHHHHHHHcC-CcEeC--CCCEEEEEEec
Confidence             5799999999999999999997 55552  38999999875

>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=99.93  E-value=1.2e-25  Score=223.21  Aligned_cols=156  Identities=20%  Similarity=0.265  Sum_probs=144.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++|+++|+++|+.||.|..|.++.+      +|||||+|.+.++|.+|+..|++..|.|++|.|.++.
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~  173 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD  173 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            4578999999999999999999999999999998643      5799999999999999999999999999999999996


Q ss_pred             c---------ccceeccCccccc-CHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeee
Q psy93           186 I---------NAAIKVKNLTSCV-TNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFL  255 (503)
Q Consensus       186 ~---------~~~L~V~nLp~~~-tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~  255 (503)
                      +         .++|||.|||..+ ++++|+++|+.||.|..+.|+.+.++.++++|||+|.+.++|.+|+..|| +..+ 
T Consensus       174 ~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~-g~~~-  251 (284)
T 3smz_A          174 AGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQAD-GLSL-  251 (284)
T ss_dssp             GGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHT-TCEE-
T ss_pred             CCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhC-CCcc-
Confidence            4         4689999999995 99999999999999999999999999999999999999999999999997 6666 


Q ss_pred             cCCCCeEEeecCCccc
Q psy93           256 TQSLRPVIVEPLELTD  271 (503)
Q Consensus       256 ~~~~rpl~V~~~~~~~  271 (503)
                        .+++|.|.++.+..
T Consensus       252 --~g~~l~v~~a~~~~  265 (284)
T 3smz_A          252 --GGSHLRVSFCAPGP  265 (284)
T ss_dssp             --TTEECEEEECCSSS
T ss_pred             --CCeEEEEEEecCCC
Confidence              68999999987654

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.93  E-value=4.1e-26  Score=214.54  Aligned_cols=150  Identities=21%  Similarity=0.302  Sum_probs=135.3

Q ss_pred             CcEEEEcCCCC-CCCHHHHHHhhccCCCeEEEEEecC-CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc----
Q psy93           113 NCRLYLGNIGG-DITENDIIELFKPYGETQELFINKE-KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI----  186 (503)
Q Consensus       113 ~~~l~V~nLp~-~~te~~L~~~F~~~G~V~~v~i~~~-kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~----  186 (503)
                      +++|||+|||+ ++++++|+++|+.||.|.+|.|+.+ ++||||+|.+.++|.+|+..||+..|.|++|.|.++.+    
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~~~   82 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQ   82 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCSCC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCCcC
Confidence            57999999999 9999999999999999999999876 59999999999999999999999999999999998742    


Q ss_pred             -------------------------------------ccceeccCcccccCHHHHHHHhccCC-CeeeeEEEeCCCCCce
Q psy93           187 -------------------------------------NAAIKVKNLTSCVTNELLELAFGVFG-DIERAIVIVDERGNSK  228 (503)
Q Consensus       187 -------------------------------------~~~L~V~nLp~~~tee~L~~~Fs~~G-~V~~~~v~~d~~g~sk  228 (503)
                                                           +++|||.|||..+++++|+++|+.|| .|..+.++.+.    +
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~----~  158 (198)
T 1qm9_A           83 LPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----R  158 (198)
T ss_dssp             CSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT----S
T ss_pred             CCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC----C
Confidence                                                 46799999999999999999999999 99999987642    7


Q ss_pred             eEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCc
Q psy93           229 CEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLEL  269 (503)
Q Consensus       229 g~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~  269 (503)
                      ++|||+|.+.++|.+|+..|| +..+  ..+++|.|.++.+
T Consensus       159 g~afV~f~~~~~A~~A~~~l~-g~~~--~~g~~l~v~~a~~  196 (198)
T 1qm9_A          159 KMALIQMGSVEEAVQALIDLH-NHDL--GENHHLRVSFSKS  196 (198)
T ss_dssp             SCEEEECSSHHHHHHHHHHHT-SSCC--SSCCSCCEEEECC
T ss_pred             cEEEEEeCCHHHHHHHHHHhc-CCcc--CCCCeEEEEeecc
Confidence            899999999999999999997 5554  1378888888654

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.93  E-value=1.8e-25  Score=222.92  Aligned_cols=156  Identities=21%  Similarity=0.381  Sum_probs=141.7

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHhhccCC-CeEEEEEec-----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           110 FANNCRLYLGNIGGDITENDIIELFKPYG-ETQELFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       110 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G-~V~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      ....++|||+|||+++++++|+++|+.|| .|..|.|+.     +++||||+|.+.++|.+|+..|++..|.|++|.|.+
T Consensus       114 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  193 (292)
T 2ghp_A          114 HLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKV  193 (292)
T ss_dssp             ECCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             ECCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            34578999999999999999999999999 999999864     579999999999999999999999999999999999


Q ss_pred             ccc-------------ccceeccCcccc-cCHHHHHHHhccCCCeeeeEEEeCCC--CCceeEEEEEeCCHHHHHHHHHH
Q psy93           184 API-------------NAAIKVKNLTSC-VTNELLELAFGVFGDIERAIVIVDER--GNSKCEGIVEFARKPAAAQALRR  247 (503)
Q Consensus       184 a~~-------------~~~L~V~nLp~~-~tee~L~~~Fs~~G~V~~~~v~~d~~--g~skg~gfV~F~s~e~A~kAl~~  247 (503)
                      +.+             .++|||.|||.. +++++|+++|+.||.|..|.|+.+..  +.+++||||+|.+.++|.+|+ .
T Consensus       194 a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~  272 (292)
T 2ghp_A          194 SNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-Q  272 (292)
T ss_dssp             CCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-G
T ss_pred             CCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-H
Confidence            853             368999999999 99999999999999999999999876  899999999999999999999 9


Q ss_pred             hhCCeeeecCCCCeEEeecCCcc
Q psy93           248 CAEGCFFLTQSLRPVIVEPLELT  270 (503)
Q Consensus       248 ln~g~~~~~~~~rpl~V~~~~~~  270 (503)
                      || +..+   .+++|.|.++.++
T Consensus       273 l~-g~~~---~g~~i~V~~a~~k  291 (292)
T 2ghp_A          273 MN-RSLL---GNREISVSLADKK  291 (292)
T ss_dssp             GT-TEEE---TTEEEEEEECCCC
T ss_pred             hc-CCEE---CCcEEEEEEecCC
Confidence            97 6666   6899999998764

>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=6.5e-20  Score=157.95  Aligned_cols=92  Identities=17%  Similarity=0.357  Sum_probs=69.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc-
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI-  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~-  186 (503)
                      .+++|||+|||+++|+++|+++|+.||.|.+|+|+.+    +|||||+|.+.++|.+||+.|++..|.|++|.|.++.+ 
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~   83 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   83 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCc
Confidence            3568999999999999999999999999999999754    68999999999999999999999999999999999853 


Q ss_pred             -------------ccceeccCcccccCHHH
Q psy93           187 -------------NAAIKVKNLTSCVTNEL  203 (503)
Q Consensus       187 -------------~~~L~V~nLp~~~tee~  203 (503)
                                   .++|||+|||+++|++.
T Consensus        84 ~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           84 KEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             CC----------------------------
T ss_pred             cccccccccccCCCCceEeCCCCCCccccc
Confidence                         24799999999998864

>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=4.6e-18  Score=142.45  Aligned_cols=82  Identities=18%  Similarity=0.404  Sum_probs=72.7

Q ss_pred             cccCcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceE
Q psy93           106 KDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSL  179 (503)
Q Consensus       106 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l  179 (503)
                      .+..+...|+|||+|||+++|+++|+++|++||+|.+|.|+++      +|||||+|.+.++|.+||+.||+..|.|++|
T Consensus        12 ~en~~~~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           12 HENLYFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI   91 (99)
T ss_dssp             ----CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             cccccCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            3445566789999999999999999999999999999999753      5799999999999999999999999999999


Q ss_pred             EEEecccc
Q psy93           180 KIRFAPIN  187 (503)
Q Consensus       180 ~V~~a~~~  187 (503)
                      +|.||.|+
T Consensus        92 ~V~~AkPS   99 (99)
T 4fxv_A           92 KVSYARPS   99 (99)
T ss_dssp             EEEECCBC
T ss_pred             EEEEeeCC
Confidence            99999763

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.73  E-value=7.6e-18  Score=136.53  Aligned_cols=72  Identities=17%  Similarity=0.194  Sum_probs=70.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ++.|||+||++.+|+++|+++|.+||+|.++++..++|||||+|.+.++|.+||+.||+..|.|++|+|++|
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcCCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            568999999999999999999999999999999999999999999999999999999999999999999987

>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=99.73  E-value=7.5e-18  Score=144.55  Aligned_cols=100  Identities=21%  Similarity=0.346  Sum_probs=91.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec---CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK---EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINA  188 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~---~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~~  188 (503)
                      .+++|||+|||+++|+++|+++|+.||.|.+|.|+.   +++||||+|.+.++|.+|+..||+..|.|+.|.|.++.+..
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   86 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANR   86 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCh
Confidence            357899999999999999999999999999999964   47899999999999999999999999999999999998754


Q ss_pred             ceeccCcccccCHHHHHHHhccCCC
Q psy93           189 AIKVKNLTSCVTNELLELAFGVFGD  213 (503)
Q Consensus       189 ~L~V~nLp~~~tee~L~~~Fs~~G~  213 (503)
                      ..  .+++...++++|.++|++||.
T Consensus        87 ~~--~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           87 AF--QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             HT--TTSCHHHHHHHHHHHHHHHCC
T ss_pred             hh--hhhhHhHhHHHHHHHHHHhCC
Confidence            43  788889999999999999985

>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=99.72  E-value=1.6e-17  Score=138.64  Aligned_cols=87  Identities=40%  Similarity=0.725  Sum_probs=80.9

Q ss_pred             cCcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           108 IKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       108 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ....+.++|||+|||+++|+++|+++|+.||+|..|.|.++++||||+|.+.++|.+|+..||+..|.|++|.|.++.+.
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   89 (99)
T 2cpj_A           10 KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   89 (99)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCC
Confidence            34456789999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             cceeccC
Q psy93           188 AAIKVKN  194 (503)
Q Consensus       188 ~~L~V~n  194 (503)
                      ..+.+.+
T Consensus        90 ~~~~~g~   96 (99)
T 2cpj_A           90 ASLTSGP   96 (99)
T ss_dssp             SCCCCCC
T ss_pred             CCCCCCC
Confidence            8777764

>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=99.72  E-value=1.8e-17  Score=150.22  Aligned_cols=121  Identities=17%  Similarity=0.112  Sum_probs=100.3

Q ss_pred             cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEE-------Eec------------ccccceeccCcccccCHHHHHHH
Q psy93           147 KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKI-------RFA------------PINAAIKVKNLTSCVTNELLELA  207 (503)
Q Consensus       147 ~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V-------~~a------------~~~~~L~V~nLp~~~tee~L~~~  207 (503)
                      +.+|||||+|.+.++|++|+..+++.......+.+       ...            .+.++|||+|||..+++++|+++
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            35799999999999999999887754322222222       111            23679999999999999999999


Q ss_pred             hccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCccc
Q psy93           208 FGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTD  271 (503)
Q Consensus       208 Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~~  271 (503)
                      |+.||.|..|.|+.| .++.++|||||+|.+.++|.+|+..|| +..+   .+++|.|.++.+..
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 FEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMD-GAVL---DGRELRVQMARYGR  151 (158)
T ss_dssp             HHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHST-TEES---SSSEEEEEEECCSS
T ss_pred             HHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhC-CCEE---CCeEEEEEECCCCC
Confidence            999999999999998 588999999999999999999999997 6665   68999999987653

>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=99.70  E-value=2e-17  Score=139.24  Aligned_cols=79  Identities=14%  Similarity=0.236  Sum_probs=73.1

Q ss_pred             CCcEEEEcCCCC-CCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCc--cccCceEEEEeccccc
Q psy93           112 NNCRLYLGNIGG-DITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH--VLKGRSLKIRFAPINA  188 (503)
Q Consensus       112 ~~~~l~V~nLp~-~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~--~l~g~~l~V~~a~~~~  188 (503)
                      ++++|||+|||+ ++|+++|+++|++||.|.+|.|+++++||||+|++.++|.+||+.|++.  .|.|++|.|.++....
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~   93 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYK   93 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCCT
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCCCC
Confidence            567999999999 9999999999999999999999999999999999999999999999865  5999999999998655


Q ss_pred             ce
Q psy93           189 AI  190 (503)
Q Consensus       189 ~L  190 (503)
                      .|
T Consensus        94 ~~   95 (102)
T 1x4d_A           94 RI   95 (102)
T ss_dssp             TS
T ss_pred             CC
Confidence            44

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=2.2e-17  Score=139.37  Aligned_cols=76  Identities=25%  Similarity=0.405  Sum_probs=71.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCC--ccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDG--HVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g--~~l~g~~l~V~~a~~~  187 (503)
                      +.++|||+|||+++|+++|+++|++||.|.+|.|+++||||||+|++.++|.+||+.|++  ..|.|++|+|.|+.+.
T Consensus        15 ~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~   92 (105)
T 1sjq_A           15 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK   92 (105)
T ss_dssp             CCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCC
Confidence            467999999999999999999999999999999999999999999999999999998864  6899999999999764

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.70  E-value=4.7e-17  Score=136.10  Aligned_cols=77  Identities=10%  Similarity=0.192  Sum_probs=72.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCcc--ccCceEEEEecccc
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHV--LKGRSLKIRFAPIN  187 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~--l~g~~l~V~~a~~~  187 (503)
                      .++++|||+|||+++|+++|+++|++||.|.+|.|+++|+||||+|++.++|.+|++.|++..  |.|++|.|.++++.
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k   97 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQ   97 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEecccc
Confidence            356789999999999999999999999999999999999999999999999999999999885  77999999998764

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.70  E-value=2.3e-17  Score=138.18  Aligned_cols=83  Identities=22%  Similarity=0.463  Sum_probs=77.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc------
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKE-KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI------  186 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~------  186 (503)
                      |+|||+|||+++|+++|+++|++||+|.+|.|+.+ ++||||+|.+.++|.+|+..||+..|.|+.|.|.++.+      
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~~   80 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSR   80 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCCSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCCccc
Confidence            58999999999999999999999999999999886 99999999999999999999999999999999999953      


Q ss_pred             ----------ccceeccCcc
Q psy93           187 ----------NAAIKVKNLT  196 (503)
Q Consensus       187 ----------~~~L~V~nLp  196 (503)
                                ..+|||++|+
T Consensus        81 ~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           81 FDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CCSCCCSCCCCSCCCSCCCC
T ss_pred             CCCCCccccCCCceecCCCC
Confidence                      4578888886

>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=99.69  E-value=3.4e-17  Score=147.34  Aligned_cols=114  Identities=23%  Similarity=0.152  Sum_probs=103.0

Q ss_pred             CCCceEEeeCCHHHHHHHHHHh-CCccccCceEEEEeccc----------------------ccceeccCcccccCHHHH
Q psy93           148 EKMFGFIRMDYKHNADKAKAKL-DGHVLKGRSLKIRFAPI----------------------NAAIKVKNLTSCVTNELL  204 (503)
Q Consensus       148 ~kg~aFV~F~~~e~A~~Ai~~l-~g~~l~g~~l~V~~a~~----------------------~~~L~V~nLp~~~tee~L  204 (503)
                      -+|+++|+|.++++|++|+..| |+..+.| +|.|.++..                      .++|||+|||+.+++++|
T Consensus        12 l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~~l   90 (150)
T 2i2y_A           12 LKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTEL   90 (150)
T ss_dssp             SCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCHHH
T ss_pred             ccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHHHH
Confidence            3789999999999999999999 9999999 999988742                      468999999999999999


Q ss_pred             HHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCcc
Q psy93           205 ELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELT  270 (503)
Q Consensus       205 ~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~  270 (503)
                      +++|+.||.|.+|.|+.+    +++||||+|.+.++|.+|+..|| +..+   .+++|.|.++.+.
T Consensus        91 ~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~v~~a~~~  148 (150)
T 2i2y_A           91 ERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELD-GRTL---CGCRVRVELSNGE  148 (150)
T ss_dssp             HHHHHHHSCEEEEEECSS----SCSEEEEEESSHHHHHHHHHHHS-SSCS---SSSCCEEEECCCC
T ss_pred             HHHHHhhCCEEEEEEeeC----CCcEEEEEECCHHHHHHHHHHcC-CCEE---CCeEEEEEEcCCC
Confidence            999999999999999876    58899999999999999999997 5555   6899999987654

>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=99.68  E-value=7.5e-17  Score=137.87  Aligned_cols=83  Identities=17%  Similarity=0.281  Sum_probs=75.2

Q ss_pred             cCCCcEEEEcCCCCC-CCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCC--ccccCceEEEEeccc
Q psy93           110 FANNCRLYLGNIGGD-ITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDG--HVLKGRSLKIRFAPI  186 (503)
Q Consensus       110 ~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g--~~l~g~~l~V~~a~~  186 (503)
                      ..++++|||+|||++ +|+++|+++|++||.|.+|.|+++++||||+|++.++|.+||+.|++  ..|.|++|.|.++..
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~  101 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK  101 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECcc
Confidence            445789999999998 99999999999999999999999999999999999999999998864  569999999999987


Q ss_pred             ccceec
Q psy93           187 NAAIKV  192 (503)
Q Consensus       187 ~~~L~V  192 (503)
                      ...+..
T Consensus       102 ~~~~~~  107 (112)
T 1x4f_A          102 YKKLVS  107 (112)
T ss_dssp             CSSSSC
T ss_pred             cccccc
Confidence            666544

>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=99.67  E-value=1e-16  Score=130.99  Aligned_cols=83  Identities=16%  Similarity=0.325  Sum_probs=78.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccccccee
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAIK  191 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~~~L~  191 (503)
                      ..++|||+|||+++++++|+++|++| .|.+|.|.++++||||+|.+.++|.+|+..||+..+.|++|+|.+++....++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~~~~   82 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDALLC   82 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCCCCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEeCCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCCceEe
Confidence            45789999999999999999999999 99999998899999999999999999999999999999999999999988888


Q ss_pred             ccCc
Q psy93           192 VKNL  195 (503)
Q Consensus       192 V~nL  195 (503)
                      +.|.
T Consensus        83 ~~n~   86 (88)
T 1wg1_A           83 SGPS   86 (88)
T ss_dssp             CCCT
T ss_pred             cCCC
Confidence            8764

>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=99.67  E-value=2.3e-16  Score=132.66  Aligned_cols=76  Identities=18%  Similarity=0.317  Sum_probs=70.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHh--CCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL--DGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l--~g~~l~g~~l~V~~a~~~  187 (503)
                      ++++|||+|||+++|+++|+++|++||.|.+|.|+++++||||+|.+.++|.+|++.|  ++..|.|++|.|.|+.+.
T Consensus        14 p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~   91 (101)
T 2cq1_A           14 PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK   91 (101)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcc
Confidence            4678999999999999999999999999999999999999999999999999999977  467899999999999753

>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=99.67  E-value=4.5e-17  Score=139.28  Aligned_cols=75  Identities=17%  Similarity=0.244  Sum_probs=72.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ..++|||+|||+++|+++|+++|++||.|..|.|+++++||||+|.+.++|.+||..||+..|.|++|.|.|+..
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   83 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            357899999999999999999999999999999999999999999999999999999999999999999999865

>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=99.67  E-value=2.2e-16  Score=131.22  Aligned_cols=76  Identities=25%  Similarity=0.435  Sum_probs=72.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCcccc--CceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLK--GRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~--g~~l~V~~a~~~  187 (503)
                      +.++|||+|||+++|+++|+++|++||.|..|.+.++++||||+|.+.++|.+|+..||+..|.  +++|+|.|+.+.
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~   93 (97)
T 1why_A           16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCCCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCC
Confidence            3568999999999999999999999999999999999999999999999999999999999999  999999999764

>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=99.67  E-value=1.5e-16  Score=137.42  Aligned_cols=77  Identities=25%  Similarity=0.400  Sum_probs=71.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCC--ccccCceEEEEecccc
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDG--HVLKGRSLKIRFAPIN  187 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g--~~l~g~~l~V~~a~~~  187 (503)
                      .++++|||+|||+++|+++|+++|++||.|.+|.|+++|+||||+|++.++|.+||+.|++  ..|.|++|.|.|+.+.
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k  107 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK  107 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGGGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCC
Confidence            3567899999999999999999999999999999999999999999999999999999874  6899999999999764

>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=99.66  E-value=2.2e-16  Score=133.49  Aligned_cols=76  Identities=9%  Similarity=0.166  Sum_probs=70.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCc--cccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH--VLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~--~l~g~~l~V~~a~~~  187 (503)
                      ++++|||+|||+++++++|+++|++||.|..|.|+++|+||||+|.+.++|.+|++.|++.  .|.|++|.|.|+.+.
T Consensus        14 p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~   91 (104)
T 1wex_A           14 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             CCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCc
Confidence            4678999999999999999999999999999999999999999999999999999988764  589999999999764

>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=99.66  E-value=2.3e-16  Score=131.01  Aligned_cols=78  Identities=14%  Similarity=0.227  Sum_probs=72.8

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHH----HhhccCCCeEEEEEecC---CCceEEeeCCHHHHHHHHHHhCCccccCceEEEE
Q psy93           110 FANNCRLYLGNIGGDITENDII----ELFKPYGETQELFINKE---KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIR  182 (503)
Q Consensus       110 ~~~~~~l~V~nLp~~~te~~L~----~~F~~~G~V~~v~i~~~---kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~  182 (503)
                      +++.++|||+|||+++++++|+    ++|++||+|.+|.|+.+   ++||||+|.+.++|.+||..||+..|.|++|+|.
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~   85 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVS   85 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            3456899999999999999999    99999999999999865   8999999999999999999999999999999999


Q ss_pred             ecccc
Q psy93           183 FAPIN  187 (503)
Q Consensus       183 ~a~~~  187 (503)
                      ++.+.
T Consensus        86 ~a~~~   90 (96)
T 2dgx_A           86 LATGA   90 (96)
T ss_dssp             ECCCS
T ss_pred             EcCCC
Confidence            99764

>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=99.66  E-value=2.1e-16  Score=127.84  Aligned_cols=74  Identities=26%  Similarity=0.532  Sum_probs=70.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHh-CCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL-DGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l-~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++++++|+++|++||.|..|.++++++||||+|.+.++|.+|+..| ++..+.|++|+|.|++
T Consensus        11 ~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A           11 TITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             SCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            4578999999999999999999999999999999999999999999999999999998 9999999999999873

>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=99.66  E-value=5e-16  Score=131.83  Aligned_cols=74  Identities=12%  Similarity=0.176  Sum_probs=70.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccC-----ceEEEEecccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKG-----RSLKIRFAPIN  187 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g-----~~l~V~~a~~~  187 (503)
                      .++|||+|||+++|+++|+++|+.||+|..|.|+.+ +||||+|.+.++|.+||+.||+..|.|     ++|.|.++.+.
T Consensus        15 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~~~   93 (108)
T 1x4c_A           15 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPR   93 (108)
T ss_dssp             CCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESSCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCCCC
Confidence            578999999999999999999999999999999887 999999999999999999999999999     99999999764

>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=99.65  E-value=3.5e-16  Score=125.79  Aligned_cols=75  Identities=20%  Similarity=0.449  Sum_probs=70.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      +++|||+|||+++++++|+++|+.||+|.+|.++.+      ++||||+|.+.++|.+|+..||+..|.|++|.|.++.+
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            368999999999999999999999999999999755      68999999999999999999999999999999999876


Q ss_pred             c
Q psy93           187 N  187 (503)
Q Consensus       187 ~  187 (503)
                      .
T Consensus        81 ~   81 (83)
T 3md1_A           81 L   81 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.65  E-value=1.9e-16  Score=132.51  Aligned_cols=75  Identities=28%  Similarity=0.379  Sum_probs=71.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ..++|||+|||.++++++|+++|+.||.|.+|.|.++++||||+|.+.++|.+|+..||+..|.|+.|+|.|+.+
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            467999999999999999999999999999999999999999999999999999999999999999999999864

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.65  E-value=2.9e-16  Score=130.18  Aligned_cols=80  Identities=28%  Similarity=0.347  Sum_probs=73.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      +++|||+|||.++++++|+++|+.||.|.+|.|+.+      ++||||+|.+.++|.+|+..||+..|.|+.|.|.++.+
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            578999999999999999999999999999999754      78999999999999999999999999999999999987


Q ss_pred             ccceec
Q psy93           187 NAAIKV  192 (503)
Q Consensus       187 ~~~L~V  192 (503)
                      ......
T Consensus        82 ~~~~~~   87 (96)
T 2x1f_A           82 SDISGV   87 (96)
T ss_dssp             SSGGGH
T ss_pred             CCCCCc
Confidence            655443

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=7.8e-16  Score=129.24  Aligned_cols=76  Identities=29%  Similarity=0.504  Sum_probs=71.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ..++|||+|||+++|+++|+++|+.||.|..|.|+.+    ++||||+|.+.++|.+||..||+..|.|++|.|.++.+.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   93 (103)
T 2cq3_A           14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR   93 (103)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcccC
Confidence            4679999999999999999999999999999999865    789999999999999999999999999999999999764

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.64  E-value=5e-16  Score=143.92  Aligned_cols=80  Identities=20%  Similarity=0.348  Sum_probs=73.3

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec-----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       110 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ....++|||+|||+++++++|+++|+.||+|..|.|+.     +++||||+|.+.++|.+||..||+..|.|++|+|.|+
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            34578999999999999999999999999999999965     4799999999999999999999999999999999999


Q ss_pred             ccccc
Q psy93           185 PINAA  189 (503)
Q Consensus       185 ~~~~~  189 (503)
                      .....
T Consensus       165 ~~~~~  169 (177)
T 2f3j_A          165 ASQID  169 (177)
T ss_dssp             SSGGG
T ss_pred             cCCCC
Confidence            76543

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.64  E-value=3.9e-16  Score=133.27  Aligned_cols=76  Identities=12%  Similarity=0.164  Sum_probs=70.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +.++|||+|||+++|+++|+++|++||.|.+|.|+.      ++|||||+|.+.++|.+||+.||+..|.|+.|.|.++.
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~   84 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDI   84 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            356899999999999999999999999999999964      36899999999999999999999999999999999986


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      ..
T Consensus        85 ~~   86 (110)
T 3s8s_A           85 KG   86 (110)
T ss_dssp             TT
T ss_pred             CC
Confidence            53

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=6.8e-16  Score=126.38  Aligned_cols=74  Identities=28%  Similarity=0.489  Sum_probs=70.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      +.++|||+|||.++|+++|+++|+.||+|..|.|.  ++||||+|.+.++|.+|+..||+..|.|++|+|.++.+.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   80 (90)
T 2dnq_A            7 GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNK   80 (90)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCC
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCC
Confidence            56899999999999999999999999999999998  799999999999999999999999999999999998754

>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=99.64  E-value=7.2e-16  Score=129.83  Aligned_cols=77  Identities=25%  Similarity=0.477  Sum_probs=71.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccccC---ceEEEE
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVLKG---RSLKIR  182 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g---~~l~V~  182 (503)
                      ...++|||+|||+++++++|+++|+.||.|..|.|+.+     ++||||+|.+.++|.+||..||+..+.+   ++|.|.
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~   92 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVK   92 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEE
Confidence            35789999999999999999999999999999999865     7899999999999999999999999998   999999


Q ss_pred             ecccc
Q psy93           183 FAPIN  187 (503)
Q Consensus       183 ~a~~~  187 (503)
                      ++.+.
T Consensus        93 ~a~~~   97 (105)
T 2dnh_A           93 FADTD   97 (105)
T ss_dssp             ESCSS
T ss_pred             ECccC
Confidence            99753

>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=99.64  E-value=4.3e-16  Score=132.33  Aligned_cols=77  Identities=25%  Similarity=0.537  Sum_probs=73.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINA  188 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~~  188 (503)
                      ..++|||+|||.++|+++|+++|+.||.|..|.|+.+++||||+|.+.++|.+||..|++..|.|++|+|.|+.+..
T Consensus        24 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  100 (109)
T 1x4g_A           24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP  100 (109)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCC
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999997654

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=3.7e-16  Score=133.03  Aligned_cols=81  Identities=27%  Similarity=0.457  Sum_probs=73.9

Q ss_pred             ccCcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEE
Q psy93           107 DIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIR  182 (503)
Q Consensus       107 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~  182 (503)
                      .......++|||+|||.++|+++|+++|+.||.|..|.|..+    ++||||+|.+.++|.+|+..||+..|.|++|.|.
T Consensus        23 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  102 (109)
T 2err_A           23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             CSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             ccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            334456789999999999999999999999999999999755    7999999999999999999999999999999999


Q ss_pred             ecccc
Q psy93           183 FAPIN  187 (503)
Q Consensus       183 ~a~~~  187 (503)
                      ++.+.
T Consensus       103 ~a~~~  107 (109)
T 2err_A          103 NATAR  107 (109)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            98754

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=8.5e-16  Score=126.87  Aligned_cols=76  Identities=28%  Similarity=0.567  Sum_probs=71.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      .+++|||+|||.++|+++|+++|+.||.|..|.|+.+      ++||||+|.+.++|.+||..||+..|.|++|+|.++.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   83 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVT   83 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcc
Confidence            4679999999999999999999999999999999754      6899999999999999999999999999999999997


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus        84 ~~   85 (95)
T 2dnz_A           84 ER   85 (95)
T ss_dssp             CC
T ss_pred             cc
Confidence            54

>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=99.64  E-value=5e-16  Score=125.43  Aligned_cols=74  Identities=20%  Similarity=0.501  Sum_probs=69.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +.++|||+|||+++++++|+++|++||+|..|.|+.      +++||||+|.+.++|.+|+..||+..|.|++|+|.|++
T Consensus         6 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~ak   85 (85)
T 3mdf_A            6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   85 (85)
T ss_dssp             CSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            467999999999999999999999999999999864      37899999999999999999999999999999999873

>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=99.64  E-value=7.2e-16  Score=131.19  Aligned_cols=76  Identities=25%  Similarity=0.475  Sum_probs=71.1

Q ss_pred             CcCCCcEEEEcCCCCC-CCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           109 KFANNCRLYLGNIGGD-ITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       109 ~~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      .....++|||+|||++ +|+++|+++|++||+|..|.|  +++||||+|.+.++|.+||..||+..|.|++|+|.++.+
T Consensus        23 ~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   99 (110)
T 1wf1_A           23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGE   99 (110)
T ss_dssp             CTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCC
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            3445689999999999 999999999999999999999  689999999999999999999999999999999999864

>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=99.64  E-value=9e-16  Score=128.85  Aligned_cols=76  Identities=25%  Similarity=0.449  Sum_probs=71.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ..++|||+|||+++++++|+++|+.||+|..|.|+.    +++||||+|.+.++|.+||..||+..|.|++|.|.|+.+.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   93 (103)
T 2cqi_A           14 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTP   93 (103)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCT
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECCCC
Confidence            467999999999999999999999999999999976    4789999999999999999999999999999999999764

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.63  E-value=4.5e-16  Score=126.27  Aligned_cols=75  Identities=25%  Similarity=0.547  Sum_probs=69.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +.++|||+|||.++++++|+++|+.||.|.+|.|+.+      ++||||+|.+.++|.+|+..||+..|.|+.|.|.|+.
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   84 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT   84 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecC
Confidence            4678999999999999999999999999999999764      5899999999999999999999999999999999986


Q ss_pred             c
Q psy93           186 I  186 (503)
Q Consensus       186 ~  186 (503)
                      +
T Consensus        85 ~   85 (87)
T 3bs9_A           85 R   85 (87)
T ss_dssp             -
T ss_pred             C
Confidence            5

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=6.6e-16  Score=129.67  Aligned_cols=76  Identities=22%  Similarity=0.452  Sum_probs=71.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ..++|||+|||+++|+++|+++|+.||.|..|.|+.    +++||||+|.+.++|.+||..||+..|.|++|.|.++.+.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~   93 (103)
T 2d9p_A           14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRK   93 (103)
T ss_dssp             SCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECSSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeccc
Confidence            467899999999999999999999999999999984    4789999999999999999999999999999999999764

>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=99.63  E-value=1.1e-15  Score=131.02  Aligned_cols=76  Identities=20%  Similarity=0.463  Sum_probs=70.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++++++|+++|+.||.|..|.|+.+      ++||||+|.+.++|.+||+.||+..|.|++|+|.|+.
T Consensus        24 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  103 (115)
T 2cpz_A           24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR  103 (115)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            4578999999999999999999999999999999754      4799999999999999999999999999999999997


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus       104 ~~  105 (115)
T 2cpz_A          104 SK  105 (115)
T ss_dssp             CS
T ss_pred             CC
Confidence            64

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.63  E-value=1.1e-15  Score=129.16  Aligned_cols=77  Identities=29%  Similarity=0.458  Sum_probs=72.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-------CCceEEeeCCHHHHHHHHHHh-CCccccCceEEEEe
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-------KMFGFIRMDYKHNADKAKAKL-DGHVLKGRSLKIRF  183 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-------kg~aFV~F~~~e~A~~Ai~~l-~g~~l~g~~l~V~~  183 (503)
                      ..++|||+|||+++|+++|+++|+.||.|..|.|+.+       ++||||+|.+.++|.+||..| |+..|.|++|.|.|
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~~   93 (107)
T 2cph_A           14 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEW   93 (107)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEEEe
Confidence            4678999999999999999999999999999999765       789999999999999999999 99999999999999


Q ss_pred             ccccc
Q psy93           184 APINA  188 (503)
Q Consensus       184 a~~~~  188 (503)
                      +.+..
T Consensus        94 a~~~~   98 (107)
T 2cph_A           94 ADSEV   98 (107)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            97654

>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=99.63  E-value=9.8e-16  Score=127.58  Aligned_cols=77  Identities=32%  Similarity=0.540  Sum_probs=71.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +.++|||+|||+++|+++|+++|+.||+|..|.|+.+      ++||||+|.+.++|.+||..||+..|.|++|.|.++.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   86 (99)
T 1whw_A            7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST   86 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            5679999999999999999999999999999999754      5899999999999999999999999999999999997


Q ss_pred             ccc
Q psy93           186 INA  188 (503)
Q Consensus       186 ~~~  188 (503)
                      +..
T Consensus        87 ~~~   89 (99)
T 1whw_A           87 IKK   89 (99)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            653

>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=1.2e-15  Score=125.73  Aligned_cols=74  Identities=27%  Similarity=0.434  Sum_probs=68.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +.++|||+|||+++++++|+++|+.||+|..|.|+.+      ++||||+|.+.++|.+|++.||+..|.|++|+|.|++
T Consensus        15 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~ak   94 (94)
T 2e5h_A           15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIAI   94 (94)
T ss_dssp             CTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEecC
Confidence            3568999999999999999999999999999999653      6899999999999999999999999999999999874

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.63  E-value=5.6e-16  Score=128.81  Aligned_cols=76  Identities=26%  Similarity=0.458  Sum_probs=70.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec---------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEE
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK---------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIR  182 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~---------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~  182 (503)
                      +.++|||+|||+++|+++|+++|+.||+|..|.|..         +++||||+|.+.++|.+||..||+..|.|++|.|.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR   83 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            457899999999999999999999999999999873         35799999999999999999999999999999999


Q ss_pred             ecccc
Q psy93           183 FAPIN  187 (503)
Q Consensus       183 ~a~~~  187 (503)
                      ++.+.
T Consensus        84 ~a~~~   88 (98)
T 2cpf_A           84 ISERA   88 (98)
T ss_dssp             CSSCS
T ss_pred             EccCC
Confidence            99764

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.63  E-value=1.6e-16  Score=130.84  Aligned_cols=76  Identities=14%  Similarity=0.258  Sum_probs=68.2

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCC-CeEEEEEec------CCCceEEeeCCHHHHHHHHHHhC-CccccCceEEEEec
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYG-ETQELFINK------EKMFGFIRMDYKHNADKAKAKLD-GHVLKGRSLKIRFA  184 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G-~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~-g~~l~g~~l~V~~a  184 (503)
                      +++|||+|||+++|+++|+++|+.|| +|.+|.|++      ++|||||+|.+.++|.+||+.++ +..|.|++|.|.|+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            46899999999999999999999999 899999864      47899999999999999998874 56899999999999


Q ss_pred             cccc
Q psy93           185 PINA  188 (503)
Q Consensus       185 ~~~~  188 (503)
                      .+..
T Consensus        81 ~~~~   84 (91)
T 2lxi_A           81 DPKP   84 (91)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            7653

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=5.3e-16  Score=128.37  Aligned_cols=76  Identities=21%  Similarity=0.428  Sum_probs=71.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEE-EEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQEL-FINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v-~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      +.++|||+|||+++|+++|+++|+.||.|..| .|+.+      ++||||+|.+.++|.+||..||+..|.|++|.|.++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA   83 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            56899999999999999999999999999999 88754      789999999999999999999999999999999999


Q ss_pred             ccc
Q psy93           185 PIN  187 (503)
Q Consensus       185 ~~~  187 (503)
                      .+.
T Consensus        84 ~~~   86 (96)
T 1x5t_A           84 FKK   86 (96)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            654

>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=99.63  E-value=1.3e-15  Score=129.54  Aligned_cols=80  Identities=30%  Similarity=0.510  Sum_probs=72.9

Q ss_pred             cCcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEE
Q psy93           108 IKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKI  181 (503)
Q Consensus       108 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V  181 (503)
                      ......++|||+|||+++|+++|+++|+.||+|..|.|+.+      +|||||+|.+.++|.+|++.|++..|.|++|+|
T Consensus        21 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  100 (108)
T 2jrs_A           21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV  100 (108)
T ss_dssp             CSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34456789999999999999999999999999999999743      589999999999999999999999999999999


Q ss_pred             Eecccc
Q psy93           182 RFAPIN  187 (503)
Q Consensus       182 ~~a~~~  187 (503)
                      .++.+.
T Consensus       101 ~~a~~k  106 (108)
T 2jrs_A          101 GHVTER  106 (108)
T ss_dssp             ECSCSS
T ss_pred             EEcccC
Confidence            998754

>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=99.62  E-value=1.2e-15  Score=127.17  Aligned_cols=78  Identities=24%  Similarity=0.484  Sum_probs=71.1

Q ss_pred             cCcCCCcEEEEcCCCC-CCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           108 IKFANNCRLYLGNIGG-DITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       108 ~~~~~~~~l~V~nLp~-~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      .....+++|||+|||. ++++++|+++|+.||.|..|.|.  ++||||+|.+.++|.+|+..||+..+.|+.|+|.++.+
T Consensus        17 ~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   94 (97)
T 2xnq_A           17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSS   94 (97)
T ss_dssp             --CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCC
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCC
Confidence            3344678999999998 99999999999999999999994  89999999999999999999999999999999999865


Q ss_pred             c
Q psy93           187 N  187 (503)
Q Consensus       187 ~  187 (503)
                      .
T Consensus        95 ~   95 (97)
T 2xnq_A           95 N   95 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=1.5e-15  Score=126.84  Aligned_cols=76  Identities=18%  Similarity=0.372  Sum_probs=70.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ..++|||+|||+++|+++|+++|+.||+|..|.|+.+     ++||||+|.+.++|.+|+..||+..|.|++|.|.++.+
T Consensus        16 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   95 (100)
T 2do4_A           16 EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNS   95 (100)
T ss_dssp             CCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            4678999999999999999999999999999999764     48999999999999999999999999999999999976


Q ss_pred             c
Q psy93           187 N  187 (503)
Q Consensus       187 ~  187 (503)
                      .
T Consensus        96 ~   96 (100)
T 2do4_A           96 G   96 (100)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.62  E-value=8.7e-16  Score=124.77  Aligned_cols=76  Identities=18%  Similarity=0.446  Sum_probs=70.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec-------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK-------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~-------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ..++|||+|||+++|+++|+++|+.||.|..|.|+.       +++||||+|.+.++|.+|+..||+..|.|+.|.|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            357899999999999999999999999999999853       6889999999999999999999999999999999998


Q ss_pred             ccc
Q psy93           185 PIN  187 (503)
Q Consensus       185 ~~~  187 (503)
                      .+.
T Consensus        83 ~~~   85 (88)
T 4a8x_A           83 LAP   85 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=8.9e-16  Score=128.88  Aligned_cols=76  Identities=25%  Similarity=0.525  Sum_probs=70.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||.++|+++|+++|+.||.|..|.|+.      +++||||+|.+.++|.+||..||+..|.|++|.|.++.
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   91 (103)
T 2dnm_A           12 GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVAR   91 (103)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEECS
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEECC
Confidence            467999999999999999999999999999999964      36899999999999999999999999999999999997


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus        92 ~~   93 (103)
T 2dnm_A           92 YG   93 (103)
T ss_dssp             SC
T ss_pred             cC
Confidence            53

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=7.7e-16  Score=128.95  Aligned_cols=76  Identities=20%  Similarity=0.467  Sum_probs=70.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +.++|||+|||+++|+++|+++|+.||+|..|.|+.      +++||||+|.+.++|.+||+.||+..|.|++|.|.++.
T Consensus        11 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   90 (102)
T 2cqb_A           11 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   90 (102)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeCC
Confidence            457899999999999999999999999999999964      37899999999999999999999999999999999997


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus        91 ~~   92 (102)
T 2cqb_A           91 PM   92 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=8.6e-16  Score=128.96  Aligned_cols=77  Identities=27%  Similarity=0.534  Sum_probs=71.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ...++|||+|||+++++++|+++|+.||+|..|.|+.+      ++||||+|.+.++|.+||..||+..|.|+.|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   92 (103)
T 2cq0_A           13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   92 (103)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEC
Confidence            34689999999999999999999999999999999754      579999999999999999999999999999999999


Q ss_pred             ccc
Q psy93           185 PIN  187 (503)
Q Consensus       185 ~~~  187 (503)
                      .+.
T Consensus        93 ~~~   95 (103)
T 2cq0_A           93 KPS   95 (103)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            764

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=1e-15  Score=128.17  Aligned_cols=76  Identities=24%  Similarity=0.546  Sum_probs=70.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +.++|||+|||+++|+++|+++|+.||+|..|.|+.      +++||||+|.+.++|.+||+.||+..|.|++|+|.++.
T Consensus        11 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   90 (102)
T 1x5s_A           11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   90 (102)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            457899999999999999999999999999999975      36899999999999999999999999999999999986


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus        91 ~~   92 (102)
T 1x5s_A           91 KS   92 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=1e-15  Score=129.13  Aligned_cols=78  Identities=22%  Similarity=0.436  Sum_probs=71.6

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       110 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      ...+++|||+|||.++++++|+++|+.||+|..|.|+.+      ++||||+|.+.++|.+|+..||+..|.|++|.|.+
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   99 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   99 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEe
Confidence            345689999999999999999999999999999999744      68999999999999999999999999999999999


Q ss_pred             cccc
Q psy93           184 APIN  187 (503)
Q Consensus       184 a~~~  187 (503)
                      +.+.
T Consensus       100 a~~~  103 (106)
T 1p27_B          100 CFVR  103 (106)
T ss_dssp             SEES
T ss_pred             ecCC
Confidence            8653

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=1.7e-15  Score=127.57  Aligned_cols=77  Identities=22%  Similarity=0.403  Sum_probs=71.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++|+++|+++|+.||.|..|.|+.+      ++||||+|.+.++|.+||..||+..|.|++|.|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   93 (105)
T 1x5u_A           14 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS   93 (105)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECC
Confidence            4679999999999999999999999999999999753      5899999999999999999999999999999999997


Q ss_pred             ccc
Q psy93           186 INA  188 (503)
Q Consensus       186 ~~~  188 (503)
                      +..
T Consensus        94 ~~~   96 (105)
T 1x5u_A           94 AHN   96 (105)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            643

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.62  E-value=8.1e-16  Score=126.23  Aligned_cols=76  Identities=21%  Similarity=0.356  Sum_probs=71.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ..++|||+|||.++++++|+++|+.||+|..|.|.+    +++||||+|.+.++|.+|+..||+..|.|+.|+|.++.+.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   86 (92)
T 2dgv_A            7 GACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNA   86 (92)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            467999999999999999999999999999999975    4689999999999999999999999999999999998764

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.62  E-value=6.2e-16  Score=132.18  Aligned_cols=75  Identities=15%  Similarity=0.149  Sum_probs=70.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCC-CeEEEEEe--cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYG-ETQELFIN--KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G-~V~~v~i~--~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ..++|||+|||+++|+++|+++|+.|| .|..|.|.  .++|||||+|.+.++|++||+.||+..|.|++|+|.++..
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~  104 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDN  104 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            457999999999999999999999999 89999985  4689999999999999999999999999999999999864

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.62  E-value=1.2e-15  Score=130.74  Aligned_cols=78  Identities=27%  Similarity=0.558  Sum_probs=72.2

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       110 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      ....++|||+|||.++|+++|+++|+.||.|..|.|+.+      ++||||+|.+.++|.+||..||+..|.|+.|.|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345789999999999999999999999999999999765      57999999999999999999999999999999999


Q ss_pred             cccc
Q psy93           184 APIN  187 (503)
Q Consensus       184 a~~~  187 (503)
                      +.+.
T Consensus        92 a~~~   95 (115)
T 2dgo_A           92 ATRK   95 (115)
T ss_dssp             SSCC
T ss_pred             ccCC
Confidence            9754

>2dgs_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=2.2e-15  Score=125.56  Aligned_cols=75  Identities=23%  Similarity=0.469  Sum_probs=70.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||.++++++|+++|+.||.|..|.|+.      +++||||+|.+.++|.+||+ |++..|.|++|.|.++.
T Consensus         9 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a~   87 (99)
T 2dgs_A            9 KSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAE   87 (99)
T ss_dssp             SCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEECC
Confidence            467899999999999999999999999999999975      37899999999999999998 99999999999999997


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus        88 ~~   89 (99)
T 2dgs_A           88 PR   89 (99)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=1.7e-15  Score=124.56  Aligned_cols=75  Identities=24%  Similarity=0.422  Sum_probs=70.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ...++|||+|||+++|+++|+++|+.||.|..|.|.  ++||||+|.+.++|.+|+..||+..|.|+.|+|.++.+.
T Consensus         8 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   82 (92)
T 2dgt_A            8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSR   82 (92)
T ss_dssp             CSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCC
Confidence            356899999999999999999999999999999997  559999999999999999999999999999999999764

>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=99.61  E-value=1.3e-15  Score=132.70  Aligned_cols=76  Identities=22%  Similarity=0.458  Sum_probs=71.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ...++|||+|||+++|+++|+++|+.||.|..|.|+.+      ++||||+|.+.++|.+||..||+..|.|+.|.|.|+
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   99 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC   99 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEe
Confidence            45689999999999999999999999999999999754      789999999999999999999999999999999998


Q ss_pred             cc
Q psy93           185 PI  186 (503)
Q Consensus       185 ~~  186 (503)
                      .+
T Consensus       100 ~~  101 (126)
T 3ex7_B          100 FV  101 (126)
T ss_dssp             EE
T ss_pred             cC
Confidence            64

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.61  E-value=1.7e-15  Score=130.41  Aligned_cols=76  Identities=22%  Similarity=0.481  Sum_probs=70.0

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       110 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      ....++|||+|||+++++++|+++|+.||.|..|.|+.+      ++||||+|.+.++|.+||+.||+..|.|++|+|.|
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            345689999999999999999999999999999999743      78999999999999999999999999999999998


Q ss_pred             cc
Q psy93           184 AP  185 (503)
Q Consensus       184 a~  185 (503)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            73

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.61  E-value=1.4e-15  Score=129.35  Aligned_cols=78  Identities=23%  Similarity=0.449  Sum_probs=71.8

Q ss_pred             cCcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           108 IKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       108 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ......++|||+|||.++|+++|+++|+.||.|..|.|.  ++||||+|.+.++|.+|+..||+..|.|++|.|.++.+.
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  103 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLP  103 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCC
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCC
Confidence            334567899999999999999999999999999999998  899999999999999999999999999999999998764

>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=99.61  E-value=3e-15  Score=127.04  Aligned_cols=76  Identities=29%  Similarity=0.596  Sum_probs=71.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC---CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE---KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~---kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ..++|||+|||+++|+++|+++|+.||.|..|.|..+   ++||||+|.+.++|.+||+.||+..|.|+.|.|.|+.+.
T Consensus        21 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~   99 (109)
T 1x4a_A           21 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG   99 (109)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcccC
Confidence            4679999999999999999999999999999999754   689999999999999999999999999999999999764

>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=99.61  E-value=1.4e-15  Score=127.81  Aligned_cols=74  Identities=26%  Similarity=0.428  Sum_probs=69.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      +.++|||+|||+++|+++|+++|+.||.|..|.|+  ++||||+|.+.++|.+||..||+..|.|++|.|.|+.+.
T Consensus        10 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   83 (103)
T 2dgu_A           10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPP   83 (103)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCC
Confidence            45789999999999999999999999999999997  679999999999999999999999999999999999764

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=3e-15  Score=124.35  Aligned_cols=75  Identities=24%  Similarity=0.401  Sum_probs=70.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ...++|||+||  ++|+++|+++|+.||+|..|.|.++++||||+|.+.++|.+||..||+..|.|++|.|.|+.+.
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~   87 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   87 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSC
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCC
Confidence            35689999996  8999999999999999999999999999999999999999999999999999999999999764

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.61  E-value=6.9e-16  Score=128.20  Aligned_cols=75  Identities=19%  Similarity=0.370  Sum_probs=67.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCC--eEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCc----cccCceE
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGE--TQELFINK------EKMFGFIRMDYKHNADKAKAKLDGH----VLKGRSL  179 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~--V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~----~l~g~~l  179 (503)
                      .-.||||+|||+++|+++|+++|++||.  |.+|+|++      ++|||||+|.+.++|.+||+.||+.    .|+|++|
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i   87 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTI   87 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEE
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEE
Confidence            3568999999999999999999999995  66888864      4789999999999999999999997    4889999


Q ss_pred             EEEeccc
Q psy93           180 KIRFAPI  186 (503)
Q Consensus       180 ~V~~a~~  186 (503)
                      .|.||++
T Consensus        88 ~V~~Aks   94 (95)
T 2lkz_A           88 GVDFAKS   94 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999864

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=1.1e-15  Score=126.13  Aligned_cols=75  Identities=27%  Similarity=0.439  Sum_probs=69.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +.++|||+|||+++++++|+++|+.||+|..|.|+.+      ++||||+|.+.++|.+|+..||+..|.|++|.|.++.
T Consensus        14 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   93 (95)
T 2cqc_A           14 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPS   93 (95)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecC
Confidence            4578999999999999999999999999999999643      5799999999999999999999999999999999986


Q ss_pred             c
Q psy93           186 I  186 (503)
Q Consensus       186 ~  186 (503)
                      +
T Consensus        94 ~   94 (95)
T 2cqc_A           94 S   94 (95)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.61  E-value=9.7e-16  Score=126.52  Aligned_cols=75  Identities=27%  Similarity=0.426  Sum_probs=70.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ..++|||+|||+++++++|+++|+.||+|..|.|+.+     ++||||+|.+.++|.+|+..||+..|.|++|.|.++..
T Consensus        15 ~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   94 (95)
T 2ywk_A           15 ADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPSS   94 (95)
T ss_dssp             GGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcCC
Confidence            4578999999999999999999999999999999764     68999999999999999999999999999999998853

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=3.3e-15  Score=124.50  Aligned_cols=78  Identities=21%  Similarity=0.323  Sum_probs=71.5

Q ss_pred             CcCCCcEEEEcCCCCCCCHHHHHHhhccC--CCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           109 KFANNCRLYLGNIGGDITENDIIELFKPY--GETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       109 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~--G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      .....++|||+|||+++|+++|+++|+.|  |.|..|.+.  ++||||+|.+.++|.+||..||+..|.|++|.|.++.+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   88 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   88 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCC
Confidence            34467899999999999999999999999  999999875  78999999999999999999999999999999999976


Q ss_pred             cc
Q psy93           187 NA  188 (503)
Q Consensus       187 ~~  188 (503)
                      ..
T Consensus        89 ~~   90 (99)
T 2cpd_A           89 VD   90 (99)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=1.4e-15  Score=128.17  Aligned_cols=74  Identities=24%  Similarity=0.254  Sum_probs=68.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec-----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ..++|||+|||+++|+++|+++|+.||+|.+|.|+.     ++|||||+|.+.++|.+||. +++..|.|++|.|.++..
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEchH
Confidence            457899999999999999999999999999999975     47999999999999999999 899999999999998753

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=1.7e-15  Score=124.00  Aligned_cols=75  Identities=24%  Similarity=0.507  Sum_probs=70.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ...++|||+|||+++|+++|+++|+.||.|..|.|+  ++||||+|.+.++|.+||..||+..|.|++|.|.++.+.
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   81 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKG   81 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC--SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE--CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCC
Confidence            346789999999999999999999999999999997  559999999999999999999999999999999999764

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.61  E-value=1.9e-15  Score=132.34  Aligned_cols=78  Identities=14%  Similarity=0.279  Sum_probs=71.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHH----HhhccCCCeEEEEEe---cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           111 ANNCRLYLGNIGGDITENDII----ELFKPYGETQELFIN---KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~----~~F~~~G~V~~v~i~---~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      .++++|||+|||+.+++++|+    ++|++||+|.+|.+.   +++|||||+|.+.++|.+||..|||..|.|++|.|.|
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~  106 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITF  106 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEE
Confidence            456899999999999999876    699999999999985   4589999999999999999999999999999999999


Q ss_pred             ccccc
Q psy93           184 APINA  188 (503)
Q Consensus       184 a~~~~  188 (503)
                      +....
T Consensus       107 a~~~~  111 (127)
T 2a3j_A          107 SETPQ  111 (127)
T ss_dssp             CCCCC
T ss_pred             ccCcc
Confidence            97643

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.61  E-value=1.5e-15  Score=126.04  Aligned_cols=75  Identities=25%  Similarity=0.533  Sum_probs=69.9

Q ss_pred             CCCcEEEEcCCCC-CCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           111 ANNCRLYLGNIGG-DITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       111 ~~~~~l~V~nLp~-~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      .+.++|||+|||+ ++|+++|+++|+.||+|.+|.|.  ++||||+|.+.++|.+|+..||+..+.|++|.|.++.+.
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~   83 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSN   83 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcC
Confidence            4578999999998 99999999999999999999995  899999999999999999999999999999999998653

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.61  E-value=2.2e-15  Score=125.63  Aligned_cols=74  Identities=22%  Similarity=0.405  Sum_probs=68.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEE--------EEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQE--------LFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGR  177 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~--------v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~  177 (503)
                      ..++|||+|||.++|+++|+++|+.||.|..        |.|+.+      +|||||+|.+.++|.+|++.||+..|.|+
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g~   91 (99)
T 2la6_A           12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGN   91 (99)
T ss_dssp             CCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            4689999999999999999999999999999        888654      57999999999999999999999999999


Q ss_pred             eEEEEecc
Q psy93           178 SLKIRFAP  185 (503)
Q Consensus       178 ~l~V~~a~  185 (503)
                      .|+|.+|+
T Consensus        92 ~l~V~~A~   99 (99)
T 2la6_A           92 PIKVSFAT   99 (99)
T ss_dssp             BCEEEECC
T ss_pred             EEEEEecC
Confidence            99999873

>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=2.1e-15  Score=129.92  Aligned_cols=75  Identities=23%  Similarity=0.492  Sum_probs=70.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ..++|||+|||.++|+++|+++|+.||.|..|.|..+     ++||||+|.+.++|.+||..||+..|.|++|.|.++.+
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   85 (116)
T 2fy1_A            6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKK   85 (116)
T ss_dssp             SCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            4578999999999999999999999999999999864     59999999999999999999999999999999999965

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=1.4e-15  Score=126.58  Aligned_cols=76  Identities=25%  Similarity=0.419  Sum_probs=70.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeE-EEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCce----EE
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQ-ELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRS----LK  180 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~-~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~----l~  180 (503)
                      ..++|||+|||+++++++|+++|+.||+|. +|.|+.+      ++||||+|.+.++|.+|+..||+..|.|+.    |+
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~   87 (99)
T 2div_A            8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFK   87 (99)
T ss_dssp             SSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEE
Confidence            568999999999999999999999999999 9999755      489999999999999999999999999999    99


Q ss_pred             EEecccc
Q psy93           181 IRFAPIN  187 (503)
Q Consensus       181 V~~a~~~  187 (503)
                      |.|+.+.
T Consensus        88 v~~a~~~   94 (99)
T 2div_A           88 LNYATYS   94 (99)
T ss_dssp             EEETTCC
T ss_pred             EeecCCC
Confidence            9998764

>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=99.60  E-value=2.1e-15  Score=128.14  Aligned_cols=76  Identities=22%  Similarity=0.331  Sum_probs=70.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhC------CccccCceE
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLD------GHVLKGRSL  179 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~------g~~l~g~~l  179 (503)
                      ..++|||+|||+++|+++|+++|+.||+|..|.|+.      +++||||+|.+.++|.+||..||      +..|.|++|
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~l   93 (111)
T 1x4h_A           14 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQL   93 (111)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEEE
Confidence            467899999999999999999999999999999973      47899999999999999999999      999999999


Q ss_pred             EEEecccc
Q psy93           180 KIRFAPIN  187 (503)
Q Consensus       180 ~V~~a~~~  187 (503)
                      .|.++.+.
T Consensus        94 ~v~~a~~~  101 (111)
T 1x4h_A           94 KVDLAVTR  101 (111)
T ss_dssp             EEECCCCC
T ss_pred             EEEECCCC
Confidence            99998764

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=3.2e-15  Score=124.21  Aligned_cols=75  Identities=20%  Similarity=0.311  Sum_probs=68.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEE--ecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFI--NKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i--~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ..++|||+|||+++|+++|+++|+.||.|. +.+  .++++||||+|.+.++|.+||..||+..|.|++|.|.++.+.
T Consensus        18 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   94 (97)
T 2e5j_A           18 LAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ   94 (97)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCC
T ss_pred             CCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            467999999999999999999999999995 444  466899999999999999999999999999999999998764

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.60  E-value=1.9e-15  Score=127.65  Aligned_cols=74  Identities=23%  Similarity=0.391  Sum_probs=69.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++|+++|+++|+.||.|.+|.|+.+     ++||||+|.+.++|.+||..||+..|.|++|.|.++.
T Consensus        28 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           28 TGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             CSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            5689999999999999999999999999999999743     7899999999999999999999999999999999875

>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=99.60  E-value=7.7e-16  Score=126.78  Aligned_cols=75  Identities=20%  Similarity=0.358  Sum_probs=68.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCC-eEEEEEecCCCceEEeeCCHHHHHHHHHHhCC-ccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGE-TQELFINKEKMFGFIRMDYKHNADKAKAKLDG-HVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~-V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g-~~l~g~~l~V~~a~~~  187 (503)
                      ..++|||+|||+++|+++|+++|++||. |..+.+ .+++||||+|.+.++|.+|+..||+ ..|.|++|+|.++.+.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~-~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~   83 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   83 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE-EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE-cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCc
Confidence            4578999999999999999999999999 555555 5799999999999999999999999 9999999999999764

>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=99.60  E-value=2.2e-15  Score=127.99  Aligned_cols=76  Identities=22%  Similarity=0.465  Sum_probs=71.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ...++|||+|||.++|+++|+++|+.||.|..|.|+.+      ++||||+|.+.++|.+||..||+..|.|++|.|.|+
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  103 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  103 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEc
Confidence            45689999999999999999999999999999999754      689999999999999999999999999999999998


Q ss_pred             cc
Q psy93           185 PI  186 (503)
Q Consensus       185 ~~  186 (503)
                      .+
T Consensus       104 ~~  105 (110)
T 1oo0_B          104 FV  105 (110)
T ss_dssp             EE
T ss_pred             cc
Confidence            65

>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=99.60  E-value=2e-15  Score=127.28  Aligned_cols=77  Identities=25%  Similarity=0.413  Sum_probs=70.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccc---cCceEEE
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVL---KGRSLKI  181 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l---~g~~l~V  181 (503)
                      ...++|||+|||.++|+++|+++|+.||.|..|.|+.      +++||||+|.+.++|.+||..||+..+   .+++|.|
T Consensus        11 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v   90 (106)
T 2dgp_A           11 HDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQV   90 (106)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEE
Confidence            3567899999999999999999999999999999975      468999999999999999999999987   8899999


Q ss_pred             Eecccc
Q psy93           182 RFAPIN  187 (503)
Q Consensus       182 ~~a~~~  187 (503)
                      .++.+.
T Consensus        91 ~~a~~~   96 (106)
T 2dgp_A           91 KPADSE   96 (106)
T ss_dssp             EECCCC
T ss_pred             EECCcc
Confidence            999764

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.60  E-value=2.3e-15  Score=127.12  Aligned_cols=76  Identities=18%  Similarity=0.227  Sum_probs=70.1

Q ss_pred             CCcEEEEcCCCCCC------CHHHHHHhhccCCCeEEEEEe----cCCCceEEeeCCHHHHHHHHHHhCCccccCc-eEE
Q psy93           112 NNCRLYLGNIGGDI------TENDIIELFKPYGETQELFIN----KEKMFGFIRMDYKHNADKAKAKLDGHVLKGR-SLK  180 (503)
Q Consensus       112 ~~~~l~V~nLp~~~------te~~L~~~F~~~G~V~~v~i~----~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~-~l~  180 (503)
                      ..++|||+|||+.+      |+++|+++|++||+|.+|.|+    +++|||||+|.+.++|.+||..||+..|.|+ +|+
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l~   93 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   93 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEEE
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceEE
Confidence            46799999999999      789999999999999999997    3479999999999999999999999999998 999


Q ss_pred             EEecccc
Q psy93           181 IRFAPIN  187 (503)
Q Consensus       181 V~~a~~~  187 (503)
                      |.++...
T Consensus        94 V~~a~~~  100 (105)
T 2nlw_A           94 VNLFTDF  100 (105)
T ss_dssp             EECSCCC
T ss_pred             EEEcchH
Confidence            9998653

>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=99.59  E-value=2.2e-15  Score=124.85  Aligned_cols=77  Identities=17%  Similarity=0.451  Sum_probs=72.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHH----HhhccCCCeEEEEEe---cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           112 NNCRLYLGNIGGDITENDII----ELFKPYGETQELFIN---KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~----~~F~~~G~V~~v~i~---~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ++++|||+|||.++++++|+    ++|+.||.|..|.|.   ++++||||+|.+.++|.+|+..||+..|.|++|.|.|+
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   86 (97)
T 1nu4_A            7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA   86 (97)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            56799999999999999999    999999999999997   45899999999999999999999999999999999999


Q ss_pred             cccc
Q psy93           185 PINA  188 (503)
Q Consensus       185 ~~~~  188 (503)
                      .+..
T Consensus        87 ~~~~   90 (97)
T 1nu4_A           87 KTDS   90 (97)
T ss_dssp             SSCC
T ss_pred             cCCC
Confidence            7654

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.59  E-value=7.4e-16  Score=129.03  Aligned_cols=76  Identities=14%  Similarity=0.135  Sum_probs=70.4

Q ss_pred             CCcEEEEcCCCC------CCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccC-ce
Q psy93           112 NNCRLYLGNIGG------DITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKG-RS  178 (503)
Q Consensus       112 ~~~~l~V~nLp~------~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g-~~  178 (503)
                      .+++|||+|||+      ++++++|+++|++||+|.+|.|+.      ++|||||+|.+.++|.+||..||+..|.| ++
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            357899999999      999999999999999999999863      47999999999999999999999999999 99


Q ss_pred             EEEEecccc
Q psy93           179 LKIRFAPIN  187 (503)
Q Consensus       179 l~V~~a~~~  187 (503)
                      |.|.++.+.
T Consensus        85 l~V~~a~~~   93 (100)
T 3ns6_A           85 LFLYTMKDV   93 (100)
T ss_dssp             CEEEESHHH
T ss_pred             EEEEECchh
Confidence            999998654

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.59  E-value=1.7e-15  Score=129.21  Aligned_cols=79  Identities=15%  Similarity=0.347  Sum_probs=72.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHH---HhhccCCCeEEEEEecC---------CCceEEeeCCHHHHHHHHHHhCCccccCce
Q psy93           111 ANNCRLYLGNIGGDITENDII---ELFKPYGETQELFINKE---------KMFGFIRMDYKHNADKAKAKLDGHVLKGRS  178 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~---~~F~~~G~V~~v~i~~~---------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~  178 (503)
                      ...++|||+|||+++++++|+   ++|++||+|..|.|+++         +|||||+|.+.++|.+||..||+..|.|++
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~   92 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   92 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEE
Confidence            346789999999999999999   99999999999999754         369999999999999999999999999999


Q ss_pred             EEEEecccccc
Q psy93           179 LKIRFAPINAA  189 (503)
Q Consensus       179 l~V~~a~~~~~  189 (503)
                      |+|.++.+..+
T Consensus        93 l~V~~a~~k~~  103 (111)
T 2cpi_A           93 LKASLGTTKYC  103 (111)
T ss_dssp             EEEESCCCCSC
T ss_pred             EEEEecccccc
Confidence            99999987654

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=3.2e-15  Score=127.74  Aligned_cols=75  Identities=15%  Similarity=0.256  Sum_probs=70.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ..++|||+|||+++++++|+++|+.||.|..|.|+.+     ++||||+|.+.++|.+||..||+..|.|+.|.|.++..
T Consensus        14 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   93 (114)
T 2do0_A           14 LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDER   93 (114)
T ss_dssp             CCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEccc
Confidence            3568999999999999999999999999999999764     68999999999999999999999999999999999864

>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=2.2e-15  Score=127.70  Aligned_cols=77  Identities=25%  Similarity=0.424  Sum_probs=71.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCC-eEEEEEe-------cCCCceEEeeCCHHHHHHHHHHhC--CccccCceEEE
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGE-TQELFIN-------KEKMFGFIRMDYKHNADKAKAKLD--GHVLKGRSLKI  181 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~-V~~v~i~-------~~kg~aFV~F~~~e~A~~Ai~~l~--g~~l~g~~l~V  181 (503)
                      +.++|||+|||+++|+++|+++|+.||. |..|.|+       ++++||||+|.+.++|.+|+..|+  +..|.|+.|+|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V   86 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAV   86 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEE
Confidence            4689999999999999999999999998 9999997       568999999999999999999996  58999999999


Q ss_pred             Eeccccc
Q psy93           182 RFAPINA  188 (503)
Q Consensus       182 ~~a~~~~  188 (503)
                      .|+.+..
T Consensus        87 ~~a~~~~   93 (109)
T 2dis_A           87 DWAEPEI   93 (109)
T ss_dssp             EESCSSC
T ss_pred             EEcCCCC
Confidence            9997643

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=1.9e-15  Score=127.02  Aligned_cols=76  Identities=18%  Similarity=0.388  Sum_probs=70.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhcc-CCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCcc-ccCceEEEEec
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKP-YGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHV-LKGRSLKIRFA  184 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~-~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~-l~g~~l~V~~a  184 (503)
                      ..++|||+|||+++|+++|+++|+. ||.|.+|.|+.+     ++||||+|.+.++|.+||..||+.. |.|++|.|.++
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~a   87 (104)
T 2dhg_A            8 PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVA   87 (104)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCBC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEEc
Confidence            4678999999999999999999999 999999999764     7899999999999999999999999 99999999998


Q ss_pred             ccc
Q psy93           185 PIN  187 (503)
Q Consensus       185 ~~~  187 (503)
                      .+.
T Consensus        88 ~~~   90 (104)
T 2dhg_A           88 IPK   90 (104)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            654

>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=99.58  E-value=2.8e-15  Score=131.62  Aligned_cols=76  Identities=28%  Similarity=0.474  Sum_probs=70.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +.++|||+|||+++|+++|+++|+.||+|..|.|+.      .++||||+|.+.++|.+||..||+..|.|++|.|.|+.
T Consensus        45 ~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a~  124 (129)
T 2kxn_B           45 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSI  124 (129)
T ss_dssp             CSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            457899999999999999999999999999999974      47899999999999999999999999999999999986


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus       125 ~~  126 (129)
T 2kxn_B          125 TK  126 (129)
T ss_dssp             SS
T ss_pred             CC
Confidence            53

>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=99.58  E-value=4.1e-15  Score=133.62  Aligned_cols=79  Identities=22%  Similarity=0.527  Sum_probs=73.9

Q ss_pred             CcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           109 KFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       109 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      .....++|||+|||+++|+++|+++|+.||.|.+|.|+++ +|||||+|.+.++|.+||..||+..|.|++|.|.|+.+.
T Consensus        69 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            3446789999999999999999999999999999999876 999999999999999999999999999999999998764

>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=99.58  E-value=2.7e-15  Score=122.15  Aligned_cols=74  Identities=23%  Similarity=0.390  Sum_probs=69.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      .++|||+|||+++|+++|+++|+.||.|..|.++.+      ++||||+|.+.++|.+|+ .||+..|.|+.|.|.++.+
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            468999999999999999999999999999999754      789999999999999999 8999999999999999865


Q ss_pred             c
Q psy93           187 N  187 (503)
Q Consensus       187 ~  187 (503)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=2.8e-15  Score=127.95  Aligned_cols=77  Identities=22%  Similarity=0.374  Sum_probs=70.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeE--------EEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccC
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQ--------ELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKG  176 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~--------~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g  176 (503)
                      ...++|||+|||+++|+++|+++|+.||.|.        .|.|+.+      ++||||+|.+.++|.+||..||+..|.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   92 (113)
T 2cpe_A           13 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   92 (113)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccCC
Confidence            4568999999999999999999999999998        5888644      6899999999999999999999999999


Q ss_pred             ceEEEEecccc
Q psy93           177 RSLKIRFAPIN  187 (503)
Q Consensus       177 ~~l~V~~a~~~  187 (503)
                      ++|+|.++.+.
T Consensus        93 ~~l~V~~a~~~  103 (113)
T 2cpe_A           93 SKLKVSLARKK  103 (113)
T ss_dssp             EECEEECSSCC
T ss_pred             CEEEEEECCCC
Confidence            99999998764

>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=99.58  E-value=4.2e-15  Score=124.99  Aligned_cols=74  Identities=23%  Similarity=0.376  Sum_probs=68.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      +.++|||+|||+++|+++|+++|+.|| |..|.|+.+       ++||||+|.+.++|.+|| .||+..|.|+.|.|.++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a   91 (104)
T 1wi8_A           14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEEc
Confidence            457999999999999999999999999 999999643       689999999999999999 89999999999999999


Q ss_pred             ccc
Q psy93           185 PIN  187 (503)
Q Consensus       185 ~~~  187 (503)
                      .+.
T Consensus        92 ~~~   94 (104)
T 1wi8_A           92 DQA   94 (104)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            764

>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=99.58  E-value=9.8e-15  Score=124.77  Aligned_cols=77  Identities=19%  Similarity=0.449  Sum_probs=70.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccc--------cCc
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVL--------KGR  177 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l--------~g~  177 (503)
                      ...++|||+|||+++|+++|+++|+.||.|..|.|+.+     ++||||+|.+.++|.+||..||+..|        .++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~  102 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE  102 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCC
Confidence            35689999999999999999999999999999999754     68999999999999999999999999        578


Q ss_pred             eEEEEecccc
Q psy93           178 SLKIRFAPIN  187 (503)
Q Consensus       178 ~l~V~~a~~~  187 (503)
                      +|.|.|+.+.
T Consensus       103 ~l~v~~a~p~  112 (114)
T 1x5o_A          103 PLLCKFSGPS  112 (114)
T ss_dssp             CBEEEECCCS
T ss_pred             ceeEEccCCC
Confidence            8999998754

>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=99.58  E-value=2.3e-15  Score=128.89  Aligned_cols=74  Identities=19%  Similarity=0.433  Sum_probs=68.5

Q ss_pred             CCcEEEE--cCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccc-----cCceEEEEec
Q psy93           112 NNCRLYL--GNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL-----KGRSLKIRFA  184 (503)
Q Consensus       112 ~~~~l~V--~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l-----~g~~l~V~~a  184 (503)
                      ++++|||  +|||.++|+++|+++|++||.|.+|.|+.+++||||+|.+.++|.+|++.|||..|     .+++|.|.++
T Consensus        24 pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~a  103 (114)
T 2cq2_A           24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFV  103 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEEE
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEec
Confidence            3568999  77999999999999999999999999998999999999999999999999999988     6889999876


Q ss_pred             c
Q psy93           185 P  185 (503)
Q Consensus       185 ~  185 (503)
                      .
T Consensus       104 ~  104 (114)
T 2cq2_A          104 E  104 (114)
T ss_dssp             S
T ss_pred             c
Confidence            4

>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=5.8e-15  Score=128.30  Aligned_cols=77  Identities=21%  Similarity=0.362  Sum_probs=71.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec-----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ..++|||+|||+++++++|+++|+.||.|..|.|..     +++||||+|.+.++|.+|+..||+..|.|++|+|.++.+
T Consensus        34 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  113 (124)
T 2kt5_A           34 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVAS  113 (124)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCC
Confidence            467999999999999999999999999999999975     478999999999999999999999999999999999976


Q ss_pred             cc
Q psy93           187 NA  188 (503)
Q Consensus       187 ~~  188 (503)
                      ..
T Consensus       114 ~~  115 (124)
T 2kt5_A          114 QI  115 (124)
T ss_dssp             TT
T ss_pred             CC
Confidence            43

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=1.1e-15  Score=123.53  Aligned_cols=74  Identities=23%  Similarity=0.375  Sum_probs=68.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +.++|||+|||+++++++|+++|+.||+|..|.|+.+      ++||||+|.+.++|.+|+..||+..|.|+.|+|.++.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            4679999999999999999999999999999999754      7899999999999999999999999999999887653

>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=99.58  E-value=5.9e-15  Score=123.45  Aligned_cols=80  Identities=23%  Similarity=0.291  Sum_probs=73.2

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ..++|||+|||.++|+++|+++|+.||.|.+|.|++| .++.++|||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~ln-g~~~---~gr~l~V   93 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLN-GLRL---QSKTIKV   93 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHT-TCEE---TTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhC-CCEE---CCEEEEE
Confidence            3578999999999999999999999999999999998 578999999999999999999999997 6666   6899999


Q ss_pred             ecCCc
Q psy93           265 EPLEL  269 (503)
Q Consensus       265 ~~~~~  269 (503)
                      .++.+
T Consensus        94 ~~AkP   98 (99)
T 4fxv_A           94 SYARP   98 (99)
T ss_dssp             EECCB
T ss_pred             EEeeC
Confidence            98864

>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=99.58  E-value=1e-15  Score=125.52  Aligned_cols=74  Identities=20%  Similarity=0.267  Sum_probs=64.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCC--CeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYG--ETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G--~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      .+|||+|||+++|+++|+++|+.||  .|.+|.|+.+      +|||||+|.+.++|.+||+.||+..|.|+.|.|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4699999999999999999999999  9999998653      5799999999999999999999999999999999886


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus        82 ~~   83 (90)
T 3p5t_L           82 KL   83 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            54

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.58  E-value=5.1e-15  Score=131.10  Aligned_cols=78  Identities=23%  Similarity=0.370  Sum_probs=71.9

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       110 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      ....++|||+|||.++|+++|+++|+.||+|.+|.|+.+      ++||||+|.+.++|.+||..||+..|.|+.|+|.+
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  118 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            345689999999999999999999999999999999743      67999999999999999999999999999999999


Q ss_pred             cccc
Q psy93           184 APIN  187 (503)
Q Consensus       184 a~~~  187 (503)
                      +.+.
T Consensus       119 a~~~  122 (139)
T 1u6f_A          119 AASG  122 (139)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            9754

>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=99.57  E-value=2.3e-15  Score=125.97  Aligned_cols=76  Identities=24%  Similarity=0.365  Sum_probs=67.6

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEE
Q psy93           110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIR  182 (503)
Q Consensus       110 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~  182 (503)
                      ....++|||+|||.++++++|+++|+.|| |.+|.|+.+       +|||||+|.+.++|.+|| .||+..|.|+.|.|.
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVD   93 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEE
Confidence            34568999999999999999999999999 999999653       689999999999999999 899999999999999


Q ss_pred             ecccc
Q psy93           183 FAPIN  187 (503)
Q Consensus       183 ~a~~~  187 (503)
                      ++.+.
T Consensus        94 ~a~~~   98 (100)
T 2j76_E           94 VADQA   98 (100)
T ss_dssp             ECCCS
T ss_pred             eccCC
Confidence            98754

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.57  E-value=1.3e-14  Score=126.28  Aligned_cols=76  Identities=26%  Similarity=0.277  Sum_probs=69.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCc-eEEeeCCHHHHHHHHHHhCCccccC--ceEEEEeccccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMF-GFIRMDYKHNADKAKAKLDGHVLKG--RSLKIRFAPINA  188 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~-aFV~F~~~e~A~~Ai~~l~g~~l~g--~~l~V~~a~~~~  188 (503)
                      ...|||+|||+.+|+++|+++|++||.|.+|.|....|| |||+|.+.++|..|++.|||..|.|  ++|+|.++.+..
T Consensus        25 vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~  103 (124)
T 2e5i_A           25 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTR  103 (124)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEESSSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSC
T ss_pred             EEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCc
Confidence            345789999999999999999999999999998765696 9999999999999999999999987  699999998765

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.57  E-value=1.8e-15  Score=121.37  Aligned_cols=69  Identities=19%  Similarity=0.287  Sum_probs=64.1

Q ss_pred             CcEEEEcCCCCCC------CHHHHHHhhccCCCeEEEEEec----CCCceEEeeCCHHHHHHHHHHhCCccccCc-eEEE
Q psy93           113 NCRLYLGNIGGDI------TENDIIELFKPYGETQELFINK----EKMFGFIRMDYKHNADKAKAKLDGHVLKGR-SLKI  181 (503)
Q Consensus       113 ~~~l~V~nLp~~~------te~~L~~~F~~~G~V~~v~i~~----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~-~l~V  181 (503)
                      +++|||+|||+++      ++++|+++|++||+|.+|.|++    ++|||||+|.+.++|.+|+..||+..|.|+ +|+|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            3689999999999      7799999999999999999873    479999999999999999999999999999 8876

>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=99.57  E-value=4.8e-15  Score=120.32  Aligned_cols=73  Identities=23%  Similarity=0.473  Sum_probs=66.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|++ +++..|.|+.|.|.+|
T Consensus         9 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A            9 EDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             SCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEeC
Confidence            35679999999999999999999999999999999754      6799999999999999996 5888999999999875

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=5.9e-15  Score=126.64  Aligned_cols=74  Identities=18%  Similarity=0.462  Sum_probs=69.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++|+++|+++|+.||+|..|.|+.+      ++||||+|.+.++|.+||..|++ .|.|++|.|.++.
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~a~   94 (116)
T 2cqd_A           16 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   94 (116)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEEcc
Confidence            5679999999999999999999999999999999754      68999999999999999999998 8999999999995


Q ss_pred             c
Q psy93           186 I  186 (503)
Q Consensus       186 ~  186 (503)
                      +
T Consensus        95 ~   95 (116)
T 2cqd_A           95 L   95 (116)
T ss_dssp             T
T ss_pred             c
Confidence            4

>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=3e-15  Score=125.66  Aligned_cols=75  Identities=24%  Similarity=0.402  Sum_probs=70.2

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      .++|||+|||+++++++|+++|+.||.|..|.|+.+      ++||||+|.+.++|.+|++.||+..|.|+.|.|.++.+
T Consensus         8 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   87 (104)
T 1p1t_A            8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             ccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCC
Confidence            468999999999999999999999999999999754      68999999999999999999999999999999999976


Q ss_pred             c
Q psy93           187 N  187 (503)
Q Consensus       187 ~  187 (503)
                      .
T Consensus        88 ~   88 (104)
T 1p1t_A           88 E   88 (104)
T ss_dssp             T
T ss_pred             c
Confidence            4

>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=99.57  E-value=4.4e-15  Score=127.04  Aligned_cols=74  Identities=15%  Similarity=0.267  Sum_probs=69.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||.++++++|+++|+.||.|..|.|+.      +++||||+|.+.++|.+|| .||+..|.|+.|.|.++.
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  102 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecC
Confidence            457999999999999999999999999999999963      4689999999999999999 999999999999999986


Q ss_pred             c
Q psy93           186 I  186 (503)
Q Consensus       186 ~  186 (503)
                      +
T Consensus       103 ~  103 (114)
T 2cq4_A          103 A  103 (114)
T ss_dssp             H
T ss_pred             C
Confidence            4

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.57  E-value=5.6e-15  Score=133.62  Aligned_cols=78  Identities=24%  Similarity=0.455  Sum_probs=71.9

Q ss_pred             CcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEE
Q psy93           109 KFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIR  182 (503)
Q Consensus       109 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~  182 (503)
                      .....++|||+|||+++|+++|+++|+.||+|..|.|+.+      ++||||+|.+.++|.+||..||+..|.+++|+|.
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  114 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD  114 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            3346789999999999999999999999999999999643      5799999999999999999999999999999999


Q ss_pred             eccc
Q psy93           183 FAPI  186 (503)
Q Consensus       183 ~a~~  186 (503)
                      |+.+
T Consensus       115 ~a~~  118 (156)
T 1h2v_Z          115 WDAG  118 (156)
T ss_dssp             EESC
T ss_pred             ECCC
Confidence            9975

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.56  E-value=7.2e-15  Score=123.36  Aligned_cols=74  Identities=24%  Similarity=0.394  Sum_probs=68.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++++++|+++|+.|| |..|.|+.+      ++||||+|.+.++|.+|| .||+..|.|++|.|.++.
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~   91 (103)
T 2dng_A           14 PPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAE   91 (103)
T ss_dssp             SCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEECC
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEec
Confidence            457999999999999999999999997 999999754      579999999999999999 899999999999999997


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus        92 ~~   93 (103)
T 2dng_A           92 GR   93 (103)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.56  E-value=4.5e-15  Score=120.34  Aligned_cols=71  Identities=35%  Similarity=0.601  Sum_probs=67.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccC----C-------CeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEE
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPY----G-------ETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLK  180 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~----G-------~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~  180 (503)
                      ..++|||+|||+++|+++|+++|+.|    |       .|.+|.+.++++||||+|.+.++|.+|+ .||+..|.|+.|+
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l~   83 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   83 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSSSSEEEEEESSHHHHHHHG-GGTTCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCCCcEEEEEcCCHHHHHHHH-hcCCCEECCeEEE
Confidence            35789999999999999999999999    8       9999999999999999999999999999 9999999999999


Q ss_pred             EEe
Q psy93           181 IRF  183 (503)
Q Consensus       181 V~~  183 (503)
                      |+.
T Consensus        84 V~r   86 (87)
T 2hzc_A           84 IRR   86 (87)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            974

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.56  E-value=3.1e-15  Score=118.42  Aligned_cols=70  Identities=24%  Similarity=0.571  Sum_probs=65.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      |+|||+|||+++++++|+++|++||+|..|.++.+      +|||||+|.+.++|.+|+..++ ..+.|++|.|.++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            57999999999999999999999999999999754      6899999999999999999999 9999999999986

>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=99.56  E-value=4.5e-15  Score=127.52  Aligned_cols=73  Identities=12%  Similarity=0.192  Sum_probs=66.4

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCce-----EEEEeccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRS-----LKIRFAPI  186 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~-----l~V~~a~~  186 (503)
                      .++|||+|||+++|+++|+++|++||+|..|.|+.+ +||||+|.+.++|.+||+.||+..|.|+.     |+|..+.+
T Consensus        16 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~~   93 (115)
T 3beg_B           16 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGP   93 (115)
T ss_dssp             -CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC-
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCCC
Confidence            468999999999999999999999999999999877 99999999999999999999999999998     66665543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.56  E-value=7.8e-15  Score=124.79  Aligned_cols=78  Identities=22%  Similarity=0.465  Sum_probs=67.4

Q ss_pred             CcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEE
Q psy93           109 KFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIR  182 (503)
Q Consensus       109 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~  182 (503)
                      .....++|||+|||.++|+++|+++|+.||.|.+|.|+.+      +|||||+|.+.++|.+||..+ +..|.|+.|.|.
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~   99 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPK   99 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEE
Confidence            3345688999999999999999999999999999999753      689999999999999999976 599999999999


Q ss_pred             ecccc
Q psy93           183 FAPIN  187 (503)
Q Consensus       183 ~a~~~  187 (503)
                      ++.+.
T Consensus       100 ~a~~~  104 (109)
T 2rs2_A          100 VAFPR  104 (109)
T ss_dssp             ECCCC
T ss_pred             EccCC
Confidence            98653

>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=99.56  E-value=3.2e-15  Score=124.23  Aligned_cols=75  Identities=13%  Similarity=0.186  Sum_probs=67.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++++++|+++|+.||.|..+.++.      +++||||+|.+.++|.+||..||+..|.|++|+|.++.
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   93 (98)
T 2cqp_A           14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGS   93 (98)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEcC
Confidence            357899999999999999999999999998665542      36899999999999999999999999999999999986


Q ss_pred             c
Q psy93           186 I  186 (503)
Q Consensus       186 ~  186 (503)
                      .
T Consensus        94 ~   94 (98)
T 2cqp_A           94 G   94 (98)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=1.2e-14  Score=124.42  Aligned_cols=77  Identities=29%  Similarity=0.379  Sum_probs=69.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCe----EEEEEe--cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGET----QELFIN--KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V----~~v~i~--~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      .++++|||+|||.++|+++|+++|+.||.|    ..+.+.  ++++||||+|.+.++|.+||..||+..|.|++|.|.|+
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            456899999999999999999999999998    566654  45799999999999999999999999999999999999


Q ss_pred             ccc
Q psy93           185 PIN  187 (503)
Q Consensus       185 ~~~  187 (503)
                      .+.
T Consensus       103 ~~~  105 (115)
T 2cpx_A          103 KNK  105 (115)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            764

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.55  E-value=2.2e-15  Score=124.41  Aligned_cols=74  Identities=14%  Similarity=0.175  Sum_probs=66.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      .++|||+|||+++|+++|+++|+.||.|..+.++.      +++||||+|.+.++|.+||..||+..|.|++|+|.++.+
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~s   94 (95)
T 2ek1_A           15 PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPSS   94 (95)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC-
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEeccC
Confidence            46899999999999999999999999998766653      368999999999999999999999999999999998753

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=1.1e-14  Score=119.33  Aligned_cols=74  Identities=14%  Similarity=0.242  Sum_probs=68.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ..++|||+|||+++|+++|+++|+.| .|..|.|+.+     +|||||+|.+.++|.+||. ||+..|.|+.|.|.++.+
T Consensus         9 ~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~~   86 (91)
T 2dgw_A            9 TCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREKS   86 (91)
T ss_dssp             CCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEESS
T ss_pred             CccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECCc
Confidence            45789999999999999999999999 9999999754     6799999999999999999 999999999999999865


Q ss_pred             c
Q psy93           187 N  187 (503)
Q Consensus       187 ~  187 (503)
                      .
T Consensus        87 ~   87 (91)
T 2dgw_A           87 G   87 (91)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=7.8e-15  Score=125.87  Aligned_cols=75  Identities=20%  Similarity=0.427  Sum_probs=69.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++|+++|+++|+.||.|..|.|+.+      ++||||+|.+.++|.+||.. ++..|.|+.|.|.++.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            4589999999999999999999999999999999754      68999999999999999997 9999999999999987


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus       105 ~~  106 (116)
T 1x4b_A          105 AR  106 (116)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.55  E-value=1.4e-14  Score=126.75  Aligned_cols=76  Identities=20%  Similarity=0.356  Sum_probs=69.8

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec-CCCc-eEEeeCCHHHHHHHHHHhCCccccC--ceEEEEeccccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINK-EKMF-GFIRMDYKHNADKAKAKLDGHVLKG--RSLKIRFAPINA  188 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~-~kg~-aFV~F~~~e~A~~Ai~~l~g~~l~g--~~l~V~~a~~~~  188 (503)
                      -..|||+||++.+|+++|+++|++||.|.+|.|.. .++| |||+|.+.++|.+|++.|||..|.+  ++|+|.|+++..
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~  107 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  107 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSS
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCc
Confidence            35789999999999999999999999999998864 4677 9999999999999999999999998  999999998764

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.55  E-value=4.9e-15  Score=116.83  Aligned_cols=69  Identities=16%  Similarity=0.444  Sum_probs=64.6

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           115 RLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       115 ~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      +|||+|||+++|+++|+++|+.||+|.+|.++.+      +|||||+|.+.++|.+|++ ||+..|.|++|.|.+|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            4999999999999999999999999999998643      5899999999999999998 9999999999999875

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.55  E-value=1.9e-14  Score=127.19  Aligned_cols=73  Identities=21%  Similarity=0.521  Sum_probs=68.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ..++|||+|||+++|+++|+++|+.||+|..|.|+.+      ++||||+|.+.++|.+|++.||+..|.|++|+|.+|
T Consensus        62 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A           62 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            4578999999999999999999999999999999653      789999999999999999999999999999999875

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.55  E-value=7.1e-15  Score=133.32  Aligned_cols=76  Identities=21%  Similarity=0.364  Sum_probs=69.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCC--CeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYG--ETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G--~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      ..++|||+|||+++|+++|+++|+.||  .|.+|.|+.+      +|||||+|.+.++|.+||..||+..|.|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            357999999999999999999999999  9999999744      68999999999999999999999999999999999


Q ss_pred             cccc
Q psy93           184 APIN  187 (503)
Q Consensus       184 a~~~  187 (503)
                      +.+.
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            9653

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=1.6e-14  Score=120.77  Aligned_cols=76  Identities=20%  Similarity=0.258  Sum_probs=66.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEE--ecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFI--NKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i--~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ..++|||+|||+++|+++|+++|+.||.|.-+..  .++++||||+|.+.++|.+||..||+..|.|++|+|.++.+.
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   91 (101)
T 2fc9_A           14 ESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPR   91 (101)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCC
Confidence            4689999999999999999999999998832221  134899999999999999999999999999999999999764

>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=99.54  E-value=9.1e-15  Score=133.64  Aligned_cols=76  Identities=22%  Similarity=0.468  Sum_probs=70.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++|+++|+.+|+.||+|..|.|+.+      ++||||+|.+.++|.+||..||+..|.|++|.|.|+.
T Consensus        71 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  150 (165)
T 1rk8_A           71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF  150 (165)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            4678999999999999999999999999999999764      6899999999999999999999999999999999986


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus       151 ~~  152 (165)
T 1rk8_A          151 VK  152 (165)
T ss_dssp             EC
T ss_pred             CC
Confidence            53

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.54  E-value=3.2e-15  Score=129.82  Aligned_cols=75  Identities=24%  Similarity=0.432  Sum_probs=69.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||.++|+++|+++|+.||.|.+|.|+.+      ++||||+|.+.++|.+|| .||+..|.|+.|.|.++.
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            4679999999999999999999999999999999753      689999999999999999 799999999999999987


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus       114 ~~  115 (124)
T 2jwn_A          114 TN  115 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=1.4e-14  Score=119.74  Aligned_cols=76  Identities=22%  Similarity=0.292  Sum_probs=69.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEE-EEecCC--CceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQEL-FINKEK--MFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v-~i~~~k--g~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ..++|||+|||+++|+++|+++|+.||.|.+| .|+.++  +.|||+|.+.++|.+||..||+..|.|++|.|.++.+.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   92 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDE   92 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCcc
Confidence            35789999999999999999999999999999 476553  45999999999999999999999999999999998764

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=2.4e-14  Score=117.16  Aligned_cols=76  Identities=16%  Similarity=0.287  Sum_probs=67.7

Q ss_pred             cEEEEcCCCCCCCHHH----HHHhhccC-CCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccccc
Q psy93           114 CRLYLGNIGGDITEND----IIELFKPY-GETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINA  188 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~----L~~~F~~~-G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~~  188 (503)
                      |.|||+|||.++++++    |+++|++| |+|.+|.    .|+|||.|.+.++|.+|++.|+|..|.|++|+|.+++...
T Consensus        10 T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~Vt----gG~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~~s   85 (96)
T 2diu_A           10 TLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSIT----GCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNR   85 (96)
T ss_dssp             EEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEECC----TTCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCCSC
T ss_pred             eEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEEe----cCEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCCCc
Confidence            4599999999999988    55899999 5999993    4999999999999999999999999999999999998876


Q ss_pred             ceecc
Q psy93           189 AIKVK  193 (503)
Q Consensus       189 ~L~V~  193 (503)
                      .++..
T Consensus        86 d~~~~   90 (96)
T 2diu_A           86 ELCET   90 (96)
T ss_dssp             CCCCC
T ss_pred             ceeEe
Confidence            65543

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.54  E-value=8.4e-15  Score=128.70  Aligned_cols=77  Identities=21%  Similarity=0.362  Sum_probs=70.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEE--EEEecC------CCceEEeeCCHHHHHHHHHHhCCc----cccCce
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQE--LFINKE------KMFGFIRMDYKHNADKAKAKLDGH----VLKGRS  178 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~--v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~----~l~g~~  178 (503)
                      ...++|||+|||+++|+++|+++|+.||.|..  |+|+++      +|||||+|.+. +|.+||..||+.    .|.|++
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~   99 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKT   99 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEE
Confidence            35679999999999999999999999999976  888643      69999999999 999999999999    999999


Q ss_pred             EEEEeccccc
Q psy93           179 LKIRFAPINA  188 (503)
Q Consensus       179 l~V~~a~~~~  188 (503)
                      |.|.++.+..
T Consensus       100 l~V~~a~~~~  109 (131)
T 2m2b_A          100 INVEFAKGSK  109 (131)
T ss_dssp             CCCEECCCSC
T ss_pred             EEEEECCCCC
Confidence            9999997643

>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=99.53  E-value=1.1e-14  Score=124.90  Aligned_cols=75  Identities=13%  Similarity=0.186  Sum_probs=68.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCe-EEEEEec-----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGET-QELFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V-~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++|+++|+++|+.||.| ..|.|+.     ++|||||+|.+.++|.+||.. |+..|.|+.|.|.++.
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a~   92 (114)
T 2cpy_A           14 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVVT   92 (114)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEEC
T ss_pred             CccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEECC
Confidence            45789999999999999999999999999 8888864     579999999999999999987 9999999999999986


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus        93 ~~   94 (114)
T 2cpy_A           93 LE   94 (114)
T ss_dssp             HH
T ss_pred             HH
Confidence            53

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=1.5e-14  Score=119.34  Aligned_cols=74  Identities=16%  Similarity=0.324  Sum_probs=66.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCC-ceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKM-FGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg-~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ..++|||+|||+++|+++|+++|+.||.|.+|.+.+..+ ||||+|.+.++|.+||. ||+..|.|+.|.|.++.+
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~   81 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQ   81 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCc
Confidence            457899999999999999999999999999984443322 99999999999999999 999999999999998864

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.53  E-value=8.4e-15  Score=129.57  Aligned_cols=76  Identities=26%  Similarity=0.545  Sum_probs=70.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++|+++|+++|+.||.|..|.|+.      +++||||+|.+.++|.+||..||+..|.|++|+|.|+.
T Consensus        46 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~  125 (135)
T 2lea_A           46 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR  125 (135)
T ss_dssp             GCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            356899999999999999999999999999999964      36899999999999999999999999999999999997


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus       126 ~~  127 (135)
T 2lea_A          126 YG  127 (135)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.53  E-value=6.3e-15  Score=121.24  Aligned_cols=82  Identities=12%  Similarity=0.129  Sum_probs=73.6

Q ss_pred             ccceeccCcccccCHHHHHHHhccCC-CeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFG-DIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G-~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +++|||+|||.++|+++|+++|+.|| .|.+|.|++| .++.++|||||+|.+.++|.+|+..++++..+   .+++|.|
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~---~gr~i~V   77 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNI---LGQKVSM   77 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEE---TTEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEE---CCEEEEE
Confidence            46899999999999999999999999 8999999988 57899999999999999999999988656656   7899999


Q ss_pred             ecCCccc
Q psy93           265 EPLELTD  271 (503)
Q Consensus       265 ~~~~~~~  271 (503)
                      .++.+..
T Consensus        78 ~~a~~~~   84 (91)
T 2lxi_A           78 HYSDPKP   84 (91)
T ss_dssp             ECCCSCC
T ss_pred             EEcCCCC
Confidence            9986653

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=6.2e-15  Score=124.14  Aligned_cols=75  Identities=23%  Similarity=0.431  Sum_probs=69.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++++++|+++|+.||+|..|.|+.+      ++||||+|.+.++|.+||.. ++..|.|+.|.|.++.
T Consensus        15 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~a~   93 (105)
T 2dh8_A           15 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCT   93 (105)
T ss_dssp             SSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCCSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEcc
Confidence            4578999999999999999999999999999999764      47999999999999999998 9999999999999986


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus        94 ~~   95 (105)
T 2dh8_A           94 PR   95 (105)
T ss_dssp             CS
T ss_pred             CC
Confidence            54

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=2.8e-14  Score=120.21  Aligned_cols=75  Identities=15%  Similarity=0.161  Sum_probs=67.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEE-EEEec-----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQE-LFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~-v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++|+++|+++|+.||.|.. |.|+.     ++|||||+|.+.++|.+||.. |+..|.++.|.|.++.
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~~   92 (104)
T 1wg5_A           14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKSS   92 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEECC
Confidence            4578999999999999999999999999987 77753     479999999999999999997 9999999999999886


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus        93 ~~   94 (104)
T 1wg5_A           93 RA   94 (104)
T ss_dssp             TT
T ss_pred             HH
Confidence            54

>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=99.53  E-value=4.6e-15  Score=156.16  Aligned_cols=82  Identities=18%  Similarity=0.250  Sum_probs=74.5

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +.++|||+|||..+|+++|.++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+||..|| +..|   .+++|.|
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~ln-g~~i---~gr~i~V  176 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHAD-GKKI---DGRRVLV  176 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcC-CCEE---CCEEEEE
Confidence            4579999999999999999999999999999999988 588899999999999999999999997 6666   6899999


Q ss_pred             ecCCccc
Q psy93           265 EPLELTD  271 (503)
Q Consensus       265 ~~~~~~~  271 (503)
                      .++....
T Consensus       177 ~~a~~~~  183 (437)
T 3pgw_S          177 DVERGRT  183 (437)
T ss_pred             EEeCCCC
Confidence            9987643

>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=2.9e-14  Score=128.95  Aligned_cols=77  Identities=26%  Similarity=0.538  Sum_probs=71.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ...++|||+|||+++|+++|+++|+.||.|..|.|+.      ++|||||+|.+.++|.+||..||+..|.|++|.|.++
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  147 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  147 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            4568999999999999999999999999999999975      3689999999999999999999999999999999999


Q ss_pred             ccc
Q psy93           185 PIN  187 (503)
Q Consensus       185 ~~~  187 (503)
                      .+.
T Consensus       148 ~~~  150 (158)
T 2kn4_A          148 RYG  150 (158)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            754

>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=99.52  E-value=3.4e-15  Score=122.01  Aligned_cols=74  Identities=28%  Similarity=0.472  Sum_probs=66.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ++|||+|||.++++++|+++|+.||+|.+|.|+.+      ++||||+|.+.+ |.+|+..||+..+.|++|+|.++.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            57999999999999999999999999999999743      789999999999 99999999999999999999999764


Q ss_pred             c
Q psy93           188 A  188 (503)
Q Consensus       188 ~  188 (503)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            3

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.52  E-value=4.9e-14  Score=120.18  Aligned_cols=83  Identities=10%  Similarity=0.035  Sum_probs=75.0

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      ++.++|||+|||..+++++|+++|++||.|.+|.|+.|. ++.++|||||+|.+.++|.+|+..|| +..+   .+++|.
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~ln-g~~~---~gr~i~   79 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLH-LTSV---MGNIIH   79 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT-TCEE---TTEECE
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhC-CCEE---CCeEEE
Confidence            457899999999999999999999999999999999984 69999999999999999999999997 6666   699999


Q ss_pred             eecCCccc
Q psy93           264 VEPLELTD  271 (503)
Q Consensus       264 V~~~~~~~  271 (503)
                      |.++....
T Consensus        80 V~~a~~~~   87 (110)
T 3s8s_A           80 AQLDIKGQ   87 (110)
T ss_dssp             EEECSTTH
T ss_pred             EEECCCCc
Confidence            99876543

>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=99.52  E-value=3.1e-14  Score=129.29  Aligned_cols=76  Identities=18%  Similarity=0.328  Sum_probs=69.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec--CCCceEEeeCCHHHHHHHHHHhCCccccC--ceEEEEeccccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINK--EKMFGFIRMDYKHNADKAKAKLDGHVLKG--RSLKIRFAPINA  188 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~--~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g--~~l~V~~a~~~~  188 (503)
                      ..+|||+|||+.+|+++|+++|++||.|.+|.|..  +++||||+|.+.++|.+|++.|||..|.+  ++|+|.|+.+..
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~~  125 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  125 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSSS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCCc
Confidence            46799999999999999999999999999999863  36799999999999999999999999976  999999998753

>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=99.51  E-value=4.1e-14  Score=118.60  Aligned_cols=74  Identities=24%  Similarity=0.400  Sum_probs=67.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++++++|+++|+.||+|..|.|+.+      ++||||+|.+.++|.+||.  ++..|.|+.|.|.++.
T Consensus        14 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~a~   91 (103)
T 2cqg_A           14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLPN   91 (103)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECCC
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEecC
Confidence            4578999999999999999999999999999999754      5799999999999999998  4779999999999987


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus        92 ~~   93 (103)
T 2cqg_A           92 SK   93 (103)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=3e-14  Score=119.17  Aligned_cols=77  Identities=19%  Similarity=0.333  Sum_probs=65.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe---cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFIN---KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~---~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ...++|||+|||+++|+++|+++|+.|+.|.-+...   ++++||||+|.+.++|.+||..||+..|.|+.|.|.|+.+.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~   92 (102)
T 2fc8_A           13 QPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPK   92 (102)
T ss_dssp             CCCSSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CCCCEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCC
Confidence            356789999999999999999999988543332221   22589999999999999999999999999999999999764

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.51  E-value=9.9e-15  Score=120.74  Aligned_cols=77  Identities=22%  Similarity=0.313  Sum_probs=68.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEE-ecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFI-NKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i-~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ...++|||+|||+++|+++|+++|+.||.|..+.. .+++|||||+|.+.++|.+|+..|++..|.|++|.|.++.+.
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   91 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK   91 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            35689999999999999999999999999987722 234789999999999999999999999999999999998653

>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=99.51  E-value=2.4e-14  Score=120.38  Aligned_cols=72  Identities=18%  Similarity=0.184  Sum_probs=65.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      .++|||+|||+++|+++|+++|+.||.| +|.|+.+     +|||||+|.+.++|.+||. +|+..|.++.|.|.++.+
T Consensus        15 ~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~~~   91 (102)
T 1wez_A           15 GHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNST   91 (102)
T ss_dssp             SCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCC
Confidence            4689999999999999999999999955 8888643     6899999999999999995 799999999999988754

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=9.2e-15  Score=127.13  Aligned_cols=75  Identities=15%  Similarity=0.239  Sum_probs=66.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEE-Ee-----cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELF-IN-----KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~-i~-----~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++|+++|+++|+.||.|..+. |.     +++|||||+|.+.++|.+||. ||+..|.|+.|.|.++.
T Consensus        24 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~  102 (124)
T 1wel_A           24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT  102 (124)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECC
Confidence            457899999999999999999999999997633 32     247899999999999999999 99999999999999986


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus       103 ~~  104 (124)
T 1wel_A          103 KK  104 (124)
T ss_dssp             HH
T ss_pred             HH
Confidence            53

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.50  E-value=8.1e-15  Score=129.69  Aligned_cols=117  Identities=19%  Similarity=0.197  Sum_probs=74.5

Q ss_pred             CceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc------cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-
Q psy93           150 MFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP------INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-  222 (503)
Q Consensus       150 g~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~------~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-  222 (503)
                      .++|++|.+...+..|+..+++....++. .+.+..      +.++|||+|||..+++++|+++|+.||.|..|.|+.+ 
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~-~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~   83 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRG-SMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDR   83 (135)
T ss_dssp             -------------------------------CCSCCSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCS
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCC-CCCcCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC
Confidence            37889999999999999999887665543 122222      3568999999999999999999999999999999888 


Q ss_pred             CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCccc
Q psy93           223 ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTD  271 (503)
Q Consensus       223 ~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~~  271 (503)
                      .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|.++....
T Consensus        84 ~~g~~~G~afV~F~~~~~A~~Ai~~l~-g~~i---~g~~l~V~~a~~~~  128 (135)
T 2lea_A           84 YTKESRGFAFVRFHDKRDAEDAMDAMD-GAVL---DGRELRVQMARYGR  128 (135)
T ss_dssp             SSSSCCSCCEEECSCHHHHHHHHTTTT-TCCS---SSSCCEEEECCCCC
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHcC-CCEE---CCEEEEEEECCCCC
Confidence            478899999999999999999999997 5555   58999999987653

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.50  E-value=2.1e-14  Score=123.92  Aligned_cols=74  Identities=8%  Similarity=0.067  Sum_probs=67.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCC---eEEEEEec-----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGE---TQELFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~---V~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      ..++|||+|||+++|+++|+++|+.||.   |..|.|+.     ++|||||+|.+.++|.+||. ||+..|.|+.|.|.+
T Consensus        16 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~   94 (118)
T 2db1_A           16 EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVFK   94 (118)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEEE
Confidence            4578999999999999999999999999   88898864     36899999999999999999 999999999999998


Q ss_pred             ccc
Q psy93           184 API  186 (503)
Q Consensus       184 a~~  186 (503)
                      +..
T Consensus        95 a~~   97 (118)
T 2db1_A           95 SHR   97 (118)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            754

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.50  E-value=5.3e-14  Score=117.52  Aligned_cols=75  Identities=15%  Similarity=0.301  Sum_probs=66.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEE-----EEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQE-----LFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~-----v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ..++|||+|||+++|+++|+++|+.||.|..     ....++++||||+|.+.++|.+||+ ||+..|.|+.|.|.++.+
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~~   94 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKG   94 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcCC
Confidence            4679999999999999999999999997765     2223568999999999999999998 999999999999999865


Q ss_pred             c
Q psy93           187 N  187 (503)
Q Consensus       187 ~  187 (503)
                      .
T Consensus        95 ~   95 (101)
T 1fj7_A           95 R   95 (101)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.50  E-value=2.2e-14  Score=126.98  Aligned_cols=74  Identities=8%  Similarity=0.064  Sum_probs=67.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCC---eEEEEEec-----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGE---TQELFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~---V~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      ..++|||+|||+++|+++|+++|+.||.   |.+|.|+.     ++|||||+|.+.++|.+||+ ||+..|.|+.|.|.+
T Consensus        43 ~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~~  121 (136)
T 2hgl_A           43 EGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFK  121 (136)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            3578999999999999999999999999   88888864     36899999999999999999 999999999999998


Q ss_pred             ccc
Q psy93           184 API  186 (503)
Q Consensus       184 a~~  186 (503)
                      +.+
T Consensus       122 a~~  124 (136)
T 2hgl_A          122 SHR  124 (136)
T ss_dssp             CCH
T ss_pred             CCh
Confidence            754

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.49  E-value=1.9e-14  Score=138.77  Aligned_cols=76  Identities=20%  Similarity=0.276  Sum_probs=69.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCC--CeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYG--ETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G--~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      ..++|||+|||+++|+++|+++|+.||  .|++|.|+.+      +|||||+|.+.++|.+||..||++.|.|+.|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            467899999999999999999999999  9999999754      68999999999999999999999999999999999


Q ss_pred             cccc
Q psy93           184 APIN  187 (503)
Q Consensus       184 a~~~  187 (503)
                      +.+.
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            8654

>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=99.49  E-value=1.9e-14  Score=121.92  Aligned_cols=75  Identities=11%  Similarity=0.084  Sum_probs=68.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCC---eEEEEEec-----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEE
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGE---TQELFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIR  182 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~---V~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~  182 (503)
                      ...++|||+|||+++|+++|+++|+.||.   |..|.|+.     ++|||||+|.+.++|.+||. +|+..|.|+.|.|.
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   87 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVY   87 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEE
Confidence            35678999999999999999999999998   88998864     47899999999999999999 99999999999999


Q ss_pred             eccc
Q psy93           183 FAPI  186 (503)
Q Consensus       183 ~a~~  186 (503)
                      ++.+
T Consensus        88 ~a~~   91 (107)
T 2lmi_A           88 EINN   91 (107)
T ss_dssp             ECCH
T ss_pred             ECCH
Confidence            8864

>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=99.49  E-value=1.4e-14  Score=114.05  Aligned_cols=69  Identities=23%  Similarity=0.397  Sum_probs=63.9

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           115 RLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       115 ~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      +|||+|||+++|+++|+++|+.||+|..|.++.      +++||||+|.+.++|.+|+.. ++..|.|+.|.|.++
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            599999999999999999999999999999864      378999999999999999984 889999999999875

>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=99.49  E-value=1.2e-13  Score=116.03  Aligned_cols=86  Identities=21%  Similarity=0.244  Sum_probs=75.8

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      +.++|||+|||..+++++|+++|+.||.|..|.|+.+.++.+++||||+|.+.++|.+|+..|| +..+.....++|.|.
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~-g~~~~gg~~~~l~V~   92 (105)
T 2dnh_A           14 RDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH-GSQTMPGASSSLVVK   92 (105)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHS-SCCCCTTCSSCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHc-CCccCCCCCccEEEE
Confidence            4689999999999999999999999999999999999889999999999999999999999997 555532223899999


Q ss_pred             cCCcccc
Q psy93           266 PLELTDE  272 (503)
Q Consensus       266 ~~~~~~~  272 (503)
                      ++.....
T Consensus        93 ~a~~~~~   99 (105)
T 2dnh_A           93 FADTDKE   99 (105)
T ss_dssp             ESCSSCC
T ss_pred             ECccCcc
Confidence            9877644

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.49  E-value=2.4e-14  Score=118.81  Aligned_cols=83  Identities=13%  Similarity=0.107  Sum_probs=71.0

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCC--eeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGD--IERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~--V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      -.+|||+|||+.+|+++|+++|++||.  |.+|.+++| .++.++|||||+|.+.++|.+|+..||+....+...+++|.
T Consensus         9 m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~   88 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIG   88 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEE
T ss_pred             cCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEE
Confidence            368999999999999999999999995  678888888 57899999999999999999999999854322223799999


Q ss_pred             eecCCc
Q psy93           264 VEPLEL  269 (503)
Q Consensus       264 V~~~~~  269 (503)
                      |.+++.
T Consensus        89 V~~Aks   94 (95)
T 2lkz_A           89 VDFAKS   94 (95)
T ss_dssp             EEECCC
T ss_pred             EEEccC
Confidence            998753

>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=99.49  E-value=1.9e-14  Score=128.14  Aligned_cols=77  Identities=27%  Similarity=0.482  Sum_probs=68.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEE--------EEE---ecCCCceEEeeCCHHHHHHHHHHhCCccccCceE
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQE--------LFI---NKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSL  179 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~--------v~i---~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l  179 (503)
                      .++++|||+|||+++|+++|+++|+.||.|..        |.+   .+++|||||+|.+.++|.+||..||+..|.|++|
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l  122 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM  122 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            35689999999999999999999999999876        333   2468999999999999999999999999999999


Q ss_pred             EEEecccc
Q psy93           180 KIRFAPIN  187 (503)
Q Consensus       180 ~V~~a~~~  187 (503)
                      .|.++.+.
T Consensus       123 ~V~~a~~~  130 (143)
T 3egn_A          123 VVQFARSA  130 (143)
T ss_dssp             EEEECCCS
T ss_pred             EEEECCCC
Confidence            99999653

>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=99.48  E-value=7.7e-14  Score=114.23  Aligned_cols=72  Identities=28%  Similarity=0.510  Sum_probs=61.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec-CCCceEEeeCCHHHHHHHHHHhCCcc--ccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK-EKMFGFIRMDYKHNADKAKAKLDGHV--LKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~-~kg~aFV~F~~~e~A~~Ai~~l~g~~--l~g~~l~V~~a~~~  187 (503)
                      ..++|||+|||+++|+++|+++|++||+|.+|.|+. ++|||||+|.+.++|.+    |++..  +.++.|.|.++.+.
T Consensus        10 ~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~~k   84 (89)
T 3d2w_A           10 HGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAEPK   84 (89)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC--
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcCCC
Confidence            457899999999999999999999999999999986 58999999999999984    45554  45899999998654

>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=99.48  E-value=9.1e-14  Score=119.26  Aligned_cols=81  Identities=32%  Similarity=0.471  Sum_probs=72.3

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      .++|||+|||..+++++|+++|+.||.|.+|+|+.+. +.+++||||+|.+.++|.+|+..|+ +..+   .+++|.|.+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~-~~~kg~afV~f~~~~~A~~Ai~~l~-~~~~---~g~~i~V~~   79 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMN-GMLL---NDRKVFVGR   79 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TEEEEEEEEEESCHHHHHHHHHHHT-TCEE---TTEECEEEE
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC-CCCCceEEEEECCHHHHHHHHHHcC-CCEE---CCEEEEEEE
Confidence            4689999999999999999999999999999999885 4479999999999999999999997 6666   689999998


Q ss_pred             CCcccc
Q psy93           267 LELTDE  272 (503)
Q Consensus       267 ~~~~~~  272 (503)
                      +.....
T Consensus        80 a~~~~~   85 (115)
T 4f25_A           80 FKSRKE   85 (115)
T ss_dssp             SSCCCC
T ss_pred             CCCccc
Confidence            876543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.22  E-value=3.1e-15  Score=128.48  Aligned_cols=77  Identities=21%  Similarity=0.385  Sum_probs=70.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEE--------EEEecC------CCceEEeeCCHHHHHHHHHHhCCccccC
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQE--------LFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKG  176 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~--------v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g  176 (503)
                      .+.++|||+|||+++++++|+++|+.||.|..        |.|+.+      ++||||+|.+.++|.+||..||+..|.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            35678999999999999999999999999998        777543      6899999999999999999999999999


Q ss_pred             ceEEEEecccc
Q psy93           177 RSLKIRFAPIN  187 (503)
Q Consensus       177 ~~l~V~~a~~~  187 (503)
                      ++|.|.++.+.
T Consensus        85 ~~l~V~~a~~~   95 (116)
T 2lcw_A           85 NPIKVSFATRR   95 (116)
Confidence            99999998653

>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=99.48  E-value=3.6e-14  Score=115.50  Aligned_cols=74  Identities=27%  Similarity=0.540  Sum_probs=63.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      .+++|||+|||+++|+++|+++|+.||+|.+|.|+++ ++||||+|.+.++|++|+..  ...+.+++|.|.++.+.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~~~   78 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEPK   78 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCCC
Confidence            4679999999999999999999999999999999754 89999999999999865321  33558999999998764

>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=99.48  E-value=8.7e-14  Score=127.10  Aligned_cols=113  Identities=16%  Similarity=0.183  Sum_probs=73.1

Q ss_pred             EeeCCHHHHHHHHHHhCCcccc--CceEEEEec--------------------------ccccceeccCcccccCHHHHH
Q psy93           154 IRMDYKHNADKAKAKLDGHVLK--GRSLKIRFA--------------------------PINAAIKVKNLTSCVTNELLE  205 (503)
Q Consensus       154 V~F~~~e~A~~Ai~~l~g~~l~--g~~l~V~~a--------------------------~~~~~L~V~nLp~~~tee~L~  205 (503)
                      .+|++.++|..|+..|++....  |+.+.+.++                          .+.++|||.|||..+++++|+
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            6788888888888888877555  444444321                          124579999999999999999


Q ss_pred             HHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCcc
Q psy93           206 LAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELT  270 (503)
Q Consensus       206 ~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~  270 (503)
                      ++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+||..|| +..+   .+++|.|.++...
T Consensus        91 ~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~-g~~~---~g~~l~V~~a~~~  152 (165)
T 1rk8_A           91 EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALN-GAEI---MGQTIQVDWCFVK  152 (165)
T ss_dssp             HHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHT-TCEE---TTEECEEEESEEC
T ss_pred             HHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhC-CCEE---CCEEEEEEEecCC
Confidence            99999999999999998 588999999999999999999999997 6555   6899999997654

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.47  E-value=2.3e-13  Score=113.39  Aligned_cols=83  Identities=18%  Similarity=0.184  Sum_probs=75.8

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..|.|+.+.++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~v   90 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD-GMTI---KENIIKV   90 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHT-TEES---SSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhC-CCEE---CCEEEEE
Confidence            45689999999999999999999999999999999999889999999999999999999999997 6665   6899999


Q ss_pred             ecCCccc
Q psy93           265 EPLELTD  271 (503)
Q Consensus       265 ~~~~~~~  271 (503)
                      .++.+..
T Consensus        91 ~~a~~~~   97 (100)
T 2do4_A           91 AISNSGP   97 (100)
T ss_dssp             EECCCCS
T ss_pred             EECCCCC
Confidence            9987653

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.47  E-value=8.8e-14  Score=118.41  Aligned_cols=72  Identities=14%  Similarity=0.171  Sum_probs=66.4

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec-----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      .++|||+|||+++|+++|+++|+.| .|..|.|+.     ++|||||+|.+.++|.+|| .+|+..|.|+.|.|..+.+
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            4689999999999999999999999 899999964     4799999999999999999 6999999999999988754

>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=99.47  E-value=2.3e-13  Score=109.06  Aligned_cols=80  Identities=25%  Similarity=0.276  Sum_probs=73.1

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      +.+|||+|||..+++++|+++|+.||.|..+.++.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|.
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 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQ-GQDL---NGRPLRIN   76 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHT-TCEE---TTEECEEE
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhc-CCee---CCcEEEEE
Confidence            358999999999999999999999999999999988 688999999999999999999999997 6666   68999999


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      ++.+.
T Consensus        77 ~a~~~   81 (83)
T 3md1_A           77 WAAKL   81 (83)
T ss_dssp             ECCCC
T ss_pred             ecCcC
Confidence            98765

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.47  E-value=2.1e-13  Score=114.30  Aligned_cols=82  Identities=30%  Similarity=0.426  Sum_probs=75.1

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      +.++|||.|||..+++++|+++|+.||.|..|.|+.+ ++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~~~g~afV~f~~~~~A~~A~~~l~-g~~~---~g~~l~V~   88 (103)
T 2d9p_A           14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMN-GRIV---ATKPLYVA   88 (103)
T ss_dssp             SCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHT-TCBS---SSSBCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhC-CCEe---CCcEEEEE
Confidence            5689999999999999999999999999999999998 88999999999999999999999997 5555   68999999


Q ss_pred             cCCcccc
Q psy93           266 PLELTDE  272 (503)
Q Consensus       266 ~~~~~~~  272 (503)
                      ++.....
T Consensus        89 ~a~~~~~   95 (103)
T 2d9p_A           89 LAQRKEE   95 (103)
T ss_dssp             ECSSCCC
T ss_pred             Eeccccc
Confidence            9877654

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.46  E-value=6.4e-14  Score=135.25  Aligned_cols=77  Identities=29%  Similarity=0.531  Sum_probs=71.6

Q ss_pred             CCCcEEEEcCCCCCC---------CHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccc-------
Q psy93           111 ANNCRLYLGNIGGDI---------TENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL-------  174 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~---------te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l-------  174 (503)
                      ..+++|||+|||..+         ++++|+++|++||+|.+|.|+.+++||||+|.+.++|+.|++.|++..|       
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~~e  211 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKE  211 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHHHTTCCCCCTTSTT
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECCCCEEEEEeCCHHHHHHHHHHhCCCEEecccccc
Confidence            356899999999998         7999999999999999999999999999999999999999999999999       


Q ss_pred             -----cCceEEEEecccc
Q psy93           175 -----KGRSLKIRFAPIN  187 (503)
Q Consensus       175 -----~g~~l~V~~a~~~  187 (503)
                           .|+.|.|.||...
T Consensus       212 ~~~~~~gr~L~V~wA~~~  229 (240)
T 3u1l_A          212 WDDRREGTGLLVKWANED  229 (240)
T ss_dssp             GGGGGGSCCCEEEECC--
T ss_pred             ccccCCCCEEEEEEccCC
Confidence                 8999999999754

>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=99.46  E-value=2.1e-13  Score=113.27  Aligned_cols=84  Identities=24%  Similarity=0.273  Sum_probs=76.0

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..|.|+.+. ++.+++||||+|.+.++|.+|+..|| +..+   .+++|.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~   81 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVD-GQVF---QGRMLH   81 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTT-TEES---SSCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhC-CCEE---CCcEEE
Confidence            356799999999999999999999999999999999885 88999999999999999999999997 6666   689999


Q ss_pred             eecCCcccc
Q psy93           264 VEPLELTDE  272 (503)
Q Consensus       264 V~~~~~~~~  272 (503)
                      |.++.....
T Consensus        82 V~~a~~~~~   90 (99)
T 1whw_A           82 VLPSTIKKE   90 (99)
T ss_dssp             EEECCCCST
T ss_pred             EEEcCCCcc
Confidence            999877654

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.46  E-value=2.6e-13  Score=111.81  Aligned_cols=84  Identities=25%  Similarity=0.387  Sum_probs=75.4

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..+.++.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~   78 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLN-GFEL---AGRPMR   78 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHT-TCCS---SSSCCE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhC-CCee---CCcEEE
Confidence            45789999999999999999999999999999999988 468899999999999999999999997 5555   689999


Q ss_pred             eecCCcccc
Q psy93           264 VEPLELTDE  272 (503)
Q Consensus       264 V~~~~~~~~  272 (503)
                      |.++.....
T Consensus        79 V~~a~~~~~   87 (95)
T 2dnz_A           79 VGHVTERLD   87 (95)
T ss_dssp             EEESSCCCC
T ss_pred             EEEcccccC
Confidence            999876644

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=9.5e-14  Score=120.76  Aligned_cols=73  Identities=11%  Similarity=0.139  Sum_probs=64.8

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCe----EEEEEec-----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGET----QELFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V----~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      .++|||+|||+++|+++|+++|+.||+|    ..|.|+.     ++|||||+|.+.++|.+||.. |+..|.++.|.|..
T Consensus        23 ~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~~  101 (123)
T 2dha_A           23 QVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELFR  101 (123)
T ss_dssp             CCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECCEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEEEE
Confidence            4689999999999999999999999976    5787764     368999999999999999986 99999999999987


Q ss_pred             ccc
Q psy93           184 API  186 (503)
Q Consensus       184 a~~  186 (503)
                      +.+
T Consensus       102 a~~  104 (123)
T 2dha_A          102 STA  104 (123)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            643

>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=99.45  E-value=2.4e-13  Score=112.02  Aligned_cols=80  Identities=24%  Similarity=0.276  Sum_probs=73.3

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..|.|+.+.++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~V   89 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN-GIRL---YGRPINV   89 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHT-TCEE---TTEECEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhC-CCEE---CCCEEEE
Confidence            45689999999999999999999999999999999999889999999999999999999999997 6555   5899999


Q ss_pred             ecCC
Q psy93           265 EPLE  268 (503)
Q Consensus       265 ~~~~  268 (503)
                      .++.
T Consensus        90 ~~a~   93 (95)
T 2ywk_A           90 SGPS   93 (95)
T ss_dssp             ECCC
T ss_pred             EEcC
Confidence            8864

>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=99.45  E-value=2.9e-13  Score=115.79  Aligned_cols=83  Identities=22%  Similarity=0.315  Sum_probs=75.4

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +.++|||.|||..+++++|+++|+.||.|..|.|+.+. ++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus        24 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~V   99 (115)
T 2cpz_A           24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMN-GFQI---GMKRLKV   99 (115)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHT-TCEE---TTEECEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcC-CCEE---CCEEEEE
Confidence            46799999999999999999999999999999999985 88999999999999999999999997 6655   6899999


Q ss_pred             ecCCcccc
Q psy93           265 EPLELTDE  272 (503)
Q Consensus       265 ~~~~~~~~  272 (503)
                      .++.+...
T Consensus       100 ~~a~~~~~  107 (115)
T 2cpz_A          100 QLKRSKND  107 (115)
T ss_dssp             ECCCCSCC
T ss_pred             EEcCCCCc
Confidence            99876644

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.45  E-value=4.9e-13  Score=114.03  Aligned_cols=83  Identities=28%  Similarity=0.300  Sum_probs=75.4

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..|.|+.+.++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~v   88 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFN-GQLL---FDRPMHV   88 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHT-TCEE---TTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhC-CCEe---CCCEEEE
Confidence            45789999999999999999999999999999999999889999999999999999999999997 6666   6899999


Q ss_pred             ecCCccc
Q psy93           265 EPLELTD  271 (503)
Q Consensus       265 ~~~~~~~  271 (503)
                      .++....
T Consensus        89 ~~a~~~~   95 (114)
T 2do0_A           89 KMDERAL   95 (114)
T ss_dssp             EECSCCC
T ss_pred             EEcccCC
Confidence            9876543

>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=99.45  E-value=2.6e-13  Score=109.84  Aligned_cols=81  Identities=27%  Similarity=0.329  Sum_probs=72.0

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||+|||..+++++|+++|+.||.|.++.++.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.
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 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMG-GQWL---GGRQIR   79 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT-TCEE---TTEECE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcC-CCEE---CCeEEE
Confidence            35678999999999999999999999999999999998 588999999999999999999999997 5655   689999


Q ss_pred             eecCCc
Q psy93           264 VEPLEL  269 (503)
Q Consensus       264 V~~~~~  269 (503)
                      |.++.+
T Consensus        80 v~~a~~   85 (87)
T 3bs9_A           80 TNWATR   85 (87)
T ss_dssp             EEEEC-
T ss_pred             EEecCC
Confidence            988754

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=2.1e-13  Score=113.96  Aligned_cols=84  Identities=24%  Similarity=0.234  Sum_probs=76.2

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~---~g~~l~   85 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN-ESEL---FGRTIR   85 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHT-TEEE---TTEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhC-CCEE---CCcEEE
Confidence            45789999999999999999999999999999999888 578899999999999999999999997 7666   699999


Q ss_pred             eecCCcccc
Q psy93           264 VEPLELTDE  272 (503)
Q Consensus       264 V~~~~~~~~  272 (503)
                      |.++.+...
T Consensus        86 V~~a~~~~~   94 (102)
T 2cqb_A           86 VNLAKPMRI   94 (102)
T ss_dssp             EEECCCCCC
T ss_pred             EEeCCCCCC
Confidence            999876644

>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=99.45  E-value=1.4e-13  Score=144.91  Aligned_cols=77  Identities=18%  Similarity=0.341  Sum_probs=71.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ...++|||+|||++||+++|.++|+.||.|+.|.|+.+      +|||||+|.+.++|.+||..||++.|.|++|.|.|+
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            34679999999999999999999999999999999743      789999999999999999999999999999999999


Q ss_pred             ccc
Q psy93           185 PIN  187 (503)
Q Consensus       185 ~~~  187 (503)
                      .+.
T Consensus       180 ~~~  182 (437)
T 3pgw_S          180 RGR  182 (437)
T ss_pred             CCC
Confidence            754

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.44  E-value=2.3e-13  Score=116.49  Aligned_cols=71  Identities=15%  Similarity=0.263  Sum_probs=60.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe---------cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEE
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFIN---------KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIR  182 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~---------~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~  182 (503)
                      ..++|||+|||+++|+++|+++|++||+|. +.++         +++|||||+|.+.++|.+||+.|+  .++|+.|.+.
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~   83 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLCV   83 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEec
Confidence            457899999999999999999999999999 6664         347899999999999999999984  3667776666


Q ss_pred             ecc
Q psy93           183 FAP  185 (503)
Q Consensus       183 ~a~  185 (503)
                      .+.
T Consensus        84 ~~~   86 (114)
T 2dnl_A           84 SSP   86 (114)
T ss_dssp             CCS
T ss_pred             cCC
Confidence            554

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=4.5e-13  Score=110.27  Aligned_cols=80  Identities=23%  Similarity=0.238  Sum_probs=72.9

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      ++.++|||.|||..+++++|+++|+.||.|..|.++.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~---~g~~l~   88 (95)
T 2cqc_A           13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERAN-GMEL---DGRRIR   88 (95)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHT-TEEE---TTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhC-CCEE---CCEEEE
Confidence            45789999999999999999999999999999999988 467899999999999999999999997 6666   689999


Q ss_pred             eecCC
Q psy93           264 VEPLE  268 (503)
Q Consensus       264 V~~~~  268 (503)
                      |.++.
T Consensus        89 v~~a~   93 (95)
T 2cqc_A           89 VSGPS   93 (95)
T ss_dssp             EECCS
T ss_pred             EEecC
Confidence            99875

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=2e-13  Score=112.69  Aligned_cols=84  Identities=27%  Similarity=0.373  Sum_probs=75.7

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeee-EEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERA-IVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPV  262 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~-~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl  262 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..+ .|+.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~-g~~~---~g~~l   78 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMN-GQYL---CNRPI   78 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTT-TCEE---TTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcC-CCEE---CCEEE
Confidence            356899999999999999999999999999999 99988 688899999999999999999999997 6655   68999


Q ss_pred             EeecCCcccc
Q psy93           263 IVEPLELTDE  272 (503)
Q Consensus       263 ~V~~~~~~~~  272 (503)
                      .|.++.+...
T Consensus        79 ~v~~a~~~~~   88 (96)
T 1x5t_A           79 TVSYAFKKDS   88 (96)
T ss_dssp             EEEESCCCCC
T ss_pred             EEEEecccCC
Confidence            9999876643

>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=99.44  E-value=5.2e-14  Score=125.07  Aligned_cols=73  Identities=16%  Similarity=0.169  Sum_probs=66.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec-----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      .++|||+|||+++|+++|+++|+.|| |++|.|+.     ++|||||+|.+.++|++|| .+|+..|.++.|.|.++.+.
T Consensus        46 ~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~  123 (139)
T 2hgn_A           46 GHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTT  123 (139)
T ss_dssp             CCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCC
Confidence            45799999999999999999999999 66898864     4789999999999999999 78999999999999887653

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=3.3e-13  Score=113.08  Aligned_cols=84  Identities=29%  Similarity=0.329  Sum_probs=75.5

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~---~g~~l~   88 (103)
T 2cq0_A           13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVS-GFGY---DHLILN   88 (103)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTT-TCEE---TTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcC-CCee---CCcEEE
Confidence            34689999999999999999999999999999999998 588999999999999999999999997 6655   689999


Q ss_pred             eecCCcccc
Q psy93           264 VEPLELTDE  272 (503)
Q Consensus       264 V~~~~~~~~  272 (503)
                      |.++.+...
T Consensus        89 v~~a~~~~~   97 (103)
T 2cq0_A           89 VEWAKPSTN   97 (103)
T ss_dssp             EEESSCCCC
T ss_pred             EEECCCCCC
Confidence            999876643

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=1.8e-13  Score=115.33  Aligned_cols=79  Identities=14%  Similarity=0.165  Sum_probs=70.2

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhC-CeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAE-GCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~-g~~~~~~~~rpl~  263 (503)
                      .+.++|||+|||+.+++++|+++|++||.|.+|.|+++     ++||||+|++.++|.+|+..|+. +..+   .+++|.
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kGfaFVeF~~~~~A~~Ai~~l~~~~~~l---~Gr~l~   85 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVL---RGQPIY   85 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTSCCEE---TTEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhccCCceE---CCEEEE
Confidence            45789999999999999999999999999999999876     79999999999999999999863 3555   689999


Q ss_pred             eecCCccc
Q psy93           264 VEPLELTD  271 (503)
Q Consensus       264 V~~~~~~~  271 (503)
                      |.++....
T Consensus        86 V~~A~~~~   93 (105)
T 1sjq_A           86 IQFSNHKE   93 (105)
T ss_dssp             BCCCSSSS
T ss_pred             EEEcCCCC
Confidence            99986653

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.44  E-value=3.1e-13  Score=113.87  Aligned_cols=84  Identities=18%  Similarity=0.249  Sum_probs=75.0

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC--CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE--RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~--~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      +.++|||.|||..+++++|+++|+.||.|..|.|+.+.  ++.+++||||+|.+.++|.+|+..|+++..+   .+++|.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~---~g~~l~   90 (107)
T 2cph_A           14 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHL---YGRRLV   90 (107)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBS---SSCBCE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeE---CCCEEE
Confidence            46899999999999999999999999999999998874  8889999999999999999999999436655   589999


Q ss_pred             eecCCcccc
Q psy93           264 VEPLELTDE  272 (503)
Q Consensus       264 V~~~~~~~~  272 (503)
                      |.++.....
T Consensus        91 v~~a~~~~~   99 (107)
T 2cph_A           91 LEWADSEVT   99 (107)
T ss_dssp             EEECCCCCC
T ss_pred             EEeCCCCCC
Confidence            999877644

>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=99.44  E-value=2.2e-13  Score=109.69  Aligned_cols=80  Identities=25%  Similarity=0.270  Sum_probs=72.6

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||+|||..+++++|+++|+.||.|..+.++.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~   80 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN-ESEL---FGRTIR   80 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHT-TCEE---TTEECE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhC-CCEE---CCcEEE
Confidence            46789999999999999999999999999999999888 678889999999999999999999997 6666   689999


Q ss_pred             eecCC
Q psy93           264 VEPLE  268 (503)
Q Consensus       264 V~~~~  268 (503)
                      |.+++
T Consensus        81 v~~ak   85 (85)
T 3mdf_A           81 VNLAK   85 (85)
T ss_dssp             EEECC
T ss_pred             EEEcC
Confidence            98863

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.44  E-value=2.9e-13  Score=121.97  Aligned_cols=76  Identities=20%  Similarity=0.462  Sum_probs=70.6

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       110 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      ....++|||+|||+++|+++|+++|+.||.|..+.+..+      +|||||+|.+.++|.+|+..||+..|.|++|.|.|
T Consensus        84 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  163 (166)
T 3md3_A           84 SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW  163 (166)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Confidence            345679999999999999999999999999999999744      67999999999999999999999999999999999


Q ss_pred             cc
Q psy93           184 AP  185 (503)
Q Consensus       184 a~  185 (503)
                      +.
T Consensus       164 a~  165 (166)
T 3md3_A          164 AA  165 (166)
T ss_dssp             SC
T ss_pred             cC
Confidence            85

>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=99.43  E-value=1.6e-13  Score=112.31  Aligned_cols=80  Identities=21%  Similarity=0.195  Sum_probs=68.0

Q ss_pred             cceeccCcccccCHHHHHHHhccCC--CeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFG--DIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G--~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .+|||+|||..+++++|+++|+.||  .|.++.++.+ .++.++|||||+|.+.++|.+|+..|| +..+   .++.|.|
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 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLP-KREL---HGQNPVV   77 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGG-GSCS---SSCCCEE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcC-CCee---CCEEEEE
Confidence            4799999999999999999999999  9999999998 589999999999999999999999998 5555   6899999


Q ss_pred             ecCCccc
Q psy93           265 EPLELTD  271 (503)
Q Consensus       265 ~~~~~~~  271 (503)
                      .++.+..
T Consensus        78 ~~~~~~~   84 (90)
T 3p5t_L           78 TPSNKLE   84 (90)
T ss_dssp             CCC----
T ss_pred             EECCCCc
Confidence            8876653

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.43  E-value=3.2e-13  Score=113.25  Aligned_cols=84  Identities=24%  Similarity=0.317  Sum_probs=75.3

Q ss_pred             ccccceeccCcccccCHHHHHHHhcc-CCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCee-eecCCCCeE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGV-FGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCF-FLTQSLRPV  262 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~-~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~-~~~~~~rpl  262 (503)
                      .+.++|||+|||..+++++|+++|+. ||.|..|.|+.+.++.+++||||+|.+.++|.+|+..|+ +.. +   .+++|
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~-g~~~~---~g~~l   82 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQ-GAVGL---GSKPV   82 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTT-TCCSS---SSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHcc-CCccc---CCEeE
Confidence            35689999999999999999999999 999999999999899999999999999999999999997 554 4   58899


Q ss_pred             EeecCCcccc
Q psy93           263 IVEPLELTDE  272 (503)
Q Consensus       263 ~V~~~~~~~~  272 (503)
                      .|.++.....
T Consensus        83 ~v~~a~~~~~   92 (104)
T 2dhg_A           83 RLSVAIPKAS   92 (104)
T ss_dssp             CCCBCCCCCS
T ss_pred             EEEEccCCCc
Confidence            9998866543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.43  E-value=5.1e-14  Score=117.82  Aligned_cols=74  Identities=23%  Similarity=0.367  Sum_probs=68.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec-----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ..++|||+|||+++++++|+++|+.||.|..|.|+.     ++|||||+|.+.++|.+|+.  ++..|.|+.|.|.++.+
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~~   85 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAIR   85 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECCc
Confidence            457899999999999999999999999999999976     36899999999999999998  99999999999998865


Q ss_pred             c
Q psy93           187 N  187 (503)
Q Consensus       187 ~  187 (503)
                      .
T Consensus        86 ~   86 (102)
T 2xs2_A           86 K   86 (102)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.43  E-value=4e-13  Score=111.38  Aligned_cols=84  Identities=23%  Similarity=0.217  Sum_probs=74.2

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC----CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCC
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE----RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLR  260 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~----~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~r  260 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..|.|+.+.    ++.+++||||+|.+.++|.+|+..|| +..+   .++
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~   78 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQ-GHTV---DGH   78 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHST-TCEE---TTE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhC-CCee---CCe
Confidence            456899999999999999999999999999999998874    34789999999999999999999997 6655   589


Q ss_pred             eEEeecCCcccc
Q psy93           261 PVIVEPLELTDE  272 (503)
Q Consensus       261 pl~V~~~~~~~~  272 (503)
                      +|.|.++.....
T Consensus        79 ~l~V~~a~~~~~   90 (98)
T 2cpf_A           79 KLEVRISERATK   90 (98)
T ss_dssp             ECEEECSSCSSC
T ss_pred             EEEEEEccCCCC
Confidence            999999876643

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.43  E-value=5e-13  Score=111.09  Aligned_cols=83  Identities=20%  Similarity=0.214  Sum_probs=74.0

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+|+. |+ +..+   .+++|.
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~-~~~~---~g~~l~   82 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MH-FHDI---MGKKVE   82 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HC-CCBS---SSCBCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hC-CCEE---CCeEEE
Confidence            35689999999999999999999999999999999988 478899999999999999999998 76 6655   689999


Q ss_pred             eecCCcccc
Q psy93           264 VEPLELTDE  272 (503)
Q Consensus       264 V~~~~~~~~  272 (503)
                      |.++.+...
T Consensus        83 V~~a~~~~~   91 (99)
T 2dgs_A           83 VKRAEPRDS   91 (99)
T ss_dssp             EEECCCCCC
T ss_pred             EEECCCCcc
Confidence            999877644

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.43  E-value=8.5e-13  Score=112.78  Aligned_cols=83  Identities=28%  Similarity=0.327  Sum_probs=75.2

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +.++|||.|||..+++++|+++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~V   89 (115)
T 2dgo_A           14 NHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMG-GQWL---GGRQIRT   89 (115)
T ss_dssp             TCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTT-TCEE---TTEECEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhC-CCEE---CCEEEEE
Confidence            4678999999999999999999999999999999998 588999999999999999999999997 6655   6899999


Q ss_pred             ecCCcccc
Q psy93           265 EPLELTDE  272 (503)
Q Consensus       265 ~~~~~~~~  272 (503)
                      .++.....
T Consensus        90 ~~a~~~~~   97 (115)
T 2dgo_A           90 NWATRKPP   97 (115)
T ss_dssp             EESSCCCC
T ss_pred             EEccCCCC
Confidence            99876643

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.43  E-value=2e-13  Score=129.73  Aligned_cols=75  Identities=17%  Similarity=0.377  Sum_probs=70.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ..++|||+|||+++|+++|+++|+.||.|..|.|+.    ++|||||+|.+.++|.+||+.||+..|.|++|.|.++.+
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            456899999999999999999999999999999975    378999999999999999999999999999999999865

>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=99.43  E-value=4.1e-13  Score=115.42  Aligned_cols=84  Identities=18%  Similarity=0.254  Sum_probs=75.9

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .+.++|||+|||.++++++|+++|+.||.|..|.|+.+.++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~-g~~~---~g~~l~V   80 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN-GKSL---HGKAIKV   80 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCS-SCBC---SSSBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhC-CCEE---CCEEEEE
Confidence            35689999999999999999999999999999999999889999999999999999999999997 5555   6899999


Q ss_pred             ecCCcccc
Q psy93           265 EPLELTDE  272 (503)
Q Consensus       265 ~~~~~~~~  272 (503)
                      .++.....
T Consensus        81 ~~a~~~~~   88 (116)
T 2fy1_A           81 EQAKKPSF   88 (116)
T ss_dssp             EECCCSSC
T ss_pred             EECCCCCC
Confidence            99876543

>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=99.43  E-value=4.1e-13  Score=113.18  Aligned_cols=80  Identities=26%  Similarity=0.378  Sum_probs=73.2

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..|.|+.+.++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~V  102 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN-GVPL---DGRPMNI  102 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHT-TCEE---TTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhC-CCEe---CCcEEEE
Confidence            45789999999999999999999999999999999999999999999999999999999999997 6655   6889999


Q ss_pred             ecCC
Q psy93           265 EPLE  268 (503)
Q Consensus       265 ~~~~  268 (503)
                      .++.
T Consensus       103 ~~a~  106 (107)
T 3ulh_A          103 QLVT  106 (107)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            8753

>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=99.42  E-value=7e-13  Score=111.01  Aligned_cols=82  Identities=27%  Similarity=0.324  Sum_probs=73.4

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      +.++|||.|||..+++++|+++|+.||.|..|.|+.+... +++||||+|.+.++|.+|+..|| +..+   .+++|.|.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~v~   88 (103)
T 2cq3_A           14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLH-GTVV---EGRKIEVN   88 (103)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHT-TCEE---TTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHHHHHHHhC-CCEE---CCEEEEEE
Confidence            4689999999999999999999999999999999988654 79999999999999999999997 6655   68999999


Q ss_pred             cCCcccc
Q psy93           266 PLELTDE  272 (503)
Q Consensus       266 ~~~~~~~  272 (503)
                      ++.....
T Consensus        89 ~a~~~~~   95 (103)
T 2cq3_A           89 NATARVM   95 (103)
T ss_dssp             ECCSSCC
T ss_pred             EcccCCC
Confidence            9876643

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.42  E-value=4.5e-13  Score=110.11  Aligned_cols=80  Identities=21%  Similarity=0.244  Sum_probs=72.3

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      ++.++|||.|||..+++++|+++|+.||.|..+.++.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~---~g~~l~   89 (94)
T 2e5h_A           14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAIN-NKQL---FGRVIK   89 (94)
T ss_dssp             CCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTT-TEEE---TTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcC-CCee---CCcEEE
Confidence            45689999999999999999999999999999999988 458889999999999999999999997 6666   689999


Q ss_pred             eecCC
Q psy93           264 VEPLE  268 (503)
Q Consensus       264 V~~~~  268 (503)
                      |.+++
T Consensus        90 v~~ak   94 (94)
T 2e5h_A           90 ASIAI   94 (94)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            98863

>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=99.42  E-value=4e-13  Score=111.08  Aligned_cols=82  Identities=18%  Similarity=0.170  Sum_probs=74.2

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      |+++|||+|||..+++++|+++|+.||.|..+.++.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
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 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLN-GYQL---GSRFLKC   76 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHT-TCEE---TTEECEE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhC-CCeE---CCeEEEE
Confidence            4678999999999999999999999999999999988 578899999999999999999999997 6655   6899999


Q ss_pred             ecCCccc
Q psy93           265 EPLELTD  271 (503)
Q Consensus       265 ~~~~~~~  271 (503)
                      .++....
T Consensus        77 ~~a~~~~   83 (96)
T 2x1f_A           77 GYSSNSD   83 (96)
T ss_dssp             EECSCSS
T ss_pred             EEcCCCC
Confidence            9987654

>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=99.42  E-value=2.6e-13  Score=114.26  Aligned_cols=86  Identities=19%  Similarity=0.211  Sum_probs=75.2

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +.++|||.|||..+++++|+++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+|+..|| +..++...+++|.|
T Consensus        12 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~-g~~~~~~~g~~l~v   90 (106)
T 2dgp_A           12 DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALH-EQKTLPGMNRPIQV   90 (106)
T ss_dssp             TCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHT-TTCCCTTCSSCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhc-CCcccCCCCceEEE
Confidence            4678999999999999999999999999999999988 468899999999999999999999998 44443446799999


Q ss_pred             ecCCcccc
Q psy93           265 EPLELTDE  272 (503)
Q Consensus       265 ~~~~~~~~  272 (503)
                      .++.....
T Consensus        91 ~~a~~~~~   98 (106)
T 2dgp_A           91 KPADSESR   98 (106)
T ss_dssp             EECCCCSC
T ss_pred             EECCcccc
Confidence            99876643

>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=99.42  E-value=1.5e-13  Score=125.15  Aligned_cols=119  Identities=15%  Similarity=0.141  Sum_probs=100.7

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCC---CceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERG---NSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g---~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .++|||+|||.++++++|+++|+.||.|.++.++.+..+   .+++||||+|.+.++|.+|+..|+ +..+.....+++.
T Consensus         3 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-~~~~~~~~~~~~~   81 (175)
T 3nmr_A            3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALH-NMKVLPGMHHPIQ   81 (175)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHT-TTCCCTTCSSCCE
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhc-CcEEccCCccceE
Confidence            578999999999999999999999999999999998644   789999999999999999999997 5555555678899


Q ss_pred             eecCCccccccCCcccccCCCCchhhhhhccCcccCCCCCcch
Q psy93           264 VEPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFEF  306 (503)
Q Consensus       264 V~~~~~~~~~~~~~~k~i~k~~~~~~kere~~~rf~~~g~~e~  306 (503)
                      +.+.............++..+++...++.++...|..+|.+..
T Consensus        82 ~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~  124 (175)
T 3nmr_A           82 MKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEE  124 (175)
T ss_dssp             EEECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEE
T ss_pred             EccccccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEE
Confidence            9888777665555566777788888888888888888887653

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.42  E-value=4.5e-13  Score=111.87  Aligned_cols=80  Identities=23%  Similarity=0.346  Sum_probs=70.0

Q ss_pred             cccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           184 APINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       184 a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+|+++|||+|||..+++++|.++|++||.|.++.++++     ++||||+|++.++|.+|+..|+...+.+  .+++|.
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~-----kg~AFVef~~~~~A~~Av~~ln~~~~~i--~Gr~i~   90 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK-----KRQALVEFEDVLGACNAVNYAADNQIYI--AGHPAF   90 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCEEE--TTEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhcCCCcee--CCcEEE
Confidence            357889999999999999999999999999999999864     7899999999999999999998443322  689999


Q ss_pred             eecCCcc
Q psy93           264 VEPLELT  270 (503)
Q Consensus       264 V~~~~~~  270 (503)
                      |.++..+
T Consensus        91 V~~S~~k   97 (100)
T 3r27_A           91 VNYSTSQ   97 (100)
T ss_dssp             EEECSCS
T ss_pred             EEecccc
Confidence            9997654

>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=99.42  E-value=7.5e-13  Score=112.26  Aligned_cols=85  Identities=22%  Similarity=0.274  Sum_probs=75.4

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhC-----CeeeecCC
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAE-----GCFFLTQS  258 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~-----g~~~~~~~  258 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+|+..||.     +..+   .
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~---~   89 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKL---D   89 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEES---S
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEE---c
Confidence            35689999999999999999999999999999999988 5688999999999999999999999962     5555   6


Q ss_pred             CCeEEeecCCcccc
Q psy93           259 LRPVIVEPLELTDE  272 (503)
Q Consensus       259 ~rpl~V~~~~~~~~  272 (503)
                      +++|.|.++.+...
T Consensus        90 g~~l~v~~a~~~~~  103 (111)
T 1x4h_A           90 GRQLKVDLAVTRDE  103 (111)
T ss_dssp             SCEEEEECCCCCCC
T ss_pred             CEEEEEEECCCCcc
Confidence            89999999877644

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.42  E-value=2e-13  Score=119.19  Aligned_cols=73  Identities=16%  Similarity=0.175  Sum_probs=64.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeE--EEEEec-----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQ--ELFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~--~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ..++|||+|||+++|+++|+++|+.| .|.  .|.|+.     ++|||||+|.+.++|.+||.. ++..|.|+.|.|.++
T Consensus        41 ~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V~~a  118 (126)
T 2hgm_A           41 NDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVFKS  118 (126)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEEEC
Confidence            35689999999999999999999999 676  888864     479999999999999999985 779999999999877


Q ss_pred             cc
Q psy93           185 PI  186 (503)
Q Consensus       185 ~~  186 (503)
                      .+
T Consensus       119 ~~  120 (126)
T 2hgm_A          119 SQ  120 (126)
T ss_dssp             CH
T ss_pred             CH
Confidence            43

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.41  E-value=1.1e-13  Score=115.67  Aligned_cols=80  Identities=19%  Similarity=0.186  Sum_probs=72.3

Q ss_pred             ccceeccCccc------ccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCC
Q psy93           187 NAAIKVKNLTS------CVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSL  259 (503)
Q Consensus       187 ~~~L~V~nLp~------~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~  259 (503)
                      .++|||.|||.      .+++++|+++|++||.|.+|.|+.+. ++.++|||||+|.+.++|.+|+..|| +..+   .+
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~ln-g~~~---~g   81 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH-GKRL---DL   81 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHT-TCBS---SS
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhC-Cccc---CC
Confidence            57899999999      99999999999999999999999885 59999999999999999999999997 6555   56


Q ss_pred             -CeEEeecCCcc
Q psy93           260 -RPVIVEPLELT  270 (503)
Q Consensus       260 -rpl~V~~~~~~  270 (503)
                       ++|.|.++.+.
T Consensus        82 ~r~l~V~~a~~~   93 (100)
T 3ns6_A           82 KHRLFLYTMKDV   93 (100)
T ss_dssp             SCBCEEEESHHH
T ss_pred             CeEEEEEECchh
Confidence             89999988654

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.41  E-value=4.1e-13  Score=126.76  Aligned_cols=77  Identities=21%  Similarity=0.449  Sum_probs=71.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ...++|||+|||.++|+++|+++|+.||.|..|.|..+      ++||||+|.+.++|.+|+..||+..|.|+.|.|.++
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            34579999999999999999999999999999999765      689999999999999999999999999999999998


Q ss_pred             ccc
Q psy93           185 PIN  187 (503)
Q Consensus       185 ~~~  187 (503)
                      .+.
T Consensus       203 ~~~  205 (216)
T 2qfj_A          203 VTP  205 (216)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            754

>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=99.41  E-value=3.9e-13  Score=112.91  Aligned_cols=84  Identities=21%  Similarity=0.208  Sum_probs=75.2

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..|.|+.+. ++.+++||||+|.+.++|.+|+..|| +..+   .+++|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~   88 (105)
T 1x5u_A           13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMD-MIKL---YGKPIR   88 (105)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSS-SCBC---SSCBCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhC-CCeE---CCeEEE
Confidence            356899999999999999999999999999999999884 88999999999999999999999997 5555   689999


Q ss_pred             eecCCcccc
Q psy93           264 VEPLELTDE  272 (503)
Q Consensus       264 V~~~~~~~~  272 (503)
                      |.++.....
T Consensus        89 v~~a~~~~~   97 (105)
T 1x5u_A           89 VNKASAHNK   97 (105)
T ss_dssp             EEETTTTSC
T ss_pred             EEECCCCCc
Confidence            999876643

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=2.8e-13  Score=113.22  Aligned_cols=84  Identities=23%  Similarity=0.289  Sum_probs=74.5

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.
T Consensus        10 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~---~g~~l~   85 (102)
T 1x5s_A           10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMN-GKSV---DGRQIR   85 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHT-TCCT---TSCCCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhC-CCEE---CCeEEE
Confidence            45689999999999999999999999999999999988 477889999999999999999999997 5555   689999


Q ss_pred             eecCCcccc
Q psy93           264 VEPLELTDE  272 (503)
Q Consensus       264 V~~~~~~~~  272 (503)
                      |.++.....
T Consensus        86 v~~a~~~~~   94 (102)
T 1x5s_A           86 VDQAGKSSD   94 (102)
T ss_dssp             EEEEECCCC
T ss_pred             EEECCCCCC
Confidence            998766543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=6.6e-13  Score=111.70  Aligned_cols=81  Identities=20%  Similarity=0.193  Sum_probs=73.0

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +.++|||+|||..+++++|+++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus        22 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~V   97 (106)
T 1p27_B           22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN-GQDL---MGQPISV   97 (106)
T ss_dssp             TBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHT-TCBS---SSSBCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhc-CCEE---CCcEEEE
Confidence            4578999999999999999999999999999999988 568899999999999999999999997 5555   5899999


Q ss_pred             ecCCcc
Q psy93           265 EPLELT  270 (503)
Q Consensus       265 ~~~~~~  270 (503)
                      .++.+.
T Consensus        98 ~~a~~~  103 (106)
T 1p27_B           98 DWCFVR  103 (106)
T ss_dssp             EESEES
T ss_pred             EeecCC
Confidence            987654

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=3.7e-13  Score=112.71  Aligned_cols=82  Identities=18%  Similarity=0.190  Sum_probs=73.8

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +.++|||.|||..+++++|+++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~---~g~~l~V   87 (103)
T 2dnm_A           12 GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMD-GAEL---DGRELRV   87 (103)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHS-SCCB---TTBCCEE
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcC-CCEE---CCcEEEE
Confidence            4689999999999999999999999999999999988 468899999999999999999999997 5555   6899999


Q ss_pred             ecCCccc
Q psy93           265 EPLELTD  271 (503)
Q Consensus       265 ~~~~~~~  271 (503)
                      .++....
T Consensus        88 ~~a~~~~   94 (103)
T 2dnm_A           88 QVARYGR   94 (103)
T ss_dssp             EECSSCC
T ss_pred             EECCcCC
Confidence            9987653

>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=99.40  E-value=9.8e-13  Score=110.13  Aligned_cols=83  Identities=23%  Similarity=0.171  Sum_probs=73.5

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..|.|+.+... +++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~V   87 (103)
T 2cqi_A           13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMN-GRKI---LGKEVKV   87 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHT-TEEE---TTEEEEE
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC-CCCEEEEEECCHHHHHHHHHHhC-CCCc---CCCeEEE
Confidence            45689999999999999999999999999999999988543 68999999999999999999997 6666   6899999


Q ss_pred             ecCCcccc
Q psy93           265 EPLELTDE  272 (503)
Q Consensus       265 ~~~~~~~~  272 (503)
                      .++.....
T Consensus        88 ~~a~~~~~   95 (103)
T 2cqi_A           88 NWATTPSS   95 (103)
T ss_dssp             EECCCTTC
T ss_pred             EECCCCcc
Confidence            99876543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.40  E-value=4e-13  Score=113.12  Aligned_cols=80  Identities=11%  Similarity=0.016  Sum_probs=71.8

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ..++|||+|||.++|+++|.++|+.||.|.+|.|+.+..+.++|||||+|.+.++|.+|+. ++ +..+   .+++|.|.
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~-~~~~---~gr~l~V~   84 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TP-GQKY---KETDLLIL   84 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SS-CCCC---TTTTCEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cC-CCEE---CCEEEEEE
Confidence            4679999999999999999999999999999999999779999999999999999999999 65 6555   68999998


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      +....
T Consensus        85 ~~~~~   89 (103)
T 1s79_A           85 FKDDY   89 (103)
T ss_dssp             EHHHH
T ss_pred             EchHH
Confidence            76543

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.40  E-value=7.9e-13  Score=108.18  Aligned_cols=82  Identities=27%  Similarity=0.240  Sum_probs=73.1

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..+.|+.+ ++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~-~g~~~g~afV~f~~~~~a~~a~~~l~-g~~~---~g~~l~v   80 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMN-GMKL---SGREIDV   80 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-SSCEEEEEEEEESSHHHHHHHHHHHT-TCCB---TTBCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-CCCcceEEEEEECCHHHHHHHHHHhC-CCEE---CCcEEEE
Confidence            35689999999999999999999999999999999885 78899999999999999999999997 5555   6888999


Q ss_pred             ecCCccc
Q psy93           265 EPLELTD  271 (503)
Q Consensus       265 ~~~~~~~  271 (503)
                      .++....
T Consensus        81 ~~a~~~~   87 (92)
T 2dgv_A           81 RIDRNAS   87 (92)
T ss_dssp             EECSCCS
T ss_pred             EEcCCCC
Confidence            8876654

>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=99.40  E-value=7.5e-13  Score=111.05  Aligned_cols=79  Identities=14%  Similarity=0.194  Sum_probs=70.0

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhh-CCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCA-EGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln-~g~~~~~~~~rpl~  263 (503)
                      ++.++|||+|||..+++++|+++|+.||.|..|.++.+     ++||||+|.+.++|.+|+..|+ ++..+   .+++|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~---~Gr~l~   84 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHL---RNQPIY   84 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEE---TTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceE---CCcEEE
Confidence            46789999999999999999999999999999988876     8899999999999999999886 35455   699999


Q ss_pred             eecCCccc
Q psy93           264 VEPLELTD  271 (503)
Q Consensus       264 V~~~~~~~  271 (503)
                      |.++....
T Consensus        85 V~~a~~~~   92 (101)
T 2cq1_A           85 IQYSNHKE   92 (101)
T ss_dssp             EEECSCSS
T ss_pred             EEEcCccc
Confidence            99987653

>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=99.40  E-value=9.6e-13  Score=112.29  Aligned_cols=84  Identities=17%  Similarity=0.262  Sum_probs=73.3

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeec-----CCC
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLT-----QSL  259 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~-----~~~  259 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..|.|+.+.++.+++||||+|.+.++|.+|+..|| +..+..     ..+
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~-g~~~~~~~~~~~~~  101 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFN-GKFIKTPPGVSAPT  101 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHB-TCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhC-CCEEcCCccccCCC
Confidence            34689999999999999999999999999999999999889999999999999999999999998 444321     147


Q ss_pred             CeEEeecCCc
Q psy93           260 RPVIVEPLEL  269 (503)
Q Consensus       260 rpl~V~~~~~  269 (503)
                      +++.|.++++
T Consensus       102 ~~l~v~~a~p  111 (114)
T 1x5o_A          102 EPLLCKFSGP  111 (114)
T ss_dssp             SCBEEEECCC
T ss_pred             CceeEEccCC
Confidence            7888888764

>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=99.40  E-value=4.2e-13  Score=122.05  Aligned_cols=73  Identities=22%  Similarity=0.406  Sum_probs=69.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ..++|||+|||+++|+++|+++|++||+|..|.+..+      +|||||+|.+.++|.+|+..||+..|.|++|.|.||
T Consensus        93 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            4678999999999999999999999999999999765      589999999999999999999999999999999987

>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=99.40  E-value=8.2e-13  Score=112.04  Aligned_cols=81  Identities=28%  Similarity=0.382  Sum_probs=73.4

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +.++|||+|||..+++++|+++|+.||.|..|.++.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus        25 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~-g~~i---~g~~l~V  100 (108)
T 2jrs_A           25 GPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLN-GFEL---AGRPMKV  100 (108)
T ss_dssp             SCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHT-TCCS---SSSCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcC-CCEE---CCEEEEE
Confidence            4678999999999999999999999999999999988 578899999999999999999999997 5555   6899999


Q ss_pred             ecCCcc
Q psy93           265 EPLELT  270 (503)
Q Consensus       265 ~~~~~~  270 (503)
                      .++.+.
T Consensus       101 ~~a~~k  106 (108)
T 2jrs_A          101 GHVTER  106 (108)
T ss_dssp             ECSCSS
T ss_pred             EEcccC
Confidence            988665

>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=99.40  E-value=7.6e-13  Score=116.02  Aligned_cols=82  Identities=22%  Similarity=0.218  Sum_probs=74.0

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.
T Consensus        44 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~ln-g~~i---~g~~l~  119 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERAN-GMEL---DGRRIR  119 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHT-TCCS---SSSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhC-CCEE---CCEEEE
Confidence            45789999999999999999999999999999999988 578899999999999999999999997 5555   689999


Q ss_pred             eecCCcc
Q psy93           264 VEPLELT  270 (503)
Q Consensus       264 V~~~~~~  270 (503)
                      |.++...
T Consensus       120 V~~a~~~  126 (129)
T 2kxn_B          120 VDFSITK  126 (129)
T ss_dssp             ESCCSSS
T ss_pred             EEEecCC
Confidence            9998665

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.39  E-value=7.7e-13  Score=109.88  Aligned_cols=82  Identities=17%  Similarity=0.226  Sum_probs=72.2

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCee-eeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCe-
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIE-RAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRP-  261 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~-~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rp-  261 (503)
                      .+.++|||.|||..+++++|+++|+.||.|. .|.|+.+ .++.+++||||+|.+.++|.+|+..|| +..+   .++. 
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~~   82 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKIN-GKPL---PGATP   82 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTT-TSEE---SSCSS
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHc-CCcc---CCCCc
Confidence            4578999999999999999999999999999 9999998 488999999999999999999999997 5555   4555 


Q ss_pred             ---EEeecCCcc
Q psy93           262 ---VIVEPLELT  270 (503)
Q Consensus       262 ---l~V~~~~~~  270 (503)
                         |.|.++...
T Consensus        83 ~~~l~v~~a~~~   94 (99)
T 2div_A           83 AKRFKLNYATYS   94 (99)
T ss_dssp             CEECCEEETTCC
T ss_pred             ceeEEEeecCCC
Confidence               888887554

>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=99.39  E-value=3.9e-13  Score=113.69  Aligned_cols=87  Identities=16%  Similarity=0.140  Sum_probs=75.2

Q ss_pred             cccccceeccCcccccCHHHHHHHhccCCC-eeeeEEE-eC-CCCCceeEEEEEeCCHHHHHHHHHHhhCC-eeeecCCC
Q psy93           184 APINAAIKVKNLTSCVTNELLELAFGVFGD-IERAIVI-VD-ERGNSKCEGIVEFARKPAAAQALRRCAEG-CFFLTQSL  259 (503)
Q Consensus       184 a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~-V~~~~v~-~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g-~~~~~~~~  259 (503)
                      +.+.++|||+|||..+++++|+++|+.||. |..+.++ .+ .++.+++||||+|.+.++|.+|+..|+++ ..+   .+
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~---~g   81 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQL---WG   81 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCB---TT
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCcee---cC
Confidence            456789999999999999999999999998 9999887 55 46788999999999999999999999544 545   68


Q ss_pred             CeEEeecCCccccc
Q psy93           260 RPVIVEPLELTDEI  273 (503)
Q Consensus       260 rpl~V~~~~~~~~~  273 (503)
                      ++|.|.++.+....
T Consensus        82 ~~l~V~~a~~~~~~   95 (109)
T 2dis_A           82 HQIAVDWAEPEIDV   95 (109)
T ss_dssp             BCCEEEESCSSCST
T ss_pred             CeEEEEEcCCCCCc
Confidence            99999998776543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.39  E-value=1.1e-12  Score=108.98  Aligned_cols=79  Identities=32%  Similarity=0.302  Sum_probs=71.4

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeee--------eEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeee
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIER--------AIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFL  255 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~--------~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~  255 (503)
                      .+.++|||+|||..+++++|+++|+.||.|..        +.++.+ .++.++|||||+|.+.++|.+|+..|| +..+ 
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~-g~~~-   88 (99)
T 2la6_A           11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFD-GKEF-   88 (99)
T ss_dssp             CCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHT-TCBS-
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhC-CCEe-
Confidence            35689999999999999999999999999999        999998 578999999999999999999999997 5555 


Q ss_pred             cCCCCeEEeecC
Q psy93           256 TQSLRPVIVEPL  267 (503)
Q Consensus       256 ~~~~rpl~V~~~  267 (503)
                        .++.|.|.++
T Consensus        89 --~g~~l~V~~A   98 (99)
T 2la6_A           89 --SGNPIKVSFA   98 (99)
T ss_dssp             --SSSBCEEEEC
T ss_pred             --CCcEEEEEec
Confidence              5888998875

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.39  E-value=9e-13  Score=112.26  Aligned_cols=84  Identities=25%  Similarity=0.257  Sum_probs=75.3

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCee--------eeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeee
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIE--------RAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFL  255 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~--------~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~  255 (503)
                      .+.++|||.|||..+++++|+++|+.||.|.        .|.|+.+ .++.+++||||+|.+.++|.+|+..|| +..+ 
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~-g~~~-   90 (113)
T 2cpe_A           13 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFD-GKDF-   90 (113)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHT-TCEE-
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcC-CCcc-
Confidence            4568999999999999999999999999999        6899888 688999999999999999999999997 6666 


Q ss_pred             cCCCCeEEeecCCcccc
Q psy93           256 TQSLRPVIVEPLELTDE  272 (503)
Q Consensus       256 ~~~~rpl~V~~~~~~~~  272 (503)
                        .+++|.|.++.....
T Consensus        91 --~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           91 --QGSKLKVSLARKKPP  105 (113)
T ss_dssp             --TTEECEEECSSCCCC
T ss_pred             --CCCEEEEEECCCCCC
Confidence              689999999877644

>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=99.39  E-value=1.4e-12  Score=111.36  Aligned_cols=81  Identities=14%  Similarity=0.180  Sum_probs=69.3

Q ss_pred             CCCcEEEEcCCCCCCC-----------HHHHHHhhccCCCeEEEEEe--cCCCceEEeeCCHHHHHHHHHHhCCccccCc
Q psy93           111 ANNCRLYLGNIGGDIT-----------ENDIIELFKPYGETQELFIN--KEKMFGFIRMDYKHNADKAKAKLDGHVLKGR  177 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~t-----------e~~L~~~F~~~G~V~~v~i~--~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~  177 (503)
                      +++++|+|.||....+           +++|+++|++||+|.+|.|.  .++|||||+|.+.++|.+|+..||+..|.|+
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   92 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGR   92 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEECCc
Confidence            3467899999944332           58999999999999999775  3489999999999999999999999999999


Q ss_pred             eEEEEeccccccee
Q psy93           178 SLKIRFAPINAAIK  191 (503)
Q Consensus       178 ~l~V~~a~~~~~L~  191 (503)
                      +|.|.++.+.....
T Consensus        93 ~l~v~~a~~~~~~~  106 (112)
T 2dit_A           93 QITAQAWDGTTDYQ  106 (112)
T ss_dssp             ECEEEECCSCCCSS
T ss_pred             EEEEEEeCCCCCcc
Confidence            99999998765443

>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=99.38  E-value=9.4e-13  Score=130.01  Aligned_cols=76  Identities=24%  Similarity=0.364  Sum_probs=71.3

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCC-CceEEeeCCHHHHHHHHHHhCCcccc-CceEEEEecc
Q psy93           110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEK-MFGFIRMDYKHNADKAKAKLDGHVLK-GRSLKIRFAP  185 (503)
Q Consensus       110 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~k-g~aFV~F~~~e~A~~Ai~~l~g~~l~-g~~l~V~~a~  185 (503)
                      ...+++|||+|||.++|+++|+++|+.||.|.+|.|..++ +||||+|.+.++|.+|+..||+..|. |+.|+|.|++
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCCCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            3456899999999999999999999999999999998775 99999999999999999999999999 9999999985

>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=99.38  E-value=6.2e-13  Score=119.91  Aligned_cols=115  Identities=18%  Similarity=0.239  Sum_probs=96.2

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ++++|||+|||..+++++|+++|+.||.|..+.++.+. ++.+++||||+|.+.++|.+|+..|+ +..+   .++++.|
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~-~~~~---~g~~l~v   76 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLN-GLRL---QTKTIKV   76 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT-TCEE---TTEECEE
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcC-CCcc---CCceEEE
Confidence            35789999999999999999999999999999999985 88999999999999999999999997 6655   6889999


Q ss_pred             ecCCccccccCCcccccCCCCchhhhhhccCcccCCCCCcc
Q psy93           265 EPLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFE  305 (503)
Q Consensus       265 ~~~~~~~~~~~~~~k~i~k~~~~~~kere~~~rf~~~g~~e  305 (503)
                      .+..+..... ....+...+++...++.++...|..+|.+.
T Consensus        77 ~~~~~~~~~~-~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~  116 (167)
T 1fxl_A           77 SYARPSSASI-RDANLYVSGLPKTMTQKELEQLFSQYGRII  116 (167)
T ss_dssp             EECCCCCGGG-TTCEEEEESCCTTCCHHHHHHHHGGGSCEE
T ss_pred             EecCCCcccC-CCCcEEECCCCCcCCHHHHHHHHHhcCCEe
Confidence            9887654422 234455667777777788888888888764

>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=99.38  E-value=2e-12  Score=124.22  Aligned_cols=76  Identities=25%  Similarity=0.367  Sum_probs=71.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCC-CeEEEEEe-cCCCceEEeeCCHHHHHHHHHHhCCcccc-CceEEEEeccc
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYG-ETQELFIN-KEKMFGFIRMDYKHNADKAKAKLDGHVLK-GRSLKIRFAPI  186 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G-~V~~v~i~-~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~-g~~l~V~~a~~  186 (503)
                      .++++|||+|||+++++++|+++|+.|| .|..|.|. .+++||||+|.+.++|.+|+..||+..|. |++|+|.|+.+
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~  227 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  227 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecC
Confidence            3468999999999999999999999999 99999994 48999999999999999999999999999 99999999875

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.38  E-value=1.5e-12  Score=109.02  Aligned_cols=82  Identities=20%  Similarity=0.160  Sum_probs=72.8

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||.|||..+++++|+++|+.|| |..|.|+.+. ++.+++||||+|.+.++|.+|+ .|| +..+   .+++|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~-g~~~---~g~~l~   86 (103)
T 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYD-GALL---GDRSLR   86 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGT-TCEE---TTEECE
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhC-CCeE---CCeEEE
Confidence            3467999999999999999999999997 9999999984 6889999999999999999999 886 6666   689999


Q ss_pred             eecCCcccc
Q psy93           264 VEPLELTDE  272 (503)
Q Consensus       264 V~~~~~~~~  272 (503)
                      |.++.....
T Consensus        87 V~~a~~~~~   95 (103)
T 2dng_A           87 VDIAEGRKQ   95 (103)
T ss_dssp             EEECCCCCC
T ss_pred             EEEecCCCC
Confidence            999876543

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.38  E-value=1.4e-12  Score=121.73  Aligned_cols=76  Identities=24%  Similarity=0.360  Sum_probs=71.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCC-CeEEEEEec-CCCceEEeeCCHHHHHHHHHHhCCcccc-CceEEEEeccc
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYG-ETQELFINK-EKMFGFIRMDYKHNADKAKAKLDGHVLK-GRSLKIRFAPI  186 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G-~V~~v~i~~-~kg~aFV~F~~~e~A~~Ai~~l~g~~l~-g~~l~V~~a~~  186 (503)
                      .++++|||+|||.++++++|+++|+.|| .|..|.|.. +++||||+|.+.++|.+|+..||+..|. |++|+|.|+.+
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~  196 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  196 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeecc
Confidence            3568999999999999999999999999 999999954 7899999999999999999999999999 99999999865

>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=99.38  E-value=1.3e-12  Score=118.23  Aligned_cols=74  Identities=24%  Similarity=0.490  Sum_probs=68.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccC--ceEEEE
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKG--RSLKIR  182 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g--~~l~V~  182 (503)
                      ...++|||+|||.++++++|+++|+.||.|..|.+.++      ++||||+|.+.++|.+|+..||+..|.|  ++|+|.
T Consensus        87 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~  166 (168)
T 1b7f_A           87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR  166 (168)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEE
Confidence            35679999999999999999999999999999999765      4899999999999999999999999987  999999


Q ss_pred             ec
Q psy93           183 FA  184 (503)
Q Consensus       183 ~a  184 (503)
                      ||
T Consensus       167 ~A  168 (168)
T 1b7f_A          167 LA  168 (168)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.38  E-value=6.2e-13  Score=123.79  Aligned_cols=77  Identities=21%  Similarity=0.403  Sum_probs=71.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ...++|||+|||+++++++|+++|+.||.|..|.+..+      ++||||+|.+.++|.+|+..||+..|.|++|.|.++
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            35689999999999999999999999999999999755      689999999999999999999999999999999999


Q ss_pred             ccc
Q psy93           185 PIN  187 (503)
Q Consensus       185 ~~~  187 (503)
                      .+.
T Consensus       192 ~~~  194 (198)
T 2yh0_A          192 SVG  194 (198)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.38  E-value=1.5e-12  Score=106.53  Aligned_cols=79  Identities=16%  Similarity=0.168  Sum_probs=72.6

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ..++|||+|||..+++++|+++|+.| .|..|.|+.+.++.+++||||+|.+.++|.+|+. || +..+   .+++|.|.
T Consensus         9 ~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~-g~~~---~gr~i~v~   82 (91)
T 2dgw_A            9 TCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CN-REYM---GGRYIEVF   82 (91)
T ss_dssp             CCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SC-SEEE---TTEEEEEE
T ss_pred             CccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hC-Ccee---CCcEEEEE
Confidence            46789999999999999999999999 9999999999889999999999999999999999 86 7776   68999999


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      ++...
T Consensus        83 ~a~~~   87 (91)
T 2dgw_A           83 REKSG   87 (91)
T ss_dssp             EESSC
T ss_pred             ECCcC
Confidence            87655

>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=99.38  E-value=8.4e-13  Score=113.92  Aligned_cols=79  Identities=14%  Similarity=0.165  Sum_probs=69.9

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhC-CeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAE-GCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~-g~~~~~~~~rpl~  263 (503)
                      ++.++|||+|||+.+++++|+++|+.||.|.+|.|+.+     ++||||+|++.++|.+|+..|+. +..+   .+++|.
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kG~AFVeF~~~e~A~~Ai~~l~~~~~~l---~Gr~l~  100 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVL---RGQPIY  100 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-----GTEEEEECSCHHHHHHHHHHHHHHCCCB---TTBCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhccCCceE---CCeEEE
Confidence            45789999999999999999999999999999999876     89999999999999999999873 2334   689999


Q ss_pred             eecCCccc
Q psy93           264 VEPLELTD  271 (503)
Q Consensus       264 V~~~~~~~  271 (503)
                      |.++....
T Consensus       101 V~~a~~k~  108 (119)
T 2ad9_A          101 IQFSNHKE  108 (119)
T ss_dssp             EEECSSSS
T ss_pred             EEEccCCC
Confidence            99986654

>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=99.38  E-value=9.4e-13  Score=106.95  Aligned_cols=78  Identities=27%  Similarity=0.336  Sum_probs=71.2

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      .++|||+|||..+++++|+++|+.||.|..+.++.+ .++.+++||||+|.+.++|.+|+ .|| +..+   .+++|.|.
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~-g~~~---~g~~l~V~   80 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALD-ESLF---RGRQIKVI   80 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGT-TCEE---TTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcC-CCEE---CCcEEEEE
Confidence            578999999999999999999999999999999998 48899999999999999999999 886 6666   68999999


Q ss_pred             cCCc
Q psy93           266 PLEL  269 (503)
Q Consensus       266 ~~~~  269 (503)
                      ++.+
T Consensus        81 ~a~~   84 (89)
T 3ucg_A           81 PKRT   84 (89)
T ss_dssp             ETTT
T ss_pred             EccC
Confidence            8754

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.38  E-value=1.3e-12  Score=115.46  Aligned_cols=83  Identities=22%  Similarity=0.280  Sum_probs=74.9

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +.++|||+|||..+++++|+++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+|+..|| +..+   .++.|.|
T Consensus        41 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~v  116 (139)
T 1u6f_A           41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLN-GFNI---LNKRLKV  116 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTT-TEEC---SSCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhC-CCEE---CCeEEEE
Confidence            3578999999999999999999999999999999988 468889999999999999999999997 6665   6899999


Q ss_pred             ecCCcccc
Q psy93           265 EPLELTDE  272 (503)
Q Consensus       265 ~~~~~~~~  272 (503)
                      .++.....
T Consensus       117 ~~a~~~~~  124 (139)
T 1u6f_A          117 ALAASGHQ  124 (139)
T ss_dssp             EESSCCCC
T ss_pred             EECCCCCC
Confidence            99877644

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.38  E-value=1.3e-12  Score=109.71  Aligned_cols=83  Identities=18%  Similarity=0.217  Sum_probs=74.7

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+|+.. + +..+   .++.|.
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~-~~~~---~g~~l~   88 (105)
T 2dh8_A           14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-R-PHTL---DGRNID   88 (105)
T ss_dssp             SSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-C-SEEE---TTEEEB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-C-CCeE---CCEEEE
Confidence            45689999999999999999999999999999999998 5789999999999999999999998 4 7766   689999


Q ss_pred             eecCCcccc
Q psy93           264 VEPLELTDE  272 (503)
Q Consensus       264 V~~~~~~~~  272 (503)
                      |.++.+...
T Consensus        89 V~~a~~~~~   97 (105)
T 2dh8_A           89 PKPCTPRGM   97 (105)
T ss_dssp             CCCSCCSSC
T ss_pred             EEEccCCCC
Confidence            999876643

>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=99.37  E-value=1e-12  Score=111.44  Aligned_cols=82  Identities=17%  Similarity=0.162  Sum_probs=74.0

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||+|||..+++++|+++|+.||.|..|.++.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~-g~~~---~g~~l~   99 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALN-GAEI---MGQTIQ   99 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHT-TCEE---TTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcC-CCEE---CCcEEE
Confidence            34678999999999999999999999999999999888 578899999999999999999999997 6655   689999


Q ss_pred             eecCCcc
Q psy93           264 VEPLELT  270 (503)
Q Consensus       264 V~~~~~~  270 (503)
                      |.++...
T Consensus       100 V~~a~~~  106 (110)
T 1oo0_B          100 VDWCFVK  106 (110)
T ss_dssp             EEESEES
T ss_pred             EEEcccC
Confidence            9987654

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.37  E-value=6.6e-13  Score=107.55  Aligned_cols=74  Identities=14%  Similarity=0.164  Sum_probs=67.7

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      .+..|+|+||++.+|+++|+++|.+||+|.+++++.     ++|||||+|.+.++|.+|++.|| ++.+   .+++|.|+
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~-----~kGfaFVey~~~~eA~~Ai~~Ln-~~~l---~gr~I~V~   76 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-----NQGIALCKYTTREEANKAQMALN-NCVL---ANTTIFAE   76 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHT-TEEE---TTEEEEEE
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC-----CCcEEEEEECCHHHHHHHHHHhc-CCEE---CCcEEEEE
Confidence            356799999999999999999999999999999976     49999999999999999999997 6776   69999999


Q ss_pred             cCC
Q psy93           266 PLE  268 (503)
Q Consensus       266 ~~~  268 (503)
                      ++.
T Consensus        77 ~A~   79 (89)
T 2wbr_A           77 SPS   79 (89)
T ss_dssp             CCC
T ss_pred             ECC
Confidence            884

>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=99.37  E-value=8e-13  Score=108.81  Aligned_cols=79  Identities=20%  Similarity=0.171  Sum_probs=70.2

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +.++|||.|||..+++++|+++|+.||.|..+.++.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~-g~~~---~gr~l~v   89 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLN-DRPI---GSRKVKL   89 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHT-TCEE---TTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhC-CCeE---CCcEEEE
Confidence            4578999999999999999999999999998888776 678899999999999999999999997 6666   6889999


Q ss_pred             ecCC
Q psy93           265 EPLE  268 (503)
Q Consensus       265 ~~~~  268 (503)
                      .++.
T Consensus        90 ~~a~   93 (95)
T 2ek1_A           90 SGPS   93 (95)
T ss_dssp             ECCC
T ss_pred             Eecc
Confidence            8764

>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=99.37  E-value=1.2e-12  Score=109.97  Aligned_cols=82  Identities=17%  Similarity=0.097  Sum_probs=73.0

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-C-CCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-R-GNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPV  262 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~-g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl  262 (503)
                      .+.++|||.|||..+++++|+++|+.|| |..|.|+.+. + +.+++||||+|.+.++|.+|| .|| +..+   .+++|
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~-g~~~---~g~~l   86 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLN-EESL---GNKRI   86 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGG-TCEE---TTEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcC-CCEe---CCcEE
Confidence            3568999999999999999999999999 9999999885 3 889999999999999999999 887 6555   68999


Q ss_pred             EeecCCcccc
Q psy93           263 IVEPLELTDE  272 (503)
Q Consensus       263 ~V~~~~~~~~  272 (503)
                      .|.++.....
T Consensus        87 ~V~~a~~~~~   96 (104)
T 1wi8_A           87 RVDVADQAQD   96 (104)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEccCCCC
Confidence            9999877654

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.37  E-value=1.3e-12  Score=113.30  Aligned_cols=81  Identities=26%  Similarity=0.362  Sum_probs=74.3

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      +.++|||+|||..+++++|+++|+.||.|..|.|+.+.++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|.
T Consensus        34 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~-g~~~---~g~~l~V~  109 (124)
T 2kt5_A           34 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK-GVPL---DGRPMDIQ  109 (124)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHT-TEES---SSCEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcC-CCEE---CCcEEEEE
Confidence            4679999999999999999999999999999999998888999999999999999999999997 6655   68999999


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      ++...
T Consensus       110 ~a~~~  114 (124)
T 2kt5_A          110 LVASQ  114 (124)
T ss_dssp             EECCT
T ss_pred             EeCCC
Confidence            87654

>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=99.37  E-value=1.8e-12  Score=117.08  Aligned_cols=82  Identities=22%  Similarity=0.197  Sum_probs=74.5

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +.++|||.|||..+++++|+++|+.||.|..|.|+.+. ++.+++||||+|.+.++|.+||..|| +..+   .+++|.|
T Consensus        38 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~-g~~~---~g~~l~V  113 (156)
T 1h2v_Z           38 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYIN-GTRL---DDRIIRT  113 (156)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTT-TSEE---TTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhC-CCEE---CCeEEEE
Confidence            56899999999999999999999999999999999984 68899999999999999999999997 6666   6899999


Q ss_pred             ecCCccc
Q psy93           265 EPLELTD  271 (503)
Q Consensus       265 ~~~~~~~  271 (503)
                      .++....
T Consensus       114 ~~a~~~~  120 (156)
T 1h2v_Z          114 DWDAGFK  120 (156)
T ss_dssp             EEESCCC
T ss_pred             EECCCCC
Confidence            9987653

>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=99.36  E-value=2.5e-12  Score=104.16  Aligned_cols=78  Identities=17%  Similarity=0.192  Sum_probs=69.0

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||+|||..+++++|+++|+.||.|..+.++.+ .++.+++||||+|.+.++|.+|+.. + +..+   .+++|.
T Consensus         9 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~-~~~~---~g~~i~   83 (87)
T 3s7r_A            9 EDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ-K-EHRL---DGRVID   83 (87)
T ss_dssp             SCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS-S-CEEE---TTEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh-C-CCEE---CCEEEE
Confidence            35679999999999999999999999999999999988 5789999999999999999999965 4 5555   788998


Q ss_pred             eecC
Q psy93           264 VEPL  267 (503)
Q Consensus       264 V~~~  267 (503)
                      |+++
T Consensus        84 v~~A   87 (87)
T 3s7r_A           84 PKKA   87 (87)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            8764

>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=99.36  E-value=1.9e-12  Score=109.23  Aligned_cols=79  Identities=18%  Similarity=0.236  Sum_probs=69.1

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCC-eeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEG-CFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g-~~~~~~~~rpl~  263 (503)
                      .+.++|||+|||..+++++|+++|++||.|..|.++++     ++||||+|.+.++|.+|+..|+.. ..+   .+++|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~i---~Gr~l~   84 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYI---AGQQAF   84 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBS---SSSBCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceE---CCEEEE
Confidence            46789999999999999999999999999999988865     789999999999999999998732 223   689999


Q ss_pred             eecCCccc
Q psy93           264 VEPLELTD  271 (503)
Q Consensus       264 V~~~~~~~  271 (503)
                      |.++....
T Consensus        85 V~~a~~~~   92 (104)
T 1wex_A           85 FNYSTSKR   92 (104)
T ss_dssp             EEECSSSS
T ss_pred             EEEccCcc
Confidence            99987654

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.36  E-value=1.3e-12  Score=118.30  Aligned_cols=81  Identities=21%  Similarity=0.173  Sum_probs=72.9

Q ss_pred             cccceeccCcccccCHHHHHHHhccCC--CeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeE
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFG--DIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPV  262 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G--~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl  262 (503)
                      ..++|||+|||..+++++|+++|+.||  .|..|.|+.| .++.++|||||+|.+.++|.+||..|| +..+   .+++|
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~ln-g~~~---~Gr~l  129 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLP-GKVL---NGEKV  129 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHST-TCEE---TTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcC-CCEE---CCeEe
Confidence            457999999999999999999999999  9999999998 589999999999999999999999997 6666   68999


Q ss_pred             EeecCCcc
Q psy93           263 IVEPLELT  270 (503)
Q Consensus       263 ~V~~~~~~  270 (503)
                      .|.++...
T Consensus       130 ~V~~a~~~  137 (156)
T 3n9u_C          130 DVRPATRQ  137 (156)
T ss_dssp             EEEECCHH
T ss_pred             EEEEcCCC
Confidence            99987553

>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=99.36  E-value=1.4e-12  Score=111.07  Aligned_cols=82  Identities=15%  Similarity=0.174  Sum_probs=72.6

Q ss_pred             cccceeccCcccccCHHHHH---HHhccCCCeeeeEEEeCC----CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCC
Q psy93           186 INAAIKVKNLTSCVTNELLE---LAFGVFGDIERAIVIVDE----RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQS  258 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~---~~Fs~~G~V~~~~v~~d~----~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~  258 (503)
                      ..++|||.|||..+++++|.   ++|++||.|..|.|+.+.    .+.+++||||+|.+.++|.+|+..|| +..+   .
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~ln-g~~~---~   89 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVN-NVVV---D   89 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHT-TEEE---T
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhC-CCEE---C
Confidence            46799999999999999999   999999999999998874    23567999999999999999999997 7666   6


Q ss_pred             CCeEEeecCCccc
Q psy93           259 LRPVIVEPLELTD  271 (503)
Q Consensus       259 ~rpl~V~~~~~~~  271 (503)
                      +++|.|.++.+..
T Consensus        90 gr~l~V~~a~~k~  102 (111)
T 2cpi_A           90 GRTLKASLGTTKY  102 (111)
T ss_dssp             TEEEEEESCCCCS
T ss_pred             CEEEEEEeccccc
Confidence            9999999987653

>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=99.36  E-value=1.5e-12  Score=107.85  Aligned_cols=79  Identities=14%  Similarity=0.155  Sum_probs=71.3

Q ss_pred             cccceeccCcccccCHHHHH----HHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCe
Q psy93           186 INAAIKVKNLTSCVTNELLE----LAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRP  261 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~----~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rp  261 (503)
                      ..++|||+|||..+++++|+    ++|+.||.|.+|.|+.+...  ++||||+|.+.++|.+|+..|| +..+   .+++
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~-g~~~---~gr~   81 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLH-RYKI---GSKK   81 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHT-TEEE---TTEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhC-CCEE---CCeE
Confidence            45789999999999999999    99999999999999988655  7899999999999999999997 7666   6999


Q ss_pred             EEeecCCcc
Q psy93           262 VIVEPLELT  270 (503)
Q Consensus       262 l~V~~~~~~  270 (503)
                      |.|.++.+.
T Consensus        82 l~V~~a~~~   90 (96)
T 2dgx_A           82 ILVSLATGA   90 (96)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEEcCCC
Confidence            999998654

>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=99.36  E-value=1.1e-12  Score=108.62  Aligned_cols=80  Identities=20%  Similarity=0.126  Sum_probs=71.2

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ..++|||.|||..+++++|+++|+.||.|..+.++.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~-g~~~---~g~~l~V   89 (98)
T 2cqp_A           14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLN-DRPI---GSRKVKL   89 (98)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTT-TCEE---TTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhC-CCee---CCeEEEE
Confidence            4578999999999999999999999999998877766 678899999999999999999999997 6555   6899999


Q ss_pred             ecCCc
Q psy93           265 EPLEL  269 (503)
Q Consensus       265 ~~~~~  269 (503)
                      .++..
T Consensus        90 ~~a~~   94 (98)
T 2cqp_A           90 VLGSG   94 (98)
T ss_dssp             EESSC
T ss_pred             EEcCC
Confidence            88653

>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=99.36  E-value=1.1e-12  Score=113.96  Aligned_cols=82  Identities=20%  Similarity=0.191  Sum_probs=73.9

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +.++|||.|||..+++++|+++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus        21 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~v   96 (126)
T 3ex7_B           21 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN-GQDL---MGQPISV   96 (126)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHT-TCBS---SSSBCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhC-CCee---CCeEEEE
Confidence            4678999999999999999999999999999999988 488899999999999999999999997 6555   6899999


Q ss_pred             ecCCccc
Q psy93           265 EPLELTD  271 (503)
Q Consensus       265 ~~~~~~~  271 (503)
                      .++....
T Consensus        97 ~~a~~~~  103 (126)
T 3ex7_B           97 DWCFVRG  103 (126)
T ss_dssp             EESEESS
T ss_pred             EEecCCC
Confidence            9986553

>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=99.36  E-value=7e-13  Score=111.36  Aligned_cols=78  Identities=15%  Similarity=0.143  Sum_probs=69.0

Q ss_pred             ccccceeccCccc-ccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCC-eeeecCCCCeE
Q psy93           185 PINAAIKVKNLTS-CVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEG-CFFLTQSLRPV  262 (503)
Q Consensus       185 ~~~~~L~V~nLp~-~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g-~~~~~~~~rpl  262 (503)
                      .+.++|||+|||+ .+++++|+++|++||.|.+|.|+++     ++||||+|++.++|.+|+..|+.. ..+   .+++|
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~---~Gr~l   84 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALV---FGKPV   84 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEE---TTEEC
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHHcCCCceE---CCcEE
Confidence            4678999999999 9999999999999999999999876     689999999999999999999832 334   69999


Q ss_pred             EeecCCcc
Q psy93           263 IVEPLELT  270 (503)
Q Consensus       263 ~V~~~~~~  270 (503)
                      .|.++...
T Consensus        85 ~V~~a~~~   92 (102)
T 1x4d_A           85 RVHLSQKY   92 (102)
T ss_dssp             EEEEECCC
T ss_pred             EEEECCCC
Confidence            99987654

>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=99.36  E-value=1.3e-12  Score=109.33  Aligned_cols=83  Identities=25%  Similarity=0.289  Sum_probs=74.4

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +.++|||+|||..+++++|+++|+.||.|..+.++.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~v   82 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLN-GREF---SGRALRV   82 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSS-SBSC---SSSCBEE
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhC-CCee---CCcEEEE
Confidence            3578999999999999999999999999999999988 578899999999999999999999997 6555   6899999


Q ss_pred             ecCCcccc
Q psy93           265 EPLELTDE  272 (503)
Q Consensus       265 ~~~~~~~~  272 (503)
                      .++.....
T Consensus        83 ~~a~~~~~   90 (104)
T 1p1t_A           83 DNAASEKN   90 (104)
T ss_dssp             EETTCTTH
T ss_pred             EeCCCccc
Confidence            99876543

>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=99.36  E-value=4.6e-12  Score=106.00  Aligned_cols=81  Identities=20%  Similarity=0.191  Sum_probs=72.4

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +.++|||.|||..+++++|+++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+|+..   +..+   .+++|.|
T Consensus        14 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~---~~~~---~g~~l~v   87 (103)
T 2cqg_A           14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ---RHMI---DGRWCDC   87 (103)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS---CEEE---TTEEEEE
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc---CCee---CCeEEEE
Confidence            4678999999999999999999999999999999998 5789999999999999999999983   4444   7899999


Q ss_pred             ecCCcccc
Q psy93           265 EPLELTDE  272 (503)
Q Consensus       265 ~~~~~~~~  272 (503)
                      .++....+
T Consensus        88 ~~a~~~~~   95 (103)
T 2cqg_A           88 KLPNSKQS   95 (103)
T ss_dssp             ECCCTTCC
T ss_pred             EecCCCCc
Confidence            99877654

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.35  E-value=2.1e-12  Score=109.08  Aligned_cols=76  Identities=25%  Similarity=0.311  Sum_probs=67.1

Q ss_pred             CCCcEEEEcCCCC-----CCCHHHHHHhhccCCCeEEEEEec-------CCCceEEeeCCHHHHHHHHHHhCCccccCce
Q psy93           111 ANNCRLYLGNIGG-----DITENDIIELFKPYGETQELFINK-------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRS  178 (503)
Q Consensus       111 ~~~~~l~V~nLp~-----~~te~~L~~~F~~~G~V~~v~i~~-------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~  178 (503)
                      .++++|+|.||..     +.++++|+++|++||+|.+|.|++       ++|||||+|.+.++|.+|+..|||..+.|++
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            3567899999963     237899999999999999999974       3689999999999999999999999999999


Q ss_pred             EEEEeccc
Q psy93           179 LKIRFAPI  186 (503)
Q Consensus       179 l~V~~a~~  186 (503)
                      |.|.+++.
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999865

>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=99.35  E-value=1e-12  Score=106.41  Aligned_cols=81  Identities=21%  Similarity=0.262  Sum_probs=70.8

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCC-ceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGN-SKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~-skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      ..++|||+|||..+++++|+++|+.||.|..+.++.+. ++. +++||||+|.+.++|.+|+..|| +..+   .+++|.
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 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMD-GGQI---DGQEIT   78 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHT-TCEE---TTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcC-CCeE---CCeEEE
Confidence            35789999999999999999999999999999998874 233 78999999999999999999997 6666   689999


Q ss_pred             eecCCcc
Q psy93           264 VEPLELT  270 (503)
Q Consensus       264 V~~~~~~  270 (503)
                      |.++.+.
T Consensus        79 v~~a~~~   85 (88)
T 4a8x_A           79 ATAVLAP   85 (88)
T ss_dssp             EEEECCC
T ss_pred             EEECCCC
Confidence            9887543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.35  E-value=1.6e-12  Score=111.37  Aligned_cols=82  Identities=32%  Similarity=0.334  Sum_probs=73.5

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+|+..++ + .+   .+++|.
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~-~-~~---~g~~l~   89 (116)
T 2cqd_A           15 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN-P-II---DGRKAN   89 (116)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSS-C-EE---TTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCC-C-cC---CCEEEE
Confidence            34689999999999999999999999999999999988 578899999999999999999999997 5 44   689999


Q ss_pred             eecCCccc
Q psy93           264 VEPLELTD  271 (503)
Q Consensus       264 V~~~~~~~  271 (503)
                      |.++....
T Consensus        90 V~~a~~~~   97 (116)
T 2cqd_A           90 VNLAYLGA   97 (116)
T ss_dssp             EEESTTTC
T ss_pred             EEEcccCC
Confidence            99986553

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.35  E-value=8.5e-13  Score=114.36  Aligned_cols=79  Identities=25%  Similarity=0.334  Sum_probs=71.7

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      .++|||+|||..+++++|+++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+|+ .|| +..+   .+++|.|.
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~-g~~~---~g~~l~V~  110 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMD-ETVF---RGRTIKVL  110 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTT-TCEE---TTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcC-CCeE---CCeEEEEE
Confidence            578999999999999999999999999999999988 58899999999999999999999 786 6666   68999999


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      ++...
T Consensus       111 ~a~~~  115 (124)
T 2jwn_A          111 PKRTN  115 (124)
T ss_dssp             ESSCC
T ss_pred             ECCCC
Confidence            87643

>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=99.35  E-value=1.1e-12  Score=110.14  Aligned_cols=79  Identities=18%  Similarity=0.122  Sum_probs=69.2

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ..++|||.|||.++++++|+++|+.||. ..|.|+.+.++++++||||+|.+.++|.+||. +| +..+   .++.|.|.
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~-~~~~---~gr~i~V~   87 (102)
T 1wez_A           14 TGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KD-KANM---QHRYVELF   87 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TS-SCCS---SSSCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hC-CCeE---CCcEEEEE
Confidence            4678999999999999999999999995 49999999999999999999999999999995 65 6665   67888887


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      ++...
T Consensus        88 ~~~~~   92 (102)
T 1wez_A           88 LNSTA   92 (102)
T ss_dssp             EECCC
T ss_pred             ECCCC
Confidence            76544

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.35  E-value=1.3e-12  Score=112.71  Aligned_cols=80  Identities=16%  Similarity=0.077  Sum_probs=72.7

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCC---eeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeE
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGD---IERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPV  262 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~---V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl  262 (503)
                      ..++|||+|||.++++++|+++|+.||.   |..|.|+.+.+++++|||||+|.+.++|.+||. +| +..+   .+++|
T Consensus        16 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~-g~~~---~gr~i   90 (118)
T 2db1_A           16 EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KD-RESM---GHRYI   90 (118)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GT-TEEE---TTEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cC-CCeE---CCeEE
Confidence            4578999999999999999999999999   899999999889999999999999999999999 75 7776   68999


Q ss_pred             EeecCCcc
Q psy93           263 IVEPLELT  270 (503)
Q Consensus       263 ~V~~~~~~  270 (503)
                      .|.++...
T Consensus        91 ~V~~a~~~   98 (118)
T 2db1_A           91 EVFKSHRT   98 (118)
T ss_dssp             EEEEECHH
T ss_pred             EEEECCHH
Confidence            99887554

>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=99.34  E-value=1.2e-12  Score=115.80  Aligned_cols=80  Identities=16%  Similarity=0.068  Sum_probs=72.7

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCC---eeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeE
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGD---IERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPV  262 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~---V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl  262 (503)
                      ..++|||+|||.++|+++|+++|+.||.   |..|.|+.|..++++|||||+|.+.++|.+||. +| +..+   .+++|
T Consensus        43 ~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~-g~~l---~gr~i  117 (136)
T 2hgl_A           43 EGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KD-RESM---GHRYI  117 (136)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TT-EEES---SSSEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cC-CCEE---CCEEE
Confidence            3678999999999999999999999999   899999999779999999999999999999999 86 6666   68999


Q ss_pred             EeecCCcc
Q psy93           263 IVEPLELT  270 (503)
Q Consensus       263 ~V~~~~~~  270 (503)
                      .|.++...
T Consensus       118 ~V~~a~~~  125 (136)
T 2hgl_A          118 EVFKSHRT  125 (136)
T ss_dssp             EEEECCHH
T ss_pred             EEEECChH
Confidence            99987554

>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=99.34  E-value=2.9e-12  Score=108.40  Aligned_cols=81  Identities=20%  Similarity=0.106  Sum_probs=71.2

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..|.|..+  +.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus        20 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~-g~~~---~g~~l~V   93 (109)
T 1x4a_A           20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRD-GYDY---DGYRLRV   93 (109)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHT-TCEE---TTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC--CCCCcEEEEEECCHHHHHHHHHHcC-CCEE---CCeEEEE
Confidence            34679999999999999999999999999999998665  4578999999999999999999997 5555   6899999


Q ss_pred             ecCCccc
Q psy93           265 EPLELTD  271 (503)
Q Consensus       265 ~~~~~~~  271 (503)
                      .++....
T Consensus        94 ~~a~~~~  100 (109)
T 1x4a_A           94 EFPRSGR  100 (109)
T ss_dssp             ECCCCCC
T ss_pred             EEcccCC
Confidence            9987653

>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=99.34  E-value=8.6e-13  Score=110.15  Aligned_cols=80  Identities=19%  Similarity=0.087  Sum_probs=70.0

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC--CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE--RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPV  262 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~--~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl  262 (503)
                      ...++|||+|||.++++++|+++|+.|| |.+|.|+.+.  ++.++|||||+|.+.++|.+|+ .|| +..+   .++.|
T Consensus        17 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~-g~~~---~g~~l   90 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLN-EESL---GNRRI   90 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTT-TCCB---TTBCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcC-CCEE---CCeEE
Confidence            3468999999999999999999999999 9999999885  7899999999999999999999 887 6555   68889


Q ss_pred             EeecCCcc
Q psy93           263 IVEPLELT  270 (503)
Q Consensus       263 ~V~~~~~~  270 (503)
                      .|.++...
T Consensus        91 ~V~~a~~~   98 (100)
T 2j76_E           91 RVDVADQA   98 (100)
T ss_dssp             CCEECCCS
T ss_pred             EEEeccCC
Confidence            99887654

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.34  E-value=6.8e-13  Score=107.01  Aligned_cols=78  Identities=18%  Similarity=0.191  Sum_probs=67.2

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..+.++.+ .++.+++||||+|.+.++|.+|+..|| +..+   .++.+.
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 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALK-ASGV---QAQMAK   78 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHH-HHTC---CEESCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhc-CCeE---eeEEEe
Confidence            45789999999999999999999999999999999988 578899999999999999999999998 4444   345454


Q ss_pred             eec
Q psy93           264 VEP  266 (503)
Q Consensus       264 V~~  266 (503)
                      +.+
T Consensus        79 ~~~   81 (85)
T 1x4e_A           79 QSG   81 (85)
T ss_dssp             SSC
T ss_pred             ecC
Confidence            443

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.34  E-value=8.8e-13  Score=103.74  Aligned_cols=74  Identities=19%  Similarity=0.209  Sum_probs=66.5

Q ss_pred             ceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecC
Q psy93           189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPL  267 (503)
Q Consensus       189 ~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~  267 (503)
                      +|||+|||..+++++|+++|+.||.|..+.++.+. ++.+++||||+|.+.++|.+|+. ++ +..+   .++++.|.++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~-~~~~---~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IH-FHEI---NNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SS-CCCS---SSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CC-CCEE---CCEEEEEEeC
Confidence            58999999999999999999999999999998884 78899999999999999999998 75 6555   6888888764

>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=99.34  E-value=6.7e-13  Score=113.59  Aligned_cols=82  Identities=17%  Similarity=0.173  Sum_probs=74.1

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCe-eeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDI-ERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V-~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||.|||..+++++|+++|+.||.| ..|.|+.|.++.+++||||+|.+.++|.+||..  ++..+   .+++|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~--~~~~~---~gr~i~   87 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL--HRKKL---NGREAF   87 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG--CSEEE---TTEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh--CCCcc---CCeEEE
Confidence            346789999999999999999999999999 899999998999999999999999999999987  47776   789999


Q ss_pred             eecCCccc
Q psy93           264 VEPLELTD  271 (503)
Q Consensus       264 V~~~~~~~  271 (503)
                      |.++....
T Consensus        88 v~~a~~~~   95 (114)
T 2cpy_A           88 VHVVTLED   95 (114)
T ss_dssp             EEEECHHH
T ss_pred             EEECCHHH
Confidence            99987654

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.34  E-value=2.6e-12  Score=107.11  Aligned_cols=80  Identities=25%  Similarity=0.229  Sum_probs=71.0

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .+.++|||.|||..+++++|+++|+.||.|   .++.+.++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~-g~~~---~g~~l~v   85 (101)
T 2fc9_A           13 GESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCN-KREI---EGRAIRL   85 (101)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTS-SEEE---TTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhC-CCEe---CCeEEEE
Confidence            457899999999999999999999999987   46666788899999999999999999999997 6666   6899999


Q ss_pred             ecCCccc
Q psy93           265 EPLELTD  271 (503)
Q Consensus       265 ~~~~~~~  271 (503)
                      .++.+..
T Consensus        86 ~~a~~~~   92 (101)
T 2fc9_A           86 ELQGPRG   92 (101)
T ss_dssp             EECSSCC
T ss_pred             EEcCCCC
Confidence            9987664

>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=99.34  E-value=3.7e-13  Score=119.53  Aligned_cols=114  Identities=13%  Similarity=0.052  Sum_probs=69.3

Q ss_pred             CceEEeeCCHHHHHHHHHHhCCccccCceEEE--------EecccccceeccCcccccCHHHHHHHhccCCCeeeeEEEe
Q psy93           150 MFGFIRMDYKHNADKAKAKLDGHVLKGRSLKI--------RFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIV  221 (503)
Q Consensus       150 g~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V--------~~a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~  221 (503)
                      ++||..|..++.+..++..+... ..+...--        .......+|||.|||.++|+++|+++|+.|| |+.|.|+.
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~-~gg~~~g~~~g~~~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~   79 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASM-TGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEI   79 (139)
T ss_dssp             --------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCC
T ss_pred             CcccccccCccccchhcccchhc-cCCCCCCCCCCCcccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEE
Confidence            57888888887777666654332 22221110        0112457899999999999999999999999 77999999


Q ss_pred             CCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCcc
Q psy93           222 DERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELT  270 (503)
Q Consensus       222 d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~  270 (503)
                      |.++++++||||+|.+.++|.+|| .+| +..+   .++.|.|.++...
T Consensus        80 d~~g~srGfaFV~F~~~e~A~~Al-~~~-g~~l---~gR~i~V~~a~~~  123 (139)
T 2hgn_A           80 GPDGRVTGEADVEFATHEEAVAAM-SKD-RANM---QHRYIELFLNSTT  123 (139)
T ss_dssp             SSSSCSSCCCEEECSHHHHHHHHT-TCC-SCSS---SSCCCCCEECCCS
T ss_pred             CCCCCCceEEEEEeCCHHHHHHHH-hhC-CCEE---CCEEEEEEECCCC
Confidence            988999999999999999999999 675 6655   5788888776554

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.34  E-value=1.3e-12  Score=110.18  Aligned_cols=79  Identities=20%  Similarity=0.289  Sum_probs=70.9

Q ss_pred             ccceeccCccccc------CHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCC
Q psy93           187 NAAIKVKNLTSCV------TNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLR  260 (503)
Q Consensus       187 ~~~L~V~nLp~~~------tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~r  260 (503)
                      .++|||+|||..+      ++++|+++|++||.|..|.|+ ..++.++|||||+|.+.++|.+|+..|| +..+   .++
T Consensus        15 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~-g~~~---~g~   89 (105)
T 2nlw_A           15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNAD-GYKL---DKQ   89 (105)
T ss_dssp             CSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCS-SEEC---STT
T ss_pred             CCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhC-Cccc---CCC
Confidence            5789999999999      789999999999999999888 5678899999999999999999999997 6666   587


Q ss_pred             -eEEeecCCcc
Q psy93           261 -PVIVEPLELT  270 (503)
Q Consensus       261 -pl~V~~~~~~  270 (503)
                       +|.|.++...
T Consensus        90 ~~l~V~~a~~~  100 (105)
T 2nlw_A           90 HTFRVNLFTDF  100 (105)
T ss_dssp             CEEEEECSCCC
T ss_pred             ceEEEEEcchH
Confidence             9999998654

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.34  E-value=1.1e-12  Score=112.52  Aligned_cols=78  Identities=24%  Similarity=0.321  Sum_probs=70.7

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +.++|||.|||.++++++|+++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+|+..|| +..+   .++.|.|
T Consensus        39 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~-g~~~---~g~~l~V  114 (118)
T 2khc_A           39 EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMN-GFQV---GTKRLKV  114 (118)
T ss_dssp             CSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCC-CCEE---TTEECCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcC-CCEE---CCEEEEE
Confidence            4578999999999999999999999999999999988 578899999999999999999999997 6555   5888888


Q ss_pred             ecC
Q psy93           265 EPL  267 (503)
Q Consensus       265 ~~~  267 (503)
                      .++
T Consensus       115 ~~a  117 (118)
T 2khc_A          115 QLK  117 (118)
T ss_dssp             EEC
T ss_pred             Eec
Confidence            875

>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=99.34  E-value=9.1e-13  Score=119.22  Aligned_cols=75  Identities=21%  Similarity=0.407  Sum_probs=69.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++|+++|+++|+.||.|.+|.|..+      +|||||+|.+.++|.+|++ +++..|.|++|.|.|+.
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecC
Confidence            3578999999999999999999999999999998754      5799999999999999998 89999999999999987


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.34  E-value=1.7e-12  Score=110.22  Aligned_cols=80  Identities=26%  Similarity=0.321  Sum_probs=71.5

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ..++|||+|||..+++++|+++|+.||.|..|.++.+.. .+++||||+|.+.++|.+|+..|| +..+   .+++|.|.
T Consensus        28 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~-g~~~---~g~~l~V~  102 (109)
T 2err_A           28 QPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREKLH-GTVV---EGRKIEVN  102 (109)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT-BCTTEEEEECCCSHHHHHHHHHHT-TCEE---TTEECEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC-CCceEEEEEECCHHHHHHHHHHcC-CCEE---CCEEEEEE
Confidence            367899999999999999999999999999999998854 479999999999999999999997 6655   68999999


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      ++...
T Consensus       103 ~a~~~  107 (109)
T 2err_A          103 NATAR  107 (109)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            87653

>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=99.34  E-value=1.7e-12  Score=109.12  Aligned_cols=80  Identities=19%  Similarity=0.196  Sum_probs=70.7

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeee-eEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIER-AIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~-~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ..++|||+|||..+++++|+++|+.||.|.. |.|+.+.++.++|||||+|.+.++|.+||.. + +..+   .++.|.|
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~-~~~~---~gr~i~v   88 (104)
T 1wg5_A           14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-H-KERI---GHRYIEI   88 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-T-TCCS---SSSCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-C-cchh---CCcEEEE
Confidence            4678999999999999999999999999987 8888888999999999999999999999997 5 6665   6788888


Q ss_pred             ecCCcc
Q psy93           265 EPLELT  270 (503)
Q Consensus       265 ~~~~~~  270 (503)
                      .++...
T Consensus        89 ~~~~~~   94 (104)
T 1wg5_A           89 FKSSRA   94 (104)
T ss_dssp             EEECTT
T ss_pred             EECCHH
Confidence            776543

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.33  E-value=9.7e-13  Score=103.86  Aligned_cols=75  Identities=20%  Similarity=0.278  Sum_probs=67.5

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      ++|||+|||..+++++|+++|++||.|..+.++.+ .++.+++||||+|.+.++|.+|+..++  ..+   .++++.|++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~--~~~---~g~~l~v~~   75 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR--HEL---DSKTIDPKV   75 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT--CCC---SSCCCEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC--Ccc---CCEEEEEEe
Confidence            47999999999999999999999999999999988 468899999999999999999999986  333   688888877


Q ss_pred             C
Q psy93           267 L  267 (503)
Q Consensus       267 ~  267 (503)
                      +
T Consensus        76 a   76 (77)
T 1uaw_A           76 A   76 (77)
T ss_dssp             C
T ss_pred             c
Confidence            5

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.33  E-value=2.2e-12  Score=109.71  Aligned_cols=78  Identities=17%  Similarity=0.228  Sum_probs=70.5

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      ..+|||+|||.++++++|+++|+.| .|..|.|+.|.+++++|||||+|.+.++|.+|| .+| +..+   .++.|.|.+
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~-~~~~---~gr~i~V~~   89 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRN-RMLM---IQRYVEVSP   89 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTT-TEEE---TTEEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcC-CCeE---CCeEEEEEE
Confidence            4689999999999999999999999 899999999988999999999999999999999 575 7776   689999988


Q ss_pred             CCcc
Q psy93           267 LELT  270 (503)
Q Consensus       267 ~~~~  270 (503)
                      +...
T Consensus        90 a~~~   93 (109)
T 2dnn_A           90 ATER   93 (109)
T ss_dssp             CCHH
T ss_pred             CCcc
Confidence            7544

>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=99.33  E-value=1.2e-12  Score=111.62  Aligned_cols=80  Identities=19%  Similarity=0.287  Sum_probs=69.2

Q ss_pred             cccccceeccCcccc-cCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhC-CeeeecCCCCe
Q psy93           184 APINAAIKVKNLTSC-VTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAE-GCFFLTQSLRP  261 (503)
Q Consensus       184 a~~~~~L~V~nLp~~-~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~-g~~~~~~~~rp  261 (503)
                      ..+.++|||+|||++ +++++|+++|+.||.|.+|.|++.     ++||||+|.+.++|.+|+..|+. +..+   .+++
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~l---~Gr~   93 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALWF---QGRC   93 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCCS---SSSC
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC-----CCEEEEEECCHHHHHHHHHHhccCCceE---CCEE
Confidence            346789999999998 999999999999999999999754     78999999999999999999872 3333   6899


Q ss_pred             EEeecCCccc
Q psy93           262 VIVEPLELTD  271 (503)
Q Consensus       262 l~V~~~~~~~  271 (503)
                      |.|.++....
T Consensus        94 l~V~~a~~~~  103 (112)
T 1x4f_A           94 VKVDLSEKYK  103 (112)
T ss_dssp             CEEEEECSCS
T ss_pred             EEEEECcccc
Confidence            9999976553

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.33  E-value=3.5e-12  Score=109.16  Aligned_cols=81  Identities=19%  Similarity=0.182  Sum_probs=73.6

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      .++|||.|||..+++++|+++|+.||.|..|.|+.+ .++.+++||||+|.+.++|.+||.. + +..+   .++.|.|.
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~-~~~~---~g~~l~V~  101 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-R-PHSI---DGRVVEPK  101 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-C-SEEE---TTEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-C-CcEE---CCEEEEEE
Confidence            578999999999999999999999999999999998 5688999999999999999999987 4 7766   78999999


Q ss_pred             cCCcccc
Q psy93           266 PLELTDE  272 (503)
Q Consensus       266 ~~~~~~~  272 (503)
                      ++.+...
T Consensus       102 ~a~~~~~  108 (116)
T 1x4b_A          102 RAVAREE  108 (116)
T ss_dssp             CCSSCCC
T ss_pred             ECCCCcc
Confidence            9877654

>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=99.32  E-value=3.2e-12  Score=105.84  Aligned_cols=79  Identities=16%  Similarity=0.119  Sum_probs=68.9

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ++.++|||.|||..+++++|+++|+.||.|..|.++.+     ++||||+|.+.++|.+|+..|| +..+ ...+++|.|
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-----~g~afV~f~~~~~A~~A~~~l~-g~~~-~~~g~~l~V   87 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMR-GFPL-GGPDRRLRV   87 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHT-TCBC-SSSSCBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-----CCEEEEEECCHHHHHHHHHHHC-CCEe-CCCCcEEEE
Confidence            45789999999999999999999999999999998765     7899999999999999999997 5555 112789999


Q ss_pred             ecCCcc
Q psy93           265 EPLELT  270 (503)
Q Consensus       265 ~~~~~~  270 (503)
                      .++.+.
T Consensus        88 ~~a~~~   93 (97)
T 1why_A           88 DFAKSG   93 (97)
T ss_dssp             EECCCC
T ss_pred             EECCCC
Confidence            998665

>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=99.32  E-value=1.2e-12  Score=111.78  Aligned_cols=80  Identities=21%  Similarity=0.242  Sum_probs=72.0

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      .++|||.|||..+++++|+++|+.||.|..|.|+.+. ++.+++||||+|.+.++|.+|+ .|| +..+   .+++|.|.
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~-g~~~---~g~~l~V~   99 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLT-GQRL---LGVPIIVQ   99 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHT-TEEE---TTEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcC-CCEe---CCeEEEEE
Confidence            4689999999999999999999999999999999884 5889999999999999999999 886 7766   68999999


Q ss_pred             cCCccc
Q psy93           266 PLELTD  271 (503)
Q Consensus       266 ~~~~~~  271 (503)
                      ++....
T Consensus       100 ~a~~~~  105 (114)
T 2cq4_A          100 ASQAEK  105 (114)
T ss_dssp             EHHHHH
T ss_pred             ecCCCc
Confidence            876543

>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=99.32  E-value=4.4e-12  Score=107.32  Aligned_cols=76  Identities=24%  Similarity=0.186  Sum_probs=67.9

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCC-----C
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSL-----R  260 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~-----r  260 (503)
                      ..++|||.|||..+++++|+++|+.||.|..|.|+.+      +||||+|.+.++|.+||..|| +..+   .+     +
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~-g~~~---~g~~~~~~   83 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLD-NTKF---RSHEGETA   83 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHHHHHHHSS-SEEE---ECTTSCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHHHHHHHHC-cCCc---cCCcCcce
Confidence            4678999999999999999999999999999999876      799999999999999999997 6665   35     8


Q ss_pred             eEEeecCCccc
Q psy93           261 PVIVEPLELTD  271 (503)
Q Consensus       261 pl~V~~~~~~~  271 (503)
                      +|.|.++.+..
T Consensus        84 ~i~V~~a~~~~   94 (108)
T 1x4c_A           84 YIRVKVDGPRS   94 (108)
T ss_dssp             EEEEEESSCCS
T ss_pred             EEEEEeCCCCC
Confidence            89999987643

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.32  E-value=8.3e-13  Score=115.87  Aligned_cols=84  Identities=20%  Similarity=0.140  Sum_probs=72.3

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeee--eEEEeCC-CCCceeEEEEEeCCHHHHHHHHHHhhCCe-eeecCCCCe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIER--AIVIVDE-RGNSKCEGIVEFARKPAAAQALRRCAEGC-FFLTQSLRP  261 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~--~~v~~d~-~g~skg~gfV~F~s~e~A~kAl~~ln~g~-~~~~~~~rp  261 (503)
                      +.++|||+|||..+++++|+++|+.||.|..  |+|+.|. ++.++|||||+|.+. +|.+|+..|| +. ..+...+++
T Consensus        22 ~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~-g~~~~~~~~gr~   99 (131)
T 2m2b_A           22 ANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQ-ALHPPLTIDGKT   99 (131)
T ss_dssp             CCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHT-TCCCSCCGGGCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhc-CCCCCccCCCEE
Confidence            4678999999999999999999999999977  9999985 899999999999999 9999999998 44 111226889


Q ss_pred             EEeecCCccc
Q psy93           262 VIVEPLELTD  271 (503)
Q Consensus       262 l~V~~~~~~~  271 (503)
                      |.|.++.+..
T Consensus       100 l~V~~a~~~~  109 (131)
T 2m2b_A          100 INVEFAKGSK  109 (131)
T ss_dssp             CCCEECCCSC
T ss_pred             EEEEECCCCC
Confidence            9999887653

>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=99.32  E-value=1.6e-12  Score=118.76  Aligned_cols=77  Identities=22%  Similarity=0.313  Sum_probs=68.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEE-ecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFI-NKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i-~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ...++|||+|||+++|+++|+++|+.||.|..+.. ..+++||||+|.+.++|.+|+..||+..|.|++|.|.|+.+.
T Consensus        97 ~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B           97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             GGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEECSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             ccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEecCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            35689999999999999999999999999988711 135899999999999999999999999999999999998653

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.32  E-value=3.7e-12  Score=108.15  Aligned_cols=82  Identities=18%  Similarity=0.222  Sum_probs=71.4

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||+|||..+++++|+++|+.||.|..|.|+.+ .++.++|||||+|.+.++|.+|+..+  +..+   .++.|.
T Consensus        23 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~--~~~l---~g~~l~   97 (109)
T 2rs2_A           23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS--RHEL---DSKTID   97 (109)
T ss_dssp             ---CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS--CEEE---TTEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC--CCcC---CCEEEE
Confidence            45789999999999999999999999999999999988 46899999999999999999999986  3555   689999


Q ss_pred             eecCCccc
Q psy93           264 VEPLELTD  271 (503)
Q Consensus       264 V~~~~~~~  271 (503)
                      |.++....
T Consensus        98 V~~a~~~~  105 (109)
T 2rs2_A           98 PKVAFPRR  105 (109)
T ss_dssp             EEECCCCC
T ss_pred             EEEccCCC
Confidence            99887653

>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=99.32  E-value=2.2e-12  Score=121.00  Aligned_cols=74  Identities=24%  Similarity=0.253  Sum_probs=66.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec-----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ..++|||+|||+++|+++|+++|+.||+|.+|.|++     ++|||||+|.+.++|.+|+..+ +..|.|++|.|.++..
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            357899999999999999999999999999999975     4789999999999999999865 4589999999998753

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.32  E-value=1e-12  Score=105.23  Aligned_cols=72  Identities=22%  Similarity=0.333  Sum_probs=62.7

Q ss_pred             cceeccCccccc------CHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCC-
Q psy93           188 AAIKVKNLTSCV------TNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLR-  260 (503)
Q Consensus       188 ~~L~V~nLp~~~------tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~r-  260 (503)
                      ++|||+|||..+      ++++|+++|++||.|..+.++ ..++.++|||||+|.+.++|.+|+..|| +..+   .++ 
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~~~g~afV~f~~~~~A~~Ai~~ln-g~~~---~g~~   76 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNAD-GYKL---DKQH   76 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSS-SCCC---SSSS
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhc-Cccc---CCce
Confidence            689999999999      679999999999999999887 5678899999999999999999999997 5555   455 


Q ss_pred             eEEe
Q psy93           261 PVIV  264 (503)
Q Consensus       261 pl~V  264 (503)
                      +|.|
T Consensus        77 ~l~V   80 (81)
T 2krb_A           77 TFRV   80 (81)
T ss_dssp             CCCC
T ss_pred             eEEe
Confidence            5544

>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=99.31  E-value=3.2e-12  Score=102.95  Aligned_cols=74  Identities=22%  Similarity=0.208  Sum_probs=66.7

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      +.++|||.|||..+++++|+++|++||.|..+.++.+     ++||||+|.+.++|.+|+..|+++..+   .+++|.|.
T Consensus        11 ~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~-----kg~afV~f~~~~~A~~a~~~l~~~~~~---~g~~l~v~   82 (85)
T 2ytc_A           11 TITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKSFNKLIV---NGRRLNVK   82 (85)
T ss_dssp             SCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHTTTTTCEE---TTEECCEE
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC-----CCEEEEEECCHHHHHHHHHHhcCCeeE---CCCEEEEE
Confidence            4679999999999999999999999999999999875     789999999999999999998447666   58888888


Q ss_pred             cC
Q psy93           266 PL  267 (503)
Q Consensus       266 ~~  267 (503)
                      ++
T Consensus        83 ~a   84 (85)
T 2ytc_A           83 WG   84 (85)
T ss_dssp             EC
T ss_pred             ec
Confidence            76

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.31  E-value=2e-12  Score=110.29  Aligned_cols=86  Identities=17%  Similarity=0.076  Sum_probs=68.1

Q ss_pred             ceEEEEecc---cccceeccCcccccCHHHHHHHhccCC-CeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCe
Q psy93           177 RSLKIRFAP---INAAIKVKNLTSCVTNELLELAFGVFG-DIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGC  252 (503)
Q Consensus       177 ~~l~V~~a~---~~~~L~V~nLp~~~tee~L~~~Fs~~G-~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~  252 (503)
                      .++.+.+..   ..++|||+|||.++++++|+++|+.|| .|..+.|+.+   .++|||||+|.+.++|.+|+..|| +.
T Consensus        15 ~~~~~~~~~~p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~---~~rGfaFV~F~~~e~A~~Ai~~ln-g~   90 (111)
T 2jvr_A           15 VPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR---DFDGTGALEFPSEEILVEALERLN-NI   90 (111)
T ss_dssp             ----------CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC---SSSCCEEEEESSHHHHHHHHHHTT-TE
T ss_pred             eecchhcCCCCCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC---CCCCEEEEEECCHHHHHHHHHHcC-CC
Confidence            345555553   357899999999999999999999999 8999888643   468999999999999999999997 77


Q ss_pred             eeecCCCCeEEeecCCc
Q psy93           253 FFLTQSLRPVIVEPLEL  269 (503)
Q Consensus       253 ~~~~~~~rpl~V~~~~~  269 (503)
                      .+   .+++|.|.++..
T Consensus        91 ~l---~Gr~i~V~~a~~  104 (111)
T 2jvr_A           91 EF---RGSVITVERDDN  104 (111)
T ss_dssp             EE---TTEEEEEEESCC
T ss_pred             EE---CCeEEEEEECCC
Confidence            66   799999988643

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.31  E-value=6.7e-12  Score=102.38  Aligned_cols=77  Identities=21%  Similarity=0.200  Sum_probs=68.4

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .+.++|||+|||..+++++|+++|+.||.|..+.++       ++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-------~g~afV~f~~~~~A~~A~~~l~-g~~~---~g~~l~v   74 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLH-HYKL---HGVNINV   74 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-------TTEEEEEESSHHHHHHHHHHHT-TCBC---SSCBCEE
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhc-CCcc---CCcEEEE
Confidence            356899999999999999999999999999999987       5699999999999999999997 5555   6899999


Q ss_pred             ecCCcccc
Q psy93           265 EPLELTDE  272 (503)
Q Consensus       265 ~~~~~~~~  272 (503)
                      .++.....
T Consensus        75 ~~a~~~~~   82 (90)
T 2dnq_A           75 EASKNKSK   82 (90)
T ss_dssp             ECSSCCCC
T ss_pred             EECCCCCC
Confidence            99876644

>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=99.31  E-value=3.1e-12  Score=118.82  Aligned_cols=117  Identities=15%  Similarity=0.142  Sum_probs=94.0

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      ...++|||+|||.++++++|+++|+.||.|.+|.|+.+ .++.+++||||+|.+.++|.+|+.. + +..+   .++++.
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~-~~~~---~g~~l~   85 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-R-PHKV---DGRVVE   85 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-C-SCEE---TTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-C-CCEE---CCEEee
Confidence            34679999999999999999999999999999999998 4788999999999999999999976 3 5555   688999


Q ss_pred             eecCCccccccC-----CcccccCCCCchhhhhhccCcccCCCCCcch
Q psy93           264 VEPLELTDEIDG-----LSERTINKKTPEFYKQRQVGPRFATVNSFEF  306 (503)
Q Consensus       264 V~~~~~~~~~~~-----~~~k~i~k~~~~~~kere~~~rf~~~g~~e~  306 (503)
                      |.++........     ....++..+++...++.++...|..+|.+..
T Consensus        86 v~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~  133 (196)
T 1l3k_A           86 PKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV  133 (196)
T ss_dssp             EEECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEE
T ss_pred             eecccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEE
Confidence            988766533221     1234566678887888888899999987753

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.30  E-value=3.2e-12  Score=111.71  Aligned_cols=82  Identities=18%  Similarity=0.243  Sum_probs=70.2

Q ss_pred             ccccceeccCcccccCHHHHH----HHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCC
Q psy93           185 PINAAIKVKNLTSCVTNELLE----LAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLR  260 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~----~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~r  260 (503)
                      .+.++|||+|||+.+++++|+    ++|++||.|.+|.+..  ++.++|||||+|.+.++|.+|+..|| +..+   .++
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~--~~~~rG~aFV~F~~~~~A~~Ai~~ln-g~~l---~gr  100 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL--SDDNSGKAYIVFATQESAQAFVEAFQ-GYPF---QGN  100 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC--CCSSCCCEEEEESSHHHHHHHHHHST-TCCC---TTS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc--CCCcCCEEEEEECCHHHHHHHHHHHC-CCEe---CCC
Confidence            456899999999999998866    6999999999887753  57789999999999999999999997 5555   589


Q ss_pred             eEEeecCCcccc
Q psy93           261 PVIVEPLELTDE  272 (503)
Q Consensus       261 pl~V~~~~~~~~  272 (503)
                      +|.|.++....+
T Consensus       101 ~l~V~~a~~~~~  112 (127)
T 2a3j_A          101 PLVITFSETPQS  112 (127)
T ss_dssp             CCEEEECCCCCH
T ss_pred             EEEEEEccCcch
Confidence            999999876543

>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=99.30  E-value=5.7e-12  Score=106.68  Aligned_cols=79  Identities=23%  Similarity=0.278  Sum_probs=70.7

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .+.++|||+|||..+++++|+++|+.||.|..|.++.+     ++||||+|.+.++|.+|+..|+ +..+   .+++|.|
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~v   93 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVN-GTTI---EGHVVKC   93 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHT-TCEE---TTEECEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHcC-CCEE---CCcEEEE
Confidence            34679999999999999999999999999999999887     7899999999999999999997 6655   6899999


Q ss_pred             ecCCcccc
Q psy93           265 EPLELTDE  272 (503)
Q Consensus       265 ~~~~~~~~  272 (503)
                      .++.....
T Consensus        94 ~~a~~~~~  101 (109)
T 1x4g_A           94 YWGKESPD  101 (109)
T ss_dssp             ECCCCCCS
T ss_pred             EecCCCCC
Confidence            99876643

>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=99.30  E-value=2.3e-12  Score=124.09  Aligned_cols=80  Identities=21%  Similarity=0.198  Sum_probs=71.5

Q ss_pred             cccceeccCcccccCHHHHHHHhccCC--CeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeE
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFG--DIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPV  262 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G--~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl  262 (503)
                      ..++|||.||+..+|+++|+++|+.||  .|..|.|+.| .++.+++||||+|.+.++|.+||..|| +..+   .++.|
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~ln-g~~~---~Gr~l  142 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLP-KREL---HGQNP  142 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTST-TSCB---TTBCC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcC-CCeE---CCEEe
Confidence            467899999999999999999999999  9999999999 589999999999999999999999997 6555   68899


Q ss_pred             EeecCCc
Q psy93           263 IVEPLEL  269 (503)
Q Consensus       263 ~V~~~~~  269 (503)
                      .|.++..
T Consensus       143 ~V~~a~~  149 (229)
T 3q2s_C          143 VVTPVNK  149 (229)
T ss_dssp             EEEECCH
T ss_pred             EEEECCC
Confidence            9988643

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.30  E-value=1.9e-12  Score=111.94  Aligned_cols=74  Identities=18%  Similarity=0.231  Sum_probs=64.7

Q ss_pred             cEEEEcCC----CCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCC----HHH----HHHHHH--HhCCcc
Q psy93           114 CRLYLGNI----GGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDY----KHN----ADKAKA--KLDGHV  173 (503)
Q Consensus       114 ~~l~V~nL----p~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~----~e~----A~~Ai~--~l~g~~  173 (503)
                      +.|||+||    |+.|++.+|+++|+.||+|.+|.++.      ++|||||+|.+    +++    |.+||.  .|++..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            57999999    99999999999999999999999974      47999999996    433    888988  789999


Q ss_pred             ccCceEEEEecccc
Q psy93           174 LKGRSLKIRFAPIN  187 (503)
Q Consensus       174 l~g~~l~V~~a~~~  187 (503)
                      |.|++|+|.+.+.+
T Consensus        83 I~Gr~irV~ln~~g   96 (136)
T 2j8a_A           83 IMGFKFEVILNKHS   96 (136)
T ss_dssp             ETTEEEEEEECCTT
T ss_pred             ecCcEEEEEECccc
Confidence            99999999987654

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.29  E-value=5.2e-12  Score=111.37  Aligned_cols=78  Identities=26%  Similarity=0.272  Sum_probs=70.7

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +.++|||+|||..+++++|+++|+.||.|..+.|+.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus        62 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~v  137 (140)
T 2ku7_A           62 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN-ESEL---FGRTIRV  137 (140)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHST-EEEE---TTEEEEE
T ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhC-CCEE---CCEEEEE
Confidence            4679999999999999999999999999999999988 678899999999999999999999997 6666   6889998


Q ss_pred             ecC
Q psy93           265 EPL  267 (503)
Q Consensus       265 ~~~  267 (503)
                      .++
T Consensus       138 ~~A  140 (140)
T 2ku7_A          138 NLA  140 (140)
T ss_dssp             EC-
T ss_pred             EeC
Confidence            864

>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=99.29  E-value=1.8e-12  Score=112.56  Aligned_cols=80  Identities=21%  Similarity=0.232  Sum_probs=70.1

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEE-EeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIV-IVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v-~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ..++|||.|||..+++++|+++|+.||.|..+.+ ..+.++.++|||||+|.+.++|.+||. || +..+   .+++|.|
T Consensus        24 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~-g~~~---~gr~i~V   98 (124)
T 1wel_A           24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RH-KQYM---GNRFIQV   98 (124)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SC-SBCS---TTSCBEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hC-CCeE---CCcEEEE
Confidence            4579999999999999999999999999998544 445789999999999999999999999 86 6666   6899999


Q ss_pred             ecCCcc
Q psy93           265 EPLELT  270 (503)
Q Consensus       265 ~~~~~~  270 (503)
                      .++...
T Consensus        99 ~~a~~~  104 (124)
T 1wel_A           99 HPITKK  104 (124)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            887654

>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=99.29  E-value=4e-12  Score=105.63  Aligned_cols=78  Identities=17%  Similarity=0.143  Sum_probs=69.5

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..|.++.+     ++||||+|.+.++|.+|+..|+ +..+   .+++|.|
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~-----kg~afV~f~~~~~a~~a~~~l~-g~~~---~g~~l~v   83 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELD-NMPL---RGKQLRV   83 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHT-TCCB---TTBCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCEEEEEECCHHHHHHHHHHhC-CCEe---CCceEEE
Confidence            35679999999999999999999999999999999865     7899999999999999999997 5555   5899999


Q ss_pred             ecCCccc
Q psy93           265 EPLELTD  271 (503)
Q Consensus       265 ~~~~~~~  271 (503)
                      .++.+..
T Consensus        84 ~~a~~~~   90 (99)
T 2cpj_A           84 RFACHSA   90 (99)
T ss_dssp             EESSCCS
T ss_pred             EEcCCCC
Confidence            9987653

>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=99.29  E-value=1.5e-12  Score=110.10  Aligned_cols=80  Identities=15%  Similarity=0.118  Sum_probs=71.6

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCC---eeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeE
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGD---IERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPV  262 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~---V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl  262 (503)
                      ..++|||+|||.++++++|+++|+.||.   |..|.|+.+..+.++|||||+|.+.++|.+||. ++ +..+   .++.|
T Consensus        10 ~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~-~~~~---~gr~i   84 (107)
T 2lmi_A           10 DVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KH-RMYM---GQRYV   84 (107)
T ss_dssp             SCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TT-TCCS---SSSCC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hC-ccee---CCeEE
Confidence            4678999999999999999999999998   899999999779999999999999999999999 76 6655   68888


Q ss_pred             EeecCCcc
Q psy93           263 IVEPLELT  270 (503)
Q Consensus       263 ~V~~~~~~  270 (503)
                      .|.++...
T Consensus        85 ~V~~a~~~   92 (107)
T 2lmi_A           85 EVYEINNE   92 (107)
T ss_dssp             CCEECCHH
T ss_pred             EEEECCHH
Confidence            88887654

>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=99.28  E-value=5.8e-12  Score=107.53  Aligned_cols=82  Identities=21%  Similarity=0.215  Sum_probs=72.0

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .++++|||+|||..+++++|+++|+.||.|..|.++.+  +.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~-g~~~---~g~~l~v   79 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLS-GFNV---SNRYLVV   79 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTCEEEEESSHHHHHHHHHHHT-TCBS---SSCBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--CCCCcEEEEEECCHHHHHHHHHHcC-CCEE---CCeEEEE
Confidence            35789999999999999999999999999999999876  4558999999999999999999997 6555   6899999


Q ss_pred             ecCCcccc
Q psy93           265 EPLELTDE  272 (503)
Q Consensus       265 ~~~~~~~~  272 (503)
                      .++.+...
T Consensus        80 ~~a~~~~~   87 (115)
T 3lqv_A           80 LYYNANRA   87 (115)
T ss_dssp             EECCHHHH
T ss_pred             EEecCChh
Confidence            99876543

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.28  E-value=4.5e-12  Score=105.66  Aligned_cols=76  Identities=24%  Similarity=0.210  Sum_probs=68.5

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecC
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPL  267 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~  267 (503)
                      ++|||+|||..+++++|+++|+.||.|..|.++.+    +++||||+|.+.++|.+|+..|+ +..+   .+++|.|.++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~V~~a   72 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLD-GKVI---CGSRVRVELS   72 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS----SSSEEEEECSSHHHHHHHHHHHH-HSCS---SSCCCEEEES
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC----CCCEEEEEECCHHHHHHHHHHHC-CCeE---CCcEEEEEEc
Confidence            47999999999999999999999999999999887    68899999999999999999998 4444   6888999998


Q ss_pred             Cccc
Q psy93           268 ELTD  271 (503)
Q Consensus       268 ~~~~  271 (503)
                      ....
T Consensus        73 ~~~~   76 (101)
T 2hvz_A           73 TGMP   76 (101)
T ss_dssp             SSCC
T ss_pred             cCCC
Confidence            7764

>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=99.28  E-value=1.1e-12  Score=106.99  Aligned_cols=79  Identities=25%  Similarity=0.300  Sum_probs=68.4

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      ++|||+|||..+++++|+++|+.||.|..+.++.+ .++.+++||||+|.+.+ |.+|+..|| +..+   .+++|.|.+
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 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLD-NTDF---MGRTIRVTE   76 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSC-SSCC---SSSSCSEEE
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhC-CCEE---CCeEEEEEE
Confidence            47999999999999999999999999999999988 46889999999999999 999999997 5555   588999998


Q ss_pred             CCccc
Q psy93           267 LELTD  271 (503)
Q Consensus       267 ~~~~~  271 (503)
                      +....
T Consensus        77 a~~~~   81 (90)
T 2ki2_A           77 ANPKK   81 (90)
T ss_dssp             C----
T ss_pred             cCCCC
Confidence            76653

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.28  E-value=2.7e-12  Score=111.56  Aligned_cols=80  Identities=20%  Similarity=0.216  Sum_probs=69.8

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCe----eeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDI----ERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRP  261 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V----~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rp  261 (503)
                      ...+|||+|||.++|+++|+++|+.||.|    ..|.|+.+.+++++|||||+|.+.++|.+||.. | +..+   .++.
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~-~~~l---~gR~   96 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-H-KDLL---GKRY   96 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-T-TEES---SSCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-C-CCee---CCeE
Confidence            45789999999999999999999999975    689999998999999999999999999999986 4 6666   5788


Q ss_pred             EEeecCCcc
Q psy93           262 VIVEPLELT  270 (503)
Q Consensus       262 l~V~~~~~~  270 (503)
                      |.|.++...
T Consensus        97 i~V~~a~~~  105 (123)
T 2dha_A           97 IELFRSTAA  105 (123)
T ss_dssp             ECCEEECHH
T ss_pred             EEEEECCHH
Confidence            888776443

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.28  E-value=1.4e-11  Score=100.86  Aligned_cols=76  Identities=20%  Similarity=0.250  Sum_probs=68.2

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .+.++|||+|||..+++++|+++|+.||.|..|.++++       ||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus         8 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~-------~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~V   76 (92)
T 2dgt_A            8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRGLD-NTEF---QGKRMHV   76 (92)
T ss_dssp             CSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS-------EEEEEESCHHHHHHHHHHHT-TEEE---TTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC-------EEEEEECCHHHHHHHHHHhC-CCee---CCcEEEE
Confidence            35689999999999999999999999999999998754       99999999999999999997 6666   6899999


Q ss_pred             ecCCccc
Q psy93           265 EPLELTD  271 (503)
Q Consensus       265 ~~~~~~~  271 (503)
                      .++....
T Consensus        77 ~~a~~~~   83 (92)
T 2dgt_A           77 QLSTSRL   83 (92)
T ss_dssp             EESSCCC
T ss_pred             EEccCCC
Confidence            9987654

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.28  E-value=4.9e-12  Score=116.97  Aligned_cols=82  Identities=26%  Similarity=0.356  Sum_probs=74.6

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..|.|+.+.++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~ln-g~~l---~Gr~l~V  161 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK-GVPL---DGRPMDI  161 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHST-TCBC---SSSBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhC-CCEE---CCEEEEE
Confidence            45689999999999999999999999999999999998888999999999999999999999997 5555   6899999


Q ss_pred             ecCCcc
Q psy93           265 EPLELT  270 (503)
Q Consensus       265 ~~~~~~  270 (503)
                      .++...
T Consensus       162 ~~a~~~  167 (177)
T 2f3j_A          162 QLVASQ  167 (177)
T ss_dssp             EEESSG
T ss_pred             EEecCC
Confidence            987654

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.27  E-value=5.9e-12  Score=104.95  Aligned_cols=75  Identities=17%  Similarity=0.023  Sum_probs=66.9

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ..++|||+|||..+++++|+++|+.||.|.++.+..     +++||||+|.+.++|.+|+..|| +..+   .++.|.|.
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~-----~~g~afV~f~~~~~A~~Ai~~l~-g~~~---~g~~l~V~   96 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP-----EKGCCFIKYDTHEQAAVCIVALA-NFPF---QGRNLRTG   96 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHT-TCEE---TTEECCCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhC-CCeE---CCeEEEEE
Confidence            357899999999999999999999999999999884     48899999999999999999997 6666   58889998


Q ss_pred             cCCc
Q psy93           266 PLEL  269 (503)
Q Consensus       266 ~~~~  269 (503)
                      ++.+
T Consensus        97 ~a~~  100 (101)
T 2la4_A           97 WGKE  100 (101)
T ss_dssp             BCCC
T ss_pred             eccC
Confidence            8754

>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=99.27  E-value=3.6e-12  Score=120.66  Aligned_cols=73  Identities=16%  Similarity=0.195  Sum_probs=65.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCe--EEEEEecC----CCceEEeeCCHHHHHHHHHHhCCccccCc----eEEE
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGET--QELFINKE----KMFGFIRMDYKHNADKAKAKLDGHVLKGR----SLKI  181 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V--~~v~i~~~----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~----~l~V  181 (503)
                      ++++|||+|||+++|+++|+++|++||.|  .+|++..+    ++||||+|.+.++|.+||..||+..|.+.    ++.|
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~v  201 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTL  201 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEEC
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEE
Confidence            45689999999999999999999999999  89998754    48999999999999999999999999875    6777


Q ss_pred             Eec
Q psy93           182 RFA  184 (503)
Q Consensus       182 ~~a  184 (503)
                      +++
T Consensus       202 k~~  204 (205)
T 3tyt_A          202 KLC  204 (205)
T ss_dssp             EEE
T ss_pred             Eec
Confidence            764

>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=99.27  E-value=1.1e-11  Score=103.73  Aligned_cols=76  Identities=25%  Similarity=0.332  Sum_probs=68.1

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      +.++|||.|||..+++++|+++|+.||.|..|.+++       +||||+|.+.++|.+|+..|| +..+   .+++|.|.
T Consensus        10 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~-------~~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~v~   78 (103)
T 2dgu_A           10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK-------DYAFIHFDERDGAVKAMEEMN-GKDL---EGENIEIV   78 (103)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS-------SCEEEEESSHHHHHHHHHHHT-TEEE---TTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC-------CEEEEEeCCHHHHHHHHHHHC-CCcc---CCCEEEEE
Confidence            467999999999999999999999999999998874       499999999999999999997 6666   68999999


Q ss_pred             cCCcccc
Q psy93           266 PLELTDE  272 (503)
Q Consensus       266 ~~~~~~~  272 (503)
                      ++.+...
T Consensus        79 ~a~~~~~   85 (103)
T 2dgu_A           79 FAKPPDQ   85 (103)
T ss_dssp             ECCCCCC
T ss_pred             EcCCCcc
Confidence            9877644

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.26  E-value=1.1e-11  Score=101.20  Aligned_cols=76  Identities=20%  Similarity=0.150  Sum_probs=68.0

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .+.++|||+|||..+++++|+++|+.||.|..+.++++       ||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~-------~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~v   75 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQLN-GKEV---KGKRINV   75 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS-------CEEEEESCHHHHHHHHHHHT-TCEE---TTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC-------EEEEEECCHHHHHHHHHHhC-CCEE---CCcEEEE
Confidence            35689999999999999999999999999999999754       99999999999999999997 6655   6899999


Q ss_pred             ecCCccc
Q psy93           265 EPLELTD  271 (503)
Q Consensus       265 ~~~~~~~  271 (503)
                      .++....
T Consensus        76 ~~a~~~~   82 (90)
T 2dnp_A           76 ELSTKGQ   82 (90)
T ss_dssp             EESCCCC
T ss_pred             EECCCCC
Confidence            9987654

>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=99.26  E-value=2.5e-11  Score=113.80  Aligned_cols=109  Identities=13%  Similarity=-0.007  Sum_probs=89.1

Q ss_pred             CHHHHHHHHHHh--CCccccCceEEEEecc---------------cccceeccCcccccCHHHHHHHhccCCCeeeeEEE
Q psy93           158 YKHNADKAKAKL--DGHVLKGRSLKIRFAP---------------INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVI  220 (503)
Q Consensus       158 ~~e~A~~Ai~~l--~g~~l~g~~l~V~~a~---------------~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~  220 (503)
                      +.+.+..|+...  ....+.+..+.|...+               ..++|||+|||..+++++|.++|+.||.|..|.|+
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~~p~p~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~  142 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMR  142 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTTSCCCCCCHHHHHHHHHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEE
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEecccCCCcccchhhhhccccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEE
Confidence            667778888776  4556666555665542               13689999999999999999999999999999999


Q ss_pred             eCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCccc
Q psy93           221 VDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELTD  271 (503)
Q Consensus       221 ~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~~  271 (503)
                      .+.++.++|||||+|.+.++|.+|+..++ . .+   .+++|.|.+.....
T Consensus       143 ~~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~-~~---~Gr~l~V~~~~~y~  188 (193)
T 2voo_A          143 RTLHKAFKGSIFVVFDSIESAKKFVETPG-Q-KY---KETDLLILFKDDYF  188 (193)
T ss_dssp             ECTTCCEEEEEEEEESSHHHHHHHHHCTT-C-EE---TTEECEEEETTTC-
T ss_pred             ECCCCCcccEEEEEECCHHHHHHHHHhCC-C-eE---CCEEEEEEEhHHHH
Confidence            99889999999999999999999998764 3 34   68999999876543

>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=99.26  E-value=5.6e-12  Score=107.77  Aligned_cols=81  Identities=10%  Similarity=0.008  Sum_probs=67.1

Q ss_pred             ccccceec--cCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCee-eecCCCCe
Q psy93           185 PINAAIKV--KNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCF-FLTQSLRP  261 (503)
Q Consensus       185 ~~~~~L~V--~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~-~~~~~~rp  261 (503)
                      .++.+|||  +||+..+++++|+++|++||.|..|.|+.+     ++||||+|.+.++|.+|+..||+..+ .....+++
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~-----rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~   97 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   97 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcE
Confidence            46788999  669999999999999999999999887643     78999999999999999999984433 12234788


Q ss_pred             EEeecCCcc
Q psy93           262 VIVEPLELT  270 (503)
Q Consensus       262 l~V~~~~~~  270 (503)
                      +.|.++...
T Consensus        98 l~v~~a~~~  106 (114)
T 2cq2_A           98 LYLNFVEKV  106 (114)
T ss_dssp             CEEEEESCC
T ss_pred             EEEEecccC
Confidence            888887654

>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=99.26  E-value=4.3e-12  Score=108.11  Aligned_cols=75  Identities=25%  Similarity=0.311  Sum_probs=66.6

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      .++|||+|||..+++++|+++|++||.|..|.|+.     +++||||+|.+.++|.+|+..|| +..+   .+++|.|.+
T Consensus        10 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~-----~~g~afV~f~~~~~A~~Ai~~l~-g~~~---~g~~l~V~~   80 (111)
T 1whx_A           10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLA-YSKF---HHVPLYLEW   80 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHT-TCBS---SSSBCEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCCEEEEEeCCHHHHHHHHHHhC-CCEE---CCeEEEEEE
Confidence            57899999999999999999999999999998875     37899999999999999999997 5555   589999998


Q ss_pred             CCcc
Q psy93           267 LELT  270 (503)
Q Consensus       267 ~~~~  270 (503)
                      +...
T Consensus        81 a~~~   84 (111)
T 1whx_A           81 APIG   84 (111)
T ss_dssp             EETT
T ss_pred             CCCC
Confidence            7543

>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=99.26  E-value=4e-12  Score=105.01  Aligned_cols=81  Identities=23%  Similarity=0.307  Sum_probs=71.0

Q ss_pred             ccccceeccCcccccCHHHHH----HHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCC
Q psy93           185 PINAAIKVKNLTSCVTNELLE----LAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLR  260 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~----~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~r  260 (503)
                      ++.++|||+|||..+++++|+    ++|+.||.|..|.++.  ++.+++||||+|.+.++|.+|+..|| +..+   .++
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~---~g~   79 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQ-GFPF---YDK   79 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHT-TCEE---TTE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc--CCCcCcEEEEEeCCHHHHHHHHHHhC-CCEE---CCc
Confidence            457899999999999999999    9999999999998874  45668999999999999999999997 5555   689


Q ss_pred             eEEeecCCccc
Q psy93           261 PVIVEPLELTD  271 (503)
Q Consensus       261 pl~V~~~~~~~  271 (503)
                      +|.|.++....
T Consensus        80 ~l~v~~a~~~~   90 (97)
T 1nu4_A           80 PMRIQYAKTDS   90 (97)
T ss_dssp             ECEEEECSSCC
T ss_pred             EEEEEEccCCC
Confidence            99999987653

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.25  E-value=8.8e-12  Score=103.22  Aligned_cols=77  Identities=17%  Similarity=0.165  Sum_probs=67.4

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ..++|||.|||..+++++|+++|+.||.|. +.++.+   .+++||||+|.+.++|.+|+..|| +..+   .+++|.|.
T Consensus        18 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~---~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~V~   89 (97)
T 2e5j_A           18 LAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ---GPRRRAFLHYPDSAAAQQAVSCLQ-GLRL---GTDTLRVA   89 (97)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE---TTTTEEEEECSSHHHHHHHHHHHT-TCCS---SSSCCEEE
T ss_pred             CCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC---CCCcEEEEEECCHHHHHHHHHHhC-CCEE---CCcEEEEE
Confidence            367999999999999999999999999997 667654   568999999999999999999997 5555   68899999


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      ++.+.
T Consensus        90 ~a~~~   94 (97)
T 2e5j_A           90 LARQQ   94 (97)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            88664

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.25  E-value=8.7e-12  Score=102.81  Aligned_cols=78  Identities=22%  Similarity=0.198  Sum_probs=68.5

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      +.++|||+|||..+++++|+++|+.||.|..+    ..++.+++||||+|.+.++|.+|+..|+ +..+   .+++|.|.
T Consensus        15 ~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~g~~l~v~   86 (96)
T 1fjc_A           15 AARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQ-GAEI---DGRSVSLY   86 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTT-EEEE---TTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhC-CCEE---CCeEEEEE
Confidence            46799999999999999999999999988766    4467889999999999999999999997 6666   68999999


Q ss_pred             cCCccc
Q psy93           266 PLELTD  271 (503)
Q Consensus       266 ~~~~~~  271 (503)
                      ++.+..
T Consensus        87 ~a~~~~   92 (96)
T 1fjc_A           87 YTGEKG   92 (96)
T ss_dssp             ECSSSC
T ss_pred             EcCCCC
Confidence            986653

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.25  E-value=8.3e-12  Score=126.67  Aligned_cols=75  Identities=20%  Similarity=0.443  Sum_probs=66.8

Q ss_pred             CCCcEEEEcC--CCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCcccc---Cc--eEEEEe
Q psy93           111 ANNCRLYLGN--IGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLK---GR--SLKIRF  183 (503)
Q Consensus       111 ~~~~~l~V~n--Lp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~---g~--~l~V~~  183 (503)
                      .++.+|||+|  |++.+|+++|+++|++||+|.+|.|..+|+||||+|.+.++|++||+.|||+.+.   |+  +|.|.+
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~   95 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNF   95 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCTTCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEE
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEEE
Confidence            3567899999  5789999999999999999999999999999999999999999999999999773   44  677777


Q ss_pred             cc
Q psy93           184 AP  185 (503)
Q Consensus       184 a~  185 (503)
                      +.
T Consensus        96 ~~   97 (345)
T 3tht_A           96 VE   97 (345)
T ss_dssp             CS
T ss_pred             ee
Confidence            63

>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=99.25  E-value=7.9e-12  Score=106.65  Aligned_cols=84  Identities=21%  Similarity=0.219  Sum_probs=70.4

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||.|||..+++++|+++|+.||.|..+.+..+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~-g~~~---~g~~l~   98 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVN-GYKL---YGKILV   98 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHST-TCBC---SSCBCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhC-CCEe---CCcEEE
Confidence            35689999999999999999999999999955433222 267889999999999999999999997 5555   689999


Q ss_pred             eecCCcccc
Q psy93           264 VEPLELTDE  272 (503)
Q Consensus       264 V~~~~~~~~  272 (503)
                      |.++.....
T Consensus        99 v~~a~~~~~  107 (115)
T 2cpx_A           99 IEFGKNKKQ  107 (115)
T ss_dssp             EEECCCCSC
T ss_pred             EEEccCCCC
Confidence            999877644

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.24  E-value=2.4e-11  Score=101.26  Aligned_cols=81  Identities=26%  Similarity=0.235  Sum_probs=70.0

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||.|||..+++++|+++|+.|+   .+.++.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~---~g~~l~   85 (102)
T 2fc8_A           13 QPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME-DGEI---DGNKVT   85 (102)
T ss_dssp             CCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHT-TCEE---TTEECE
T ss_pred             CCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhC-CCeE---CCeEEE
Confidence            3568999999999999999999999873   5667777 578899999999999999999999997 6555   689999


Q ss_pred             eecCCcccc
Q psy93           264 VEPLELTDE  272 (503)
Q Consensus       264 V~~~~~~~~  272 (503)
                      |.++.+..+
T Consensus        86 V~~a~~~~~   94 (102)
T 2fc8_A           86 LDWAKPKGE   94 (102)
T ss_dssp             EEECCCCCS
T ss_pred             EEEecCCCC
Confidence            999877654

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.24  E-value=2e-12  Score=107.86  Aligned_cols=81  Identities=19%  Similarity=0.181  Sum_probs=69.5

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +.++|||+|||..+++++|+++|+.||.|.. .++.+ .++.+++||||+|.+.++|.+|+. || +..+   .+++|.|
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~-g~~~---~g~~l~V   89 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LT-GLKV---FGNEIKL   89 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GG-GCCB---TTBCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cC-CcEE---CCcEEEE
Confidence            4678999999999999999999999999988 44444 567889999999999999999998 87 5555   5899999


Q ss_pred             ecCCcccc
Q psy93           265 EPLELTDE  272 (503)
Q Consensus       265 ~~~~~~~~  272 (503)
                      .++.+...
T Consensus        90 ~~a~~~~~   97 (101)
T 1fj7_A           90 EKPKGRDG   97 (101)
T ss_dssp             ECCSCCCC
T ss_pred             EEcCCCCC
Confidence            99876543

>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=99.24  E-value=1e-11  Score=105.26  Aligned_cols=73  Identities=18%  Similarity=0.236  Sum_probs=65.7

Q ss_pred             ccceeccCcccc-cCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSC-VTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~-~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      .++|||.|||.. +++++|+++|+.||.|..|.+       +++||||+|.+.++|.+|+..|+ +..+   .+++|.|.
T Consensus        27 ~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~A~~~l~-g~~~---~g~~l~V~   95 (110)
T 1wf1_A           27 NSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGEN-GRVL---AGQTLDIN   95 (110)
T ss_dssp             SSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-------ETTEEEEECSSSHHHHHHHHHHT-TCEE---TTEECCEE
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-------eCCEEEEEECCHHHHHHHHHHcC-CCEE---CCeEEEEE
Confidence            479999999999 999999999999999999988       37899999999999999999997 6655   68999999


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      ++...
T Consensus        96 ~a~~~  100 (110)
T 1wf1_A           96 MAGEP  100 (110)
T ss_dssp             ESCCC
T ss_pred             ECCCC
Confidence            87644

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.24  E-value=2.1e-11  Score=103.27  Aligned_cols=74  Identities=26%  Similarity=0.351  Sum_probs=67.3

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      +.++|||+|||..+++++|+++|+.||.|..|.++       ++||||+|.+.++|.+|+..|| +..+   .+++|.|.
T Consensus        30 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-------kg~afV~f~~~~~A~~Ai~~l~-g~~~---~g~~l~V~   98 (108)
T 2jvo_A           30 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVH-GKSF---ANQPLEVV   98 (108)
T ss_dssp             SCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHHHHHHHHT-TCEE---TTEECEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHcC-CCEE---CCeEEEEE
Confidence            46899999999999999999999999999999987       6799999999999999999997 6655   68999999


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      ++...
T Consensus        99 ~a~~~  103 (108)
T 2jvo_A           99 YSKLP  103 (108)
T ss_dssp             SCSCC
T ss_pred             EecCC
Confidence            98665

>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=99.23  E-value=1.3e-11  Score=104.18  Aligned_cols=75  Identities=17%  Similarity=0.212  Sum_probs=65.6

Q ss_pred             CCcEEEEcCC--CCCCC--------HHHHHHhhccCCCeEEEEEec--------CCCceEEeeCCHHHHHHHHHHhCCcc
Q psy93           112 NNCRLYLGNI--GGDIT--------ENDIIELFKPYGETQELFINK--------EKMFGFIRMDYKHNADKAKAKLDGHV  173 (503)
Q Consensus       112 ~~~~l~V~nL--p~~~t--------e~~L~~~F~~~G~V~~v~i~~--------~kg~aFV~F~~~e~A~~Ai~~l~g~~  173 (503)
                      +++.|+|.|+  |.++.        +++|++.|++||+|.+|.|++        ++|||||+|.+.++|.+|+..|||..
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            4568999998  43443        468999999999999999974        36999999999999999999999999


Q ss_pred             ccCceEEEEeccc
Q psy93           174 LKGRSLKIRFAPI  186 (503)
Q Consensus       174 l~g~~l~V~~a~~  186 (503)
                      +.|++|+|.+++.
T Consensus        84 f~GR~i~v~~~~~   96 (105)
T 3v4m_A           84 FANRVVVTKYCDP   96 (105)
T ss_dssp             ETTEECEEEEECH
T ss_pred             eCCCEEEEEEeCH
Confidence            9999999998764

>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=99.23  E-value=1.3e-11  Score=101.29  Aligned_cols=79  Identities=14%  Similarity=0.095  Sum_probs=66.8

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCC-eeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGD-IERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~-V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||+|||..+++++|+++|+.||. |..+.+.      +++||||+|.+.++|.+|+..||+...+   .+++|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~~A~~~l~g~~~~---~g~~l~   76 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVEL---HGKIME   76 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEE---TTEECE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHHHHHHHccCCeeE---CCEEEE
Confidence            35679999999999999999999999999 6666553      3789999999999999999999731555   689999


Q ss_pred             eecCCcccc
Q psy93           264 VEPLELTDE  272 (503)
Q Consensus       264 V~~~~~~~~  272 (503)
                      |.++.+...
T Consensus        77 v~~a~~~~~   85 (93)
T 2cqh_A           77 VDYSVSKKL   85 (93)
T ss_dssp             EEECCCCCC
T ss_pred             EEEccCccc
Confidence            999876543

>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=99.23  E-value=2.8e-11  Score=100.45  Aligned_cols=75  Identities=17%  Similarity=0.204  Sum_probs=66.6

Q ss_pred             ccccceeccCccc-ccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTS-CVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~-~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      ++.++|||+|||. .+++++|+++|+.||.|..+.+.       ++||||+|.+.++|.+|+..|| +..+   .++.|.
T Consensus        20 ~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~Ai~~l~-g~~~---~g~~l~   88 (97)
T 2xnq_A           20 HMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXES-QEMN---FGKKLI   88 (97)
T ss_dssp             CTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHT-TSEE---TTEECE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcC-CCEE---CCEEEE
Confidence            4578999999998 99999999999999999999883       6899999999999999999997 5555   589999


Q ss_pred             eecCCcc
Q psy93           264 VEPLELT  270 (503)
Q Consensus       264 V~~~~~~  270 (503)
                      |.++...
T Consensus        89 V~~a~~~   95 (97)
T 2xnq_A           89 LEVSSSN   95 (97)
T ss_dssp             EEECCCC
T ss_pred             EEecCCC
Confidence            9887543

>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=99.23  E-value=1.2e-11  Score=109.95  Aligned_cols=84  Identities=25%  Similarity=0.349  Sum_probs=71.3

Q ss_pred             cccccceeccCcccccCHHHHHHHhccCCCeeee------EEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecC
Q psy93           184 APINAAIKVKNLTSCVTNELLELAFGVFGDIERA------IVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQ  257 (503)
Q Consensus       184 a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~------~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~  257 (503)
                      ..++++|||+|||..+++++|+++|+.||.|..+      .+....++.+++||||+|.+.++|.+|+..|| +..+   
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~ln-g~~~---  117 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEAN-GYVL---  117 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHT-TBEE---
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhC-CCEe---
Confidence            3567899999999999999999999999999875      22222467889999999999999999999997 6666   


Q ss_pred             CCCeEEeecCCccc
Q psy93           258 SLRPVIVEPLELTD  271 (503)
Q Consensus       258 ~~rpl~V~~~~~~~  271 (503)
                      .+++|.|.++....
T Consensus       118 ~g~~l~V~~a~~~~  131 (143)
T 3egn_A          118 FGKPMVVQFARSAR  131 (143)
T ss_dssp             TTEECEEEECCCSC
T ss_pred             CCcEEEEEECCCCC
Confidence            68999999986543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.22  E-value=7e-12  Score=104.68  Aligned_cols=79  Identities=16%  Similarity=0.255  Sum_probs=70.1

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      +.++|||+|||..+++++|+++|+.||.|..|.++.+.++.+++||||+|.+.++|.+|+.  + +..+   .++.+.|.
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~-~~~~---~g~~l~v~   81 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--S-QINF---HGKKLKLG   81 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--C-CCEE---TTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--C-CCeE---CCEEEEEE
Confidence            3578999999999999999999999999999999999888999999999999999999998  3 5555   67888887


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      ++...
T Consensus        82 ~a~~~   86 (102)
T 2xs2_A           82 PAIRK   86 (102)
T ss_dssp             EEEEC
T ss_pred             ECCcC
Confidence            76544

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.22  E-value=1.8e-11  Score=104.68  Aligned_cols=63  Identities=13%  Similarity=0.144  Sum_probs=57.0

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-C---CCceeEEEEEeCCHHHHHHHHHHhh
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-R---GNSKCEGIVEFARKPAAAQALRRCA  249 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-~---g~skg~gfV~F~s~e~A~kAl~~ln  249 (503)
                      ..++|||+|||..+++++|+++|++||.|. +.++.+. +   +.+++||||+|.+.++|.+|+..|+
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~   73 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL   73 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh
Confidence            467899999999999999999999999999 7777663 3   6899999999999999999999983

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.22  E-value=4.5e-11  Score=99.21  Aligned_cols=77  Identities=23%  Similarity=0.352  Sum_probs=67.9

Q ss_pred             ccccceeccCcccccCHHHHHHHhccC--CCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVF--GDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPV  262 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~--G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl  262 (503)
                      .+.++|||+|||..+++++|+++|+.|  |.|..+.+.       ++||||+|.+.++|.+|+..|| +..+   .+++|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-------~g~afV~f~~~~~A~~A~~~l~-g~~~---~g~~l   81 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-------RDYAFVHFSNREDAVEAMKALN-GKVL---DGSPI   81 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHS-SEEE---TTEEE
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-------CCeEEEEeCCHHHHHHHHHHhC-CCEe---CCcEE
Confidence            356899999999999999999999999  999988775       5699999999999999999997 6666   68999


Q ss_pred             EeecCCcccc
Q psy93           263 IVEPLELTDE  272 (503)
Q Consensus       263 ~V~~~~~~~~  272 (503)
                      .|.++.+...
T Consensus        82 ~v~~a~~~~~   91 (99)
T 2cpd_A           82 EVTLAKPVDK   91 (99)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEECCCCCC
Confidence            9999876543

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.21  E-value=4.1e-12  Score=99.73  Aligned_cols=73  Identities=16%  Similarity=0.236  Sum_probs=64.2

Q ss_pred             ceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       189 ~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      +|||+|||..+++++|+++|+.||.|..+.++.+ .++.+++||||+|.+.++|.+|+.. + +..+   .++.+.|.+
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~-~~~~---~g~~l~v~~   74 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-K-YHNV---GLSKCEIKV   74 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-S-SCCB---TTBCCCEEE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-C-CCeE---CCEEEEEEE
Confidence            5899999999999999999999999999999888 5688999999999999999999985 3 4444   577777765

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.21  E-value=1.5e-11  Score=101.72  Aligned_cols=76  Identities=18%  Similarity=0.205  Sum_probs=65.7

Q ss_pred             cccccceeccCccc-ccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeE
Q psy93           184 APINAAIKVKNLTS-CVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPV  262 (503)
Q Consensus       184 a~~~~~L~V~nLp~-~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl  262 (503)
                      .++.++|||+|||. .+++++|+++|+.||.|..|.+.       ++||||+|.+.++|.+|+..|| +..+   .+++|
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~A~~~l~-g~~~---~g~~l   75 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECES-QEMN---FGKKL   75 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-------TTEEEEEESCHHHHHHHHHHHT-CSSC---BTTTB
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcC-CCee---CCcEE
Confidence            35678999999998 99999999999999999999884       6799999999999999999997 5544   48888


Q ss_pred             EeecCCcc
Q psy93           263 IVEPLELT  270 (503)
Q Consensus       263 ~V~~~~~~  270 (503)
                      .|.++...
T Consensus        76 ~V~~a~~~   83 (96)
T 2kvi_A           76 ILEVSSSN   83 (96)
T ss_dssp             CEEEEECC
T ss_pred             EEEEcCcC
Confidence            88887554

>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=99.21  E-value=1.1e-10  Score=114.20  Aligned_cols=104  Identities=16%  Similarity=0.215  Sum_probs=86.9

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      +.++|||+|||.++|+++|+++|+.||.|..|.+.++     ++||||+|.+.++|.+|+..|| +..+   .+++|.|.
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~A~~A~~~l~-g~~i---~g~~l~v~   91 (261)
T 3sde_A           21 QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELD-GTIL---KSRPLRIR   91 (261)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHT-TCEE---TTEECEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CcEEEEEECCHHHHHHHHHHcC-CcEE---CCceeEee
Confidence            3578999999999999999999999999999999755     7899999999999999999997 6666   68999999


Q ss_pred             cCCccccccCCcccccCCCCchhhhhhccCcccCCCCCcc
Q psy93           266 PLELTDEIDGLSERTINKKTPEFYKQRQVGPRFATVNSFE  305 (503)
Q Consensus       266 ~~~~~~~~~~~~~k~i~k~~~~~~kere~~~rf~~~g~~e  305 (503)
                      ++.+.       ..+++.+++...++..+...|..+|.+.
T Consensus        92 ~a~~~-------~~l~v~nl~~~~t~~~l~~~F~~~G~i~  124 (261)
T 3sde_A           92 FATHG-------AALTVKNLSPVVSNELLEQAFSQFGPVE  124 (261)
T ss_dssp             ECCCS-------SEEEEESCCTTCCHHHHHHHHGGGSCEE
T ss_pred             ecccC-------CcccccCCCCCCCHHHHHHHHHhcCCeE
Confidence            87643       3455666776667777777777777664

>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=99.21  E-value=3.3e-11  Score=97.92  Aligned_cols=75  Identities=19%  Similarity=0.145  Sum_probs=67.0

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ..++|||+|||..+++++|+++|++| .|..+.+.     .+++||||+|.+.++|.+|+..|| +..+   .++++.|.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~~Ai~~l~-g~~~---~g~~l~V~   73 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFH-QYSF---RGKDLIVQ   73 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHT-TEEE---TTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHHHHHHHhC-CCeE---CCcEEEEE
Confidence            45789999999999999999999999 99999884     568999999999999999999997 6666   68999999


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      ++...
T Consensus        74 ~a~~~   78 (88)
T 1wg1_A           74 LQPTD   78 (88)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            87553

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=98.84  E-value=1.4e-12  Score=111.80  Aligned_cols=84  Identities=30%  Similarity=0.284  Sum_probs=74.1

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeee--------eEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeee
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIER--------AIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFL  255 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~--------~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~  255 (503)
                      .+.++|||+|||..+++++|+++|+.||.|..        |.|+.+ .++.+++||||+|.+.++|.+|+..|| +..+ 
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~-g~~~-   82 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFD-GKEF-   82 (116)
Confidence            35678999999999999999999999999998        888888 578899999999999999999999997 5555 


Q ss_pred             cCCCCeEEeecCCcccc
Q psy93           256 TQSLRPVIVEPLELTDE  272 (503)
Q Consensus       256 ~~~~rpl~V~~~~~~~~  272 (503)
                        .+++|.|.++.....
T Consensus        83 --~g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           83 --SGNPIKVSFATRRAD   97 (116)
Confidence              588999999876543

>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=99.20  E-value=7e-12  Score=109.31  Aligned_cols=78  Identities=22%  Similarity=0.207  Sum_probs=67.7

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCee--eeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIE--RAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~--~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      ..++|||+|||.++|+++|+++|+.| .|.  .|.|+.|.+++++|||||+|.+.++|.+||.. + +..+   .+++|.
T Consensus        41 ~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~-~~~l---~gR~I~  114 (126)
T 2hgm_A           41 NDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-H-KERI---GHRYIE  114 (126)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-T-TCCB---TTBCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-C-CCEE---CCEEEE
Confidence            46789999999999999999999999 676  89999997899999999999999999999985 4 4544   688888


Q ss_pred             eecCCc
Q psy93           264 VEPLEL  269 (503)
Q Consensus       264 V~~~~~  269 (503)
                      |.++..
T Consensus       115 V~~a~~  120 (126)
T 2hgm_A          115 VFKSSQ  120 (126)
T ss_dssp             CEEECH
T ss_pred             EEECCH
Confidence            877644

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.20  E-value=7.3e-11  Score=97.60  Aligned_cols=76  Identities=20%  Similarity=0.148  Sum_probs=66.7

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      +.++|||.||  .+++++|+++|+.||.|..|.|.     .+++||||+|.+.++|.+|+..|| +..+   .+++|.|.
T Consensus        14 ~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~-----~~~g~afV~f~~~~~a~~Ai~~l~-g~~~---~g~~l~v~   82 (97)
T 1x5p_A           14 KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD-----PPRNCAFVTYEKMESADQAVAELN-GTQV---ESVQLKVN   82 (97)
T ss_dssp             CCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE-----TTTTEEEEEESSHHHHHHHHHHTT-TEEE---TTEEEEEE
T ss_pred             CCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec-----CCCCEEEEEECCHHHHHHHHHHhC-CCeE---CCeEEEEE
Confidence            4678999996  89999999999999999999885     348899999999999999999997 6666   68999999


Q ss_pred             cCCcccc
Q psy93           266 PLELTDE  272 (503)
Q Consensus       266 ~~~~~~~  272 (503)
                      ++.....
T Consensus        83 ~a~~~~~   89 (97)
T 1x5p_A           83 IARKQPM   89 (97)
T ss_dssp             CCSSCCC
T ss_pred             ECCCCCC
Confidence            9876543

>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=99.20  E-value=3.9e-11  Score=97.95  Aligned_cols=78  Identities=17%  Similarity=0.114  Sum_probs=61.8

Q ss_pred             cccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           184 APINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       184 a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      ..+.++|||+|||.++|+++|+++|++||.|.+|.|+.+    ++|||||+|.+.++|.+    ++...+  ...++.|.
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~~----~~~~~~--~~~g~~v~   77 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQS----LCGEDL--IIKGISVH   77 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHHH----HTTCEE--EETTEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHHH----HcCCCc--ccCCEEEE
Confidence            346789999999999999999999999999999999875    68999999999999983    443322  23688899


Q ss_pred             eecCCccc
Q psy93           264 VEPLELTD  271 (503)
Q Consensus       264 V~~~~~~~  271 (503)
                      |.++.+..
T Consensus        78 v~~a~~k~   85 (89)
T 3d2w_A           78 ISNAEPKH   85 (89)
T ss_dssp             EEECC---
T ss_pred             EEEcCCCC
Confidence            98887654

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.19  E-value=4.8e-11  Score=98.10  Aligned_cols=77  Identities=21%  Similarity=0.204  Sum_probs=64.2

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ...+|||+|||..+++++|+++|+.||.|..| +....++.   ||||+|.+.++|.+|+. || +..+   .+++|.|.
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v-~~~~~~g~---~afV~f~~~~~a~~ai~-l~-g~~~---~g~~l~V~   77 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV-VMDKDKGV---FAIVEMGDVGAREAVLS-QS-QHSL---GGHRLRVR   77 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE-EECSSSCC---EEEEEESSHHHHHHHHT-CS-CCEE---TTEECCCB
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE-EEcCCCCc---EEEEEECCHHHHHHHHh-cC-CeEE---CCEEEEEE
Confidence            45689999999999999999999999999987 33223443   99999999999999999 86 6666   68999998


Q ss_pred             cCCccc
Q psy93           266 PLELTD  271 (503)
Q Consensus       266 ~~~~~~  271 (503)
                      ++....
T Consensus        78 ~a~~~~   83 (94)
T 2e5g_A           78 PREQKE   83 (94)
T ss_dssp             CSCCSC
T ss_pred             ECCcCC
Confidence            775543

>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=99.19  E-value=2.9e-11  Score=104.17  Aligned_cols=75  Identities=21%  Similarity=0.316  Sum_probs=65.1

Q ss_pred             CCcEEEEcCCC--CCC---CHHHHHHhhccCCCeEEEEEecC----------CCceEEeeCCHHHHHHHHHHhCCccccC
Q psy93           112 NNCRLYLGNIG--GDI---TENDIIELFKPYGETQELFINKE----------KMFGFIRMDYKHNADKAKAKLDGHVLKG  176 (503)
Q Consensus       112 ~~~~l~V~nLp--~~~---te~~L~~~F~~~G~V~~v~i~~~----------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g  176 (503)
                      ++++|+|.|+-  .++   .+++|++.|++||+|.+|.|+++          +||+||+|.+.++|.+|+..|||..+.|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            35689999993  222   37899999999999999999743          3899999999999999999999999999


Q ss_pred             ceEEEEeccc
Q psy93           177 RSLKIRFAPI  186 (503)
Q Consensus       177 ~~l~V~~a~~  186 (503)
                      ++|.|.+++.
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999998764

>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=99.19  E-value=2.4e-11  Score=104.11  Aligned_cols=65  Identities=26%  Similarity=0.262  Sum_probs=58.1

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCe
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRP  261 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rp  261 (503)
                      .++|||.|||..+++++|+++|++||.|..|.|+.+      +||||+|.+.++|.+||..|| +..+   .++.
T Consensus        16 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~-g~~~---~gr~   80 (115)
T 3beg_B           16 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLD-NTKF---RSHE   80 (115)
T ss_dssp             -CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHT-TCBC---CCTT
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHHHHHHHhC-CCEE---CCcE
Confidence            578999999999999999999999999999999765      799999999999999999997 5555   4555

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.19  E-value=4e-11  Score=98.78  Aligned_cols=79  Identities=19%  Similarity=0.187  Sum_probs=67.9

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeee-EEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERA-IVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~-~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ..++|||+|||..+++++|+++|+.||.|..| .|+.+..   .+.|||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~---~~~afV~f~~~~~a~~Ai~~l~-g~~~---~g~~l~V   86 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNVTYSSKDQARQALDKLN-GFQL---ENFTLKV   86 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSS---SEEEEEEESSHHHHHHHHHHHT-TCBC---SSCBCEE
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCC---CCEEEEEECCHHHHHHHHHHhC-CCEE---CCcEEEE
Confidence            46889999999999999999999999999999 4777632   3349999999999999999997 5555   5899999


Q ss_pred             ecCCccc
Q psy93           265 EPLELTD  271 (503)
Q Consensus       265 ~~~~~~~  271 (503)
                      .++.+.+
T Consensus        87 ~~a~~~~   93 (96)
T 2e44_A           87 AYIPDEM   93 (96)
T ss_dssp             EECCCCC
T ss_pred             EEcCccc
Confidence            9987663

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.17  E-value=1.2e-10  Score=97.39  Aligned_cols=73  Identities=22%  Similarity=0.279  Sum_probs=61.6

Q ss_pred             CcEEEEcCCC-------CCCCHHHHHHhhccCCCeEEEEEe-cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           113 NCRLYLGNIG-------GDITENDIIELFKPYGETQELFIN-KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       113 ~~~l~V~nLp-------~~~te~~L~~~F~~~G~V~~v~i~-~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ..+|.|.-.+       .++++++|+++|++||.|..|.|+ +++|||||+|.+.++|.+||..+++  +.+++|+|.|+
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a   87 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWL   87 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECS
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEc
Confidence            3456666544       468999999999999999999997 5689999999999999999997544  67999999998


Q ss_pred             ccc
Q psy93           185 PIN  187 (503)
Q Consensus       185 ~~~  187 (503)
                      .+.
T Consensus        88 ~~~   90 (100)
T 2d9o_A           88 EGQ   90 (100)
T ss_dssp             SCC
T ss_pred             cCC
Confidence            654

>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=99.17  E-value=5.8e-12  Score=106.17  Aligned_cols=68  Identities=16%  Similarity=0.411  Sum_probs=59.8

Q ss_pred             EcCCCCCCCHHHHHHhh------------ccCCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccccCceEE
Q psy93           118 LGNIGGDITENDIIELF------------KPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLK  180 (503)
Q Consensus       118 V~nLp~~~te~~L~~~F------------~~~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~  180 (503)
                      +.+||..+++++|.++|            ++||+|.+|.|+++     +|||||+|.+.++|.+|+..|||..+.|++|.
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            56777777887777666            99999999999754     78999999999999999999999999999999


Q ss_pred             EEecc
Q psy93           181 IRFAP  185 (503)
Q Consensus       181 V~~a~  185 (503)
                      |.|++
T Consensus       100 v~~sp  104 (104)
T 1jmt_A          100 AELSP  104 (104)
T ss_dssp             EEECC
T ss_pred             EEEcC
Confidence            99874

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.16  E-value=1.1e-10  Score=98.53  Aligned_cols=82  Identities=15%  Similarity=0.167  Sum_probs=69.5

Q ss_pred             ccccceeccCccc-----ccCHHHHHHHhccCCCeeeeEEEeCC--CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecC
Q psy93           185 PINAAIKVKNLTS-----CVTNELLELAFGVFGDIERAIVIVDE--RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQ  257 (503)
Q Consensus       185 ~~~~~L~V~nLp~-----~~tee~L~~~Fs~~G~V~~~~v~~d~--~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~  257 (503)
                      .++++|+|.||..     +.++++|+++|++||.|.+|.|+.++  ++.++||+||+|.+.++|.+|+..|| +..+   
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~ln-G~~~---   81 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLN-GRYF---   81 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHT-TCEE---
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHC-CCEE---
Confidence            4577899999863     23679999999999999999999874  36789999999999999999999997 6666   


Q ss_pred             CCCeEEeecCCcc
Q psy93           258 SLRPVIVEPLELT  270 (503)
Q Consensus       258 ~~rpl~V~~~~~~  270 (503)
                      .+|+|.|.++...
T Consensus        82 ~Gr~i~v~~a~~~   94 (105)
T 2pe8_A           82 GGRVVKACFYNLD   94 (105)
T ss_dssp             TTEECEEEECCHH
T ss_pred             CCcEEEEEEcCHH
Confidence            6999999998653

>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=99.15  E-value=7.8e-11  Score=106.88  Aligned_cols=79  Identities=22%  Similarity=0.280  Sum_probs=67.2

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecC
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPL  267 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~  267 (503)
                      .+|||.||+..+++++|+++|++||.|.+|.|+.+.   +++||||+|.+.++|.+|+..|| +..+. ...++|.|.++
T Consensus        47 l~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~---~rgfAFVeF~d~~~A~~Ai~~Ln-G~~i~-g~g~~L~V~~A  121 (164)
T 1sjr_A           47 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLD-GQNIY-NACCTLRIDFS  121 (164)
T ss_dssp             EEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS---SCEEEEEEESCHHHHHHHHHHST-TBCSS-SSCSCEEEEEC
T ss_pred             EEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC---CCCEEEEEECCHHHHHHHHHHhC-CCEec-CCCcEEEEEEe
Confidence            457899999999999999999999999999987652   47899999999999999999998 55542 12488999998


Q ss_pred             Cccc
Q psy93           268 ELTD  271 (503)
Q Consensus       268 ~~~~  271 (503)
                      ....
T Consensus       122 k~~~  125 (164)
T 1sjr_A          122 KLTS  125 (164)
T ss_dssp             SSSS
T ss_pred             cCCc
Confidence            7653

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.14  E-value=5.5e-11  Score=102.76  Aligned_cols=75  Identities=20%  Similarity=0.220  Sum_probs=64.8

Q ss_pred             cceeccCc----ccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCC----HHH----HHHHHH--HhhCCe
Q psy93           188 AAIKVKNL----TSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFAR----KPA----AAQALR--RCAEGC  252 (503)
Q Consensus       188 ~~L~V~nL----p~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s----~e~----A~kAl~--~ln~g~  252 (503)
                      +.|||.||    |+.+++.+|+++|+.||+|.+|.++.| .|+.++|||||+|.+    +.+    |.+|+.  .+| ++
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~ln-g~   81 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESS-GC   81 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTT-CE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhc-CC
Confidence            68999999    999999999999999999999999999 588999999999996    322    788888  454 77


Q ss_pred             eeecCCCCeEEeec
Q psy93           253 FFLTQSLRPVIVEP  266 (503)
Q Consensus       253 ~~~~~~~rpl~V~~  266 (503)
                      .+   .++++.|..
T Consensus        82 ~I---~Gr~irV~l   92 (136)
T 2j8a_A           82 FI---MGFKFEVIL   92 (136)
T ss_dssp             EE---TTEEEEEEE
T ss_pred             ee---cCcEEEEEE
Confidence            77   799999874

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.13  E-value=1.9e-10  Score=100.53  Aligned_cols=77  Identities=22%  Similarity=0.246  Sum_probs=65.0

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeE-EEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCE-GIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~-gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      -.|||.||+..+|+++|+++|++||.|.+|.++.+.    ++| |||+|.+.++|.+|+..|| +..+.. ..++|.|.+
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~----~gfqAFVef~~~~~A~~Ai~~Ln-G~~i~g-~~~~LrI~~  102 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLD-GQNIYN-ACCTLRIDF  102 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHT-TCEEET-TEEEEEEEE
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC----CCcEEEEEECCHHHHHHHHHHcC-CCeecC-CCcEEEEEe
Confidence            356799999999999999999999999999887642    577 9999999999999999998 554422 237899998


Q ss_pred             CCcc
Q psy93           267 LELT  270 (503)
Q Consensus       267 ~~~~  270 (503)
                      +++.
T Consensus       103 ak~~  106 (130)
T 3zzy_A          103 SKLT  106 (130)
T ss_dssp             CSCS
T ss_pred             cCCC
Confidence            8765

>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=99.13  E-value=7.1e-11  Score=95.29  Aligned_cols=72  Identities=19%  Similarity=0.209  Sum_probs=63.5

Q ss_pred             ccccceeccCcccccCHHHHHHHhccC----C-------CeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCee
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVF----G-------DIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCF  253 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~----G-------~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~  253 (503)
                      .+.++|||+|||..+++++|+++|+.|    |       .|.++.+..+     ++||||+|.+.++|.+|+ .|| +..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-----kg~afV~f~~~~~a~~A~-~l~-g~~   76 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAM-AFD-GII   76 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-----SSEEEEEESSHHHHHHHG-GGT-TCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-----CcEEEEEcCCHHHHHHHH-hcC-CCE
Confidence            456899999999999999999999999    8       8999988765     889999999999999999 887 666


Q ss_pred             eecCCCCeEEeec
Q psy93           254 FLTQSLRPVIVEP  266 (503)
Q Consensus       254 ~~~~~~rpl~V~~  266 (503)
                      +   .++++.|+.
T Consensus        77 ~---~g~~l~V~r   86 (87)
T 2hzc_A           77 F---QGQSLKIRR   86 (87)
T ss_dssp             E---TTEECEEEC
T ss_pred             E---CCeEEEEeC
Confidence            5   688887763

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.12  E-value=1.9e-10  Score=99.91  Aligned_cols=75  Identities=17%  Similarity=0.191  Sum_probs=63.1

Q ss_pred             ceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeE-EEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecC
Q psy93           189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCE-GIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPL  267 (503)
Q Consensus       189 ~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~-gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~  267 (503)
                      .|||.||+..+++++|+++|++||.|.+|.|+..     .|| |||+|.+.++|.+|+..|| +..+.. ..++|.|.++
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-----~Gf~aFVef~~~~~A~~A~~~Ln-G~~i~g-~~~~l~V~~A   99 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-----NGIQAMVEFESVLCAQKAKAALN-GADIYA-GCCTLKIEYA   99 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-----SSEEEEEEESSHHHHHHHHHHHT-TCCCBT-TBSEEEEECC
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhC-CCEecC-CCeEEEEEEe
Confidence            3679999999999999999999999999998753     376 9999999999999999998 554421 2368999988


Q ss_pred             Ccc
Q psy93           268 ELT  270 (503)
Q Consensus       268 ~~~  270 (503)
                      .+.
T Consensus       100 k~~  102 (124)
T 2e5i_A          100 RPT  102 (124)
T ss_dssp             SCS
T ss_pred             cCC
Confidence            765

>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=99.11  E-value=5.7e-11  Score=96.36  Aligned_cols=78  Identities=17%  Similarity=0.133  Sum_probs=64.3

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .+.++|||+|||..+++++|+++|+.||.|..|.|+.+    +++||||+|.+.++|.+|    +...+  ...+++|.|
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~~----~~~~~--~~~g~~l~v   72 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSL----CGEDL--IIKGISVHI   72 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHT----TTCEE--EETTEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC----CCCEEEEEECCHHHHHHH----hcCCc--eeCCEEEEE
Confidence            35689999999999999999999999999999998865    588999999999999754    32322  236788999


Q ss_pred             ecCCcccc
Q psy93           265 EPLELTDE  272 (503)
Q Consensus       265 ~~~~~~~~  272 (503)
                      .++.+...
T Consensus        73 ~~a~~~~~   80 (88)
T 1wf0_A           73 SNAEPKHN   80 (88)
T ss_dssp             ECCCCCCC
T ss_pred             EecCCCCC
Confidence            98876644

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.10  E-value=3.3e-10  Score=97.51  Aligned_cols=78  Identities=15%  Similarity=0.144  Sum_probs=70.1

Q ss_pred             ccCcCCCcEEEEcCCCCC-CCHHHHHHhhccCCCeEEEEEecCCCceEEeeCC-HHHHHHHHHHhC--CccccCceEEEE
Q psy93           107 DIKFANNCRLYLGNIGGD-ITENDIIELFKPYGETQELFINKEKMFGFIRMDY-KHNADKAKAKLD--GHVLKGRSLKIR  182 (503)
Q Consensus       107 ~~~~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~-~e~A~~Ai~~l~--g~~l~g~~l~V~  182 (503)
                      ...+...+.|||+||+.+ ++.++|+++|+.||+|..|.+.+....|||.|.+ ..+|..|+..||  +..|.+..++++
T Consensus        12 ~~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~e   91 (121)
T 1owx_A           12 SLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   91 (121)
T ss_dssp             CCSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             cccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEE
Confidence            345567889999999999 9999999999999999999999998899999999 899999999995  678889888887


Q ss_pred             ec
Q psy93           183 FA  184 (503)
Q Consensus       183 ~a  184 (503)
                      ..
T Consensus        92 vL   93 (121)
T 1owx_A           92 VL   93 (121)
T ss_dssp             EC
T ss_pred             EC
Confidence            54

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.10  E-value=2.8e-10  Score=97.43  Aligned_cols=75  Identities=17%  Similarity=0.275  Sum_probs=64.6

Q ss_pred             CCcEEEEcCCC--CCC--------CHHHHHHhhccCCCeEEEEEecC--CCceEEeeCCHHHHHHHHHHhCCccccCceE
Q psy93           112 NNCRLYLGNIG--GDI--------TENDIIELFKPYGETQELFINKE--KMFGFIRMDYKHNADKAKAKLDGHVLKGRSL  179 (503)
Q Consensus       112 ~~~~l~V~nLp--~~~--------te~~L~~~F~~~G~V~~v~i~~~--kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l  179 (503)
                      +++.|.|.|+=  .+.        .+++|++.|++||.|.+|.|.++  +|||||+|.+.++|.+|+..|||..+.|+.|
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i   85 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMI   85 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            45679999983  221        24578999999999999999765  7999999999999999999999999999999


Q ss_pred             EEEeccc
Q psy93           180 KIRFAPI  186 (503)
Q Consensus       180 ~V~~a~~  186 (503)
                      .|.+++.
T Consensus        86 ~v~~~~~   92 (114)
T 3s6e_A           86 TAAYVPL   92 (114)
T ss_dssp             EEEEECH
T ss_pred             EEEEEcH
Confidence            9999853

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.08  E-value=2.3e-10  Score=93.56  Aligned_cols=74  Identities=19%  Similarity=0.141  Sum_probs=61.8

Q ss_pred             cccc-eeccCcccccCHHH----HHHHhccC-CCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCC
Q psy93           186 INAA-IKVKNLTSCVTNEL----LELAFGVF-GDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSL  259 (503)
Q Consensus       186 ~~~~-L~V~nLp~~~tee~----L~~~Fs~~-G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~  259 (503)
                      |..+ |||.|||.++++++    |+++|++| |+|.+|      +   .|+|||.|.+.++|.+|++.|+ +..+   .+
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V------t---gG~AfV~F~~~esA~~A~~~l~-G~~l---~g   73 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI------T---GCSAILRFINQDSAERAQKRME-NEDV---FG   73 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC------C---TTCEEEEESSHHHHHHHHHHHT-TCCS---SS
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE------e---cCEEEEEECCHHHHHHHHHHhc-CCcc---CC
Confidence            3444 89999999999987    55899999 599988      2   2899999999999999999998 5544   49


Q ss_pred             CeEEeecCCcccc
Q psy93           260 RPVIVEPLELTDE  272 (503)
Q Consensus       260 rpl~V~~~~~~~~  272 (503)
                      |++.|.++....+
T Consensus        74 r~i~v~~A~~~sd   86 (96)
T 2diu_A           74 NRIIVSFTPKNRE   86 (96)
T ss_dssp             SCCEEESSCCSCC
T ss_pred             ceEEEEecCCCcc
Confidence            9999999876643

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.05  E-value=2.3e-10  Score=110.36  Aligned_cols=81  Identities=19%  Similarity=0.258  Sum_probs=68.6

Q ss_pred             ccccceeccCccccc---------CHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeee
Q psy93           185 PINAAIKVKNLTSCV---------TNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFL  255 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~---------tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~  255 (503)
                      ...++|||+||+..+         ++++|+++|++||.|.+|.|+.+     ++||||+|.+.++|..|+..|++..+++
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~-----kG~AFV~F~~~~~Ae~A~~am~g~~l~~  206 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES-----KNCGFVKFKYQANAEFAKEAMSNQTLLL  206 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHHHTTCCCCC
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC-----CCEEEEEeCCHHHHHHHHHHhCCCEEec
Confidence            457899999999998         79999999999999999999865     8999999999999999999998555422


Q ss_pred             c--------CCCCeEEeecCCcc
Q psy93           256 T--------QSLRPVIVEPLELT  270 (503)
Q Consensus       256 ~--------~~~rpl~V~~~~~~  270 (503)
                      .        ..+++|.|.|+...
T Consensus       207 ~~~~e~~~~~~gr~L~V~wA~~~  229 (240)
T 3u1l_A          207 PSDKEWDDRREGTGLLVKWANED  229 (240)
T ss_dssp             TTSTTGGGGGGSCCCEEEECC--
T ss_pred             cccccccccCCCCEEEEEEccCC
Confidence            1        15789999998654

>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=99.02  E-value=4e-10  Score=95.01  Aligned_cols=82  Identities=13%  Similarity=0.067  Sum_probs=67.4

Q ss_pred             ccccceeccCc--ccccC--------HHHHHHHhccCCCeeeeEEEeCCC---CCceeEEEEEeCCHHHHHHHHHHhhCC
Q psy93           185 PINAAIKVKNL--TSCVT--------NELLELAFGVFGDIERAIVIVDER---GNSKCEGIVEFARKPAAAQALRRCAEG  251 (503)
Q Consensus       185 ~~~~~L~V~nL--p~~~t--------ee~L~~~Fs~~G~V~~~~v~~d~~---g~skg~gfV~F~s~e~A~kAl~~ln~g  251 (503)
                      .|+++|+|.|+  |..+.        .++|++.|++||.|.+|.|+++..   +.++|++||+|.+.++|.+|+..|| +
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~ln-G   81 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLT-G   81 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHT-T
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhC-C
Confidence            35677888887  33333        378999999999999999988753   3678999999999999999999997 6


Q ss_pred             eeeecCCCCeEEeecCCcc
Q psy93           252 CFFLTQSLRPVIVEPLELT  270 (503)
Q Consensus       252 ~~~~~~~~rpl~V~~~~~~  270 (503)
                      ..+   .+|+|.|.+++..
T Consensus        82 ~~f---~GR~i~v~~~~~~   97 (105)
T 3v4m_A           82 RKF---ANRVVVTKYCDPD   97 (105)
T ss_dssp             CEE---TTEECEEEEECHH
T ss_pred             CEe---CCCEEEEEEeCHH
Confidence            666   7999999887554

>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=99.00  E-value=2.9e-10  Score=95.66  Aligned_cols=72  Identities=19%  Similarity=0.260  Sum_probs=61.6

Q ss_pred             ccCcccccCHHHHHHHh------------ccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCC
Q psy93           192 VKNLTSCVTNELLELAF------------GVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSL  259 (503)
Q Consensus       192 V~nLp~~~tee~L~~~F------------s~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~  259 (503)
                      +.+|+..+++++|.+.|            ++||.|.+|.|+.+.++.++|||||+|.+.++|.+|+..|| +..+   .+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~ln-g~~~---~G   95 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLN-NRWF---NG   95 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHT-TCEE---TT
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHC-CCEE---CC
Confidence            56777777887776666            99999999999998778899999999999999999999997 6666   68


Q ss_pred             CeEEeecC
Q psy93           260 RPVIVEPL  267 (503)
Q Consensus       260 rpl~V~~~  267 (503)
                      ++|.|.++
T Consensus        96 r~i~v~~s  103 (104)
T 1jmt_A           96 QPIHAELS  103 (104)
T ss_dssp             EECCEEEC
T ss_pred             EEEEEEEc
Confidence            99888765

>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=99.00  E-value=1.1e-09  Score=93.03  Aligned_cols=80  Identities=19%  Similarity=0.292  Sum_probs=65.9

Q ss_pred             ccccceeccCccccc-----------CHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCee
Q psy93           185 PINAAIKVKNLTSCV-----------TNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCF  253 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~-----------tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~  253 (503)
                      .++++|+|.||....           ++++|+++|++||.|..|.| .+.  .++|||||+|.+.++|.+|+..|| +..
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~--~~~G~afV~f~~~~~A~~Ai~~ln-g~~   88 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR--HPDGVASVSFRDPEEADYCIQTLD-GRW   88 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT--CTTCEEEEECSCHHHHHHHHHHST-TCE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC--CCCEEEEEEECCHHHHHHHHHHcC-CCE
Confidence            457889999994332           25799999999999999965 543  378999999999999999999997 666


Q ss_pred             eecCCCCeEEeecCCccc
Q psy93           254 FLTQSLRPVIVEPLELTD  271 (503)
Q Consensus       254 ~~~~~~rpl~V~~~~~~~  271 (503)
                      +   .+++|.|.++.+..
T Consensus        89 ~---~gr~l~v~~a~~~~  103 (112)
T 2dit_A           89 F---GGRQITAQAWDGTT  103 (112)
T ss_dssp             E---TTEECEEEECCSCC
T ss_pred             E---CCcEEEEEEeCCCC
Confidence            6   69999999987653

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=98.94  E-value=1.8e-09  Score=92.89  Aligned_cols=82  Identities=18%  Similarity=0.322  Sum_probs=67.7

Q ss_pred             ccccceeccCcc--ccc---CHHHHHHHhccCCCeeeeEEEeCC-----CCCceeEEEEEeCCHHHHHHHHHHhhCCeee
Q psy93           185 PINAAIKVKNLT--SCV---TNELLELAFGVFGDIERAIVIVDE-----RGNSKCEGIVEFARKPAAAQALRRCAEGCFF  254 (503)
Q Consensus       185 ~~~~~L~V~nLp--~~~---tee~L~~~Fs~~G~V~~~~v~~d~-----~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~  254 (503)
                      +++++|+|.|+-  ..+   .+++|++.|++||.|.+|.|+.+.     ++.++|++||+|.+.++|.+|+..|| +.++
T Consensus        18 ~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~Ln-Gr~f   96 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALN-GRWF   96 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHT-TCEE
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHC-CCEE
Confidence            367788888873  222   358899999999999999999873     34678999999999999999999997 6666


Q ss_pred             ecCCCCeEEeecCCcc
Q psy93           255 LTQSLRPVIVEPLELT  270 (503)
Q Consensus       255 ~~~~~rpl~V~~~~~~  270 (503)
                         .+|+|.|.+++..
T Consensus        97 ---~GR~i~v~~~~~~  109 (118)
T 3ue2_A           97 ---AGRKVVAEVYDQE  109 (118)
T ss_dssp             ---TTEECEEEEECHH
T ss_pred             ---CCcEEEEEEcChH
Confidence               7999999987553

>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=109.50  Aligned_cols=80  Identities=13%  Similarity=0.098  Sum_probs=66.2

Q ss_pred             cccccceeccC--cccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCC-
Q psy93           184 APINAAIKVKN--LTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLR-  260 (503)
Q Consensus       184 a~~~~~L~V~n--Lp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~r-  260 (503)
                      +.++.+|||+|  |+..+|+++|+++|++||+|.+|.+..     +++||||+|.+.++|.+|++.|| +..++...++ 
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~~Ai~~ln-G~~~~~~~g~~   88 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLN-GKEVVDDLGQK   88 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHHHHHHHTT-TCEEECTTSCE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhC-CCccccccCCc
Confidence            56788999999  678999999999999999999876653     47999999999999999999998 5555544445 


Q ss_pred             -eEEeecCCc
Q psy93           261 -PVIVEPLEL  269 (503)
Q Consensus       261 -pl~V~~~~~  269 (503)
                       ++.+.+.+.
T Consensus        89 ~~ly~~~~~~   98 (345)
T 3tht_A           89 ITLYLNFVEK   98 (345)
T ss_dssp             EECEEEECSS
T ss_pred             eEEEEEEeec
Confidence             677777643

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.90  E-value=3e-09  Score=86.17  Aligned_cols=71  Identities=14%  Similarity=0.272  Sum_probs=61.3

Q ss_pred             cEEEEcCCCC----CCCH----HHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           114 CRLYLGNIGG----DITE----NDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       114 ~~l~V~nLp~----~~te----~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      .||+|.-+|.    ++-.    .+|.+.|+.||.|..++|+.++  +||+|.+.++|.+||+ |||..+.|+.|+|+++.
T Consensus         8 ~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~lkt   84 (91)
T 2dnr_A            8 GTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--MWVTFLEGSSALNVLS-LNGKELLNRTITIALKS   84 (91)
T ss_dssp             CEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--EEEEESSHHHHHHGGG-GTTCEETTEEEEEEECC
T ss_pred             CeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--EEEEECChHHHHHHHh-cCCeEeCCeEEEEEeCC
Confidence            4788888762    3333    5789999999999999998766  8999999999999998 99999999999999987


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus        85 ~d   86 (91)
T 2dnr_A           85 PS   86 (91)
T ss_dssp             CS
T ss_pred             CC
Confidence            64

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.89  E-value=8.4e-09  Score=86.04  Aligned_cols=82  Identities=18%  Similarity=0.237  Sum_probs=64.5

Q ss_pred             CceEEEEecccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeee
Q psy93           176 GRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFL  255 (503)
Q Consensus       176 g~~l~V~~a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~  255 (503)
                      ...|.|.|.....    ...+..+++++|+++|++||.|..|.|+    +.++|||||+|.+.++|.+|+..++ +    
T Consensus        10 ~~~~~v~w~~~~~----~~~~~~~te~~L~~~F~~~G~V~~v~i~----~~~rGfaFVeF~~~~~A~~Ai~~~~-~----   76 (100)
T 2d9o_A           10 TPKLKLKWKCKKE----DESKGGYSKDVLLRLLQKYGEVLNLVLS----SKKPGTAVVEFATVKAAELAVQNEV-G----   76 (100)
T ss_dssp             SCEEEEECCCCSS----CSCCCSCCHHHHHHHHHTTSCEEEEEEE----SSSSSEEEEEESCHHHHHHHHHTCC-B----
T ss_pred             cceEEEeeeccCc----cCcCCCCCHHHHHHHHHhcCCEEEEEEc----cCCCCEEEEEECCHHHHHHHHHhcC-C----
Confidence            4678888754221    1124679999999999999999999988    3568999999999999999999854 2    


Q ss_pred             cCCCCeEEeecCCccc
Q psy93           256 TQSLRPVIVEPLELTD  271 (503)
Q Consensus       256 ~~~~rpl~V~~~~~~~  271 (503)
                       ..+++|.|.|+....
T Consensus        77 -~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           77 -LVDNPLKISWLEGQP   91 (100)
T ss_dssp             -CSSSBCEEECSSCCC
T ss_pred             -CCCCeEEEEEccCCC
Confidence             258899999976653

>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=98.69  E-value=2.8e-08  Score=84.90  Aligned_cols=79  Identities=13%  Similarity=0.112  Sum_probs=63.3

Q ss_pred             cccceeccCcccc----------cCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeee
Q psy93           186 INAAIKVKNLTSC----------VTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFL  255 (503)
Q Consensus       186 ~~~~L~V~nLp~~----------~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~  255 (503)
                      ++++|.+.|+-..          -.+++|++.|++||.|.+|.|.++.   ++||+||+|.+.++|.+|+..|| +.++ 
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~---~~G~~fV~f~~~e~A~~Ai~~ln-G~~f-   80 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS---AQGNVYVKCPSIAAAIAAVNALH-GRWF-   80 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC---TTCCEEEECSSHHHHHHHHHHHT-TCEE-
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC---CcEEEEEEECCHHHHHHHHHHhC-CCEE-
Confidence            4566777776321          1236889999999999999886652   58999999999999999999997 6666 


Q ss_pred             cCCCCeEEeecCCccc
Q psy93           256 TQSLRPVIVEPLELTD  271 (503)
Q Consensus       256 ~~~~rpl~V~~~~~~~  271 (503)
                        .+|+|.|.++...+
T Consensus        81 --~GR~i~v~~~~~~~   94 (114)
T 3s6e_A           81 --AGKMITAAYVPLPT   94 (114)
T ss_dssp             --TTEECEEEEECHHH
T ss_pred             --CCEEEEEEEEcHHH
Confidence              79999999876553

>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=98.67  E-value=2e-08  Score=81.79  Aligned_cols=69  Identities=20%  Similarity=0.297  Sum_probs=59.8

Q ss_pred             cEEEEcCCCCC-----C-CH---HHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           114 CRLYLGNIGGD-----I-TE---NDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       114 ~~l~V~nLp~~-----~-te---~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      .||+|.-++++     + .+   .+|.+.|+.||.|..++|..++  +||+|.+.++|.+||+ |||..+.|+.|+|++.
T Consensus        16 ~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V~~k   92 (95)
T 1ufw_A           16 ATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--MLVTFADSHSALSVLD-VDGMKVKGRAVKISGP   92 (95)
T ss_dssp             CEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--EEEECSCSHHHHHHHH-GGGSEETTEEEEEECC
T ss_pred             CeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--EEEEEcChHHHHHHHh-cCCeeeCCeEEEEecc
Confidence            47999988743     2 31   4688999999999999999877  9999999999999998 9999999999999865


Q ss_pred             c
Q psy93           185 P  185 (503)
Q Consensus       185 ~  185 (503)
                      .
T Consensus        93 ~   93 (95)
T 1ufw_A           93 S   93 (95)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.66  E-value=4.6e-08  Score=84.07  Aligned_cols=79  Identities=23%  Similarity=0.229  Sum_probs=64.9

Q ss_pred             ccccceeccCcccc-cCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCC-HHHHHHHHHHhhCCeeeecCCCCeE
Q psy93           185 PINAAIKVKNLTSC-VTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFAR-KPAAAQALRRCAEGCFFLTQSLRPV  262 (503)
Q Consensus       185 ~~~~~L~V~nLp~~-~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s-~e~A~kAl~~ln~g~~~~~~~~rpl  262 (503)
                      ++.+.|+|.||+.. ++.++|+++|+.||+|.+|.++.+.     ..|||.|.+ ..+|..|+..+|++...+  ++..+
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~-----~tgfVrf~~~~~~A~~av~~ln~~~~~i--~g~~~   88 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA-----KEGIILFKEKAKEALGKAKDANNGNLQL--RNKEV   88 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC-----SEEEEEESSCHHHHHHHHHHTTTSCBCT--TSSSE
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-----CEEEEEECCChHHHHHHHHHhhcCCcEE--eCcEE
Confidence            35678999999999 9999999999999999999998873     369999999 899999999998665443  44566


Q ss_pred             EeecCCcc
Q psy93           263 IVEPLELT  270 (503)
Q Consensus       263 ~V~~~~~~  270 (503)
                      .++.+.-.
T Consensus        89 ~~evL~Ge   96 (121)
T 1owx_A           89 TWEVLEGE   96 (121)
T ss_dssp             EEEECCHH
T ss_pred             EEEECCCH
Confidence            66655433

>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=98.40  E-value=3.6e-07  Score=86.85  Aligned_cols=62  Identities=18%  Similarity=0.247  Sum_probs=56.5

Q ss_pred             CCHHHHHHhhccCCCeEEEEEe----------cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           125 ITENDIIELFKPYGETQELFIN----------KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       125 ~te~~L~~~F~~~G~V~~v~i~----------~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      -.+++|.+.|++||.|.+|.|+          +.+|++||+|.+.++|.+|+..|||..+.|++|.|.+++.
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            4577899999999999999996          3468999999999999999999999999999999998764

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.30  E-value=1.2e-06  Score=70.96  Aligned_cols=74  Identities=18%  Similarity=0.168  Sum_probs=59.4

Q ss_pred             ccccceeccCccc----ccCH----HHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeec
Q psy93           185 PINAAIKVKNLTS----CVTN----ELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLT  256 (503)
Q Consensus       185 ~~~~~L~V~nLp~----~~te----e~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~  256 (503)
                      +|..+|+|..++.    ...+    .+|.+.|++||.|..++++.+       .+||+|.+.++|.+|+. || +..+  
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d-------~~fVtF~d~~sAlaAi~-mn-G~~v--   73 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED-------KMWVTFLEGSSALNVLS-LN-GKEL--   73 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS-------SEEEEESSHHHHHHGGG-GT-TCEE--
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC-------CEEEEECChHHHHHHHh-cC-CeEe--
Confidence            5566777776652    2333    568999999999999999987       38999999999999998 87 6666  


Q ss_pred             CCCCeEEeecCCcc
Q psy93           257 QSLRPVIVEPLELT  270 (503)
Q Consensus       257 ~~~rpl~V~~~~~~  270 (503)
                       .+|.+.|..+.+.
T Consensus        74 -~Gr~LkV~lkt~d   86 (91)
T 2dnr_A           74 -LNRTITIALKSPS   86 (91)
T ss_dssp             -TTEEEEEEECCCS
T ss_pred             -CCeEEEEEeCCCC
Confidence             7999999887654

>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=98.28  E-value=5.3e-06  Score=78.64  Aligned_cols=107  Identities=15%  Similarity=0.168  Sum_probs=73.7

Q ss_pred             EeeCCHHHHHHHHHHhCCc-cccCceEEEEecccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC-----CCCc
Q psy93           154 IRMDYKHNADKAKAKLDGH-VLKGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE-----RGNS  227 (503)
Q Consensus       154 V~F~~~e~A~~Ai~~l~g~-~l~g~~l~V~~a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~-----~g~s  227 (503)
                      +-+.+.++....|..+-.. ......+.+.      .++.......-.+++|.+.|++||.|.++.|+.+.     ++.+
T Consensus       101 ~G~~~~~~l~~~l~~~l~~~~~~s~v~~l~------n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~  174 (222)
T 3dxb_A          101 VGALSKGQLKEFLDANLAGSAMESTVMVLR------NMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEI  174 (222)
T ss_dssp             ESCCCHHHHHHHHHHHSCCSCCBCSEEEEE------SSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCE
T ss_pred             ccccChHHHHHHHHhhccccccccccchhh------cCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCc
Confidence            3345666666666654332 2222333322      11111222334567899999999999999998652     4488


Q ss_pred             eeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCcc
Q psy93           228 KCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLELT  270 (503)
Q Consensus       228 kg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~~  270 (503)
                      +|++||+|.+.++|.+|+..|| +.++   .+|+|.+..++..
T Consensus       175 ~G~~fv~f~~~~~a~~a~~~l~-gr~~---~gr~i~~~~~~~~  213 (222)
T 3dxb_A          175 IVKIFVEFSIASETHKAIQALN-GRWF---AGRKVVAEVYDQE  213 (222)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHT-TCBS---SSSBCEEEECCHH
T ss_pred             eeEEEEEECCHHHHHHHHHHhc-CceE---CCeEEEEEEcCHH
Confidence            9999999999999999999998 6666   7999999987643

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.20  E-value=4.4e-06  Score=69.38  Aligned_cols=70  Identities=11%  Similarity=0.172  Sum_probs=66.2

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccC-----CCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEE
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPY-----GETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIR  182 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~-----G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~  182 (503)
                      .++|-+-|||..++...|+.|+.+|     |.|+.|.+..+-+-|+|+|.+..+|-+|.-.|+|.+|.|++|+|.
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~g   95 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSG   95 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCCceEEEEccchhhHHHHhhcCCeeecCeEEEec
Confidence            4578899999999999999999999     999999999999999999999999999998999999999999985

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.19  E-value=1.2e-05  Score=66.12  Aligned_cols=86  Identities=16%  Similarity=0.211  Sum_probs=73.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccC-----CCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPY-----GETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~-----G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ..++|.|.|||+.++++.|.-+|+.-     |+|.+|....  +-|+|+|.+...|++.++. ....|++.+|.|....+
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P~~~   83 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--CGGVLTFREPADAERVLAQ-ADHELHGAQLSLRPAPP   83 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEECCC
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--CcEEEEEcChHHHHHHhcC-CcceecCeEEEEEcCCC
Confidence            35689999999999999999999872     5999998876  7899999999999999863 46788999999976654


Q ss_pred             --ccceeccCcccccC
Q psy93           187 --NAAIKVKNLTSCVT  200 (503)
Q Consensus       187 --~~~L~V~nLp~~~t  200 (503)
                        ..+|++.+|++.++
T Consensus        84 ~~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           84 RAPARLLLQGLPPGTS   99 (104)
T ss_dssp             CCCCCCCCCSCCCCCC
T ss_pred             CCcceEeeecCCCCCC
Confidence              67899999998765

>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=98.08  E-value=4.2e-06  Score=68.08  Aligned_cols=73  Identities=21%  Similarity=0.230  Sum_probs=59.2

Q ss_pred             cccccceeccCcccc-----cCH----HHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeee
Q psy93           184 APINAAIKVKNLTSC-----VTN----ELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFF  254 (503)
Q Consensus       184 a~~~~~L~V~nLp~~-----~te----e~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~  254 (503)
                      -+|..+|+|..+++.     ..+    .+|.+.|+.||.|..++++.|       -+||+|.+.++|.+||. || +..+
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d-------~~fVtF~d~~sAl~AI~-ld-G~~v   82 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG-------QMLVTFADSHSALSVLD-VD-GMKV   82 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT-------EEEEECSCSHHHHHHHH-GG-GSEE
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC-------cEEEEEcChHHHHHHHh-cC-Ceee
Confidence            367788888877632     222    568899999999999999988       39999999999999998 87 6666


Q ss_pred             ecCCCCeEEeecCC
Q psy93           255 LTQSLRPVIVEPLE  268 (503)
Q Consensus       255 ~~~~~rpl~V~~~~  268 (503)
                         .+|.+.|....
T Consensus        83 ---~Gr~L~V~~k~   93 (95)
T 1ufw_A           83 ---KGRAVKISGPS   93 (95)
T ss_dssp             ---TTEEEEEECCC
T ss_pred             ---CCeEEEEeccC
Confidence               69999998754

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.75  E-value=3.4e-05  Score=63.82  Aligned_cols=74  Identities=19%  Similarity=0.236  Sum_probs=65.8

Q ss_pred             CcEEEEcCCCCCC-C----HHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           113 NCRLYLGNIGGDI-T----ENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       113 ~~~l~V~nLp~~~-t----e~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      .++|+|.||+.+| +    .+.++++|..|+++......++=.-..|.|.++++|.+|...||+..+.|+.|+|-++.+
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~   83 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcceEEEEEeCChHHHHHHHHHhccceecCceeEEEecCC
Confidence            3679999998765 2    257799999999999999888877789999999999999999999999999999999874

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.22  E-value=0.00081  Score=55.88  Aligned_cols=71  Identities=20%  Similarity=0.170  Sum_probs=61.9

Q ss_pred             ccceeccCcccccCHHHHHHHhccC-----CCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCe
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVF-----GDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRP  261 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~-----G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rp  261 (503)
                      .++|-+-|||+.+++..|+.++..+     |.|..+.+..|     .+=|+|+|.+...|-+|.-.|+ +..+   .++.
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD-----H~GAivef~d~~~AgKasLaL~-G~ef---~gr~   91 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD-----FNGAIIIFRDSKFAAKMLMILN-GSQF---QGKV   91 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT-----TTEEEEECSCHHHHHHHHHHHS-SEEE---TTEE
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC-----CCceEEEEccchhhHHHHhhcC-Ceee---cCeE
Confidence            5678888999999999999999999     99999999988     4569999999999999999997 7777   4777


Q ss_pred             EEeec
Q psy93           262 VIVEP  266 (503)
Q Consensus       262 l~V~~  266 (503)
                      +.|-.
T Consensus        92 Lr~gT   96 (117)
T 2l9w_A           92 IRSGT   96 (117)
T ss_dssp             EEEEC
T ss_pred             EEecC
Confidence            77643

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.13  E-value=0.0013  Score=53.32  Aligned_cols=63  Identities=13%  Similarity=0.230  Sum_probs=53.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC--------CCceEEeeCCHHHHHHHHHHhCCccccC
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKE--------KMFGFIRMDYKHNADKAKAKLDGHVLKG  176 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~--------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g  176 (503)
                      ++|.|.+||+.+|++++.+.++.+..+........        -.-|||.|.+.+++....+.++|..+.+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D   72 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEc
Confidence            57999999999999999999999988776665432        2469999999999999999999997653

>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=96.93  E-value=0.0025  Score=51.81  Aligned_cols=54  Identities=17%  Similarity=0.300  Sum_probs=44.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhC
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLD  170 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~  170 (503)
                      ..++| ++|+.+...||.++|+.||.|.--.|  +-..|||.|.+++.|..|+..+.
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fggv~I~Wi--dDTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGNIQISWI--DDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCSCCCEEE--ETTEEEEECSCHHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCCEEEEEE--cCCeEEEEecCHHHHHHHHHhcc
Confidence            45666 99999999999999999996543334  35689999999999999998753

>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=96.85  E-value=0.0032  Score=53.37  Aligned_cols=71  Identities=17%  Similarity=0.215  Sum_probs=59.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccC-ceEEEEec
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKG-RSLKIRFA  184 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g-~~l~V~~a  184 (503)
                      ..+.|.|-+.|+.. ...|...|++||.|.+........+-.|.|.++.+|++|+. .||..|.+ ..|-|.+.
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            35689999999774 67788899999999999886678899999999999999997 59998874 55666554

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.61  E-value=0.0084  Score=49.29  Aligned_cols=74  Identities=22%  Similarity=0.319  Sum_probs=58.6

Q ss_pred             ccceeccCcccccCHHHHHHHhccC-----CCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCe
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVF-----GDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRP  261 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~-----G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rp  261 (503)
                      ..+|.|.|||+.++++.|.-+|++-     |.|..+....       .-|+|+|.+...|.+.+..-  .+.+   ++.+
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-------~~AvItF~d~~va~rVL~k~--~H~L---~~~~   75 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-------CGGVLTFREPADAERVLAQA--DHEL---HGAQ   75 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-------TEEEEEESSHHHHHHHHTCS--CCBS---SSSB
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-------CcEEEEEcChHHHHHHhcCC--ccee---cCeE
Confidence            5688999999999999999999872     5788776643       37899999999999998762  3333   5688


Q ss_pred             EEeecCCcccc
Q psy93           262 VIVEPLELTDE  272 (503)
Q Consensus       262 l~V~~~~~~~~  272 (503)
                      +.|.|+.+.+.
T Consensus        76 LsV~P~~~~~~   86 (104)
T 2dhx_A           76 LSLRPAPPRAP   86 (104)
T ss_dssp             CEEEECCCCCC
T ss_pred             EEEEcCCCCCc
Confidence            89988766654

>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=96.24  E-value=0.0027  Score=51.81  Aligned_cols=53  Identities=17%  Similarity=0.312  Sum_probs=43.6

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhC
Q psy93           115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLD  170 (503)
Q Consensus       115 ~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~  170 (503)
                      .++| ++|+.+...||..+|+.||.|.--.|  +-..|||.|.+++.|..|+..+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fggv~I~Wi--dDTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGNIQISWI--DDTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEEEEEEEE--ETTEEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCCEEEEEE--cCCeEEEEecCHHHHHHHHHhcc
Confidence            4556 99999999999999999995443333  35689999999999999998764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.12  E-value=0.011  Score=48.27  Aligned_cols=73  Identities=12%  Similarity=0.221  Sum_probs=53.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC--------CCceEEeeCCHHHHHHHHHHhCCccccCc-----eE
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKE--------KMFGFIRMDYKHNADKAKAKLDGHVLKGR-----SL  179 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~--------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~-----~l  179 (503)
                      +-+|.|..||+.+|++++.+.++.+=++........        -.-|||.|.+.+++....+.++|..+.+.     +-
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a   88 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPA   88 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeee
Confidence            346999999999999999888887655433222211        24699999999999999999999976532     34


Q ss_pred             EEEecc
Q psy93           180 KIRFAP  185 (503)
Q Consensus       180 ~V~~a~  185 (503)
                      .|++|+
T Consensus        89 ~VE~AP   94 (97)
T 2l08_A           89 VVEFAP   94 (97)
T ss_dssp             EEEECC
T ss_pred             EEEecC
Confidence            455554

>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=95.99  E-value=0.035  Score=44.83  Aligned_cols=71  Identities=13%  Similarity=0.179  Sum_probs=55.4

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC---CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCC
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE---RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSL  259 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~---~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~  259 (503)
                      ++|.|.+||+.+|++++.+.++.+..+.....+...   .....+-|||.|.+.+++..-...++ ++.+....+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~-g~~F~D~kg   75 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFD-GYVFLDNKG   75 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHT-TCEEECTTC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhC-CcEEEcCCC
Confidence            478999999999999999999999887766665542   11234579999999999999999997 555554444

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.95  E-value=0.003  Score=66.08  Aligned_cols=54  Identities=11%  Similarity=0.249  Sum_probs=43.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCC-ceEEeeCCHHHHHHHHH
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKM-FGFIRMDYKHNADKAKA  167 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg-~aFV~F~~~e~A~~Ai~  167 (503)
                      .++|||. .|..+++.+|.++|++||+|.++.+.+++| ||.|+|.+.+++..++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHh
Confidence            4679997 799999999999999999999999998876 99999999999987754

>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=95.69  E-value=0.023  Score=48.07  Aligned_cols=84  Identities=19%  Similarity=0.215  Sum_probs=57.0

Q ss_pred             cCceEEEEecccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeee
Q psy93           175 KGRSLKIRFAPINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFF  254 (503)
Q Consensus       175 ~g~~l~V~~a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~  254 (503)
                      .+.+|...-....+.|.|-+.|+.. ...|...|++||.|.+.....     ...+-.|.|.+..+|.+||.+  ++.++
T Consensus        12 ~~~~l~~~~~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~-----~~NWihI~Y~s~~~A~rAL~k--NG~ii   83 (119)
T 1wwh_A           12 QGDSLTSEDHLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN-----TGNWMHIRYQSKLQARKALSK--DGRIF   83 (119)
T ss_dssp             ---------CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS-----SSSEEEEEESSHHHHHHHHTT--TTCEE
T ss_pred             CCcccCCCCCCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC-----CCCeEEEEeCCHHHHHHHHHh--CCeEe
Confidence            3455555544556778888888885 556778999999999876621     245899999999999999987  57776


Q ss_pred             ecCCCCeEEeecCC
Q psy93           255 LTQSLRPVIVEPLE  268 (503)
Q Consensus       255 ~~~~~rpl~V~~~~  268 (503)
                      .  ..-.|-|.|..
T Consensus        84 ~--g~~mIGV~p~~   95 (119)
T 1wwh_A           84 G--ESIMIGVKPCI   95 (119)
T ss_dssp             T--TTEECEEEECC
T ss_pred             c--CCEEEEEEECC
Confidence            1  23556777754

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.45  E-value=0.0089  Score=51.37  Aligned_cols=71  Identities=20%  Similarity=0.231  Sum_probs=53.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEE-Ee-------------------cCCCceEEeeCCHHHHHHHHHHhCCc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELF-IN-------------------KEKMFGFIRMDYKHNADKAKAKLDGH  172 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~-i~-------------------~~kg~aFV~F~~~e~A~~Ai~~l~g~  172 (503)
                      .+.|.|-+.|++. ...|...|++||.|.+-. +.                   ...++..|+|+++.+|.+||. .||.
T Consensus         7 e~~VtVFGFp~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            4568888997654 456678899999997621 11                   124677999999999999997 5999


Q ss_pred             cccCceEEEEecc
Q psy93           173 VLKGRSLKIRFAP  185 (503)
Q Consensus       173 ~l~g~~l~V~~a~  185 (503)
                      .|.|..|-|.+.+
T Consensus        85 ii~G~mIGV~Py~   97 (132)
T 3p3d_A           85 VFNGVLLGVIPYT   97 (132)
T ss_dssp             EETTEECEEEECC
T ss_pred             EeCcEEEEEEECC
Confidence            9999877777654

>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=95.20  E-value=0.058  Score=44.43  Aligned_cols=75  Identities=12%  Similarity=-0.005  Sum_probs=59.2

Q ss_pred             ccceeccCccccc-CH----HHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCe
Q psy93           187 NAAIKVKNLTSCV-TN----ELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRP  261 (503)
Q Consensus       187 ~~~L~V~nLp~~~-te----e~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rp  261 (503)
                      .++|+|.||+..+ ..    +.++++|..|+++......+.     -.-..|.|.+.++|.+|...|+ +..+   .++.
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS-----FRRirv~F~~~~~A~~AR~~Lh-~~~f---~g~~   75 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLH-KTEF---LGKE   75 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTST-TSEE---TTEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc-----ceEEEEEeCChHHHHHHHHHhc-ccee---cCce
Confidence            5789999998765 22    567899999999988877765     2246899999999999999997 5555   4778


Q ss_pred             EEeecCCcc
Q psy93           262 VIVEPLELT  270 (503)
Q Consensus       262 l~V~~~~~~  270 (503)
                      +.|.+..+.
T Consensus        76 ~r~YFgq~~   84 (104)
T 1wey_A           76 MKLYFAQTL   84 (104)
T ss_dssp             CEEECCCCS
T ss_pred             eEEEecCCC
Confidence            888887744

>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=95.16  E-value=0.047  Score=44.35  Aligned_cols=54  Identities=19%  Similarity=0.236  Sum_probs=44.3

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhh
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCA  249 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln  249 (503)
                      ..++| ..|+.+...||..+|+.||-| .|..+.|      ..|||.|.+++.|..|+..++
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidD------TsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDD------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEET------TEEEEECSCHHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcC------CeEEEEecCHHHHHHHHHhcc
Confidence            34555 999999999999999999954 3455554      279999999999999999875

>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=93.77  E-value=0.059  Score=43.92  Aligned_cols=54  Identities=19%  Similarity=0.235  Sum_probs=44.0

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhh
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCA  249 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln  249 (503)
                      ..++| ..|+.+...+|..+|+.||.| .|..+.|      ..|||.|.+++.|..|+..++
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidD------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDD------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEET------TEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcC------CeEEEEecCHHHHHHHHHhcc
Confidence            34556 999999999999999999943 3445544      279999999999999999875

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=92.41  E-value=0.18  Score=41.01  Aligned_cols=73  Identities=14%  Similarity=0.127  Sum_probs=51.5

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC--C-CCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCC
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE--R-GNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLR  260 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~--~-g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~r  260 (503)
                      +-+|.|..||+.+|++++.+.++.+=.+.....+...  . ...-.-|||.|.+.++...-.+.++ +..+....+.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~-g~~F~D~kg~   84 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFD-GYIFLDSKGL   84 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHST-TEEEECTTCC
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcC-CcEEEeCCCC
Confidence            4578999999999999988888776554332222211  1 1123468999999999999999997 6666655443

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=91.58  E-value=0.094  Score=54.80  Aligned_cols=55  Identities=13%  Similarity=0.180  Sum_probs=40.4

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHH
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALR  246 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~  246 (503)
                      .+.|+|. .|..+++.+|.++|++||+|.++....+.    .-|++|+|.+.+++..++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~----g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF----GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS----SEEEEEECC---CCHHHHS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC----CeEEEEEeCCHHHHHHHHh
Confidence            3578886 68889999999999999999998777652    3699999999998886654

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=89.61  E-value=0.23  Score=42.58  Aligned_cols=78  Identities=21%  Similarity=0.204  Sum_probs=52.6

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeE-EEeCC----------CC----CceeEEEEEeCCHHHHHHHHHHhhCC
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAI-VIVDE----------RG----NSKCEGIVEFARKPAAAQALRRCAEG  251 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~-v~~d~----------~g----~skg~gfV~F~s~e~A~kAl~~ln~g  251 (503)
                      ...|.|-+.|+..+. .|.+.|++||.|.+-. +..+.          ..    ....+-.|+|++..+|.+||..  ++
T Consensus         7 e~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~--NG   83 (132)
T 3p3d_A            7 ELAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE--NG   83 (132)
T ss_dssp             -CEEEEECCCGGGHH-HHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT--TT
T ss_pred             ceEEEEEecCHHHHH-HHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh--CC
Confidence            345667777776555 4667999999987721 11100          00    0245789999999999999986  68


Q ss_pred             eeeecCCCCeEEeecCCcc
Q psy93           252 CFFLTQSLRPVIVEPLELT  270 (503)
Q Consensus       252 ~~~~~~~~rpl~V~~~~~~  270 (503)
                      ..+   .+..|-|.|+.+.
T Consensus        84 ~ii---~G~mIGV~Py~~~   99 (132)
T 3p3d_A           84 AVF---NGVLLGVIPYTKD   99 (132)
T ss_dssp             CEE---TTEECEEEECCHH
T ss_pred             eEe---CcEEEEEEECCHH
Confidence            777   4568888888643

>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=85.63  E-value=1.7  Score=46.04  Aligned_cols=56  Identities=16%  Similarity=0.269  Sum_probs=45.4

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCC
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDG  171 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g  171 (503)
                      ...++|+ +|..+...+|.++|+.||.|.-..|  +...|||.|.++++|..++..+..
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v~V~wi--ddt~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNIQISWI--DDTSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCCEEEEC--SSSEEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCEEEEEE--cCCeEEEEECCHHHHHHHHHHHHh
Confidence            4467776 8999999999999999996543333  556799999999999999988753

---

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	503
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-17
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	6e-17
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-13
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-04
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	5e-13
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	7e-13
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-12
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-12
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-04
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-12
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-12
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	0.003
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	5e-12
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	8e-12
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-05
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	9e-12
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-11
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-11
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-11
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-11
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-11
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	6e-11
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	7e-11
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-10
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-10
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	1e-10
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-10
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-10
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	4e-10
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	4e-10
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	4e-10
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	4e-10
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	7e-10
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	8e-10
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-09
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-09
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-09
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-09
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-09
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-09
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-09
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	4e-09
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	4e-09
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	4e-09
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-09
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	5e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	5e-09
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	6e-09
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-08
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-08
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	3e-08
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-08
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	6e-06
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	4e-08
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	5e-08
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-07
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-07
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-07
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-07
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-07
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	2e-07
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	3e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-07
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	4e-07
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	5e-07
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	6e-07
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	8e-07
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	9e-07
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-06
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	4e-06
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	5e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	7e-06
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	8e-06
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	8e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	3e-05
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	4e-05
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	6e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	9e-05
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	1e-04
d1x4fa1	99	d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus)	1e-04
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	2e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	2e-04
d1gs9a_	144	a.24.1.1 (A:) Apolipoprotein E {Human (Homo sapien	6e-04
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	0.001
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.001
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	0.002

>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 = 74.2 bits (182), Expect = 3e-17
 Identities = 35/82 (42%), Positives = 58/82 (70%)

Query: 109 KFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAK 168
            F    RL++GN+  DITE ++ +LF+ YG+  E+FI+K+K FGFIR++ +  A+ AK +
Sbjct: 4   TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVE 63

Query: 169 LDGHVLKGRSLKIRFAPINAAI 190
           LD   L+G+ L++RFA  +A++
Sbjct: 64  LDNMPLRGKQLRVRFACHSASL 85

>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 = 73.9 bits (181), Expect = 6e-17
 Identities = 19/73 (26%), Positives = 37/73 (50%)

Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDG 171
            NC +Y G I   +T+  + + F P+G+  E+ +  EK + F+R     +A  A   ++G
Sbjct: 17  KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNG 76

Query: 172 HVLKGRSLKIRFA 184
             ++G  +K  + 
Sbjct: 77  TTIEGHVVKCYWG 89

>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 = 63.4 bits (154), Expect = 2e-13
 Identities = 17/76 (22%), Positives = 35/76 (46%), Gaps = 5/76 (6%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINK-----EKMFGFIRMDYKHNADKAKAKL 169
           +L + N+   +++ DI ELF  +G  ++  ++            +  + K +A KA  + 
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 170 DGHVLKGRSLKIRFAP 185
           +G  L GR + I+   
Sbjct: 62  NGVPLDGRPMNIQLVT 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 = 37.2 bits (86), Expect = 3e-04
 Identities = 18/57 (31%), Positives = 29/57 (50%)

Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALR 246
           + V NL   V++  ++  F  FG +++A V  D  G S     V F RK  A +A++
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMK 59

>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 = 62.7 bits (152), Expect = 5e-13
 Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 6/82 (7%)

Query: 110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNAD 163
              +C LY+GN+    TE  I ELF   G+ +++ +  +KM      F F+    + +A+
Sbjct: 4   LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 63

Query: 164 KAKAKLDGHVLKGRSLKIRFAP 185
            A   ++G  L  R ++  +  
Sbjct: 64  NAMRYINGTRLDDRIIRTDWDA 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 = 62.0 bits (150), Expect = 7e-13
 Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 6/76 (7%)

Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAK 166
           +  LY+  +   +T+ ++ +LF  YG      I  +++       GFIR D +  A++A 
Sbjct: 6   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 65

Query: 167 AKLDGHVLKGRSLKIR 182
             L+G    G +  I 
Sbjct: 66  KGLNGQKPSGATEPIT 81

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 60.8 bits (147), Expect = 1e-12
 Identities = 16/79 (20%), Positives = 37/79 (46%), Gaps = 6/79 (7%)

Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFG------FIRMDYKHNADKA 165
           +N  L +  +  D+T+ ++  LF+  G      I ++   G      F+    + ++ +A
Sbjct: 1   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

Query: 166 KAKLDGHVLKGRSLKIRFA 184
              L+G  ++ + LK+ +A
Sbjct: 61  IKVLNGITVRNKRLKVSYA 79

>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 = 60.8 bits (147), Expect = 2e-12
 Identities = 16/70 (22%), Positives = 31/70 (44%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
            LY+ N+    +E  I + F          + K + + F+    + +A +A   L+G VL
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVL 69

Query: 175 KGRSLKIRFA 184
            G  +++  A
Sbjct: 70  DGSPIEVTLA 79

>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 = 60.7 bits (147), Expect = 2e-12
 Identities = 16/75 (21%), Positives = 40/75 (53%), Gaps = 6/75 (8%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKL 169
           LY+G++  D+TE  + E F P G    + + ++ +      + ++      +A++A   +
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 170 DGHVLKGRSLKIRFA 184
           +  V+KG+ ++I ++
Sbjct: 63  NFDVIKGKPVRIMWS 77

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.2 bits (86), Expect = 3e-04
 Identities = 15/60 (25%), Positives = 22/60 (36%), Gaps = 1/60 (1%)

Query: 188 AAIKVKNLTSCVTNELLELAFGVFGDIERA-IVIVDERGNSKCEGIVEFARKPAAAQALR 246
           A++ V +L   VT  +L   F   G I    +        S     V F +   A +AL 
Sbjct: 1   ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 60

>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 = 60.4 bits (146), Expect = 3e-12
 Identities = 19/78 (24%), Positives = 31/78 (39%), Gaps = 9/78 (11%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI---------NKEKMFGFIRMDYKHNADKAK 166
           L++ N+    TE  +  +F   G  +   I              FGF+       A KA 
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 167 AKLDGHVLKGRSLKIRFA 184
            +L GH + G  L++R +
Sbjct: 61  KQLQGHTVDGHKLEVRIS 78

>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 = 60.0 bits (145), Expect = 4e-12
 Identities = 19/80 (23%), Positives = 40/80 (50%), Gaps = 8/80 (10%)

Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAK 166
           +  LY+ N+   IT++ +  +F  YG   +  I ++K+        F+R + +  A +A 
Sbjct: 6   DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 65

Query: 167 AKLDGHVLKG--RSLKIRFA 184
           + L+  + +G  + L +R A
Sbjct: 66  SALNNVIPEGGSQPLSVRLA 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 34.9 bits (80), Expect = 0.003
 Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 187 NAAIKVKNLTSCVTNELLELAFGVFGDIE-RAIVIVDERGNSKCEGIVEFARKPAAAQAL 245
           +  + V NL   +T++ L+  FG +G I  + I+     G  +    V + ++  A +A+
Sbjct: 6   DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 65

Query: 246 R 246
            
Sbjct: 66  S 66

>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 = 59.2 bits (143), Expect = 5e-12
 Identities = 14/77 (18%), Positives = 33/77 (42%), Gaps = 7/77 (9%)

Query: 114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFG------FIRMDYKHNADKAKA 167
           C++++G +    T+  + E F  +GE +E  + ++ +        F+    +   DK   
Sbjct: 1   CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV-L 59

Query: 168 KLDGHVLKGRSLKIRFA 184
               H L  +++  + A
Sbjct: 60  AQSRHELDSKTIDPKVA 76

>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 = 59.2 bits (143), Expect = 8e-12
 Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 8/87 (9%)

Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEK-------MFGFIRMDYKHNADKA 165
             ++ + NI     + +I ELF  +GE + + + K+         FGF+    K +A KA
Sbjct: 8   TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 67

Query: 166 KAKL-DGHVLKGRSLKIRFAPINAAIK 191
              L     L GR L + +A     ++
Sbjct: 68  FNALCHSTHLYGRRLVLEWADSEVTVQ 94

>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 = 41.1 bits (96), Expect = 2e-05
 Identities = 14/73 (19%), Positives = 25/73 (34%), Gaps = 2/73 (2%)

Query: 190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDER--GNSKCEGIVEFARKPAAAQALRR 247
           I V+N+        +   F  FG+++   +       G  +  G V+F  K  A +A   
Sbjct: 11  ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNA 70

Query: 248 CAEGCFFLTQSLR 260
                    + L 
Sbjct: 71  LCHSTHLYGRRLV 83

>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 = 59.3 bits (143), Expect = 9e-12
 Identities = 17/79 (21%), Positives = 36/79 (45%), Gaps = 6/79 (7%)

Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKA 165
            +  +Y+G +   ++E  + ELF   G      + K+      + +GF+    + +AD A
Sbjct: 8   QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 67

Query: 166 KAKLDGHVLKGRSLKIRFA 184
              +D   L G+ +++  A
Sbjct: 68  IKIMDMIKLYGKPIRVNKA 86

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 2e-11
 Identities = 15/92 (16%), Positives = 37/92 (40%), Gaps = 5/92 (5%)

Query: 99  PPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFI-----NKEKMFGF 153
           P +  Q+ D   +    + +     +  E    E+ + YGE +E+ +     +      +
Sbjct: 13  PQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVY 72

Query: 154 IRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP 185
           ++   + +A+KA   L+     G+ +    +P
Sbjct: 73  VKFRREEDAEKAVIDLNNRWFNGQPIHAELSP 104

>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 = 57.5 bits (138), Expect = 2e-11
 Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 7/81 (8%)

Query: 113 NCRLYLGNIGGDITENDIIELFKPYGE------TQELFINKEKMFGFIRMDYKHNADKAK 166
            C L++ N     T+ +I +L +             L  N  + F +I +  K +A    
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 60

Query: 167 AKLDGHVLKGRSLKIRFA-PI 186
            KL+G  ++G +L  + + P+
Sbjct: 61  EKLNGLKIEGYTLVTKVSNPL 81

>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 = 57.7 bits (139), Expect = 3e-11
 Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 6/79 (7%)

Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKA 165
           +N  + + N+  D  E D+ ELF+P+G    +++ K+K       F FI    + +A +A
Sbjct: 7   DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 66

Query: 166 KAKLDGHVLKGRSLKIRFA 184
            A + G       L + +A
Sbjct: 67  IAGVSGFGYDHLILNVEWA 85

>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 = 57.6 bits (139), Expect = 4e-11
 Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 3/75 (4%)

Query: 111 ANNCRLYLGNIGGDIT-ENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL 169
           + N R+++GN+   +  ++D+  +F  YG+     ++K   F F++   + NA  A A  
Sbjct: 13  SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--GFAFVQYVNERNARAAVAGE 70

Query: 170 DGHVLKGRSLKIRFA 184
           DG ++ G+ L I  A
Sbjct: 71  DGRMIAGQVLDINLA 85

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 6e-11
 Identities = 15/76 (19%), Positives = 33/76 (43%), Gaps = 6/76 (7%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFIN------KEKMFGFIRMDYKHNADKAKAK 168
           +L++G +   + ++ + EL   +G  +   +         K + F      +  D+A A 
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 169 LDGHVLKGRSLKIRFA 184
           L+G  L  + L ++ A
Sbjct: 63  LNGMQLGDKKLLVQRA 78

>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 = 56.6 bits (136), Expect = 6e-11
 Identities = 20/82 (24%), Positives = 31/82 (37%), Gaps = 10/82 (12%)

Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFI--------NKEKMFGFIRMDYKHNADK 164
           NCRL++G I       +I+E      E     I         K + F F+  +    A  
Sbjct: 1   NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAM 60

Query: 165 AKAKLDGH--VLKGRSLKIRFA 184
           A+ KL      L G  + + +A
Sbjct: 61  ARRKLMPGRIQLWGHQIAVDWA 82

>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 = 56.1 bits (135), Expect = 7e-11
 Identities = 15/76 (19%), Positives = 30/76 (39%), Gaps = 7/76 (9%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEK------MFGFIRMDYKHNADKAKAK 168
           ++++G +  D  E  I E F  +GE + + +  +        F FI    +    K   +
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI-ME 59

Query: 169 LDGHVLKGRSLKIRFA 184
              H +     +I+ A
Sbjct: 60  KKYHNVGLSKCEIKVA 75

>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 = 55.5 bits (133), Expect = 1e-10
 Identities = 16/76 (21%), Positives = 36/76 (47%), Gaps = 6/76 (7%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKAKAK 168
            L +  +  ++T+ +   LF   GE +   +       +   +GF+      +A+KA   
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 169 LDGHVLKGRSLKIRFA 184
           L+G  L+ +++K+ +A
Sbjct: 64  LNGLRLQTKTIKVSYA 79

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 1e-10
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 3/83 (3%)

Query: 112 NNCRLYLGNIGGDITENDIIELFKPYG---ETQELFINKEKMFGFIRMDYKHNADKAKAK 168
            N  LY+ N+   IT  ++ ++F  YG   + +     + +   ++  +   +A  A   
Sbjct: 6   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 169 LDGHVLKGRSLKIRFAPINAAIK 191
           L G  +  R L + +   N A +
Sbjct: 66  LSGFNVCNRYLVVLYYNANRAFQ 88

>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 = 55.0 bits (132), Expect = 1e-10
 Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 2/72 (2%)

Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH 172
              LY+     D+T   +   F P+G   +L ++  +   F+  +   +AD+A A+L+G 
Sbjct: 5   GNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGT 62

Query: 173 VLKGRSLKIRFA 184
            ++   LK+  A
Sbjct: 63  QVESVQLKVNIA 74

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 2e-10
 Identities = 14/73 (19%), Positives = 29/73 (39%), Gaps = 1/73 (1%)

Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDG 171
            +  +  G +G  ++ N ++ + +  G    L +   K + F R      + +A   L+G
Sbjct: 19  QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNG 78

Query: 172 H-VLKGRSLKIRF 183
             V+     KI  
Sbjct: 79  KEVVDDLGQKITL 91

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 55.0 bits (132), Expect = 3e-10
 Identities = 17/90 (18%), Positives = 41/90 (45%), Gaps = 6/90 (6%)

Query: 96  LDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKM-FGFI 154
           L+ P +  + +         L   N+  +ITE+++ E+F+   E + +  + +     +I
Sbjct: 4   LEDPCTSKKVRA-----ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYI 58

Query: 155 RMDYKHNADKAKAKLDGHVLKGRSLKIRFA 184
               + +A+K   +  G  + GRS+ + + 
Sbjct: 59  EFKSEADAEKNLEEKQGAEIDGRSVSLYYT 88

>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 = 54.3 bits (130), Expect = 4e-10
 Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 4/78 (5%)

Query: 111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEK----MFGFIRMDYKHNADKAK 166
                LY+GN+  D+TE  I++LF   G  +   +  E      + F+      +A  A 
Sbjct: 6   GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAAL 65

Query: 167 AKLDGHVLKGRSLKIRFA 184
           A ++G  + G+ +K+ +A
Sbjct: 66  AAMNGRKILGKEVKVNWA 83

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.3 bits (130), Expect = 4e-10
 Identities = 13/79 (16%), Positives = 31/79 (39%), Gaps = 3/79 (3%)

Query: 116 LYLGNIG-GDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKA--KLDGH 172
           +++ +   G      +++L +P+G      I  +    FI M    +A  A         
Sbjct: 11  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPA 70

Query: 173 VLKGRSLKIRFAPINAAIK 191
           ++ G+ +++  +     IK
Sbjct: 71  LVFGKPVRVHLSQKYKRIK 89

>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 = 54.3 bits (130), Expect = 4e-10
 Identities = 12/79 (15%), Positives = 36/79 (45%), Gaps = 7/79 (8%)

Query: 113 NCRLYLGNIGGDITENDI----IELFKPYGETQELFINKE---KMFGFIRMDYKHNADKA 165
           N  +Y+ N+   I ++++      +F  +G+  ++ +++    +   F+      +A  A
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62

Query: 166 KAKLDGHVLKGRSLKIRFA 184
              + G     + ++I++A
Sbjct: 63  LRSMQGFPFYDKPMRIQYA 81

>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 = 54.3 bits (130), Expect = 4e-10
 Identities = 19/78 (24%), Positives = 41/78 (52%), Gaps = 4/78 (5%)

Query: 111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFG----FIRMDYKHNADKAK 166
           +   RL++ NI     + D+ ++F  +G+  ++ I   +       F+  +   +AD+A+
Sbjct: 9   STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAR 68

Query: 167 AKLDGHVLKGRSLKIRFA 184
            KL G V++GR +++  A
Sbjct: 69  EKLHGTVVEGRKIEVNNA 86

>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 = 53.9 bits (129), Expect = 7e-10
 Identities = 13/78 (16%), Positives = 34/78 (43%), Gaps = 6/78 (7%)

Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFG------FIRMDYKHNADKAK 166
              L++ ++  +  + D++++F P+G      +  +K         F+  D   +A  A 
Sbjct: 18  GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 77

Query: 167 AKLDGHVLKGRSLKIRFA 184
             ++G  +  + LK++  
Sbjct: 78  QSMNGFQIGMKRLKVQLK 95

>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 = 53.2 bits (127), Expect = 8e-10
 Identities = 15/71 (21%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDG-HV 173
           +LY+GN+   +T +D+ +LF          +  +  + F+    ++ A +A   L G   
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVE 62

Query: 174 LKGRSLKIRFA 184
           L G+ +++ ++
Sbjct: 63  LHGKIMEVDYS 73

>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 = 53.2 bits (127), Expect = 1e-09
 Identities = 16/78 (20%), Positives = 37/78 (47%), Gaps = 6/78 (7%)

Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMF------GFIRMDYKHNADKAK 166
              L++ +I  +  E++I E F  YGE + + +N ++          +  +    A  AK
Sbjct: 7   GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 66

Query: 167 AKLDGHVLKGRSLKIRFA 184
             L+G  + G+++++ + 
Sbjct: 67  EALNGAEIMGQTIQVDWC 84

>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 = 52.3 bits (125), Expect = 1e-09
 Identities = 16/76 (21%), Positives = 33/76 (43%), Gaps = 7/76 (9%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEK------MFGFIRMDYKHNADKAKAK 168
           ++++G +  D T+ D+ + F  +GE  +  +  +        FGF+      + DK    
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKV-MD 59

Query: 169 LDGHVLKGRSLKIRFA 184
              H L G+ +  + A
Sbjct: 60  QKEHKLNGKVIDPKRA 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 = 52.0 bits (124), Expect = 2e-09
 Identities = 11/76 (14%), Positives = 36/76 (47%), Gaps = 7/76 (9%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAK 168
           ++++G +  + T  D+   F+ +G+  +  +  +      + FGF+  + +   +K   +
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-E 59

Query: 169 LDGHVLKGRSLKIRFA 184
           +  H +  + ++ + A
Sbjct: 60  IHFHEINNKMVECKKA 75

>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 = 52.0 bits (124), Expect = 2e-09
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 6/75 (8%)

Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAK 166
           NC L +  +    TE D+ E+F  YG   ++ I  +      + F F+  +   +A +AK
Sbjct: 9   NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 68

Query: 167 AKLDGHVLKGRSLKI 181
            + +G  L GR +++
Sbjct: 69  ERANGMELDGRRIRV 83

>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 = 52.4 bits (125), Expect = 2e-09
 Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 3/76 (3%)

Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK---EKMFGFIRMDYKHNADKAKAK 168
           N+CR+Y+GN+  DI   DI ++F  YG  +++ +        F F+  +   +A+ A   
Sbjct: 13  NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYG 72

Query: 169 LDGHVLKGRSLKIRFA 184
            DG+   G  L++ F 
Sbjct: 73  RDGYDYDGYRLRVEFP 88

>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 = 52.3 bits (125), Expect = 2e-09
 Identities = 14/77 (18%), Positives = 33/77 (42%), Gaps = 4/77 (5%)

Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFI----NKEKMFGFIRMDYKHNADKAKA 167
               +++ N+   I    + + F  +G      +    N  K +GF+  + +  A++A  
Sbjct: 7   GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIE 66

Query: 168 KLDGHVLKGRSLKIRFA 184
           K++G +L  R + +   
Sbjct: 67  KMNGMLLNDRKVFVGRF 83

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.4 bits (125), Expect = 2e-09
 Identities = 17/70 (24%), Positives = 32/70 (45%)

Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH 172
             RL++G +G + +   +   F  +G  + +   K   F +I+ +    A  A AK+ G 
Sbjct: 17  TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGF 76

Query: 173 VLKGRSLKIR 182
            L G   ++R
Sbjct: 77  PLGGPDRRLR 86

>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 = 51.6 bits (123), Expect = 4e-09
 Identities = 14/76 (18%), Positives = 33/76 (43%), Gaps = 7/76 (9%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAK 168
           +L++G +  + T+  +   F+ +G   +  + ++      + FGF+        D A   
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-N 66

Query: 169 LDGHVLKGRSLKIRFA 184
              H + GR ++ + A
Sbjct: 67  ARPHKVDGRVVEPKRA 82

>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 = 51.7 bits (123), Expect = 4e-09
 Identities = 12/77 (15%), Positives = 29/77 (37%), Gaps = 1/77 (1%)

Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDG 171
            +  + + N+  D    ++ +L K Y          ++   F+ +     A  A      
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTA-FVTLLNGEQAQNAIQMFHQ 62

Query: 172 HVLKGRSLKIRFAPINA 188
           +  +G+ L ++  P +A
Sbjct: 63  YSFRGKDLIVQLQPTDA 79

>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 = 52.0 bits (124), Expect = 4e-09
 Identities = 18/96 (18%), Positives = 42/96 (43%), Gaps = 9/96 (9%)

Query: 95  TLDLPPSEPQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKM---- 150
           TL+  P E + ++ +     +L++G +  + TE  +   ++ +G+  +  + ++      
Sbjct: 4   TLETVPLERKKREKE--QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRS 61

Query: 151 --FGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA 184
             FGF+        D A      H + GR ++ + A
Sbjct: 62  RGFGFVTFSSMAEVDAAM-AARPHSIDGRVVEPKRA 96

>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 = 51.6 bits (123), Expect = 4e-09
 Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 6/80 (7%)

Query: 111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEK------MFGFIRMDYKHNADK 164
           + + RL++ N+    +E D+ +LF  YG   EL    +        F F+   +  +A K
Sbjct: 6   SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVK 65

Query: 165 AKAKLDGHVLKGRSLKIRFA 184
           A A++DG V +GR L +  +
Sbjct: 66  AYAEVDGQVFQGRMLHVLPS 85

>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 = 51.6 bits (123), Expect = 5e-09
 Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 2/72 (2%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQE--LFINKEKMFGFIRMDYKHNADKAKAKLDGH 172
           R+ + N+   +T + + ++F  +G   +   F    +    ++     +A  AK  LDG 
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQ 68

Query: 173 VLKGRSLKIRFA 184
            +      +R  
Sbjct: 69  NIYNACCTLRID 80

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (121), Expect = 5e-09
 Identities = 15/76 (19%), Positives = 31/76 (40%), Gaps = 7/76 (9%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFI-------NKEKMFGFIRMDYKHNADKAKAK 168
           +++GN+  +I E  + + F  +G   +             K + FI       +D A   
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 169 LDGHVLKGRSLKIRFA 184
           ++G  L  R + + +A
Sbjct: 61  MNGQYLCNRPITVSYA 76

>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 = 51.3 bits (122), Expect = 6e-09
 Identities = 16/87 (18%), Positives = 29/87 (33%), Gaps = 14/87 (16%)

Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIR--------------MD 157
           +N  +Y+  +   +T +D+ + FK  G  +      + M                    +
Sbjct: 7   DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE 66

Query: 158 YKHNADKAKAKLDGHVLKGRSLKIRFA 184
               A  A    DG   +G  LK+  A
Sbjct: 67  DPPTAKAAVEWFDGKDFQGSKLKVSLA 93

>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 = 50.0 bits (119), Expect = 1e-08
 Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDG 171
            +  +++G   GD+TE+++ E F  YG+  ++FI K     F  + +  +        + 
Sbjct: 4   GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-PFRAFAFVTFADDQIAQSLCGED 62

Query: 172 HVLKGRSLKIRFA 184
            ++KG S+ I  A
Sbjct: 63  LIIKGISVHISNA 75

>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 = 49.7 bits (118), Expect = 1e-08
 Identities = 15/76 (19%), Positives = 35/76 (46%), Gaps = 6/76 (7%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAK 168
            LY+G +  ++ +  +   F P+G+  ++ I  +        F F+  +   +A  A   
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 169 LDGHVLKGRSLKIRFA 184
           ++   L GR++++  A
Sbjct: 67  MNESELFGRTIRVNLA 82

>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 = 49.4 bits (117), Expect = 3e-08
 Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 6/78 (7%)

Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEK------MFGFIRMDYKHNADKAK 166
           N  LYL N+   +TE D++ LF  + E +   I             FI    K  A +A 
Sbjct: 18  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 77

Query: 167 AKLDGHVLKGRSLKIRFA 184
             ++G+ L G+ L I F 
Sbjct: 78  HLVNGYKLYGKILVIEFG 95

>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 = 51.2 bits (121), Expect = 3e-08
 Identities = 23/150 (15%), Positives = 50/150 (33%), Gaps = 18/150 (12%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIR----MDYKHNADKAKA-KL 169
           +L++G +  + T+  +   F+ +G   +  + ++      R    + Y    +   A   
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 170 DGHVLKGRSLKIRFAPIN------------AAIKVKNLTSCVTNELLELAFGVFGDIERA 217
             H + GR ++ + A                 I V  +        L   F  +G IE  
Sbjct: 68  RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 127

Query: 218 IVIVD-ERGNSKCEGIVEFARKPAAAQALR 246
            ++ D   G  +    V F    +  + + 
Sbjct: 128 EIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 157

>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 = 44.6 bits (104), Expect = 6e-06
 Identities = 17/88 (19%), Positives = 37/88 (42%), Gaps = 7/88 (7%)

Query: 103 PQNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELF------INKEKMFGFIRM 156
              +        ++++G I  D  E+ + + F+ YG+ + +         K++ F F+  
Sbjct: 87  DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146

Query: 157 DYKHNADKAKAKLDGHVLKGRSLKIRFA 184
           D   + DK       H + G + ++R A
Sbjct: 147 DDHDSVDKI-VIQKYHTVNGHNCEVRKA 173

>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 = 49.0 bits (116), Expect = 4e-08
 Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 7/78 (8%)

Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAK 166
               +LGN+  D+TE  I E F+    +      +       K FG+   +   +   A 
Sbjct: 15  PYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 74

Query: 167 AKLDGHVLKGRSLKIRFA 184
             L+   L  + +++  A
Sbjct: 75  -SLNEESLGNKRIRVDVA 91

>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 = 48.0 bits (113), Expect = 5e-08
 Identities = 17/75 (22%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLK 175
           + +  + GD+T  ++ +L   Y E +  F++K K   F+ +     A+ A        L+
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDY-ELKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLR 59

Query: 176 GRSLKIRFAPINAAI 190
            R L ++  P +A +
Sbjct: 60  ERELSVQLQPTDALL 74

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (112), Expect = 1e-07
 Identities = 17/76 (22%), Positives = 30/76 (39%), Gaps = 8/76 (10%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAK 168
            L +  +    TE D+ E F  +GE   + + K+        FGF+R        K  ++
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 169 LDGHVLKGRSLKIRFA 184
              H++ GR    +  
Sbjct: 70  R--HMIDGRWCDCKLP 83

>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 = 47.4 bits (112), Expect = 1e-07
 Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 12/79 (15%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFI-----------NKEKMFGFIRMDYKHNAD 163
           RLY+GNI   ITE  +++ F        L             N++K F F+         
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 164 KAKAKLDGHVLKGRSLKIR 182
           +A    DG + +G+SLKIR
Sbjct: 63  QAM-AFDGIIFQGQSLKIR 80

>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 = 47.0 bits (111), Expect = 1e-07
 Identities = 16/76 (21%), Positives = 36/76 (47%), Gaps = 7/76 (9%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEK------MFGFIRMDYKHNADKAKAK 168
           ++++G I  D  E+ + + F+ YG+ + + I  ++       F F+  D  H++      
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD-DHDSVDKIVI 62

Query: 169 LDGHVLKGRSLKIRFA 184
              H + G + ++R A
Sbjct: 63  QKYHTVNGHNCEVRKA 78

>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 = 47.5 bits (112), Expect = 2e-07
 Identities = 8/78 (10%), Positives = 29/78 (37%), Gaps = 2/78 (2%)

Query: 109 KFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAK 168
           K + +  +++  +   + E D++E  + +G    + +   K    +  +   +A +    
Sbjct: 11  KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTF 70

Query: 169 LDGH--VLKGRSLKIRFA 184
                  + G+     ++
Sbjct: 71  AADVPVYIAGQQAFFNYS 88

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 2e-07
 Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 2/74 (2%)

Query: 113 NCRLYLGNIGGD-ITENDIIELFKPYGETQELFINKE-KMFGFIRMDYKHNADKAKAKLD 170
           N  L + N+  + +T   +  LF  YG+ Q + I    K    ++M   + A  A + L+
Sbjct: 2   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 61

Query: 171 GHVLKGRSLKIRFA 184
           GH L G+ ++I  +
Sbjct: 62  GHKLHGKPIRITLS 75

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.9 bits (111), Expect = 2e-07
 Identities = 14/93 (15%), Positives = 33/93 (35%), Gaps = 8/93 (8%)

Query: 99  PPSEP-QNKDIKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMF 151
           P  EP  N   +  +   ++   +   I   D+ + F   G+ +++ I  +      K  
Sbjct: 3   PVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGI 62

Query: 152 GFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA 184
            ++      +       L G  L G  + ++ +
Sbjct: 63  AYVEFCEIQSVPL-AIGLTGQRLLGVPIIVQAS 94

>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 = 46.7 bits (110), Expect = 2e-07
 Identities = 18/80 (22%), Positives = 41/80 (51%), Gaps = 6/80 (7%)

Query: 111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADK 164
           ++  +L++G +  D  E  + ++F  YG+  E+ + K+      + FGF+  +   +A  
Sbjct: 3   SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 62

Query: 165 AKAKLDGHVLKGRSLKIRFA 184
           A   ++G  + GR +++  A
Sbjct: 63  AMMAMNGKSVDGRQIRVDQA 82

>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 = 46.4 bits (109), Expect = 3e-07
 Identities = 14/74 (18%), Positives = 35/74 (47%), Gaps = 2/74 (2%)

Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKA--KAKLD 170
           +  L++  + G++TE ++I L  P+G+   + + K K   F+ +  +  A          
Sbjct: 8   SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAV 67

Query: 171 GHVLKGRSLKIRFA 184
              L+ + + I+++
Sbjct: 68  TPHLRNQPIYIQYS 81

>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 = 46.3 bits (109), Expect = 3e-07
 Identities = 22/83 (26%), Positives = 35/83 (42%), Gaps = 3/83 (3%)

Query: 105 NKDIKFANNCRLYLGNIGGDITENDIIELFKPYGE--TQELFINKEKMFGFIRMDYKHNA 162
           N    F  +  L+L NI   ++E D+  LF   G       F  K++    I+M     A
Sbjct: 2   NFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEA 61

Query: 163 DKAKAKLDGHVL-KGRSLKIRFA 184
            +A   L  H L +   L++ F+
Sbjct: 62  VQALIDLHNHDLGENHHLRVSFS 84

>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 = 45.4 bits (107), Expect = 4e-07
 Identities = 9/79 (11%), Positives = 25/79 (31%), Gaps = 6/79 (7%)

Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFI------NKEKMFGFIRMDYKHNADKA 165
               + + N+   ++ ++I++ F  Y                      +  + +  A  A
Sbjct: 8   GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 67

Query: 166 KAKLDGHVLKGRSLKIRFA 184
              L+   +  R +K+   
Sbjct: 68  VIDLNDRPIGSRKVKLVLG 86

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.9 bits (108), Expect = 5e-07
 Identities = 14/83 (16%), Positives = 39/83 (46%), Gaps = 7/83 (8%)

Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEK------MFGFIRMDYKHNADKA 165
              ++++G +    T+  + + F+ +G+ +E  +  ++       +GF+ M  +  A++A
Sbjct: 9   TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 68

Query: 166 KAKLDGHVLKGRSLKIRFAPINA 188
               +  ++ GR   +  A + A
Sbjct: 69  CKDPN-PIIDGRKANVNLAYLGA 90

>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 = 44.9 bits (106), Expect = 6e-07
 Identities = 14/74 (18%), Positives = 25/74 (33%), Gaps = 3/74 (4%)

Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDG 171
           ++  + +           I+  F  YG   +  ++    +  IR   K  A KA    DG
Sbjct: 3   DDTWVTVFGFPQASAS-YILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKAL-SKDG 60

Query: 172 HVLKGRSLKIRFAP 185
            +     + I   P
Sbjct: 61  RIFGESIM-IGVKP 73

>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 = 45.2 bits (106), Expect = 8e-07
 Identities = 14/81 (17%), Positives = 29/81 (35%), Gaps = 6/81 (7%)

Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGE-----TQELFINKEKMFGFIRMDYKHNADKAK 166
           +   LY+ N+   + E ++  + KP+G+              +  GF RM+     +   
Sbjct: 17  DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVI 76

Query: 167 AKLDGHVLKGRSLKIRFA-PI 186
              +G  +K          P+
Sbjct: 77  GHFNGKFIKTPPGVSAPTEPL 97

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 46.1 bits (108), Expect = 9e-07
 Identities = 21/101 (20%), Positives = 41/101 (40%), Gaps = 7/101 (6%)

Query: 91  IQGPTLDLPPSEPQNKDIKFANNCR-LYLGNIGGDITENDIIELFKPYGETQELFINKEK 149
           +Q          P  +     +  R L +  I   + E  + +LF+ YG  + + I  ++
Sbjct: 19  LQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDR 78

Query: 150 MF------GFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA 184
                   GF++     +A +A A L+G  +  + LK+  A
Sbjct: 79  ETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA 119

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.8 bits (105), Expect = 1e-06
 Identities = 14/78 (17%), Positives = 24/78 (30%), Gaps = 5/78 (6%)

Query: 112 NNCRLYLGNIGGDITE-----NDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAK 166
            +  L       D+            LF+ Y +       K      I      +A  A+
Sbjct: 4   GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADAR 63

Query: 167 AKLDGHVLKGRSLKIRFA 184
            +L      G+ +K+ FA
Sbjct: 64  LRLHKTEFLGKEMKLYFA 81

>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 = 44.0 bits (103), Expect = 2e-06
 Identities = 11/80 (13%), Positives = 36/80 (45%), Gaps = 9/80 (11%)

Query: 113 NCRLYLGNIGGDITENDIIE-LFKPYGETQELFIN-------KEKMFGFIRMDYKHNADK 164
              + + N+  ++ + +++   F+ +G  +++ I              F+  + K +A++
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 165 AKAKLDGHVLKGRSLKIRFA 184
           A  +++  +L  R + +  A
Sbjct: 64  AL-QMNRSLLGNREISVSLA 82

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.6 bits (102), Expect = 3e-06
 Identities = 9/73 (12%), Positives = 27/73 (36%), Gaps = 1/73 (1%)

Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDG 171
           ++ R+ +  +    +  D+ +  +  G+       ++   G +    K + + A  KLD 
Sbjct: 14  SDFRVLVSGLPPSGSWQDLKDHMREAGDVCY-ADVQKDGMGMVEYLRKEDMEYALRKLDD 72

Query: 172 HVLKGRSLKIRFA 184
              +    +  + 
Sbjct: 73  TKFRSHEGETSYI 85

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (102), Expect = 4e-06
 Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 6/76 (7%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGET----QELFINKEKMFGFIRMDYKH--NADKAKAK 168
            +++GNI  + TE  + ++F   G              K  G+   +Y+    A  A   
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 169 LDGHVLKGRSLKIRFA 184
           L+G    GR+L++  A
Sbjct: 70  LNGREFSGRALRVDNA 85

>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 = 42.4 bits (99), Expect = 4e-06
 Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 6/71 (8%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKM------FGFIRMDYKHNADKAKAKL 169
           LY+  +    T+ D+++L +PYG+        +K       +GF+  D    A KA   L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 170 DGHVLKGRSLK 180
               ++ +  K
Sbjct: 61  KASGVQAQMAK 71

>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 = 42.6 bits (99), Expect = 5e-06
 Identities = 12/78 (15%), Positives = 31/78 (39%), Gaps = 6/78 (7%)

Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFI-----NKEKMFGFIRMDYKHNADKAK 166
               L++GN+  + +  ++           +L +        + FG++  +   + +KA 
Sbjct: 12  TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKA- 70

Query: 167 AKLDGHVLKGRSLKIRFA 184
            +L G  + G  +K+   
Sbjct: 71  LELTGLKVFGNEIKLEKP 88

>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 = 42.5 bits (99), Expect = 7e-06
 Identities = 16/84 (19%), Positives = 31/84 (36%), Gaps = 12/84 (14%)

Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEK------MFGFIRMDYKHNADKAK 166
              +++ N+  D  E  + E+ + +G+ + + +             F +   +  A K  
Sbjct: 8   GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 67

Query: 167 AKL------DGHVLKGRSLKIRFA 184
           A         G  L GR LK+  A
Sbjct: 68  AAASLEAEGGGLKLDGRQLKVDLA 91

>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 = 42.1 bits (98), Expect = 8e-06
 Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 2/74 (2%)

Query: 113 NCRLYLGNIGGDITENDIIELFKP-YGETQELFINKEKMFGFIRMDYKHNADKAKAKLDG 171
           N  L+L N+  +  E  +  LF    G  +   +       F+    +  ++ AK  L G
Sbjct: 8   NQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQG 67

Query: 172 HVL-KGRSLKIRFA 184
             +    ++KI FA
Sbjct: 68  FKITPTHAMKITFA 81

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.6 bits (99), Expect = 8e-06
 Identities = 13/75 (17%), Positives = 24/75 (32%)

Query: 113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH 172
              +   N+       +I E F  +G    + + +  +   +       A KA   L   
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYS 69

Query: 173 VLKGRSLKIRFAPIN 187
                 L + +API 
Sbjct: 70  KFHHVPLYLEWAPIG 84

>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 = 40.5 bits (94), Expect = 3e-05
 Identities = 15/77 (19%), Positives = 25/77 (32%), Gaps = 4/77 (5%)

Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKA---- 167
            N  +Y+     D T +DI E  +  G+   + + +     F    +        A    
Sbjct: 5   KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV 64

Query: 168 KLDGHVLKGRSLKIRFA 184
           +  G   K   L I F 
Sbjct: 65  ETPGQKYKETDLLILFK 81

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.9 bits (95), Expect = 4e-05
 Identities = 12/69 (17%), Positives = 26/69 (37%), Gaps = 1/69 (1%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKH-NADKAKAKLDGHVL 174
            + G++       D+  LF  +GE + +   +    G I    K   A       +   L
Sbjct: 14  KFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNL 73

Query: 175 KGRSLKIRF 183
           + R+ ++ +
Sbjct: 74  QLRNKEVTW 82

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.5 bits (91), Expect = 6e-05
 Identities = 9/70 (12%), Positives = 22/70 (31%), Gaps = 1/70 (1%)

Query: 115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVL 174
           R+ +  +    +  D+ +  +  G+            G +    K +   A  KLD    
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREAGDVCY-ADVYRDGTGVVEFVRKEDMTYAVRKLDNTKF 60

Query: 175 KGRSLKIRFA 184
           +    +  + 
Sbjct: 61  RSHEGETAYI 70

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.5 bits (92), Expect = 9e-05
 Identities = 11/60 (18%), Positives = 19/60 (31%), Gaps = 2/60 (3%)

Query: 127 ENDIIELFKPYGETQEL--FINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA 184
             D+      +G+ ++L  F         +       AD     LDG    GR +  +  
Sbjct: 33  REDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAW 92

>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 = 39.0 bits (90), Expect = 1e-04
 Identities = 10/79 (12%), Positives = 32/79 (40%), Gaps = 12/79 (15%)

Query: 115 RLYLGNIGGDITENDIIELF---KPYGETQELFINKEKM---------FGFIRMDYKHNA 162
            +++  +   + + ++++       +G+  ++ IN               ++      +A
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 163 DKAKAKLDGHVLKGRSLKI 181
            +A   ++  V+ GR+LK 
Sbjct: 70  LRAIQCVNNVVVDGRTLKA 88

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {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: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.8 bits (89), Expect = 1e-04
 Identities = 19/90 (21%), Positives = 41/90 (45%), Gaps = 4/90 (4%)

Query: 99  PPSEPQNK-DIKFANNCRLYLGNIG-GDITENDIIELFKPYGETQELFINKEKMFGFIRM 156
           P  +P  K D K      ++L N+     +++ +++L +PYG+ +   + + K   FI M
Sbjct: 3   PEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEM 62

Query: 157 DYKHNADK--AKAKLDGHVLKGRSLKIRFA 184
           + + +A              +GR +K+  +
Sbjct: 63  ETREDAMAMVDHCLKKALWFQGRCVKVDLS 92

>d1sa0e_ a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 138

class: All alpha proteins
fold: Non-globular all-alpha subunits of globular proteins
superfamily: Stathmin
family: Stathmin
domain: Stathmin 4
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 39.1 bits (91), Expect = 2e-04
 Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 7/72 (9%)

Query: 313 KQLHELYEHETEMLRK--ELAQREIDRERQKAEWEMKERQAEELKRRDEELMK-----KH 365
           K L E  EHE E+++K  E     I   ++K   +M+  +          L +     KH
Sbjct: 67  KHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQEKDKH 126

Query: 366 AEEMQLRLAQQE 377
           AEE++     +E
Sbjct: 127 AEEVRKNKELKE 138

>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 = 37.5 bits (86), Expect = 2e-04
 Identities = 9/73 (12%), Positives = 23/73 (31%), Gaps = 5/73 (6%)

Query: 116 LYLGNIGGDITENDIIELFKPYGETQELFINKE----KMFGFIRMDYKHNADKAKAKLDG 171
           + + N+     +N + + FK  G    + +         F  I    +++   A      
Sbjct: 3   VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEF-ARYDGALAAITKTH 61

Query: 172 HVLKGRSLKIRFA 184
            V+    + +   
Sbjct: 62  KVVGQNEIIVSHL 74

>d1gs9a_ a.24.1.1 (A:) Apolipoprotein E {Human (Homo sapiens), E4 [TaxId: 9606]} Length = 144

class: All alpha proteins
fold: Four-helical up-and-down bundle
superfamily: Apolipoprotein
family: Apolipoprotein
domain: Apolipoprotein E
species: Human (Homo sapiens), E4 [TaxId: 9606]

 Score = 37.9 bits (88), Expect = 6e-04
 Identities = 14/77 (18%), Positives = 32/77 (41%), Gaps = 11/77 (14%)

Query: 313 KQLHELYEHETEMLRKELAQREIDRERQKAEWEMKE------RQAEELKRRDEELMKKHA 366
           ++       E +  +  L   +++  R +      E      +  EEL+ R    +  H 
Sbjct: 66  EETRARLSKELQAAQARL-GADMEDVRGRLVQYRGEVQAMLGQSTEELRVR----LASHL 120

Query: 367 EEMQLRLAQQEEDLRRR 383
            +++ RL +  +DL++R
Sbjct: 121 RKLRKRLLRDADDLQKR 137

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.0 bits (90), Expect = 0.001
 Identities = 13/73 (17%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 311 RWKQLHELYEHETEMLRKELAQREIDRERQKAEWEMKERQAEELKRRDEELMKKHAEEMQ 370
           + +Q+ E  E   +   K+L   +++ +R +   E +   A +L+ +++ L +   +E +
Sbjct: 229 KNEQMMEQKERSYQEHLKQL-TEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKESR 287

Query: 371 LRLAQQEEDLRRR 383
             +  + +DL+ +
Sbjct: 288 -IMKNEIQDLQTK 299

>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 = 36.3 bits (83), Expect = 0.001
 Identities = 12/76 (15%), Positives = 27/76 (35%), Gaps = 3/76 (3%)

Query: 112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEK--MFGFIRMDYKHNADKAKA-K 168
               +++  +    TENDI   F P    +          + G   +++  + D   A  
Sbjct: 14  TGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA 73

Query: 169 LDGHVLKGRSLKIRFA 184
            D   ++ R +++   
Sbjct: 74  KDKANMQHRYVELFLN 89

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	503
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.93
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.77
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.73
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	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
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.71
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.7
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.7
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.69
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.69
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.69
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.68
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.68
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.68
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.68
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.68
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.68
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.68
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.68
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.68
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.68
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.68
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.68
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.68
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.67
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.67
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.67
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.67
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.67
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.66
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.66
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.66
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.65
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.65
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.64
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.64
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.64
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.64
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.64
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.63
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.63
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.63
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.62
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.62
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.62
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.62
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.61
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.61
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.61
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.61
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.61
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.61
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.61
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.6
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.6
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.6
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.6
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.6
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.6
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.59
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.59
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.59
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.59
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.59
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.58
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.58
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.57
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.57
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.56
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.56
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.56
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.56
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.56
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.55
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.55
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.55
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.54
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.54
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.53
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.53
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.53
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.53
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.53
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.52
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.52
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.52
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.52
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.52
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.51
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.51
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.5
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.5
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.49
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.48
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.48
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.48
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.47
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.47
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.47
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.47
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.47
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.47
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.46
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.46
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.46
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.46
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.46
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.45
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.44
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.43
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.43
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.43
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.42
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.42
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.41
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.41
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.41
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.4
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.4
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.4
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.4
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.4
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.4
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.4
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.39
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.39
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.39
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.38
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.38
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.37
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.37
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.36
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.36
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.36
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.34
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.34
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.34
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.34
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.32
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.32
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.32
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.32
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.32
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.31
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.31
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.31
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.3
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.3
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.3
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.3
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.29
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.28
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.28
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	99.28
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.27
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.26
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.25
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.22
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.21
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.19
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.18
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	99.18
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.17
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.13
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.07
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.0
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.98
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	98.87
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.82
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.79
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.21
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.76
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.47
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.06
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.17
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	93.69
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	92.18
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	86.28

>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=99.93  E-value=2.2e-25  Score=205.09  Aligned_cols=154  Identities=18%  Similarity=0.242  Sum_probs=134.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc-
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP-  185 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~-  185 (503)
                      .++|||+|||+++|+++|+++|++||.|.++.+++      +++||||+|.+.++|.+|+.. ++..+..+.+.+.+.. 
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhhhh
Confidence            36899999999999999999999999999999864      368999999999999999974 5666777778777653 


Q ss_pred             -----------cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCee
Q psy93           186 -----------INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCF  253 (503)
Q Consensus       186 -----------~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~  253 (503)
                                 ..++|||+|||..+|+++|+++|+.||.|..+.|+.+ .++.+++||||+|.+.++|.+|+. ++ +..
T Consensus        85 ~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~-~~~  162 (183)
T d1u1qa_          85 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QK-YHT  162 (183)
T ss_dssp             TTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SS-CEE
T ss_pred             cccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hC-CCe
Confidence                       2468999999999999999999999999999999998 568899999999999999999997 54 555


Q ss_pred             eecCCCCeEEeecCCcccc
Q psy93           254 FLTQSLRPVIVEPLELTDE  272 (503)
Q Consensus       254 ~~~~~~rpl~V~~~~~~~~  272 (503)
                      +   .+++|.|.++.++.+
T Consensus       163 ~---~G~~i~V~~A~~k~e  178 (183)
T d1u1qa_         163 V---NGHNCEVRKALSKQE  178 (183)
T ss_dssp             E---TTEEEEEEECCCHHH
T ss_pred             E---CCEEEEEEecCCccc
Confidence            5   689999998866543

>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=99.77  E-value=4.2e-19  Score=143.03  Aligned_cols=83  Identities=42%  Similarity=0.772  Sum_probs=77.7

Q ss_pred             cCcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           108 IKFANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       108 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      +.++..++|||+|||+++++++|+++|+.||+|.+|.+.++++||||+|.+.++|.+|+..||+..|.|++|+|.||.+.
T Consensus         3 k~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~   82 (86)
T d2cpja1           3 KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   82 (86)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             CCccCCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCc
Confidence            45566789999999999999999999999999999999999999999999999999999999999999999999999877


Q ss_pred             cce
Q psy93           188 AAI  190 (503)
Q Consensus       188 ~~L  190 (503)
                      ..|
T Consensus        83 ~~l   85 (86)
T d2cpja1          83 ASL   85 (86)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            644

>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=99.73  E-value=2.6e-18  Score=136.87  Aligned_cols=74  Identities=20%  Similarity=0.413  Sum_probs=69.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      +|+|||+|||+++|+++|+++|++||+|.+|+|++      +++||||+|.++++|.+||+.||+..|.|++|+|.|++|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            57899999999999999999999999999999864      368999999999999999999999999999999999976

>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=99.72  E-value=5.7e-18  Score=139.16  Aligned_cols=76  Identities=25%  Similarity=0.542  Sum_probs=72.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ..++|||+|||+++++++|+++|++||+|.+|+|+++++||||+|.+.++|.+||..||+..|.|++|+|.|+.+.
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~   92 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEecceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            3578999999999999999999999999999999999999999999999999999999999999999999999764

>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=6.1e-18  Score=134.61  Aligned_cols=75  Identities=21%  Similarity=0.402  Sum_probs=69.8

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      .++|||+|||+++++++|+++|++||+|.+|.|+++      +|||||+|.++++|.+|+..||+..|.|++|+|.||+|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            468999999999999999999999999999999643      57999999999999999999999999999999999976


Q ss_pred             c
Q psy93           187 N  187 (503)
Q Consensus       187 ~  187 (503)
                      +
T Consensus        82 s   82 (82)
T d1fxla1          82 S   82 (82)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=9.8e-18  Score=136.88  Aligned_cols=77  Identities=25%  Similarity=0.470  Sum_probs=71.2

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       110 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      ...+|+|||+|||+++|+++|+++|+.||+|.+|.|+++      +|||||+|.+.++|..||+.||+..|.|++|+|.|
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~   83 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW   83 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            346789999999999999999999999999999999753      57999999999999999999999999999999999


Q ss_pred             ccc
Q psy93           184 API  186 (503)
Q Consensus       184 a~~  186 (503)
                      +..
T Consensus        84 a~~   86 (93)
T d1h2vz_          84 DAG   86 (93)
T ss_dssp             ESC
T ss_pred             cCC
Confidence            854

>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=99.71  E-value=6.7e-18  Score=142.17  Aligned_cols=76  Identities=17%  Similarity=0.243  Sum_probs=72.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      .+|+|||+|||+++++++|+++|+.||+|..|.|.++++||||+|.+.++|.+||+.||+..|.|++|.|.|++..
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeeccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            4578999999999999999999999999999999999999999999999999999999999999999999998653

>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=99.71  E-value=1.1e-17  Score=141.71  Aligned_cols=99  Identities=21%  Similarity=0.340  Sum_probs=84.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec---CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINK---EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAA  189 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~---~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~~~  189 (503)
                      +++|||+|||.++|+++|+++|+.||+|.+|.+..   ++|||||+|.+.++|..||+.||+..|.|++|.|.++.+...
T Consensus         7 ~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~~   86 (114)
T d2f9da1           7 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRA   86 (114)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCch
Confidence            57899999999999999999999999999999974   478999999999999999999999999999999999875432


Q ss_pred             eeccCcccccCHHHHHHHhccCCC
Q psy93           190 IKVKNLTSCVTNELLELAFGVFGD  213 (503)
Q Consensus       190 L~V~nLp~~~tee~L~~~Fs~~G~  213 (503)
                        .........++.+..+...||.
T Consensus        87 --~~~~~~~~~~~~~~~~~~~~g~  108 (114)
T d2f9da1          87 --FQKMDTKKKEEQLKLLKEKYGI  108 (114)
T ss_dssp             --TTTSCHHHHHHHHHHHHHHHCC
T ss_pred             --hhhhHHHHHHHHHHHHHHHhCC
Confidence              2234444566778888887775

>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=99.70  E-value=1.6e-17  Score=134.67  Aligned_cols=77  Identities=27%  Similarity=0.537  Sum_probs=71.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++|+++|+++|+.||+|.+|.|+.+      +|||||+|.+.++|.+||+.||+..|.|++|+|.|+.
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~ak   86 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAK   86 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            4678999999999999999999999999999999753      5799999999999999999999999999999999998


Q ss_pred             ccc
Q psy93           186 INA  188 (503)
Q Consensus       186 ~~~  188 (503)
                      |..
T Consensus        87 p~~   89 (90)
T d2cq0a1          87 PST   89 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            753

>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=2.8e-17  Score=134.13  Aligned_cols=77  Identities=22%  Similarity=0.393  Sum_probs=71.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++|+++|+++|++||+|.+|+|++      ++|||||+|.+.++|.+||+.||+..|.|++|+|.||.
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~   87 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS   87 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            357899999999999999999999999999999864      46899999999999999999999999999999999997


Q ss_pred             ccc
Q psy93           186 INA  188 (503)
Q Consensus       186 ~~~  188 (503)
                      +..
T Consensus        88 ~~~   90 (93)
T d1x5ua1          88 AHN   90 (93)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            643

>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=99.69  E-value=1.8e-17  Score=133.90  Aligned_cols=78  Identities=17%  Similarity=0.368  Sum_probs=70.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccccce
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAI  190 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~~~L  190 (503)
                      .+++|||+|||+++++++|+++|++|| |..+.+.++++||||+|.+.++|.+||..||+..|.|++|.|+++++...+
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~~~   81 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDALL   81 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeeeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCCC
Confidence            456899999999999999999999999 455677788999999999999999999999999999999999999776544

>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=99.69  E-value=5.1e-17  Score=127.15  Aligned_cols=74  Identities=22%  Similarity=0.433  Sum_probs=70.0

Q ss_pred             EEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccccce
Q psy93           116 LYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPINAAI  190 (503)
Q Consensus       116 l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~~~L  190 (503)
                      |||+|||+++++++|+++|++|| |..+.+.++++||||+|.+.++|.+|+..||+..+.|++|+|+|++....|
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~~l   74 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDALL   74 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTTCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCCcc
Confidence            79999999999999999999999 778888999999999999999999999999999999999999999876654

>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=4e-17  Score=132.30  Aligned_cols=76  Identities=26%  Similarity=0.461  Sum_probs=70.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      +.++|||+|||+++|+++|+++|+.||+|.+|.|+.+    ++||||+|.+.++|.+|+..||+..|.|++|+|.|+.+.
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~   86 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTP   86 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCT
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCC
Confidence            3568999999999999999999999999999999643    689999999999999999999999999999999999653

>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=2.2e-17  Score=133.56  Aligned_cols=76  Identities=20%  Similarity=0.467  Sum_probs=70.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++|+++|+++|+.||+|.+|.|+.      ++|||||+|.+.++|.+||..||+..|.|++|.|.|+.
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            356899999999999999999999999999999864      47899999999999999999999999999999999997


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus        84 p~   85 (89)
T d2cqba1          84 PM   85 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.68  E-value=4.3e-17  Score=130.92  Aligned_cols=76  Identities=21%  Similarity=0.283  Sum_probs=72.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ..++|||+|||+++|+++|+++|+.||.|..+.+.++++||||+|.+.++|..||..||+..|.|+.|.|.|+.|.
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~   82 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV   82 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCC
Confidence            3468999999999999999999999999999999999999999999999999999999999999999999999764

>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=99.68  E-value=2.5e-17  Score=130.74  Aligned_cols=74  Identities=20%  Similarity=0.345  Sum_probs=67.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe------cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFIN------KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~------~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      .|+|||+|||+++|+++|+++|+.||+|..+.++      ++++||||+|.+.++|.+|++.||+..+.|++|.|.+++|
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            3799999999999999999999999999887764      3478999999999999999999999999999999999876

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=8.2e-17  Score=131.27  Aligned_cols=77  Identities=29%  Similarity=0.502  Sum_probs=71.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ...++|||+|||+++++++|+++|+.||+|.+|.|+.+    ++||||+|.++++|.+||..||+..|.|+.|+|.||.+
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~   88 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA   88 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCc
Confidence            34568999999999999999999999999999999754    78999999999999999999999999999999999976


Q ss_pred             c
Q psy93           187 N  187 (503)
Q Consensus       187 ~  187 (503)
                      .
T Consensus        89 r   89 (93)
T d2cq3a1          89 R   89 (93)
T ss_dssp             S
T ss_pred             C
Confidence            4

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=4.3e-17  Score=128.85  Aligned_cols=74  Identities=23%  Similarity=0.388  Sum_probs=70.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      .+++|||+|||  +|+++|+++|++||.|.+|.+.++++||||+|.+.++|.+|+..||+..|.|++|+|.|+.+.
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            45789999996  999999999999999999999999999999999999999999999999999999999999653

>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=99.68  E-value=4.9e-17  Score=132.91  Aligned_cols=77  Identities=29%  Similarity=0.454  Sum_probs=70.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec-------CCCceEEeeCCHHHHHHHHHHh-CCccccCceEEEEe
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK-------EKMFGFIRMDYKHNADKAKAKL-DGHVLKGRSLKIRF  183 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~-------~kg~aFV~F~~~e~A~~Ai~~l-~g~~l~g~~l~V~~  183 (503)
                      .+++|||+|||+++++++|+++|+.||.|.+|.|++       ++|||||+|.+.++|.+||..| |+..|.|++|.|.|
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~   86 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEW   86 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEE
Confidence            356799999999999999999999999999999853       3789999999999999999998 89999999999999


Q ss_pred             ccccc
Q psy93           184 APINA  188 (503)
Q Consensus       184 a~~~~  188 (503)
                      |+...
T Consensus        87 A~~~~   91 (94)
T d2cpha1          87 ADSEV   91 (94)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            97654

>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=99.68  E-value=5.5e-17  Score=132.85  Aligned_cols=76  Identities=29%  Similarity=0.590  Sum_probs=70.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec---CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK---EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~---~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ++|+|||+|||+++|+++|+++|+.||.|..+.+..   .++||||+|.+.++|.+||+.||++.|.|++|+|+|+.+.
T Consensus        13 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~~   91 (95)
T d1x4aa1          13 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG   91 (95)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccCC
Confidence            457899999999999999999999999999999864   4789999999999999999999999999999999998754

>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=99.68  E-value=1.2e-17  Score=132.36  Aligned_cols=74  Identities=20%  Similarity=0.349  Sum_probs=69.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCc-cccCceEEEEecccc
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGH-VLKGRSLKIRFAPIN  187 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~-~l~g~~l~V~~a~~~  187 (503)
                      ++|||+|||+++|+++|+++|++||.|.++.+.++++||||+|.+.++|.+|++.|||. .+.|++|.|.|+.+.
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k   76 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   76 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCc
Confidence            46999999999999999999999999999888889999999999999999999999996 699999999999764

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.68  E-value=3.8e-17  Score=131.92  Aligned_cols=75  Identities=23%  Similarity=0.471  Sum_probs=69.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++|+++|+++|+.||+|.+|+|+.+      ++||||+|.+.++|.+|+..||+..|.|++|+|+|+.
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~   85 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF   85 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEec
Confidence            4678999999999999999999999999999998743      5799999999999999999999999999999999986


Q ss_pred             c
Q psy93           186 I  186 (503)
Q Consensus       186 ~  186 (503)
                      +
T Consensus        86 ~   86 (88)
T d1rk8a_          86 V   86 (88)
T ss_dssp             E
T ss_pred             C
Confidence            5

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.68  E-value=6.5e-17  Score=133.41  Aligned_cols=77  Identities=32%  Similarity=0.533  Sum_probs=71.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      +.+++|||+|||+++|+++|+++|++||+|.+|.|+.      +++||||+|.+.++|.+||+.||+..|.|++|+|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3467899999999999999999999999999999964      3689999999999999999999999999999999998


Q ss_pred             ccc
Q psy93           185 PIN  187 (503)
Q Consensus       185 ~~~  187 (503)
                      .+.
T Consensus        86 ~~~   88 (99)
T d1whwa_          86 TIK   88 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=3.3e-17  Score=129.82  Aligned_cols=71  Identities=23%  Similarity=0.506  Sum_probs=67.4

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           115 RLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       115 ~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +|||+|||+++|+++|+++|+.||+|.+|+|+++      ++||||+|.++++|.+||+.||+..|.|++|+|.|+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            6999999999999999999999999999999753      5799999999999999999999999999999999985

>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=99.68  E-value=1e-16  Score=127.81  Aligned_cols=74  Identities=23%  Similarity=0.363  Sum_probs=68.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-CCceEEeeCCHHHHHHHHHHhCCcccc-CceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-KMFGFIRMDYKHNADKAKAKLDGHVLK-GRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-kg~aFV~F~~~e~A~~Ai~~l~g~~l~-g~~l~V~~a~  185 (503)
                      ++++|||+|||.++|+++|.++|+.||+|..|.+.+. ++||||+|.+.++|..|+..||+..|. +++|+|.||+
T Consensus         7 P~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            4678999999999999999999999999999999764 689999999999999999999999885 6999999985

>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=99.68  E-value=6e-17  Score=129.80  Aligned_cols=73  Identities=25%  Similarity=0.500  Sum_probs=67.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccC--ceEEEEe
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKG--RSLKIRF  183 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g--~~l~V~~  183 (503)
                      .+++|||+|||+++|+++|+++|++||+|.+|+|+++      +|||||+|.+.++|.+||+.||+..+.|  ++|.|.|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            4578999999999999999999999999999999753      5799999999999999999999999976  8999998


Q ss_pred             c
Q psy93           184 A  184 (503)
Q Consensus       184 a  184 (503)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.67  E-value=3.9e-17  Score=132.10  Aligned_cols=76  Identities=17%  Similarity=0.384  Sum_probs=70.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ..++|||+|||+++|+++|+++|+.||.|.+|.|+.+    +|||||+|.+.++|.+||+.||+..|.|++|.|.++.+.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            3568999999999999999999999999999999754    789999999999999999999999999999999998754

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.67  E-value=5.3e-17  Score=128.00  Aligned_cols=71  Identities=24%  Similarity=0.401  Sum_probs=67.3

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec-----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           115 RLYLGNIGGDITENDIIELFKPYGETQELFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       115 ~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +|||+|||+++|+++|+++|++||+|.+|.|..     ++|||||+|.+.++|.+|++.||+..|.|++|+|++++
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            599999999999999999999999999999964     36899999999999999999999999999999999875

>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=99.67  E-value=6.4e-17  Score=129.67  Aligned_cols=72  Identities=28%  Similarity=0.543  Sum_probs=66.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccC--ceEEEEec
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKG--RSLKIRFA  184 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g--~~l~V~~a  184 (503)
                      +++|||+|||+++|+++|+++|++||+|.+|+|+.+      ++||||+|.+.++|.+|++.||+..+.|  ++|.|.||
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            578999999999999999999999999999999743      5799999999999999999999999987  66999886

>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=99.67  E-value=8.1e-17  Score=133.63  Aligned_cols=77  Identities=19%  Similarity=0.445  Sum_probs=70.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +.++|||+|||+++|+++|+++|+.||.|.+|.++.      ++|||||+|.+.++|..||+.||+..|.|++|+|+|+.
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~   96 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR   96 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            456899999999999999999999999999998864      36799999999999999999999999999999999997


Q ss_pred             ccc
Q psy93           186 INA  188 (503)
Q Consensus       186 ~~~  188 (503)
                      +..
T Consensus        97 ~k~   99 (102)
T d2cpza1          97 SKN   99 (102)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            643

>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=99.67  E-value=1.2e-16  Score=131.41  Aligned_cols=76  Identities=26%  Similarity=0.463  Sum_probs=71.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccC--ceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKG--RSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g--~~l~V~~a~~~  187 (503)
                      ++++|||+|||+++++++|+++|++||+|..|.+.++++||||+|.+.++|.+|++.||+..|.+  ++|+|.|+++.
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~   93 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeeccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCC
Confidence            35689999999999999999999999999999999999999999999999999999999999986  58999999764

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=6.1e-17  Score=129.79  Aligned_cols=73  Identities=22%  Similarity=0.418  Sum_probs=69.0

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           115 RLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       115 ~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      +|||+|||+++|+++|+++|+.||+|.+|+|++      +++||||+|.++++|..|+..||+..|.|++|.|.|+.+.
T Consensus         3 rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            699999999999999999999999999999964      3789999999999999999999999999999999999764

>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=99.66  E-value=8.1e-17  Score=130.39  Aligned_cols=76  Identities=24%  Similarity=0.546  Sum_probs=70.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ...+|||+|||+++|+++|+++|+.||+|..|.++.      ++|||||+|.++++|.+||..||+..|.|++|+|+++.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            456899999999999999999999999999998863      47899999999999999999999999999999999986


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus        84 ~~   85 (90)
T d1x5sa1          84 KS   85 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.66  E-value=6.7e-17  Score=128.88  Aligned_cols=70  Identities=29%  Similarity=0.501  Sum_probs=65.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEE
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKI  181 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V  181 (503)
                      ++++|||+|||+++|+++|+++|++||+|.+|.|+.+      ++||||+|.+.++|.+||..||+..|.|++|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            3568999999999999999999999999999998643      579999999999999999999999999999987

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=2.7e-16  Score=126.73  Aligned_cols=76  Identities=26%  Similarity=0.381  Sum_probs=68.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe--cCCCceEEeeCCHHHHHHHHHHhCCccc-cCceEEEEeccc
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFIN--KEKMFGFIRMDYKHNADKAKAKLDGHVL-KGRSLKIRFAPI  186 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~--~~kg~aFV~F~~~e~A~~Ai~~l~g~~l-~g~~l~V~~a~~  186 (503)
                      +++++|||+|||+++|+++|+++|+.||.|..+.+.  ++++||||+|.+.++|.+|+..|++..| .|++|+|.|+++
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCC
Confidence            346789999999999999999999999999887765  4588999999999999999999999988 589999999865

>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=99.65  E-value=8.7e-17  Score=128.77  Aligned_cols=72  Identities=28%  Similarity=0.481  Sum_probs=67.1

Q ss_pred             EEEcCCCCCCCHHHHHHhhccCCCeEEEEEec---------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           116 LYLGNIGGDITENDIIELFKPYGETQELFINK---------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       116 l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~---------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      |||+|||+++|+++|+++|++||+|.+|.|++         ++|||||+|.+.++|.+|++.||+..|.|++|.|.|+.+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            79999999999999999999999999999863         367999999999999999999999999999999999864


Q ss_pred             c
Q psy93           187 N  187 (503)
Q Consensus       187 ~  187 (503)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.64  E-value=1.9e-16  Score=132.74  Aligned_cols=75  Identities=27%  Similarity=0.440  Sum_probs=69.4

Q ss_pred             CcEEEEcCCCC-CCCHHHHHHhhccCCCeEEEEEecC-CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           113 NCRLYLGNIGG-DITENDIIELFKPYGETQELFINKE-KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       113 ~~~l~V~nLp~-~~te~~L~~~F~~~G~V~~v~i~~~-kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      +++|||+|||+ .+|+++|+++|+.||+|..|.|+++ +|||||+|.+.++|.+||+.||+..|.|++|+|.|+...
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~   78 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   78 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            57899999965 5999999999999999999999865 689999999999999999999999999999999998644

>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=99.64  E-value=4.3e-16  Score=125.56  Aligned_cols=77  Identities=19%  Similarity=0.323  Sum_probs=71.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHh--CCccccCceEEEEecccc
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL--DGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l--~g~~l~g~~l~V~~a~~~  187 (503)
                      .++++|||+|||+++++++|+++|++||.|.+|.+.++++||||+|.+.++|.+|++.+  ++..+.|++|+|.|++..
T Consensus         6 ~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~   84 (88)
T d2cq1a1           6 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK   84 (88)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCCC
Confidence            35678999999999999999999999999999999999999999999999999999865  567899999999998653

>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=2.7e-16  Score=130.65  Aligned_cols=75  Identities=17%  Similarity=0.446  Sum_probs=68.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++|+++|+++|+.||+|.+|.|+.      +++||||+|.+.++|.+||+.+++ .|.|++|.|.++.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            457899999999999999999999999999999964      478999999999999999998876 6999999999986


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      ..
T Consensus        88 ~~   89 (103)
T d2cqda1          88 LG   89 (103)
T ss_dssp             TT
T ss_pred             CC
Confidence            43

>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=99.64  E-value=9.2e-17  Score=126.30  Aligned_cols=70  Identities=24%  Similarity=0.553  Sum_probs=65.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      |+|||+|||+++|+++|+++|++||+|.+|.|++      ++|||||+|.+.++|.+|+. +++..|.|++|.|++|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            6899999999999999999999999999999864      47899999999999999997 7999999999999876

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=1.7e-16  Score=130.70  Aligned_cols=74  Identities=28%  Similarity=0.486  Sum_probs=67.7

Q ss_pred             CCcEEEEcCCC-CCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIG-GDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp-~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ..++|||+||| ..+++++|+++|++||+|..|.|  +++||||+|.+.++|.+||+.||++.|.|++|+|.|+.+.
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   88 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEP   88 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            34679999997 56889999999999999999999  4799999999999999999999999999999999999653

>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=99.63  E-value=2.8e-16  Score=137.66  Aligned_cols=76  Identities=24%  Similarity=0.384  Sum_probs=70.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ...++|||+|||+++|+++|+++|+.||+|.+|.|++      ++|||||+|.+.++|.+||+.||+..|.|+.|+|.++
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            3456899999999999999999999999999999864      3689999999999999999999999999999999998


Q ss_pred             cc
Q psy93           185 PI  186 (503)
Q Consensus       185 ~~  186 (503)
                      .+
T Consensus       120 ~~  121 (139)
T d1u6fa1         120 AS  121 (139)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>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=99.63  E-value=2e-16  Score=130.91  Aligned_cols=75  Identities=19%  Similarity=0.371  Sum_probs=68.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ..++|||+|||+++|+++|+++|+.||+|..+.+..+     ++||||+|.+.++|.+||+.|||..|.|++|.|.++.|
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCCC
Confidence            4578999999999999999999999999999888643     67999999999999999999999999999998877654

>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=99.63  E-value=3.1e-16  Score=129.34  Aligned_cols=80  Identities=18%  Similarity=0.325  Sum_probs=72.8

Q ss_pred             CCCcEEEEcCCCCC-CCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHH--HhCCccccCceEEEEecccc
Q psy93           111 ANNCRLYLGNIGGD-ITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKA--KLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       111 ~~~~~l~V~nLp~~-~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~--~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ..+++|||+|||.+ +|+++|.++|+.||.|.+|.|.++++||||+|.+.++|.+|++  .+++..|.|++|+|.|++..
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~~   95 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKY   95 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSC
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCCc
Confidence            45678999999985 8999999999999999999999999999999999999999998  47888999999999999766


Q ss_pred             cce
Q psy93           188 AAI  190 (503)
Q Consensus       188 ~~L  190 (503)
                      ..|
T Consensus        96 ~~l   98 (99)
T d1x4fa1          96 KKL   98 (99)
T ss_dssp             SSS
T ss_pred             ccC
Confidence            554

>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=99.62  E-value=3.3e-16  Score=130.12  Aligned_cols=74  Identities=20%  Similarity=0.415  Sum_probs=68.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      .++|||+|||+++|+++|+++|++||.|..+.|+.      ++|||||+|.+.++|.+||+ +++..|.|++|.|.++.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            46899999999999999999999999999999964      47999999999999999996 799999999999999865


Q ss_pred             c
Q psy93           187 N  187 (503)
Q Consensus       187 ~  187 (503)
                      .
T Consensus        99 k   99 (103)
T d1x4ba1          99 R   99 (103)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.62  E-value=1.1e-15  Score=127.09  Aligned_cols=77  Identities=9%  Similarity=0.150  Sum_probs=70.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHh--CCccccCceEEEEecccc
Q psy93           111 ANNCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL--DGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l--~g~~l~g~~l~V~~a~~~  187 (503)
                      .++.+|||+|||+++|+++|.++|+.||.|..|.+.++|+||||+|.+.++|..|+..|  +...+.|++|+|.|+...
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~   91 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCC
Confidence            35678999999999999999999999999999999999999999999999999999987  456788999999999654

>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=99.62  E-value=1.2e-16  Score=128.65  Aligned_cols=70  Identities=13%  Similarity=0.156  Sum_probs=65.8

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       115 ~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +|||+|||+++|+++|+++|+.||+|.+|.|.+ +|||||+|.+.++|.+||..||+..|.|+.|.|.++.
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~-~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~   71 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   71 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhcccccccccc-cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEe
Confidence            699999999999999999999999999999865 5899999999999999999999999999999887653

>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=99.62  E-value=2e-16  Score=129.70  Aligned_cols=79  Identities=23%  Similarity=0.326  Sum_probs=71.5

Q ss_pred             CcCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe-cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           109 KFANNCRLYLGNIGGDITENDIIELFKPYGETQELFIN-KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       109 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~-~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ...+.++|||+|||+++|+++|+++|+.||.|..+... ++++||||+|.+.++|.+|+..||+..|.|++|+|.|+.+.
T Consensus        12 ~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k   91 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK   91 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCC
Confidence            33456899999999999999999999999999877654 56899999999999999999999999999999999999764

>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=99.61  E-value=3e-16  Score=130.52  Aligned_cols=74  Identities=24%  Similarity=0.421  Sum_probs=68.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      ++|||+|||+++|+++|+++|+.||+|.+|.|+.+      +|||||+|.+.++|.+||+.||+..|.|++|+|.++.+.
T Consensus         9 rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~~   88 (104)
T d1p1ta_           9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCT
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            47999999999999999999999999999998643      579999999999999999999999999999999998653

>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=3.4e-16  Score=124.65  Aligned_cols=72  Identities=22%  Similarity=0.439  Sum_probs=65.6

Q ss_pred             EEEcCCCCCCCHHHHHHhhccCCCeEEE-EEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           116 LYLGNIGGDITENDIIELFKPYGETQEL-FINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       116 l~V~nLp~~~te~~L~~~F~~~G~V~~v-~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      |||+|||+++|+++|+++|++||.|.++ .|++      ++|||||+|.+.++|.+||+.|++..|.|++|+|.|+.+.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCC
Confidence            8999999999999999999999999764 5543      4789999999999999999999999999999999998754

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=5.3e-16  Score=123.96  Aligned_cols=72  Identities=19%  Similarity=0.388  Sum_probs=66.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      .++|||+|||+++|+++|+++|+.||+|..|.|+.      ++|||||+|.++++|.+||+ +++..|.|+.|.|..|.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            46899999999999999999999999999999864      36899999999999999997 68999999999998874

>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=99.61  E-value=9.2e-16  Score=125.86  Aligned_cols=76  Identities=22%  Similarity=0.331  Sum_probs=68.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhC------CccccCceE
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLD------GHVLKGRSL  179 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~------g~~l~g~~l  179 (503)
                      ..++|||+|||+++|+++|+++|+.||+|.++.+..      ++|||||+|.+.++|.+||+.|+      +..|.|++|
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l   86 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQL   86 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEE
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEE
Confidence            457899999999999999999999999999998863      47899999999999999999886      567889999


Q ss_pred             EEEecccc
Q psy93           180 KIRFAPIN  187 (503)
Q Consensus       180 ~V~~a~~~  187 (503)
                      +|.|+.+.
T Consensus        87 ~v~~a~~k   94 (98)
T d1x4ha1          87 KVDLAVTR   94 (98)
T ss_dssp             EEECCCCC
T ss_pred             EEEECCCC
Confidence            99998653

>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=99.61  E-value=4.7e-16  Score=121.52  Aligned_cols=69  Identities=23%  Similarity=0.500  Sum_probs=63.7

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           115 RLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       115 ~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      +|||+|||+++|+++|+++|++||+|.+|.|+.      ++|||||+|.++++|++||+ +++..|.|+.|.|..|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            499999999999999999999999999999864      47899999999999999997 7999999999999754

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=5.3e-16  Score=125.59  Aligned_cols=74  Identities=24%  Similarity=0.402  Sum_probs=66.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC------CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINKE------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++|+++|+++|+.||+|.+|.|+.+      +|||||+|.++++|.+||+.  ...|.|+.|.|+++.
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECCC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeCC
Confidence            4568999999999999999999999999999999743      68999999999999999985  447899999999986


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus        85 ~k   86 (90)
T d2cqga1          85 SK   86 (90)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>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=99.61  E-value=3.4e-16  Score=126.17  Aligned_cols=74  Identities=27%  Similarity=0.531  Sum_probs=67.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec-CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK-EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~-~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~~  187 (503)
                      .+++|||+|||+++|+++|+++|++||+|.+|++.. +++||||+|.+.++|++||.  ++..|.|++|.|.++.+.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k   78 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPK   78 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCC
Confidence            467999999999999999999999999999998864 58999999999999999985  788999999999998654

>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=99.60  E-value=6.3e-16  Score=125.37  Aligned_cols=77  Identities=16%  Similarity=0.449  Sum_probs=69.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHH----HhhccCCCeEEEEEec---CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           112 NNCRLYLGNIGGDITENDII----ELFKPYGETQELFINK---EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~----~~F~~~G~V~~v~i~~---~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ++++|||+|||+++|+++|+    ++|++||+|.+|.+.+   +++||||+|.+.++|.+|+..||+..+.|++|.|.|+
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~a   81 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA   81 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            35789999999999999886    4689999999999864   4899999999999999999999999999999999999


Q ss_pred             cccc
Q psy93           185 PINA  188 (503)
Q Consensus       185 ~~~~  188 (503)
                      .+..
T Consensus        82 k~~~   85 (91)
T d1nu4a_          82 KTDS   85 (91)
T ss_dssp             SSCC
T ss_pred             CCCc
Confidence            7643

>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=99.60  E-value=4.1e-16  Score=125.17  Aligned_cols=74  Identities=19%  Similarity=0.393  Sum_probs=66.4

Q ss_pred             CCcEEEEcCCCCCCC-HHHHHHhhccCCCeEEEEEec-------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           112 NNCRLYLGNIGGDIT-ENDIIELFKPYGETQELFINK-------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       112 ~~~~l~V~nLp~~~t-e~~L~~~F~~~G~V~~v~i~~-------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      ..++|||+|||+++| +++|+++|++||.|.+|.|..       ++|||||+|.+.++|.+|++ ||+..|.|++|+|.+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            457899999999876 567999999999999999853       36899999999999999996 999999999999999


Q ss_pred             ccc
Q psy93           184 API  186 (503)
Q Consensus       184 a~~  186 (503)
                      +.+
T Consensus        82 a~~   84 (86)
T d2ghpa3          82 ADK   84 (86)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            865

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=6.2e-16  Score=127.96  Aligned_cols=73  Identities=15%  Similarity=0.268  Sum_probs=67.8

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      .++|||+|||+++|+++|+++|+.||+|.+|.|++      ++|||||+|.+.++|.+|+. ||+..|.|++|.|.++.+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            46899999999999999999999999999999974      47899999999999999995 999999999999998754

>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=99.60  E-value=5.2e-16  Score=121.00  Aligned_cols=69  Identities=16%  Similarity=0.433  Sum_probs=64.1

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           115 RLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       115 ~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      +|||+|||+++|+++|+++|+.||.|..+.++.      +++||||+|.+.++|.+|++ ||+..|.|++|.|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            499999999999999999999999999998853      36899999999999999996 9999999999999876

>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=99.60  E-value=1.1e-15  Score=125.71  Aligned_cols=72  Identities=13%  Similarity=0.189  Sum_probs=67.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      .++|||+|||+++++++|+++|+.||+|..|.|. .++||||+|.+.++|.+||+.||+..|.|+.|.|.++.
T Consensus        15 ~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~-~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~   86 (98)
T d1wg4a_          15 DFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ-KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIR   86 (98)
T ss_dssp             SCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEE-TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhhccccccccc-ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEe
Confidence            4579999999999999999999999999999987 47999999999999999999999999999999998874

>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=99.60  E-value=1e-15  Score=123.64  Aligned_cols=78  Identities=13%  Similarity=0.216  Sum_probs=71.0

Q ss_pred             CCcEEEEcCCCCC-CCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHh--CCccccCceEEEEeccccc
Q psy93           112 NNCRLYLGNIGGD-ITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKL--DGHVLKGRSLKIRFAPINA  188 (503)
Q Consensus       112 ~~~~l~V~nLp~~-~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l--~g~~l~g~~l~V~~a~~~~  188 (503)
                      .+.+|||+|||.. +|+++|.++|++||.|.+|.+.+++++|||+|++.++|..|++.|  ++..+.|++|+|.|++...
T Consensus         7 ~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~~~   86 (89)
T d1x4da1           7 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYK   86 (89)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCCT
T ss_pred             CCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCCcc
Confidence            4568999999986 889999999999999999999999999999999999999999966  6778999999999997654


Q ss_pred             c
Q psy93           189 A  189 (503)
Q Consensus       189 ~  189 (503)
                      .
T Consensus        87 ~   87 (89)
T d1x4da1          87 R   87 (89)
T ss_dssp             T
T ss_pred             c
Confidence            4

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.59  E-value=5.4e-16  Score=125.29  Aligned_cols=71  Identities=17%  Similarity=0.355  Sum_probs=64.7

Q ss_pred             CCcEEEEcCCCCCCCHHHH---HHhhccCCCeEEEEEecC---------CCceEEeeCCHHHHHHHHHHhCCccccCceE
Q psy93           112 NNCRLYLGNIGGDITENDI---IELFKPYGETQELFINKE---------KMFGFIRMDYKHNADKAKAKLDGHVLKGRSL  179 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L---~~~F~~~G~V~~v~i~~~---------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l  179 (503)
                      ..++|||+|||+++++++|   .++|++||+|.+|.|+++         ++||||+|.++++|.+||+.||+..|.|++|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            4567999999999999999   678999999999999753         3799999999999999999999999999999


Q ss_pred             EEE
Q psy93           180 KIR  182 (503)
Q Consensus       180 ~V~  182 (503)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            984

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=1.2e-15  Score=120.10  Aligned_cols=70  Identities=24%  Similarity=0.480  Sum_probs=64.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      .+|||+|||+++|+++|+++|+.||.|..+.+..      ++|||||+|.++++|.+|+. +++..|.|++|.|+.|
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            5899999999999999999999999999999864      36899999999999999985 8999999999999876

>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=99.59  E-value=5.5e-16  Score=128.32  Aligned_cols=76  Identities=30%  Similarity=0.386  Sum_probs=69.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe------cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFIN------KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~------~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ++++|||+|||+++++++|+++|+.||.|..+.+.      ++++||||+|.+.++|.+||..||+..|.|++|+|.|+.
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak   96 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK   96 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCC
Confidence            46899999999999999999999999998877664      357999999999999999999999999999999999997


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus        97 ~k   98 (102)
T d2cpxa1          97 NK   98 (102)
T ss_dssp             CC
T ss_pred             Cc
Confidence            64

>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=99.59  E-value=1e-15  Score=119.55  Aligned_cols=70  Identities=14%  Similarity=0.158  Sum_probs=64.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKE----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      |+|||+|||+++++++|+++|+.||+|..|.|..+    ++||||+|.+.++|.+|+. +|+..|.|++|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            58999999999999999999999999999999754    4699999999999999995 8999999999999864

>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=9.9e-16  Score=125.45  Aligned_cols=75  Identities=24%  Similarity=0.422  Sum_probs=67.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCC-eEEEEEec-------CCCceEEeeCCHHHHHHHHHHhCCc--cccCceEEEE
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGE-TQELFINK-------EKMFGFIRMDYKHNADKAKAKLDGH--VLKGRSLKIR  182 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~-V~~v~i~~-------~kg~aFV~F~~~e~A~~Ai~~l~g~--~l~g~~l~V~  182 (503)
                      +|+|||+|||.++|+++|+++|+.||+ |.+|.|++       ++|||||+|.+.++|..|++.|++.  .+.|++|.|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            589999999999999999999999996 88999853       4689999999999999999999754  5579999999


Q ss_pred             ecccc
Q psy93           183 FAPIN  187 (503)
Q Consensus       183 ~a~~~  187 (503)
                      ||.+.
T Consensus        81 ~A~p~   85 (96)
T d2disa1          81 WAEPE   85 (96)
T ss_dssp             ESCSS
T ss_pred             EcCCC
Confidence            99764

>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=99.58  E-value=7.8e-16  Score=127.08  Aligned_cols=76  Identities=24%  Similarity=0.358  Sum_probs=67.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEE--------EEe------cCCCceEEeeCCHHHHHHHHHHhCCccccCc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQEL--------FIN------KEKMFGFIRMDYKHNADKAKAKLDGHVLKGR  177 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v--------~i~------~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~  177 (503)
                      ..++|||+|||.++|+++|+++|+.||+|..+        .+.      ++++||||+|.+.++|.+||+.||+..|.|+
T Consensus         7 ~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr   86 (101)
T d2cpea1           7 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGS   86 (101)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECCE
Confidence            46799999999999999999999999998533        332      3368999999999999999999999999999


Q ss_pred             eEEEEecccc
Q psy93           178 SLKIRFAPIN  187 (503)
Q Consensus       178 ~l~V~~a~~~  187 (503)
                      +|+|.++.+.
T Consensus        87 ~i~V~~a~~~   96 (101)
T d2cpea1          87 KLKVSLARKK   96 (101)
T ss_dssp             ECEEECSSCC
T ss_pred             EEEEEEcCCC
Confidence            9999998653

>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=99.58  E-value=2.4e-16  Score=127.94  Aligned_cols=74  Identities=16%  Similarity=0.323  Sum_probs=67.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe-----cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFIN-----KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~-----~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ...+|||+|||+++|+++|+++|+.||.|.++.|+     +++|||||+|.+.++|.+||+ ||+..|.|++|.|.++..
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak~   90 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKG   90 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCC
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecCC
Confidence            45689999999999999999999999998877663     568999999999999999996 999999999999999864

>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=99.57  E-value=1.3e-15  Score=127.45  Aligned_cols=76  Identities=18%  Similarity=0.309  Sum_probs=68.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec--CCCceEEeeCCHHHHHHHHHHhCCcccc--CceEEEEecccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK--EKMFGFIRMDYKHNADKAKAKLDGHVLK--GRSLKIRFAPIN  187 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~--~kg~aFV~F~~~e~A~~Ai~~l~g~~l~--g~~l~V~~a~~~  187 (503)
                      +..+|||+|||+++|+++|+++|++||.|..|.|..  +++||||+|.++++|.+||..||+..|.  ++.|.|.++.+.
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~   85 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT   85 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSC
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCc
Confidence            456899999999999999999999999999998864  5789999999999999999999999884  788999998764

>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=99.57  E-value=2.2e-15  Score=120.57  Aligned_cols=72  Identities=25%  Similarity=0.293  Sum_probs=66.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC-----CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKE-----KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~-----kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      .++|||+|||.++|+++|+++|+.||+|..|.|..+     +|||||+|.++++|.+||+ +++..+.|++|.|.|..
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            468999999999999999999999999999999643     6899999999999999996 79999999999999864

>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=99.56  E-value=2.7e-15  Score=118.96  Aligned_cols=79  Identities=20%  Similarity=0.239  Sum_probs=72.0

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      +++|||+|||..+++++|+++|++||.|.+++|+.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|.
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~ln-g~~~---~g~~l~v~   77 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLN-GITV---RNKRLKVS   77 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHT-TCEE---TTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhC-CCEE---CCEEEEEE
Confidence            467999999999999999999999999999999887 578899999999999999999999997 6666   68999999


Q ss_pred             cCCc
Q psy93           266 PLEL  269 (503)
Q Consensus       266 ~~~~  269 (503)
                      ++.+
T Consensus        78 ~a~p   81 (82)
T d1b7fa1          78 YARP   81 (82)
T ss_dssp             ECCC
T ss_pred             EcCC
Confidence            8754

>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=99.56  E-value=4.9e-15  Score=122.97  Aligned_cols=73  Identities=22%  Similarity=0.356  Sum_probs=64.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec-------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINK-------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~-------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      .++|||+|||+++|+++|+++|+.|| |..+.++.       +++||||+|.+.++|++|+ .||+..|.|+.|+|.++.
T Consensus        15 ~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a~   92 (104)
T d1wi8a_          15 PYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVAD   92 (104)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEECC
Confidence            47899999999999999999999999 66666642       3689999999999998777 599999999999999987


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus        93 ~~   94 (104)
T d1wi8a_          93 QA   94 (104)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.56  E-value=1.2e-15  Score=119.09  Aligned_cols=69  Identities=22%  Similarity=0.372  Sum_probs=63.0

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           115 RLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       115 ~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      +|||+|||+++|+++|+++|++||+|..|.|+.      ++|||||+|.+.++|++||+ +++..|.|+.|.|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            599999999999999999999999999999864      47899999999999999997 4777899999999865

>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=99.56  E-value=3.4e-15  Score=120.45  Aligned_cols=83  Identities=25%  Similarity=0.259  Sum_probs=75.1

Q ss_pred             cccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeE
Q psy93           184 APINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPV  262 (503)
Q Consensus       184 a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl  262 (503)
                      +..+++|||+|||.++++++|+++|+.||.|.+|.|+.| .++.++|||||+|.+.++|.+|+..|| +..+   .+++|
T Consensus         2 a~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~-~~~i---~g~~l   77 (89)
T d2cqba1           2 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN-ESEL---FGRTI   77 (89)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHT-TEEE---TTEEE
T ss_pred             CCCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcC-CCEE---CCEEE
Confidence            345689999999999999999999999999999999988 468999999999999999999999997 7666   68999


Q ss_pred             EeecCCcc
Q psy93           263 IVEPLELT  270 (503)
Q Consensus       263 ~V~~~~~~  270 (503)
                      .|.++.+.
T Consensus        78 ~v~~a~p~   85 (89)
T d2cqba1          78 RVNLAKPM   85 (89)
T ss_dssp             EEEECCCC
T ss_pred             EEEEeCCC
Confidence            99998654

>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=99.56  E-value=7.2e-15  Score=116.45  Aligned_cols=79  Identities=23%  Similarity=0.312  Sum_probs=72.1

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      .++|||+|||..+++++|+++|++||.|.+|.++.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|.
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 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLN-GLRL---QTKTIKVS   77 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT-TCEE---TTEECEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhC-CCEE---CCEEEEEE
Confidence            457999999999999999999999999999999987 578899999999999999999999997 6666   68999999


Q ss_pred             cCCc
Q psy93           266 PLEL  269 (503)
Q Consensus       266 ~~~~  269 (503)
                      ++.+
T Consensus        78 ~AkP   81 (82)
T d1fxla1          78 YARP   81 (82)
T ss_dssp             ECCC
T ss_pred             EeeC
Confidence            8764

>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=99.55  E-value=1e-15  Score=127.29  Aligned_cols=77  Identities=18%  Similarity=0.221  Sum_probs=70.5

Q ss_pred             CCCcEEEEcCCCCCC-C----HHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           111 ANNCRLYLGNIGGDI-T----ENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       111 ~~~~~l~V~nLp~~~-t----e~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +.+++|||+||+.++ +    .++|+++|+.||.|.+|.+.++++||||+|.+.++|.+||..||+..|.|++|+|.|+.
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   82 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecc
Confidence            356789999999876 3    35799999999999999999999999999999999999999999999999999999996


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus        83 ~~   84 (104)
T d1weya_          83 TL   84 (104)
T ss_dssp             CS
T ss_pred             cC
Confidence            54

>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=99.55  E-value=1.5e-15  Score=117.44  Aligned_cols=65  Identities=26%  Similarity=0.429  Sum_probs=60.9

Q ss_pred             EEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEE
Q psy93           116 LYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLK  180 (503)
Q Consensus       116 l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~  180 (503)
                      |||+|||+++|+++|+++|+.||+|..+++..      +++||||+|.+.++|.+|+..||+..|.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999999999999999999998864      478999999999999999999999999998764

>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=99.55  E-value=8.5e-15  Score=121.17  Aligned_cols=84  Identities=23%  Similarity=0.344  Sum_probs=76.2

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      ++.++|||+|||.++++++|+++|+.||.|.++.++.+ .++.++|||||+|.+.++|..||..|| +..+   .+++|.
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~ln-g~~~---~g~~i~   91 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMN-GFQI---GMKRLK   91 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHT-TCEE---TTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhC-CCEE---CCEEEE
Confidence            45678999999999999999999999999999999887 578999999999999999999999997 6666   689999


Q ss_pred             eecCCcccc
Q psy93           264 VEPLELTDE  272 (503)
Q Consensus       264 V~~~~~~~~  272 (503)
                      |+++.+.++
T Consensus        92 V~~a~~k~~  100 (102)
T d2cpza1          92 VQLKRSKND  100 (102)
T ss_dssp             EECCCCSCC
T ss_pred             EEEeCCCCC
Confidence            999887755

>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=99.54  E-value=7.2e-15  Score=119.76  Aligned_cols=84  Identities=18%  Similarity=0.254  Sum_probs=75.2

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC--CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD--ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPV  262 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d--~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl  262 (503)
                      .++++|||+|||..+++++|+++|+.||.|.+|.|+.+  .++.++|||||+|.+.++|.+|+..|+++..+   .+++|
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~---~Gr~l   82 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHL---YGRRL   82 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBS---SSCBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEE---CCEEE
Confidence            35678999999999999999999999999999999877  47889999999999999999999999657665   68999


Q ss_pred             EeecCCccc
Q psy93           263 IVEPLELTD  271 (503)
Q Consensus       263 ~V~~~~~~~  271 (503)
                      .|++++...
T Consensus        83 ~V~~A~~~~   91 (94)
T d2cpha1          83 VLEWADSEV   91 (94)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEcCCCC
Confidence            999987664

>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=99.54  E-value=5.3e-15  Score=116.29  Aligned_cols=76  Identities=28%  Similarity=0.399  Sum_probs=70.7

Q ss_pred             ceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCC
Q psy93           189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLE  268 (503)
Q Consensus       189 ~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~  268 (503)
                      +|||+|||+.+++++|+++|++||.|.++.|..+.++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|++++
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~-g~~l---~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN-GVPL---DGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHT-TCEE---TTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhC-CCEE---CCEEEEEEEee
Confidence            5899999999999999999999999999999999999999999999999999999999997 6666   68999998764

>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=99.53  E-value=9.9e-15  Score=117.91  Aligned_cols=82  Identities=29%  Similarity=0.333  Sum_probs=74.5

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .+.++|||+|||.++++++|+++|+.||.|.++.|+.| .++.++|||||+|.+.++|.+|+..|| +..+   .+++|.
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~-g~~~---~g~~i~   81 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVS-GFGY---DHLILN   81 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTT-TCEE---TTEECE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhC-CCEE---CCEEEE
Confidence            35678999999999999999999999999999999998 578899999999999999999999997 6666   689999


Q ss_pred             eecCCcc
Q psy93           264 VEPLELT  270 (503)
Q Consensus       264 V~~~~~~  270 (503)
                      |.++.+.
T Consensus        82 v~~akp~   88 (90)
T d2cq0a1          82 VEWAKPS   88 (90)
T ss_dssp             EEESSCC
T ss_pred             EEeeeCC
Confidence            9998765

>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=99.53  E-value=1.3e-14  Score=117.99  Aligned_cols=82  Identities=22%  Similarity=0.180  Sum_probs=73.9

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      ..+++|||+|||.++|+++|+++|+.||.|.+|.++.+ .++.++|||||+|.+.++|..|+..|| +..+   .+++|.
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~-g~~~---~gr~i~   80 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYIN-GTRL---DDRIIR   80 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTT-TSEE---TTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhC-CCEE---CCEEEE
Confidence            45789999999999999999999999999999999998 578899999999999999999999997 6666   689999


Q ss_pred             eecCCcc
Q psy93           264 VEPLELT  270 (503)
Q Consensus       264 V~~~~~~  270 (503)
                      |.|+...
T Consensus        81 V~~a~~~   87 (93)
T d1h2vz_          81 TDWDAGF   87 (93)
T ss_dssp             EEEESCC
T ss_pred             EEEcCCC
Confidence            9986543

>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=99.53  E-value=1.1e-14  Score=117.11  Aligned_cols=80  Identities=18%  Similarity=0.173  Sum_probs=72.5

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ...+|||+|||..+++++|.++|+.||.|.+|+++.| .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~ln-g~~l---~g~~l~V   81 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALN-GAEI---MGQTIQV   81 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHT-TCEE---TTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcC-CCEE---CCEEEEE
Confidence            3568999999999999999999999999999999998 578999999999999999999999997 6666   6899999


Q ss_pred             ecCCc
Q psy93           265 EPLEL  269 (503)
Q Consensus       265 ~~~~~  269 (503)
                      +|+.+
T Consensus        82 ~~a~~   86 (88)
T d1rk8a_          82 DWCFV   86 (88)
T ss_dssp             EESEE
T ss_pred             EEecC
Confidence            99754

>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=99.53  E-value=1.1e-14  Score=115.06  Aligned_cols=76  Identities=24%  Similarity=0.153  Sum_probs=70.4

Q ss_pred             ceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecC
Q psy93           189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPL  267 (503)
Q Consensus       189 ~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~  267 (503)
                      +|||+|||+.+|+++|.++|+.||.|.+++|+.| .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|.|+
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 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMN-FDVI---KGKPVRIMWS   77 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTST-TCEE---TTEECEEEEC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcC-CCEE---CCEEEEEEEe
Confidence            6999999999999999999999999999999998 568999999999999999999999997 6666   6899999987


Q ss_pred             C
Q psy93           268 E  268 (503)
Q Consensus       268 ~  268 (503)
                      .
T Consensus        78 ~   78 (80)
T d1cvja1          78 Q   78 (80)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.53  E-value=1.5e-14  Score=115.56  Aligned_cols=80  Identities=20%  Similarity=0.365  Sum_probs=70.3

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ..++|||+|||.++++++|+++|++||.|..++++++ .++.+++||||+|.+.++|.+|++.|| +..+ ....++|.|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~-g~~~-~g~~~~l~V   82 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN-NVIP-EGGSQPLSV   82 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT-TCCC-TTCSSCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHC-CCEe-CCCCeEEEE
Confidence            3567999999999999999999999999999999998 578999999999999999999999997 5444 223588999


Q ss_pred             ecC
Q psy93           265 EPL  267 (503)
Q Consensus       265 ~~~  267 (503)
                      .|+
T Consensus        83 ~~A   85 (85)
T d1b7fa2          83 RLA   85 (85)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            875

>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=99.52  E-value=1.8e-14  Score=118.49  Aligned_cols=83  Identities=24%  Similarity=0.263  Sum_probs=75.0

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ..++|||+|||..+++++|+++|++||.|.+|.|+.| .++.+++||||+|.+.++|.+||..|| +..+   .+++|.|
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~-g~~~---~gr~i~V   82 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVD-GQVF---QGRMLHV   82 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTT-TEES---SSCEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcC-CCEE---CCEEEEE
Confidence            4568999999999999999999999999999999987 578999999999999999999999997 6666   6899999


Q ss_pred             ecCCcccc
Q psy93           265 EPLELTDE  272 (503)
Q Consensus       265 ~~~~~~~~  272 (503)
                      .++....+
T Consensus        83 ~~a~~~~~   90 (99)
T d1whwa_          83 LPSTIKKE   90 (99)
T ss_dssp             EECCCCST
T ss_pred             EECCCCCc
Confidence            99876543

>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=99.52  E-value=3.5e-15  Score=119.49  Aligned_cols=72  Identities=13%  Similarity=0.239  Sum_probs=64.2

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEE-EEEe-----cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQE-LFIN-----KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~-v~i~-----~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      .++|||+|||+++++++|+++|+.||.|.. +.+.     +++|||||+|.+.++|.+||..||+..|.|++|+|.++
T Consensus         9 ~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           9 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            467999999999999999999999999865 3443     23689999999999999999999999999999999875

>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=99.52  E-value=3e-14  Score=115.06  Aligned_cols=81  Identities=20%  Similarity=0.191  Sum_probs=72.2

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .+++|||+|||+++|+++|+++|+.||.|.+|.|+.| .++.++|||||+|.+.++|.+||+.   ...+   .++.|.|
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~---~~~l---~Gr~i~v   80 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ---RHMI---DGRWCDC   80 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS---CEEE---TTEEEEE
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc---CCcc---CCEEeEE
Confidence            4678999999999999999999999999999999998 5799999999999999999999974   3344   6899999


Q ss_pred             ecCCcccc
Q psy93           265 EPLELTDE  272 (503)
Q Consensus       265 ~~~~~~~~  272 (503)
                      .++.+.+.
T Consensus        81 ~~a~~k~~   88 (90)
T d2cqga1          81 KLPNSKQS   88 (90)
T ss_dssp             ECCCTTCC
T ss_pred             EeCCCCCC
Confidence            99877643

>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=99.52  E-value=2.4e-14  Score=113.75  Aligned_cols=76  Identities=24%  Similarity=0.266  Sum_probs=68.7

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      ++.++|||.|||..+|+++|+++|++||.|.+|.|+.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.
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 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERAN-GMEL---DGRRIR   82 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHT-TEEE---TTEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcC-CCEE---CCEEeE
Confidence            35679999999999999999999999999999999988 468999999999999999999999997 7666   577776


Q ss_pred             e
Q psy93           264 V  264 (503)
Q Consensus       264 V  264 (503)
                      |
T Consensus        83 V   83 (83)
T d2cqca1          83 V   83 (83)
T ss_dssp             E
T ss_pred             C
Confidence            5

>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=99.52  E-value=2.1e-14  Score=114.69  Aligned_cols=79  Identities=25%  Similarity=0.391  Sum_probs=69.4

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      .++|||+|||+.+++++|+++|++||+|.+++|+.| .++.+++||||+|.+.++|.+|+..|| +..+ ....++|.|.
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~ln-g~~~-~G~~~~i~V~   83 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN-GQKP-SGATEPITVK   83 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT-TCCC-TTCSSCCEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhC-CCEe-CCCCEEEEEE
Confidence            467999999999999999999999999999999998 478999999999999999999999997 5444 2235778888


Q ss_pred             cC
Q psy93           266 PL  267 (503)
Q Consensus       266 ~~  267 (503)
                      |+
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            74

>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=99.51  E-value=1.4e-14  Score=117.80  Aligned_cols=82  Identities=22%  Similarity=0.202  Sum_probs=74.3

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ..++|||+|||..+++++|+++|++||.|.++.|+.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~-g~~~---~g~~l~V   83 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMD-MIKL---YGKPIRV   83 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSS-SCBC---SSCBCEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcC-CCEE---CCEEEEE
Confidence            3578999999999999999999999999999999987 578999999999999999999999997 6655   6899999


Q ss_pred             ecCCccc
Q psy93           265 EPLELTD  271 (503)
Q Consensus       265 ~~~~~~~  271 (503)
                      .++.+..
T Consensus        84 ~~A~~~~   90 (93)
T d1x5ua1          84 NKASAHN   90 (93)
T ss_dssp             EETTTTS
T ss_pred             EEcCCCC
Confidence            9987664

>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=99.51  E-value=1.3e-14  Score=115.96  Aligned_cols=79  Identities=15%  Similarity=0.242  Sum_probs=72.3

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      .+|||+|||..+|+++|+++|++||+|.+++|+.| .++.+++||||+|.+.++|..|+..|| +..+   .+++|.|.+
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 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN-GMQL---GDKKLLVQR   77 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSS-SCCC---SSSCCEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhC-CCEE---CCEEEEEEE
Confidence            47999999999999999999999999999999998 578999999999999999999999997 6555   689999999


Q ss_pred             CCcc
Q psy93           267 LELT  270 (503)
Q Consensus       267 ~~~~  270 (503)
                      +...
T Consensus        78 A~~~   81 (85)
T d2u2fa_          78 ASVG   81 (85)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8754

>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=99.50  E-value=2.8e-14  Score=118.38  Aligned_cols=75  Identities=13%  Similarity=0.118  Sum_probs=66.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEe------cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFIN------KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~------~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +..+|||+|||+++|+++|+++|..||.|..+.++      +.+|||||+|.++++|++|++ +|+..|.++.|.|.++.
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~   92 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSS   92 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECC
Confidence            45579999999999999999999999998875553      247899999999999999996 89999999999999886


Q ss_pred             cc
Q psy93           186 IN  187 (503)
Q Consensus       186 ~~  187 (503)
                      +.
T Consensus        93 ~~   94 (104)
T d1wg5a_          93 RA   94 (104)
T ss_dssp             TT
T ss_pred             HH
Confidence            54

>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=99.50  E-value=1.3e-14  Score=120.00  Aligned_cols=74  Identities=18%  Similarity=0.175  Sum_probs=64.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec-----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEeccc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAPI  186 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~~  186 (503)
                      ...+|||+|||+++|+++|+++|..|+.| .|.++.     .++||||+|.+.++|++|++ ||+..|.|+.|.|.++.+
T Consensus        14 ~~~~v~v~nLp~~~te~dl~~~F~~~~~~-~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~~   91 (102)
T d1weza_          14 TGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNST   91 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHhccCcc-eeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcCC
Confidence            45689999999999999999999999855 455543     26899999999999999986 899999999999999865


Q ss_pred             c
Q psy93           187 N  187 (503)
Q Consensus       187 ~  187 (503)
                      .
T Consensus        92 ~   92 (102)
T d1weza_          92 A   92 (102)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.49  E-value=2.1e-14  Score=113.47  Aligned_cols=78  Identities=9%  Similarity=0.066  Sum_probs=66.2

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      ++|||+|||+++|+++|+++|+.||.|..+.++.+ .++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|.+
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 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLN-GLKI---EGYTLVTKV   77 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHT-TCEE---TTEECEEEE
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhC-CCEE---CCEEEEEEE
Confidence            68999999999999999999999999998877665 678899999999999999999999997 6666   699999998


Q ss_pred             CCc
Q psy93           267 LEL  269 (503)
Q Consensus       267 ~~~  269 (503)
                      +++
T Consensus        78 a~P   80 (81)
T d2ghpa1          78 SNP   80 (81)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            765

>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=99.48  E-value=2.5e-14  Score=113.60  Aligned_cols=78  Identities=29%  Similarity=0.408  Sum_probs=69.6

Q ss_pred             eeccCcccccCHHHHHHHhccCCCeeee-EEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecC
Q psy93           190 IKVKNLTSCVTNELLELAFGVFGDIERA-IVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPL  267 (503)
Q Consensus       190 L~V~nLp~~~tee~L~~~Fs~~G~V~~~-~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~  267 (503)
                      |||+|||.++++++|+++|++||.|..+ .|+.+ .++.+++||||+|.+.++|.+|+..|+ +..+   .+++|.|.++
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 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMN-GQYL---CNRPITVSYA   76 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTT-TCEE---TTEECEEEES
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCC-CcEE---CCEEEEEEEe
Confidence            7999999999999999999999999775 67776 578899999999999999999999997 6666   6899999998


Q ss_pred             Cccc
Q psy93           268 ELTD  271 (503)
Q Consensus       268 ~~~~  271 (503)
                      .+.+
T Consensus        77 ~~k~   80 (83)
T d1x5ta1          77 FKKD   80 (83)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            7654

>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=99.48  E-value=1.8e-14  Score=119.23  Aligned_cols=72  Identities=15%  Similarity=0.230  Sum_probs=64.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEE-EEEe-----cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQE-LFIN-----KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~-v~i~-----~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      .++|||+|||+++|+++|+++|+.||.|.. +.+.     +++|||||+|.+.++|.+||. ||+..|.|+.|.|.++.
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            457999999999999999999999998876 4443     348999999999999999996 89999999999998764

>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=99.48  E-value=5.3e-14  Score=112.18  Aligned_cols=77  Identities=25%  Similarity=0.269  Sum_probs=68.2

Q ss_pred             eeccCcccccCHHHHHHHhccCCCeeeeEEEeCCC-C---CceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDER-G---NSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       190 L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~-g---~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      |||+|||.++|+++|+++|+.||.|.++.|+.+.. +   .++|||||+|.+.++|.+|+..|| +..+   .+++|.|.
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 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQ-GHTV---DGHKLEVR   76 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHST-TCEE---TTEECEEE
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhC-CCEE---CCEEEEEE
Confidence            79999999999999999999999999999988732 2   468999999999999999999997 6666   68999999


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      ++...
T Consensus        77 ~a~~~   81 (85)
T d2cpfa1          77 ISERA   81 (85)
T ss_dssp             CSSCS
T ss_pred             ECCCC
Confidence            97543

>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=99.47  E-value=8e-14  Score=113.19  Aligned_cols=81  Identities=27%  Similarity=0.336  Sum_probs=72.5

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ..++|||+|||..+++++|+++|+.||.|.+|.++.+..+ +++||||+|.+.++|.+|+..|| +..+   .++.|.|+
T Consensus        10 ~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~~Ai~~l~-~~~~---~g~~l~V~   84 (93)
T d2cq3a1          10 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLH-GTVV---EGRKIEVN   84 (93)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHT-TCEE---TTEECEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHHHHHHHcC-CCEE---CCEEEEEE
Confidence            3568999999999999999999999999999999988544 68999999999999999999997 6666   68999999


Q ss_pred             cCCccc
Q psy93           266 PLELTD  271 (503)
Q Consensus       266 ~~~~~~  271 (503)
                      ++.+..
T Consensus        85 ~A~~r~   90 (93)
T d2cq3a1          85 NATARV   90 (93)
T ss_dssp             ECCSSC
T ss_pred             ecCcCC
Confidence            987653

>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=99.47  E-value=2.5e-14  Score=115.39  Aligned_cols=84  Identities=23%  Similarity=0.289  Sum_probs=73.9

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      ....+|||+|||+++++++|.++|+.||.|..+.++.+ .++.++|||||+|.+.++|.+|+..|| +..+   .+++|.
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~-~~~~---~g~~l~   78 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMN-GKSV---DGRQIR   78 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHT-TCCT---TSCCCE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcC-CCEE---CCEEEE
Confidence            34568999999999999999999999999999988776 678899999999999999999999997 5555   689999


Q ss_pred             eecCCcccc
Q psy93           264 VEPLELTDE  272 (503)
Q Consensus       264 V~~~~~~~~  272 (503)
                      |+++.+..+
T Consensus        79 V~~a~~~~~   87 (90)
T d1x5sa1          79 VDQAGKSSD   87 (90)
T ss_dssp             EEEEECCCC
T ss_pred             EEEcCCCCC
Confidence            999766543

>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=99.47  E-value=2.4e-14  Score=115.35  Aligned_cols=80  Identities=31%  Similarity=0.449  Sum_probs=71.5

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      ..+|||+|||.++++++|+++|+.||.|..+.|+.+.. .+++||||+|.+.++|.+|+..|| +..+   .+++|.|.+
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~-g~~~---~g~~i~V~~   82 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMN-GMLL---NDRKVFVGR   82 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT-BCCSCEEEEESCHHHHHHHTTSSS-EEEE---TTEEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC-CCcceeEEEECCHHHHHHHHHHcC-CCEE---CCEEEEEEE
Confidence            35799999999999999999999999999999998853 468999999999999999999997 7766   689999999


Q ss_pred             CCccc
Q psy93           267 LELTD  271 (503)
Q Consensus       267 ~~~~~  271 (503)
                      +.+..
T Consensus        83 a~~~~   87 (89)
T d1cvja2          83 FKSRK   87 (89)
T ss_dssp             CCCTT
T ss_pred             CCCCC
Confidence            87654

>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=99.47  E-value=2e-14  Score=112.60  Aligned_cols=75  Identities=20%  Similarity=0.263  Sum_probs=67.2

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      ++|||+|||+++|+++|+++|++||.|.++.|+.| .++.++|||||+|.+.++|.+|+. +| ++.+   .+++|.|+.
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~-~~~i---~Gr~i~V~~   75 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QS-RHEL---DSKTIDPKV   75 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TT-TCCC---SSCCCEEEE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cC-CCEE---CCeEEEEEE
Confidence            57999999999999999999999999999999998 468999999999999999999997 55 6655   678888876


Q ss_pred             C
Q psy93           267 L  267 (503)
Q Consensus       267 ~  267 (503)
                      +
T Consensus        76 A   76 (77)
T d1uawa_          76 A   76 (77)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.47  E-value=3.6e-14  Score=117.11  Aligned_cols=80  Identities=19%  Similarity=0.308  Sum_probs=71.3

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ..++|||+|||.++++++|+++|+.||.|..+.+..+.++.+++||||+|.+.++|.+|+..|| +..+   .++++.|.
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~ln-g~~i---~gr~~~v~   92 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFN-GKFI---KTPPGVSA   92 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHB-TCCC---CCCTTSCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhC-CCEE---CCcCCccC
Confidence            3578999999999999999999999999999999998889999999999999999999999998 5555   57777777


Q ss_pred             cCCc
Q psy93           266 PLEL  269 (503)
Q Consensus       266 ~~~~  269 (503)
                      |.++
T Consensus        93 ~~~P   96 (101)
T d1x5oa1          93 PTEP   96 (101)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            6554

>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=99.47  E-value=6.2e-14  Score=122.40  Aligned_cols=81  Identities=22%  Similarity=0.267  Sum_probs=73.8

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      .++|||+|||.++++++|+++|+.||.|.+|.|+.+ .++.++|||||+|.+.++|.+||..|| +..+   .++.|.|.
T Consensus        42 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~ln-g~~~---~gr~l~V~  117 (139)
T d1u6fa1          42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLN-GFNI---LNKRLKVA  117 (139)
T ss_dssp             TSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTT-TEEC---SSCEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhC-CCEE---CCEEEEEE
Confidence            457999999999999999999999999999999988 578899999999999999999999997 7766   68999999


Q ss_pred             cCCccc
Q psy93           266 PLELTD  271 (503)
Q Consensus       266 ~~~~~~  271 (503)
                      ++....
T Consensus       118 ~a~~~~  123 (139)
T d1u6fa1         118 LAASGH  123 (139)
T ss_dssp             ESSCCC
T ss_pred             EcCCCC
Confidence            986554

>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=99.46  E-value=4.4e-14  Score=117.13  Aligned_cols=80  Identities=26%  Similarity=0.301  Sum_probs=72.2

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      .++|||+|||.++++++|+++|+.||+|.+|.|+.+ .++.++|||||+|.+.++|.+|+..|| +..+   .+++|.|.
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 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLN-GREF---SGRALRVD   83 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSS-SBSC---SSSCBEEE
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcC-CCEE---CCEEEEEE
Confidence            357999999999999999999999999999999887 578899999999999999999999997 6665   68999999


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      ++...
T Consensus        84 ~a~~~   88 (104)
T d1p1ta_          84 NAASE   88 (104)
T ss_dssp             ETTCT
T ss_pred             ECCCC
Confidence            87654

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=3.5e-14  Score=116.04  Aligned_cols=86  Identities=19%  Similarity=0.176  Sum_probs=73.6

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCC-eeeeEEEeCC--CCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGD-IERAIVIVDE--RGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~-V~~~~v~~d~--~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      +++|||+|||..+++++|+++|+.||. |..+.++.+.  ++.++|||||+|.+.++|..|+..|+...+.+  .+++|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~--~g~~i~   78 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQL--WGHQIA   78 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCB--TTBCCE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEE--CCEEEE
Confidence            367999999999999999999999996 8889888873  57889999999999999999999997544432  578999


Q ss_pred             eecCCcccccc
Q psy93           264 VEPLELTDEID  274 (503)
Q Consensus       264 V~~~~~~~~~~  274 (503)
                      |.|+++..+.+
T Consensus        79 V~~A~p~~~~~   89 (96)
T d2disa1          79 VDWAEPEIDVD   89 (96)
T ss_dssp             EEESCSSCSTT
T ss_pred             EEEcCCCCCCC
Confidence            99998765543

>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=99.46  E-value=5.6e-14  Score=118.36  Aligned_cols=71  Identities=17%  Similarity=0.194  Sum_probs=64.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCH-HHHHHHHHHhCCccccCceEEEEec
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYK-HNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~-e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      ..+||+|||+++|+++|+++|++||+|.+|.|+++++||||.|.++ ++|..|+..|++..+.++.+.|.|+
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            4569999999999999999999999999999999999999999995 7899999999999888777777665

>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=99.46  E-value=1e-13  Score=111.79  Aligned_cols=80  Identities=24%  Similarity=0.181  Sum_probs=71.3

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      +.++|||+|||.++++++|+++|+.||.|..|.++.+... .++||||+|.+.++|.+|+..|+ +..+   .+++|.|.
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~-~~~~afV~f~~~~~A~~A~~~l~-~~~~---~g~~i~v~   81 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMN-GRKI---LGKEVKVN   81 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHT-TEEE---TTEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc-cceeeEEEECCHHHHHHHHHHcC-CCEE---CCEEEEEE
Confidence            4578999999999999999999999999999999988543 37899999999999999999997 7766   68999999


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      ++.+.
T Consensus        82 ~a~~~   86 (90)
T d2cqia1          82 WATTP   86 (90)
T ss_dssp             ECCCT
T ss_pred             EcCCC
Confidence            98654

>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=99.46  E-value=8.1e-14  Score=115.36  Aligned_cols=81  Identities=19%  Similarity=0.186  Sum_probs=72.1

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      .++|||+|||.++++++|+++|++||.|..+.|+.| .++.++|||||+|.+.++|.+|+. ++ +..+   .+++|.|.
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~-~~~l---~G~~i~V~   94 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-AR-PHSI---DGRVVEPK   94 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SC-SEEE---TTEEEEEE
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hC-CCeE---CCEEEEEE
Confidence            368999999999999999999999999999999998 467899999999999999999996 54 6655   79999999


Q ss_pred             cCCcccc
Q psy93           266 PLELTDE  272 (503)
Q Consensus       266 ~~~~~~~  272 (503)
                      ++.+.++
T Consensus        95 ~a~~ke~  101 (103)
T d1x4ba1          95 RAVAREE  101 (103)
T ss_dssp             CCSSCCC
T ss_pred             ECcccCC
Confidence            9887654

>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=99.45  E-value=5.6e-14  Score=109.46  Aligned_cols=73  Identities=16%  Similarity=0.187  Sum_probs=65.1

Q ss_pred             ceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       189 ~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      +|||+|||+++++++|.++|++||.|..+.|+.+ .++.++|||||+|.+.++|.+|+. ++ +..+   .++.|.|+.
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~-~~~l---~Gr~i~V~r   74 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QK-EHKL---NGKVIDPKR   74 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TC-CCCB---TTBCCEECC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cC-CCEE---CCCEEEeeE
Confidence            5899999999999999999999999999999988 578899999999999999999997 54 5545   688888764

>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=99.44  E-value=9.2e-14  Score=115.02  Aligned_cols=79  Identities=33%  Similarity=0.341  Sum_probs=70.8

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      .++|||+|||..+++++|+++|+.||.|.++.|+.+ .++.+++||||+|.+.++|.+|++.+| +. +   .+++|.|.
T Consensus        10 ~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~-~~-l---~Gr~l~V~   84 (103)
T d2cqda1          10 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN-PI-I---DGRKANVN   84 (103)
T ss_dssp             SSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSS-CE-E---TTEECEEE
T ss_pred             CcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCC-Cc-C---CCEEEEEE
Confidence            356999999999999999999999999999999988 568999999999999999999999885 53 4   68999998


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      ++...
T Consensus        85 ~a~~~   89 (103)
T d2cqda1          85 LAYLG   89 (103)
T ss_dssp             ESTTT
T ss_pred             EcCCC
Confidence            87654

>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=99.43  E-value=1.8e-13  Score=108.88  Aligned_cols=77  Identities=19%  Similarity=0.191  Sum_probs=68.5

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ..+|||+|||..+++++|.++|+.||.|..+.|+.| .++.++|||||+|.+.++|.+|+. ++ +..+   .++.|.|.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~-~~~i---~Gr~i~V~   80 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-AR-PHKV---DGRVVEPK   80 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TC-SCEE---TTEECEEE
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hC-CCEE---CCEEEEEE
Confidence            468999999999999999999999999999999998 579999999999999999999997 44 4555   68899887


Q ss_pred             cCC
Q psy93           266 PLE  268 (503)
Q Consensus       266 ~~~  268 (503)
                      .+.
T Consensus        81 ~A~   83 (84)
T d1l3ka1          81 RAV   83 (84)
T ss_dssp             ECC
T ss_pred             eee
Confidence            653

>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=99.43  E-value=1.9e-13  Score=111.70  Aligned_cols=84  Identities=23%  Similarity=0.277  Sum_probs=73.1

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhC-----CeeeecCCC
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAE-----GCFFLTQSL  259 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~-----g~~~~~~~~  259 (503)
                      ..++|||+|||..+|+++|+++|+.||.|..+.++.+ .++.++|||||+|.+.++|.+|+..|++     +..+   .+
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~---~g   83 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKL---DG   83 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEES---SS
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEE---CC
Confidence            3578999999999999999999999999999998877 4778899999999999999999999872     3433   68


Q ss_pred             CeEEeecCCcccc
Q psy93           260 RPVIVEPLELTDE  272 (503)
Q Consensus       260 rpl~V~~~~~~~~  272 (503)
                      ++|.|.++.+.++
T Consensus        84 r~l~v~~a~~k~~   96 (98)
T d1x4ha1          84 RQLKVDLAVTRDE   96 (98)
T ss_dssp             CEEEEECCCCCCC
T ss_pred             EEEEEEECCCCCc
Confidence            9999999876543

>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=99.43  E-value=1.8e-13  Score=114.20  Aligned_cols=76  Identities=26%  Similarity=0.422  Sum_probs=66.9

Q ss_pred             ccceeccCccc-ccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTS-CVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~-~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      +++|||.|||+ .+++++|+++|+.||.|..|.|+.+.    ++||||+|.+.++|.+|+..|| +..+   .+++|.|.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~----kg~afV~f~~~~~A~~ai~~ln-g~~l---~g~~l~v~   73 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLN-GHKL---HGKPIRIT   73 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHT-TCBC---SSSBCEEE
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc----cceEEEEECCHHHHHHHHHHhC-CCEE---CCEEEEEE
Confidence            46899999965 59999999999999999999998873    6899999999999999999997 6655   58999999


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      ++...
T Consensus        74 ~s~~~   78 (109)
T d2adca1          74 LSKHQ   78 (109)
T ss_dssp             CCSCC
T ss_pred             ECCCC
Confidence            97644

>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=99.42  E-value=6.8e-14  Score=115.43  Aligned_cols=78  Identities=22%  Similarity=0.248  Sum_probs=70.3

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      .++|||+|||..+++++|+++|+.||.|.+|.|+.+ .++.++|||||+|.+.++|.+|+. || +..+   .+++|.|.
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~-g~~~---~G~~l~V~   92 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LT-GQRL---LGVPIIVQ   92 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HT-TEEE---TTEEEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HC-CCEE---CCEEEEEE
Confidence            357999999999999999999999999999999998 578999999999999999999995 86 7766   68999998


Q ss_pred             cCCc
Q psy93           266 PLEL  269 (503)
Q Consensus       266 ~~~~  269 (503)
                      ++..
T Consensus        93 ~a~~   96 (101)
T d2cq4a1          93 ASQA   96 (101)
T ss_dssp             EHHH
T ss_pred             ECCC
Confidence            7643

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=1.1e-13  Score=114.18  Aligned_cols=70  Identities=19%  Similarity=0.386  Sum_probs=61.5

Q ss_pred             CCcEEEEc--CCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCcccc-CceEEE
Q psy93           112 NNCRLYLG--NIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLK-GRSLKI  181 (503)
Q Consensus       112 ~~~~l~V~--nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~-g~~l~V  181 (503)
                      ++++|||.  |||+++|+++|+++|++||.|..|.+.++++||||+|.+.++|.+|+..|||..|. ++.+.|
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k~~aFV~f~~~e~A~~A~~~lng~~i~~~~~~~i   89 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   89 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCccEEEEEECCHHHHHHHHHHhCCCCCCCCCCcEE
Confidence            34678885  59999999999999999999999999999999999999999999999999999763 443333

>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=99.41  E-value=7.1e-14  Score=117.50  Aligned_cols=74  Identities=14%  Similarity=0.217  Sum_probs=64.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEE-e-----cCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           112 NNCRLYLGNIGGDITENDIIELFKPYGETQELFI-N-----KEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       112 ~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i-~-----~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      ..++|||+|||+++|+++|.++|+.||.|..+.+ .     ..+|||||+|.+.++|.+|+. ||+..|.|+.|.|.++.
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcC
Confidence            4568999999999999999999999998865333 2     236899999999999999996 89999999999998764


Q ss_pred             c
Q psy93           186 I  186 (503)
Q Consensus       186 ~  186 (503)
                      +
T Consensus        96 ~   96 (112)
T d1wela1          96 K   96 (112)
T ss_dssp             H
T ss_pred             h
Confidence            4

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.41  E-value=1.4e-13  Score=110.09  Aligned_cols=79  Identities=24%  Similarity=0.383  Sum_probs=66.6

Q ss_pred             ccceeccCcccccC-HHHHHHHhccCCCeeeeEEEeC--CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           187 NAAIKVKNLTSCVT-NELLELAFGVFGDIERAIVIVD--ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       187 ~~~L~V~nLp~~~t-ee~L~~~Fs~~G~V~~~~v~~d--~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      .++|||+|||.+++ +++|+++|++||.|.+|.|+.+  .++.++|||||+|.+.++|.+|+. || +..+   .+++|.
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n-~~~~---~gr~l~   78 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MN-RSLL---GNREIS   78 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GT-TEEE---TTEEEE
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cC-CCEE---CCEEEE
Confidence            46899999999876 5569999999999999998765  478899999999999999999996 86 7777   689999


Q ss_pred             eecCCcc
Q psy93           264 VEPLELT  270 (503)
Q Consensus       264 V~~~~~~  270 (503)
                      |.+++++
T Consensus        79 V~~a~~k   85 (86)
T d2ghpa3          79 VSLADKK   85 (86)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCC
Confidence            9998653

>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=99.41  E-value=2.1e-13  Score=114.74  Aligned_cols=78  Identities=21%  Similarity=0.204  Sum_probs=69.3

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      .+++|||+|||..+++++|.++|++||.|.+|.+..+  +.++|||||+|.+.++|.+|+..|| +..+   .+++|.|.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~--~~~kG~afV~f~~~~~A~~Ai~~l~-g~~~---~gr~l~V~   79 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNACDHLS-GFNV---CNRYLVVL   79 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTEEEEEESSHHHHHHHHHHHT-TCEE---TTEECEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc--CCcCCeEEEEECCHHHHHHHHHHhC-CCEE---CCEEEEEE
Confidence            3578999999999999999999999999999988765  4568999999999999999999997 6656   68999999


Q ss_pred             cCCc
Q psy93           266 PLEL  269 (503)
Q Consensus       266 ~~~~  269 (503)
                      ++..
T Consensus        80 ~a~~   83 (114)
T d2f9da1          80 YYNA   83 (114)
T ss_dssp             ECCH
T ss_pred             EcCC
Confidence            8754

>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=99.40  E-value=2.6e-13  Score=108.18  Aligned_cols=76  Identities=12%  Similarity=0.040  Sum_probs=69.0

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      .++|||+|||.++|+++|.++|+.||.|..|.+..+.++.++|||||+|.+.++|.+||+ ++ +..+   .++++.|.+
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 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TP-GQKY---KETDLLILF   80 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CC-CCEE---TTEECEEEE
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HC-CCEE---CCEEEEEEE
Confidence            468999999999999999999999999999999999899999999999999999999996 54 6655   688999887


Q ss_pred             C
Q psy93           267 L  267 (503)
Q Consensus       267 ~  267 (503)
                      .
T Consensus        81 ~   81 (85)
T d1zh5a2          81 K   81 (85)
T ss_dssp             G
T ss_pred             c
Confidence            4

>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=99.40  E-value=4.2e-13  Score=105.29  Aligned_cols=75  Identities=16%  Similarity=0.135  Sum_probs=67.2

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      ++|||+|||+++|+++|+++|++||.|..+.++.+ .++.+++||||+|.+.++|.+|+. ++ +..+   .+++|.|+.
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~-~~~l---~Gr~i~V~~   77 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QK-YHTV---NGHNCEVRK   77 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CS-CCEE---TTEECEEEE
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hC-CCEE---CCEEEEEEE
Confidence            58999999999999999999999999999999987 577899999999999999999985 65 6666   689999876


Q ss_pred             C
Q psy93           267 L  267 (503)
Q Consensus       267 ~  267 (503)
                      +
T Consensus        78 A   78 (79)
T d1l3ka2          78 A   78 (79)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.40  E-value=5.7e-14  Score=115.87  Aligned_cols=85  Identities=21%  Similarity=0.219  Sum_probs=75.7

Q ss_pred             cccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeE
Q psy93           184 APINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPV  262 (503)
Q Consensus       184 a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl  262 (503)
                      ..++++|||+|||.++++++|+++|+.||.|..+.++.+ .++.+++||||+|.+.++|..|+..|| +..+   .+++|
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 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVN-GYKL---YGKIL   90 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHST-TCBC---SSCBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhC-CCEE---CCEEE
Confidence            356789999999999999999999999999999988776 578899999999999999999999997 6555   68999


Q ss_pred             EeecCCcccc
Q psy93           263 IVEPLELTDE  272 (503)
Q Consensus       263 ~V~~~~~~~~  272 (503)
                      .|.++.+.++
T Consensus        91 ~V~~ak~k~~  100 (102)
T d2cpxa1          91 VIEFGKNKKQ  100 (102)
T ss_dssp             EEEECCCCSC
T ss_pred             EEEeCCCccc
Confidence            9999987654

>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=99.40  E-value=2.8e-13  Score=107.45  Aligned_cols=77  Identities=16%  Similarity=0.213  Sum_probs=67.4

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +|+++|||+|||..+++++|.++|+.||.|..|.++.+.    ++||||+|.+.++|..|+..|+ +..+.  .+++|.|
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~A~~~l~-g~~~~--~~~~i~v   78 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFTTELQSNAAKEALQ-GFKIT--PTHAMKI   78 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT----CSCEEEEESSHHHHHHHHHHHT-TCBSS--TTCBCEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc----ceeEEEecCCHHHHHHHHHHhC-CcEeC--CCcEEEE
Confidence            567899999999999999999999999999999997652    6799999999999999999997 54442  4678999


Q ss_pred             ecCC
Q psy93           265 EPLE  268 (503)
Q Consensus       265 ~~~~  268 (503)
                      .|++
T Consensus        79 ~~ak   82 (83)
T d2b0ga1          79 TFAK   82 (83)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9875

>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=99.40  E-value=1.6e-13  Score=106.56  Aligned_cols=74  Identities=19%  Similarity=0.204  Sum_probs=66.3

Q ss_pred             ceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecC
Q psy93           189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPL  267 (503)
Q Consensus       189 ~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~  267 (503)
                      +|||+|||.++|+++|+++|+.||.|..+.++.+ .++.+++||||+|.+.++|.+|++ +| +..+   .+++|.|.++
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~-~~~l---~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IH-FHEI---NNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CS-SCCB---TTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cC-CCEE---CCeEEEEEEC
Confidence            5899999999999999999999999999988877 468899999999999999999996 76 6666   6899998764

>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=99.40  E-value=1.4e-13  Score=108.52  Aligned_cols=76  Identities=16%  Similarity=0.103  Sum_probs=67.2

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecC
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPL  267 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~  267 (503)
                      ++|||+|||.++++++|+++|++||.|..+.+...     ++||||+|.+.++|.+|++.||+...+   .+++|.|.++
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-----rg~aFV~f~~~~~A~~Ai~~lng~~~~---~G~~i~V~~a   73 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIETLSGKVEL---HGKIMEVDYS   73 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE-----TTEEEECCSCHHHHHHHHHHHTTTCEE---TTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc-----cceEEEEECCHHHHHHHHHHhCCCeEE---CCEEEEEEEc
Confidence            47999999999999999999999999988888765     789999999999999999999743445   6899999998


Q ss_pred             Cccc
Q psy93           268 ELTD  271 (503)
Q Consensus       268 ~~~~  271 (503)
                      .+..
T Consensus        74 ~~k~   77 (80)
T d2cqha1          74 VSKK   77 (80)
T ss_dssp             CCCC
T ss_pred             CCcC
Confidence            7654

>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=99.40  E-value=2.5e-13  Score=110.91  Aligned_cols=76  Identities=22%  Similarity=0.246  Sum_probs=68.8

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ..++|||+|||..+++++|+++|+.||.|.+|+++.+     ++||||+|.+.++|.+|+..|| +..+   .+++|.|.
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~-----kg~afV~f~~~~~A~~Ai~~l~-~~~i---~g~~l~v~   87 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVN-GTTI---EGHVVKCY   87 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHT-TCEE---TTEECEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHHHHHHHhC-CCEE---CCEEEEEE
Confidence            4568999999999999999999999999999999977     7899999999999999999997 6656   68999999


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      |+...
T Consensus        88 ~ak~~   92 (96)
T d1x4ga1          88 WGKES   92 (96)
T ss_dssp             CCCCC
T ss_pred             EcCCC
Confidence            97553

>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=99.39  E-value=4.2e-14  Score=114.43  Aligned_cols=79  Identities=16%  Similarity=0.105  Sum_probs=71.4

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ...+|||+|||.++++++|+++|+.||.|..+.|+.+.++.+++||||+|.+.++|.+||+ || +..+   .+++|.|.
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~-g~~~---~g~~i~V~   86 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LT-GLKV---FGNEIKLE   86 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GG-GEEE---TTEEEEEE
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cC-CcEE---CCEEEEEE
Confidence            3568999999999999999999999999999988877889999999999999999999995 86 6666   69999999


Q ss_pred             cCCc
Q psy93           266 PLEL  269 (503)
Q Consensus       266 ~~~~  269 (503)
                      ++..
T Consensus        87 ~ak~   90 (91)
T d1fjeb1          87 KPKG   90 (91)
T ss_dssp             CCCC
T ss_pred             ecCC
Confidence            8764

>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=99.39  E-value=5.2e-15  Score=119.53  Aligned_cols=71  Identities=35%  Similarity=0.542  Sum_probs=62.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEE-----------ecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEE
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFI-----------NKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIR  182 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i-----------~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~  182 (503)
                      .+|||+|||+++|+++|+++|+.||.|..+.+           .++++||||+|.+.++|++|+. ||+..|.|++|+|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            47999999999999999999999998765443           3568999999999999999985 99999999999997


Q ss_pred             ecc
Q psy93           183 FAP  185 (503)
Q Consensus       183 ~a~  185 (503)
                      .++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.39  E-value=1.5e-13  Score=115.04  Aligned_cols=75  Identities=25%  Similarity=0.311  Sum_probs=66.2

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      +++|||+|||..+++++|+++|+.||+|..|.|..     +++||||+|.+.++|.+|+..|| +..+   .+++|.|+|
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~-----~kg~afV~f~~~~~A~~A~~~ln-g~~~---~gr~l~v~~   80 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLA-YSKF---HHVPLYLEW   80 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHT-TCBS---SSSBCEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec-----cCceEEEEEcCHHHHHHHHHHHc-CCcc---CCCeEEEEE
Confidence            56899999999999999999999999999988753     37899999999999999999997 6655   589999988


Q ss_pred             CCcc
Q psy93           267 LELT  270 (503)
Q Consensus       267 ~~~~  270 (503)
                      +...
T Consensus        81 a~~~   84 (111)
T d1whxa_          81 APIG   84 (111)
T ss_dssp             EETT
T ss_pred             CCCC
Confidence            6543

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.38  E-value=2.5e-13  Score=108.57  Aligned_cols=75  Identities=17%  Similarity=0.158  Sum_probs=68.1

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      .++|||+|||.++++++|+++|+.||+|.+|.+.++     ++||||+|.+.++|.+|+..|| +..+   .+++|.|++
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-----k~~afV~f~~~~~A~~A~~~l~-g~~i---~g~~l~V~~   78 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELD-NMPL---RGKQLRVRF   78 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHT-TCCB---TTBCCEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-----cceEEEEECCHHHHHHHHHHhC-CCEE---CCEEEEEEE
Confidence            457999999999999999999999999999999876     7899999999999999999997 6655   689999999


Q ss_pred             CCcc
Q psy93           267 LELT  270 (503)
Q Consensus       267 ~~~~  270 (503)
                      +.+.
T Consensus        79 A~~~   82 (86)
T d2cpja1          79 ACHS   82 (86)
T ss_dssp             SSCC
T ss_pred             CCCc
Confidence            8765

>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=99.38  E-value=4.8e-13  Score=108.89  Aligned_cols=80  Identities=20%  Similarity=0.109  Sum_probs=69.7

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .+.++|||+|||+.+++++|+++|+.||.|..+.+..+  ..+++||||+|.+.++|.+||..|| +..+   .+++|.|
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~--~~~~g~afV~f~~~e~a~~Ai~~l~-g~~~---~g~~l~V   85 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRD-GYDY---DGYRLRV   85 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHT-TCEE---TTEECEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc--ccccceEEEEECCHHHHHHHHHHhC-CCEE---CCEEEEE
Confidence            34678999999999999999999999999999887655  3458999999999999999999997 6666   6899999


Q ss_pred             ecCCcc
Q psy93           265 EPLELT  270 (503)
Q Consensus       265 ~~~~~~  270 (503)
                      +++...
T Consensus        86 ~~a~~~   91 (95)
T d1x4aa1          86 EFPRSG   91 (95)
T ss_dssp             ECCCCC
T ss_pred             EeccCC
Confidence            997653

>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=99.37  E-value=2.9e-13  Score=106.89  Aligned_cols=73  Identities=15%  Similarity=0.152  Sum_probs=64.2

Q ss_pred             CcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCce-EEEEecccc
Q psy93           113 NCRLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRS-LKIRFAPIN  187 (503)
Q Consensus       113 ~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~-l~V~~a~~~  187 (503)
                      .+.|+|++||++++++.| .+|++||+|.++.+.++++||||+|.++++|.+||+ +||..|.|+. |.|..+..+
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~k   77 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDK   77 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCH
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCCh
Confidence            568999999999986655 579999999999999999999999999999999996 8999999975 568776543

>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=99.37  E-value=1.2e-13  Score=107.48  Aligned_cols=73  Identities=16%  Similarity=0.225  Sum_probs=63.5

Q ss_pred             ceeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       189 ~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      +|||+|||+++|+++|+++|++||.|..|.|+.| .++.++|||||+|.+.++|.+||+..  .+.+   .++.|.|+.
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~--~~~i---~g~~i~vk~   74 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK--YHNV---GLSKCEIKV   74 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCS--SCCB---TTBCCEEEC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhC--CCEE---CCEEeEEEE
Confidence            5899999999999999999999999999999988 57899999999999999999999753  3334   566676654

>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=99.36  E-value=6.4e-13  Score=106.49  Aligned_cols=79  Identities=16%  Similarity=0.204  Sum_probs=67.5

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      +|+++|||+|||.++++++|.++|+.||.|..+.+..+   ++++||||+|.+.++|.+|+..|++..+.   .+++|.|
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~---~~~~~afV~f~~~~~A~~A~~~l~~~~i~---~g~~l~v   81 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDLHNHDLG---ENHHLRV   81 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS---SSTTCEEEEESSHHHHHHHHHHHTTCBSS---SSCBCEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee---cccceeEEEECCHHHHHHHHHhccCCEec---CCCEEEE
Confidence            56789999999999999999999999999988877654   34779999999999999999999844332   5799999


Q ss_pred             ecCCc
Q psy93           265 EPLEL  269 (503)
Q Consensus       265 ~~~~~  269 (503)
                      .+++.
T Consensus        82 ~~sk~   86 (88)
T d2adca2          82 SFSKS   86 (88)
T ss_dssp             EECSS
T ss_pred             EeCCC
Confidence            98754

>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=99.36  E-value=7.5e-13  Score=109.49  Aligned_cols=82  Identities=17%  Similarity=0.097  Sum_probs=69.3

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeC--CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeE
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVD--ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPV  262 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d--~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl  262 (503)
                      .+.++|||+|||.++++++|+++|+.|| |..+.++.+  .++.+++||||+|.+.++|.+|+ .|| +..+   .++.|
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~-~~~~---~gr~l   86 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLN-EESL---GNKRI   86 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGG-TCEE---TTEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcC-CCEE---CCEEE
Confidence            3568999999999999999999999999 677777665  46788999999999999998776 586 6666   68999


Q ss_pred             EeecCCcccc
Q psy93           263 IVEPLELTDE  272 (503)
Q Consensus       263 ~V~~~~~~~~  272 (503)
                      .|.++.+...
T Consensus        87 ~V~~a~~~~~   96 (104)
T d1wi8a_          87 RVDVADQAQD   96 (104)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEECCCCCC
Confidence            9999876654

>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=99.36  E-value=8e-13  Score=105.41  Aligned_cols=77  Identities=21%  Similarity=0.157  Sum_probs=68.0

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeee-eEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIER-AIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~-~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ..++|||+|||.++++++|+++|+.||.|.. +.+..+.++.++|+|||+|.+.++|.+|+..|| +..+   .+++|.|
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~-~~~l---~gr~i~v   83 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLN-DRPI---GSRKVKL   83 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTT-TCEE---TTEECEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcC-CCEE---CCEEEEE
Confidence            3567999999999999999999999999976 466677889999999999999999999999997 6555   6888888


Q ss_pred             ec
Q psy93           265 EP  266 (503)
Q Consensus       265 ~~  266 (503)
                      ..
T Consensus        84 ~l   85 (86)
T d2cqpa1          84 VL   85 (86)
T ss_dssp             EE
T ss_pred             EE
Confidence            75

>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=99.34  E-value=1.2e-12  Score=107.53  Aligned_cols=81  Identities=26%  Similarity=0.270  Sum_probs=69.5

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeee--------eEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeec
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIER--------AIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLT  256 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~--------~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~  256 (503)
                      ..++|||+|||..+++++|.++|+.||.|..        +.+..+ .++.+++||||+|.+.++|.+|+..|| +..+  
T Consensus         7 ~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~-g~~~--   83 (101)
T d2cpea1           7 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFD-GKDF--   83 (101)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHT-TCEE--
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhC-CCEE--
Confidence            3579999999999999999999999998753        344454 468889999999999999999999997 6666  


Q ss_pred             CCCCeEEeecCCcc
Q psy93           257 QSLRPVIVEPLELT  270 (503)
Q Consensus       257 ~~~rpl~V~~~~~~  270 (503)
                       .+++|.|.++...
T Consensus        84 -~gr~i~V~~a~~~   96 (101)
T d2cpea1          84 -QGSKLKVSLARKK   96 (101)
T ss_dssp             -TTEECEEECSSCC
T ss_pred             -CCEEEEEEEcCCC
Confidence             6999999998764

>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=99.34  E-value=8.1e-13  Score=106.24  Aligned_cols=75  Identities=16%  Similarity=0.256  Sum_probs=64.8

Q ss_pred             ccceeccCcccccCHHHH---HHHhccCCCeeeeEEEeCC-CC---CceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCC
Q psy93           187 NAAIKVKNLTSCVTNELL---ELAFGVFGDIERAIVIVDE-RG---NSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSL  259 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L---~~~Fs~~G~V~~~~v~~d~-~g---~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~  259 (503)
                      .++|||+|||+.+++++|   .++|++||+|..|.++++. ++   ...+||||+|.+.++|.+|+..|| +..+   .+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~ln-g~~~---~g   83 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVN-NVVV---DG   83 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHT-TEEE---TT
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhC-CCEE---CC
Confidence            467999999999999999   6789999999999999874 32   345899999999999999999997 7776   68


Q ss_pred             CeEEee
Q psy93           260 RPVIVE  265 (503)
Q Consensus       260 rpl~V~  265 (503)
                      ++|.|.
T Consensus        84 r~lkvS   89 (89)
T d2cpia1          84 RTLKAS   89 (89)
T ss_dssp             EEEEEE
T ss_pred             EEEEEC
Confidence            888763

>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=99.34  E-value=1.1e-12  Score=107.07  Aligned_cols=80  Identities=18%  Similarity=0.128  Sum_probs=69.6

Q ss_pred             cccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEE
Q psy93           184 APINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVI  263 (503)
Q Consensus       184 a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~  263 (503)
                      +.|+++|||.|||+++++++|+++|++||.|..+.+.++     ++||||+|.+.++|.+|+..|| +..+ ....++|.
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~-----~~~afV~f~~~~~A~~A~~~l~-~~~i-~g~~~~l~   86 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMR-GFPL-GGPDRRLR   86 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHT-TCBC-SSSSCBCE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-----ccEEEeccCCHHHHHHHHHHhC-CCEe-CCCceEEE
Confidence            457799999999999999999999999999999999876     7899999999999999999998 5444 33457899


Q ss_pred             eecCCcc
Q psy93           264 VEPLELT  270 (503)
Q Consensus       264 V~~~~~~  270 (503)
                      |++++..
T Consensus        87 v~~ak~~   93 (97)
T d1whya_          87 VDFAKSG   93 (97)
T ss_dssp             EEECCCC
T ss_pred             EEeCCCC
Confidence            9998653

>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=99.34  E-value=1.8e-12  Score=103.33  Aligned_cols=77  Identities=19%  Similarity=0.216  Sum_probs=68.2

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      .++|||+|||..+++++|+++|+.||.|..+.+...     ++||||+|.+.++|..|+..|| +..+   .+++|.|.+
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~-----rg~afV~f~~~~~A~~Ai~~l~-~~~i---~g~~i~V~~   78 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-----RDYAFVHFSNREDAVEAMKALN-GKVL---DGSPIEVTL   78 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-----SSEEEEEESSHHHHHHHHHHHS-SEEE---TTEEEEEEC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccc-----cEEEEEEeCCHHHHHHHHHHcC-CCEE---CCEEEEEEe
Confidence            367999999999999999999999999988877554     7899999999999999999997 7766   699999999


Q ss_pred             CCcccc
Q psy93           267 LELTDE  272 (503)
Q Consensus       267 ~~~~~~  272 (503)
                      +.+.+.
T Consensus        79 akP~~~   84 (86)
T d2cpda1          79 AKPVDK   84 (86)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            876643

>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=99.32  E-value=1.2e-12  Score=102.70  Aligned_cols=74  Identities=20%  Similarity=0.169  Sum_probs=65.6

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      .+++|||+||+  +|+++|+++|++||.|.++.+.++     ++||||+|.+.++|.+|+..|| +..+   .+++|.|.
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~-----~~~afV~f~~~~~A~~Ai~~ln-g~~~---~g~~l~V~   72 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAELN-GTQV---ESVQLKVN   72 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT-----TTEEEEECSSHHHHHHHHHHHT-TCBC---SSCBCEEE
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC-----CCEEEEEEcccHHHHHHHHHhC-CCEE---CCEEEEEE
Confidence            46789999996  899999999999999999999765     7799999999999999999997 6665   68999999


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      |+.+.
T Consensus        73 ~a~~~   77 (79)
T d2bz2a1          73 IARKQ   77 (79)
T ss_dssp             ECCSS
T ss_pred             EecCC
Confidence            98643

>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=99.32  E-value=5.5e-13  Score=106.72  Aligned_cols=72  Identities=24%  Similarity=0.214  Sum_probs=62.1

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecC
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPL  267 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~  267 (503)
                      ++|||+|||+.+++++|+++|++||.|.++.++.+      +||||+|.+.++|.+||..|| +..+   .++.+.|.++
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~-g~~~---~g~~i~v~~~   70 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLD-NTKF---RSHEGETAYI   70 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHT-TCBC---CCTTSCCCBC
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc------ceeeEEeCCHHHHHHHHHHhC-CCEE---CCcEeEEeEE
Confidence            46999999999999999999999999999988654      799999999999999999997 6555   4666666665


Q ss_pred             Cc
Q psy93           268 EL  269 (503)
Q Consensus       268 ~~  269 (503)
                      ..
T Consensus        71 ~~   72 (87)
T d3begb1          71 RV   72 (87)
T ss_dssp             EE
T ss_pred             ec
Confidence            43

>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=99.32  E-value=5.2e-13  Score=102.82  Aligned_cols=64  Identities=22%  Similarity=0.276  Sum_probs=59.1

Q ss_pred             eeccCcccccCHHHHHHHhccCCCeeeeEEEeC-CCCCceeEEEEEeCCHHHHHHHHHHhhCCeee
Q psy93           190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVD-ERGNSKCEGIVEFARKPAAAQALRRCAEGCFF  254 (503)
Q Consensus       190 L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d-~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~  254 (503)
                      |||+|||.++|+++|+++|+.||.|..++++.+ .++.+++||||+|.+.++|.+|+..|| +..+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~ln-g~~~   65 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALK-ASGV   65 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHH-HHTC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhC-CCEE
Confidence            799999999999999999999999999999887 578899999999999999999999998 4444

>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=99.32  E-value=1.7e-12  Score=105.84  Aligned_cols=79  Identities=22%  Similarity=0.169  Sum_probs=69.0

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      +.++|||+|||.++++++|+++|+.||.|..+..    ++.+++||||+|.+.++|.+|+..|| +..+   .+++|.|.
T Consensus        15 ~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~----~~~~~~~afV~f~~~~~A~~A~~~l~-~~~~---~gr~i~V~   86 (96)
T d1fjca_          15 AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAEKNLEEKQ-GAEI---DGRSVSLY   86 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE----TTEEEEEEEEEESSHHHHHHHHHHTT-EEEE---TTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee----cCccccEEEEEeCCHHHHHHHHHHcC-CCEE---CCEEEEEE
Confidence            4678999999999999999999999998876542    56779999999999999999999997 7766   79999999


Q ss_pred             cCCcccc
Q psy93           266 PLELTDE  272 (503)
Q Consensus       266 ~~~~~~~  272 (503)
                      ++.+...
T Consensus        87 ~a~~k~~   93 (96)
T d1fjca_          87 YTGEKGG   93 (96)
T ss_dssp             ECSSSCC
T ss_pred             EeCCCCC
Confidence            9877643

>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=99.32  E-value=2.1e-12  Score=100.27  Aligned_cols=74  Identities=24%  Similarity=0.181  Sum_probs=64.7

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecC
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPL  267 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~  267 (503)
                      ++|||+|||.++++++|+++|+.||.|..+.+..+..+. ++||||+|.+.++|.+|+. +| +..+   .+++|.|..+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN-FRFARIEFARYDGALAAIT-KT-HKVV---GQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS-SEEEEEEESSHHHHHHHHT-TT-TCEE---TTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc-ceEEEEEEcchHHhHHHHH-hc-CcEE---CCEEEEEEEC
Confidence            479999999999999999999999999999999886554 5799999999999999985 65 5666   6888888754

>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=99.31  E-value=1.8e-12  Score=103.89  Aligned_cols=79  Identities=14%  Similarity=0.185  Sum_probs=69.1

Q ss_pred             cccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhh-CCeeeecCCCCeE
Q psy93           184 APINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCA-EGCFFLTQSLRPV  262 (503)
Q Consensus       184 a~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln-~g~~~~~~~~rpl  262 (503)
                      .+|+++|||+|||.++++++|.++|+.||.|.++.+..+     +++|||+|.+.++|..|+..++ ++..+   .+++|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~-----~~~afV~f~~~e~A~~a~~~~~~~~~~~---~g~~l   76 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHL---RNQPI   76 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEE---TTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc-----ceEEEEEeCCHHHHHHHHHHHccCCCcc---CCCEE
Confidence            357889999999999999999999999999999998866     6799999999999999999875 24444   68999


Q ss_pred             EeecCCcc
Q psy93           263 IVEPLELT  270 (503)
Q Consensus       263 ~V~~~~~~  270 (503)
                      .|.+....
T Consensus        77 ~v~~sk~~   84 (88)
T d2cq1a1          77 YIQYSNHK   84 (88)
T ss_dssp             EEEECSCS
T ss_pred             EEEECCCC
Confidence            99997654

>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=99.31  E-value=7.2e-13  Score=106.93  Aligned_cols=80  Identities=24%  Similarity=0.315  Sum_probs=68.7

Q ss_pred             cccceeccCcccccCHHHHH----HHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCe
Q psy93           186 INAAIKVKNLTSCVTNELLE----LAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRP  261 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~----~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rp  261 (503)
                      |+++|||+|||..+++++|+    ++|++||+|.+|.+..  ++.+++||||+|.+.++|.+|+..+| +..+   .+++
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~--~~~~~g~afV~F~~~~~A~~A~~~~~-~~~~---~g~~   75 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQ-GFPF---YDKP   75 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHT-TCEE---TTEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee--eccCCCceEEEECCHHHHHHHHHHhC-CCEE---CCEE
Confidence            57899999999999999886    4689999999987754  35568999999999999999999997 6666   6899


Q ss_pred             EEeecCCccc
Q psy93           262 VIVEPLELTD  271 (503)
Q Consensus       262 l~V~~~~~~~  271 (503)
                      |.|.+++...
T Consensus        76 l~v~~ak~~~   85 (91)
T d1nu4a_          76 MRIQYAKTDS   85 (91)
T ss_dssp             CEEEECSSCC
T ss_pred             EEEEEeCCCc
Confidence            9999987653

>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=99.31  E-value=2e-12  Score=105.83  Aligned_cols=74  Identities=19%  Similarity=0.214  Sum_probs=64.9

Q ss_pred             cccceeccCcc-cccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLT-SCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp-~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ..++|||.||| ..+++++|+++|++||.|.+|.|.       ++||||+|.+.++|.+||..|| +..+   .+++|.|
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~-------rg~aFV~f~~~~~A~~Ai~~ln-g~~~---~g~~l~V   82 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-------KGFAFVQYVNERNARAAVAGED-GRMI---AGQVLDI   82 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE-------TEEEEEEESSHHHHHHHHHTTT-TCEE---TTEECEE
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe-------CCeEEEEECCHHHHHHHHHHcC-CCEE---CCEEEEE
Confidence            35689999997 567888999999999999999883       6899999999999999999997 6666   6899999


Q ss_pred             ecCCcc
Q psy93           265 EPLELT  270 (503)
Q Consensus       265 ~~~~~~  270 (503)
                      +++...
T Consensus        83 ~~a~~~   88 (98)
T d1wf2a_          83 NLAAEP   88 (98)
T ss_dssp             EETTSC
T ss_pred             EECCCC
Confidence            998654

>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=99.30  E-value=2.6e-12  Score=107.00  Aligned_cols=80  Identities=21%  Similarity=0.268  Sum_probs=67.5

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      +..+|||+|||..+|+++|+++|++||.|..|.++.+   ++++||||+|.+.++|.+|+..||+..+.  ..++.|.|.
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~---~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~--~~~~~l~v~   80 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDGQNIY--NACCTLRID   80 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEE---TTEEEEEEEESCHHHHHHHHHHHHSCCSS--TTCCCCEEE
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEee---CCCCeEEEEECCHHHHHHHHHHHCCCEec--cCCcEEEEE
Confidence            4467899999999999999999999999999999877   34899999999999999999999844332  246778888


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      +..+.
T Consensus        81 ~s~~~   85 (108)
T d2adba1          81 FSKLT   85 (108)
T ss_dssp             ECSSC
T ss_pred             ecCCc
Confidence            76554

>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=99.30  E-value=3e-12  Score=116.08  Aligned_cols=76  Identities=22%  Similarity=0.412  Sum_probs=68.5

Q ss_pred             cCCCcEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec------CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEe
Q psy93           110 FANNCRLYLGNIGGDITENDIIELFKPYGETQELFINK------EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRF  183 (503)
Q Consensus       110 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~------~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~  183 (503)
                      ....++|||+|||.++|+++|+++|+.||.|..+.|+.      +++||||+|.+.++|.+||. +++..|.|++|.|.+
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~  172 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRK  172 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEE
T ss_pred             ccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEe
Confidence            34567899999999999999999999999999998864      35799999999999999997 788999999999999


Q ss_pred             ccc
Q psy93           184 API  186 (503)
Q Consensus       184 a~~  186 (503)
                      |.+
T Consensus       173 A~~  175 (183)
T d1u1qa_         173 ALS  175 (183)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            854

>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=99.30  E-value=3.4e-12  Score=102.27  Aligned_cols=75  Identities=17%  Similarity=0.125  Sum_probs=63.6

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      .+++|||+|||.++++++|+++|+.|| +..+.+.     .+++||||+|.+.++|.+|+..|| +..+   .+++|.|+
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~-----~~kg~afV~f~~~~~A~~Ai~~ln-~~~~---~G~~l~V~   73 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFH-QYSF---RGKDLIVQ   73 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHT-TEEE---TTEEEEEE
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeee-----ccCCceEEEECCHHHHHHHHHHhC-CCEE---CCEEEEEE
Confidence            357899999999999999999999999 3334443     348899999999999999999997 6666   79999999


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      +++..
T Consensus        74 ~a~~~   78 (88)
T d1wg1a_          74 LQPTD   78 (88)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            98554

>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=99.30  E-value=1.8e-12  Score=106.88  Aligned_cols=79  Identities=18%  Similarity=0.114  Sum_probs=69.1

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ...+|||+|||.++|+++|+++|+.|+ |..+.++.+.++.+++||||+|.+.++|.+|+. +| +..+   .+|.|.|.
T Consensus        14 ~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~-~~~i---~gR~I~V~   87 (102)
T d1weza_          14 TGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KD-KANM---QHRYVELF   87 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TS-SCCS---SSSCCEEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cC-CCEE---CCEEEEEE
Confidence            456899999999999999999999997 557888888889999999999999999999986 75 6666   68999998


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      +....
T Consensus        88 ~s~~~   92 (102)
T d1weza_          88 LNSTA   92 (102)
T ss_dssp             EECCC
T ss_pred             EcCCC
Confidence            86654

>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=99.29  E-value=3.9e-12  Score=105.17  Aligned_cols=79  Identities=18%  Similarity=0.213  Sum_probs=68.2

Q ss_pred             ccccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           185 PINAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       185 ~~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      .++.+|||+|||..+++++|.++|+.||.|..+.+.++     +++|||+|.+.++|..|+..|+...+.  ..+++|.|
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~-----k~~AfV~f~~~e~A~~ai~~~~~~~~~--~~g~~l~v   85 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVY--IAGQQAFF   85 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCB--SSSSBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec-----ceeEEEEeCCHHHHHHHHHHHcCCCcE--EeeEEEEE
Confidence            45789999999999999999999999999999998765     789999999999999999988633222  26889999


Q ss_pred             ecCCcc
Q psy93           265 EPLELT  270 (503)
Q Consensus       265 ~~~~~~  270 (503)
                      .+++..
T Consensus        86 ~~s~~~   91 (104)
T d1wexa_          86 NYSTSK   91 (104)
T ss_dssp             EECSSS
T ss_pred             EEcCCC
Confidence            998654

>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=99.28  E-value=1.7e-12  Score=104.03  Aligned_cols=77  Identities=18%  Similarity=0.161  Sum_probs=65.8

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      .+++|||+|||..+|+++|+++|++||.|.+|++..+    +++||||+|.+.++|.+|+.   ++..+   .+++|.|.
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 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCG---EDLII---KGISVHIS   73 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTT---CEEEE---TTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec----cCceEEEEECCHHHHHHHHh---CCCEE---CCEEeEEE
Confidence            4679999999999999999999999999999876543    57899999999999999974   35555   79999999


Q ss_pred             cCCcccc
Q psy93           266 PLELTDE  272 (503)
Q Consensus       266 ~~~~~~~  272 (503)
                      ++.+..+
T Consensus        74 ~a~~k~~   80 (88)
T d1wf0a_          74 NAEPKHN   80 (88)
T ss_dssp             CCCCCCC
T ss_pred             eCCCCCC
Confidence            9876543

>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=99.28  E-value=1.6e-12  Score=107.29  Aligned_cols=79  Identities=19%  Similarity=0.204  Sum_probs=68.8

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeE-EEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAI-VIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~-v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ...+|||+|||.++++++|.++|+.||.|..+. +..+.++.++|||||+|.+.++|.+|+. || +..+   .++.|.|
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n-~~~i---~gr~i~V   81 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LH-RKKL---NGREAFV   81 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GC-SEEE---TTEEEEE
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cC-CCeE---CCcEEEE
Confidence            456899999999999999999999999998754 4455789999999999999999999996 75 7777   7899999


Q ss_pred             ecCCc
Q psy93           265 EPLEL  269 (503)
Q Consensus       265 ~~~~~  269 (503)
                      .++..
T Consensus        82 ~~~~~   86 (103)
T d2cpya1          82 HVVTL   86 (103)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            88644

>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=99.28  E-value=1.1e-13  Score=114.84  Aligned_cols=72  Identities=17%  Similarity=0.302  Sum_probs=66.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEec-----CCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINK-----EKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~-----~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      +.++|.+++.++++++|+++|++||+|.+|.|++     ++|||||+|.+.++|.+|+..|||..+.|++|.|++++
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~sP  104 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELSP  104 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEECC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEECC
Confidence            4588999999999999999999999999999964     36999999999999999999999999999999999874

>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=99.27  E-value=4e-12  Score=105.07  Aligned_cols=80  Identities=19%  Similarity=0.229  Sum_probs=68.1

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEE-eCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVI-VDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~-~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ..+|||+|||.++|+++|+++|+.||.|..+.++ .+.++.++|||||+|.+.++|.+|+. +| +..+   .+|.|.|.
T Consensus        15 ~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~-~~~i---~gR~i~V~   89 (104)
T d1wg5a_          15 DGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KH-KERI---GHRYIEIF   89 (104)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TT-TCCS---SSSCCEEE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hC-CCEE---cceEEEEE
Confidence            4579999999999999999999999998875554 45788999999999999999999996 65 6666   68889998


Q ss_pred             cCCccc
Q psy93           266 PLELTD  271 (503)
Q Consensus       266 ~~~~~~  271 (503)
                      +....+
T Consensus        90 ~~~~~~   95 (104)
T d1wg5a_          90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            876553

>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=99.26  E-value=8.1e-12  Score=96.93  Aligned_cols=71  Identities=17%  Similarity=0.146  Sum_probs=61.1

Q ss_pred             eeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecCCc
Q psy93           190 IKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPLEL  269 (503)
Q Consensus       190 L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~~~  269 (503)
                      |||+|||+++++++|+++|++|| +..+.+.     .+++||||+|.+.++|.+|+..|| +..+   .+++|.|.++..
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~-----~~~g~afv~f~~~~~A~~Ai~~ln-~~~~---~g~~l~V~~a~~   70 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD-----KYKGTAFVTLLNGEQAEAAINTFH-QSRL---RERELSVQLQPT   70 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE-----TTTTEEEEEESSHHHHHHHHHHHT-TEES---SSCEEEEEECCS
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec-----ccceeEEEEECCHHHHHHHHHHhC-CccC---CCCEEEEEEeCC
Confidence            79999999999999999999999 4444443     348899999999999999999997 6666   699999999854


Q ss_pred             c
Q psy93           270 T  270 (503)
Q Consensus       270 ~  270 (503)
                      .
T Consensus        71 d   71 (75)
T d1wi6a1          71 D   71 (75)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.25  E-value=4.4e-12  Score=103.75  Aligned_cols=73  Identities=22%  Similarity=0.151  Sum_probs=62.6

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEee
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVE  265 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~  265 (503)
                      ...+|||.|||..+++++|+++|+.||+|..+.|..      ++||||+|.+.++|.+||+.|| +..+   .++.+.|.
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~ln-g~~~---~g~~i~v~   83 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK------DGMGMVEYLRKEDMEYALRKLD-DTKF---RSHEGETS   83 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET------TTEEEEEESSHHHHHHHHHHHS-SEEE---ECTTSCEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc------cceEEEEECCHHHHHHHHHHhC-CCEe---CCeEEEEE
Confidence            356799999999999999999999999999998864      4799999999999999999997 7777   45566665


Q ss_pred             cCC
Q psy93           266 PLE  268 (503)
Q Consensus       266 ~~~  268 (503)
                      +..
T Consensus        84 ~~~   86 (98)
T d1wg4a_          84 YIR   86 (98)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            543

>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=99.22  E-value=9.9e-12  Score=101.78  Aligned_cols=77  Identities=16%  Similarity=0.216  Sum_probs=67.0

Q ss_pred             CCcEEEEcCC--CCCCC---------HHHHHHhhccCCCeEEEEEecC--CCceEEeeCCHHHHHHHHHHhCCccccCce
Q psy93           112 NNCRLYLGNI--GGDIT---------ENDIIELFKPYGETQELFINKE--KMFGFIRMDYKHNADKAKAKLDGHVLKGRS  178 (503)
Q Consensus       112 ~~~~l~V~nL--p~~~t---------e~~L~~~F~~~G~V~~v~i~~~--kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~  178 (503)
                      .+.+|+|.||  |.++.         .++|++.|++||.|..|.+..+  +|||||+|.+.++|.+|+..|||..+.|++
T Consensus         7 ~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr~   86 (99)
T d2dita1           7 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQ   86 (99)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTEE
T ss_pred             CccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEECCEE
Confidence            4678999999  54431         3689999999999999998754  689999999999999999999999999999


Q ss_pred             EEEEeccccc
Q psy93           179 LKIRFAPINA  188 (503)
Q Consensus       179 l~V~~a~~~~  188 (503)
                      |.|.++.+.+
T Consensus        87 i~v~~~~g~~   96 (99)
T d2dita1          87 ITAQAWDGTT   96 (99)
T ss_dssp             CEEEECCSCC
T ss_pred             EEEEEeCCcC
Confidence            9999987654

>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=99.21  E-value=7.3e-12  Score=100.50  Aligned_cols=78  Identities=15%  Similarity=0.144  Sum_probs=67.3

Q ss_pred             ccccceeccCcccc-cCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhh-CCeeeecCCCCeE
Q psy93           185 PINAAIKVKNLTSC-VTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCA-EGCFFLTQSLRPV  262 (503)
Q Consensus       185 ~~~~~L~V~nLp~~-~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln-~g~~~~~~~~rpl  262 (503)
                      .++.+|||.|||.. +|+++|.++|+.||.|.++.++.+     +++|||+|++.++|..|+..|+ ++..+   .+++|
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~-----k~~afV~f~~~~~A~~A~~~l~~~~~~~---~gr~l   77 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALV---FGKPV   77 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEE---TTEEC
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc-----ceEEEEEEcchhhHHHHHHHHhhCCCcc---CCceE
Confidence            45678999999986 889999999999999999999876     6799999999999999999885 34444   79999


Q ss_pred             EeecCCcc
Q psy93           263 IVEPLELT  270 (503)
Q Consensus       263 ~V~~~~~~  270 (503)
                      .|.++...
T Consensus        78 ~V~~s~~~   85 (89)
T d1x4da1          78 RVHLSQKY   85 (89)
T ss_dssp             EEEEECCC
T ss_pred             EEEECCCc
Confidence            99997543

>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=99.19  E-value=8e-12  Score=102.32  Aligned_cols=77  Identities=19%  Similarity=0.299  Sum_probs=65.5

Q ss_pred             cccceeccCcccc-cCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhh-CCeeeecCCCCeEE
Q psy93           186 INAAIKVKNLTSC-VTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCA-EGCFFLTQSLRPVI  263 (503)
Q Consensus       186 ~~~~L~V~nLp~~-~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln-~g~~~~~~~~rpl~  263 (503)
                      ++++|||.|||.+ +|+++|.++|+.||.|.++.++.+     +++|||+|.+.++|..|+..++ ++..+   .+++|.
T Consensus        17 ~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~-----k~~afV~f~~~~~A~~Ai~~~~~~~~~~---~gr~l~   88 (99)
T d1x4fa1          17 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALWF---QGRCVK   88 (99)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCCS---SSSCCE
T ss_pred             CCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec-----CCcEEEEecchHHHHHHHHHHhcCCceE---CCEEEE
Confidence            4578999999975 899999999999999999999876     7899999999999999998654 34444   689999


Q ss_pred             eecCCcc
Q psy93           264 VEPLELT  270 (503)
Q Consensus       264 V~~~~~~  270 (503)
                      |.++...
T Consensus        89 V~~s~~~   95 (99)
T d1x4fa1          89 VDLSEKY   95 (99)
T ss_dssp             EEEECSC
T ss_pred             EEEcCCc
Confidence            9987544

>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=99.18  E-value=1.3e-11  Score=101.94  Aligned_cols=78  Identities=12%  Similarity=-0.034  Sum_probs=67.1

Q ss_pred             cccceeccCccccc-CH----HHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCC
Q psy93           186 INAAIKVKNLTSCV-TN----ELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLR  260 (503)
Q Consensus       186 ~~~~L~V~nLp~~~-te----e~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~r  260 (503)
                      .+++|||.||+.++ ++    ++|.++|+.||.|.++.+++.     +++|||+|.+.++|.+|+..|| +..+   .++
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~-----~~~afV~f~~~~~A~~Ai~~ln-g~~~---~g~   74 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLH-KTEF---LGK   74 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTST-TSEE---TTE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC-----CCEEEEEECCHHHHHHHHHHhc-cccc---CCC
Confidence            46789999999886 33    569999999999999999864     7899999999999999999997 6666   699


Q ss_pred             eEEeecCCcccc
Q psy93           261 PVIVEPLELTDE  272 (503)
Q Consensus       261 pl~V~~~~~~~~  272 (503)
                      +|.|.|+.....
T Consensus        75 ~l~v~~a~~~~~   86 (104)
T d1weya_          75 EMKLYFAQTLHI   86 (104)
T ss_dssp             ECEEECCCCSSC
T ss_pred             EeEEeecccCCC
Confidence            999999876543

>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=99.18  E-value=5.5e-12  Score=104.29  Aligned_cols=76  Identities=16%  Similarity=0.184  Sum_probs=69.5

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecC
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPL  267 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~  267 (503)
                      ..++|.+++..+++++|.++|++||.|.+|.|+++.++.++|+|||+|.+.++|.+|+..|| +.++   .+++|.|++.
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~ln-g~~~---~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLN-NRWF---NGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHT-TCEE---TTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHC-CCEE---CCEEEEEEEC
Confidence            46888999999999999999999999999999988899999999999999999999999997 6666   7899888764

>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=99.17  E-value=7.1e-12  Score=105.02  Aligned_cols=80  Identities=21%  Similarity=0.232  Sum_probs=68.6

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEE-EeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEe
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIV-IVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIV  264 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v-~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V  264 (503)
                      ...+|||+|||..+|+++|.++|+.||.|..+.+ ..+.++.++|||||+|.+.++|.+|+. || +..+   .++.|.|
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~-~~~i---~gR~i~V   91 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RH-KQYM---GNRFIQV   91 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SC-SBCS---TTSCBEE
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cC-CCcC---CCEEEEE
Confidence            3568999999999999999999999999977544 556789999999999999999999996 75 7766   7899999


Q ss_pred             ecCCcc
Q psy93           265 EPLELT  270 (503)
Q Consensus       265 ~~~~~~  270 (503)
                      .++...
T Consensus        92 ~~~~~~   97 (112)
T d1wela1          92 HPITKK   97 (112)
T ss_dssp             EEECHH
T ss_pred             EEcChH
Confidence            876444

>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=99.13  E-value=3e-11  Score=99.23  Aligned_cols=73  Identities=12%  Similarity=0.109  Sum_probs=60.7

Q ss_pred             cccccceeccC--cccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCe
Q psy93           184 APINAAIKVKN--LTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRP  261 (503)
Q Consensus       184 a~~~~~L~V~n--Lp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rp  261 (503)
                      +.|+.+|+|.|  ||..+|+++|+++|++||.|..+.++.+     ++||||+|.+.++|.+|+..|| +..+....+..
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-----k~~aFV~f~~~e~A~~A~~~ln-g~~i~~~~~~~   88 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLN-GKEVVDDLGQK   88 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTT-TCEEECTTSCE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-----ccEEEEEECCHHHHHHHHHHhC-CCCCCCCCCcE
Confidence            35677888855  9999999999999999999999988766     7799999999999999999998 55554433443


Q ss_pred             E
Q psy93           262 V  262 (503)
Q Consensus       262 l  262 (503)
                      +
T Consensus        89 i   89 (101)
T d2cq2a1          89 I   89 (101)
T ss_dssp             E
T ss_pred             E
Confidence            3

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.07  E-value=6.5e-11  Score=97.67  Aligned_cols=75  Identities=17%  Similarity=0.214  Sum_probs=64.6

Q ss_pred             CCcEEEEcCC--CCCCC--------HHHHHHhhccCCCeEEEEEecC--------CCceEEeeCCHHHHHHHHHHhCCcc
Q psy93           112 NNCRLYLGNI--GGDIT--------ENDIIELFKPYGETQELFINKE--------KMFGFIRMDYKHNADKAKAKLDGHV  173 (503)
Q Consensus       112 ~~~~l~V~nL--p~~~t--------e~~L~~~F~~~G~V~~v~i~~~--------kg~aFV~F~~~e~A~~Ai~~l~g~~  173 (503)
                      ++..|+|.||  |.++.        .+||++.|++||.|.+|.|+++        .|++||+|.+.++|.+|+..|||..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            3567999999  55443        4578999999999999999642        4799999999999999999999999


Q ss_pred             ccCceEEEEeccc
Q psy93           174 LKGRSLKIRFAPI  186 (503)
Q Consensus       174 l~g~~l~V~~a~~  186 (503)
                      +.|++|.|.+.+.
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999998764

>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=99.00  E-value=5.9e-12  Score=101.16  Aligned_cols=74  Identities=16%  Similarity=0.139  Sum_probs=62.0

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEe------CCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCe
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIV------DERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRP  261 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~------d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rp  261 (503)
                      ++|||+|||.++|+++|+++|+.||.|..+.+..      ..++.+++||||+|.+.++|.+|+. || +..+   .+++
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~-g~~~---~Gr~   76 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FD-GIIF---QGQS   76 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GS-SCCS---SSSC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hC-CcEE---CCEE
Confidence            5799999999999999999999999887765532      2456789999999999999999985 86 7666   5888


Q ss_pred             EEeec
Q psy93           262 VIVEP  266 (503)
Q Consensus       262 l~V~~  266 (503)
                      |.|..
T Consensus        77 l~V~r   81 (90)
T d1u2fa_          77 LKIRR   81 (90)
T ss_dssp             CCCBC
T ss_pred             EEECC
Confidence            88864

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.98  E-value=1.6e-10  Score=96.67  Aligned_cols=61  Identities=21%  Similarity=0.236  Sum_probs=53.8

Q ss_pred             ceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCH-HHHHHHHHHhhCCeee
Q psy93           189 AIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARK-PAAAQALRRCAEGCFF  254 (503)
Q Consensus       189 ~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~-e~A~kAl~~ln~g~~~  254 (503)
                      .+||+|||+.+|+++|+++|++||+|.+|.|+.+     ++||||.|.+. ++|..|+..+|+..+.
T Consensus        13 ~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~-----kg~gfV~F~~~~~~A~~a~~~~~~~~l~   74 (113)
T d1owxa_          13 LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEALGKAKDANNGNLQ   74 (113)
T ss_dssp             EEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-----CSEEEEEESSCHHHHHHHHHHTTTSCBC
T ss_pred             EEEECCCCCCCCHHHHHHHHHhcCChheEEEecC-----CceEEEEecCcHHHHHHHHHHhcCCcee
Confidence            4589999999999999999999999999999866     78999999985 7899999999854443

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.87  E-value=1.9e-09  Score=87.83  Aligned_cols=79  Identities=18%  Similarity=0.267  Sum_probs=65.0

Q ss_pred             cccceeccCc--cccc---------CHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeee
Q psy93           186 INAAIKVKNL--TSCV---------TNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFF  254 (503)
Q Consensus       186 ~~~~L~V~nL--p~~~---------tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~  254 (503)
                      ...+|+|.||  |.++         ..++|.+.|++||.|..+.+..+   .++|++||+|.+.++|.+|+..|| +.++
T Consensus         7 ~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~---~~~G~~fV~f~~~e~A~~A~~~ln-g~~~   82 (99)
T d2dita1           7 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLD-GRWF   82 (99)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT---CTTCEEEEECSCHHHHHHHHHHST-TCEE
T ss_pred             CccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC---CCccEEEEEECCHHHHHHHHHHhC-CcEE
Confidence            4567899998  4432         23679999999999999988765   457899999999999999999997 7666


Q ss_pred             ecCCCCeEEeecCCccc
Q psy93           255 LTQSLRPVIVEPLELTD  271 (503)
Q Consensus       255 ~~~~~rpl~V~~~~~~~  271 (503)
                         .+++|.|.+++...
T Consensus        83 ---~gr~i~v~~~~g~~   96 (99)
T d2dita1          83 ---GGRQITAQAWDGTT   96 (99)
T ss_dssp             ---TTEECEEEECCSCC
T ss_pred             ---CCEEEEEEEeCCcC
Confidence               79999999986653

>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=98.82  E-value=3e-09  Score=83.33  Aligned_cols=73  Identities=19%  Similarity=0.231  Sum_probs=58.9

Q ss_pred             ccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCe-EEee
Q psy93           187 NAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRP-VIVE  265 (503)
Q Consensus       187 ~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rp-l~V~  265 (503)
                      .+.|+|.++|++.+++.| .+|++||+|.++.+..+     ++||||+|.+.++|.+||. +| +..+   .++. |.|.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~-----~~~~fV~f~~~~~A~~Al~-~n-G~~~---~g~~~vgV~   72 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT-----GNWMHIRYQSKLQARKALS-KD-GRIF---GESIMIGVK   72 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS-----SSEEEEEESSHHHHHHHHT-TT-TCEE---TTTEECEEE
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC-----CCEEEEEEcccHHHHHHHh-cC-CCeE---CCcEEEEEE
Confidence            456899999999987655 57999999999987544     7899999999999999996 76 6666   5664 5687


Q ss_pred             cCCcc
Q psy93           266 PLELT  270 (503)
Q Consensus       266 ~~~~~  270 (503)
                      |...+
T Consensus        73 ~~~~k   77 (81)
T d1wwha1          73 PCIDK   77 (81)
T ss_dssp             ECCCH
T ss_pred             eCCCh
Confidence            76543

>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=98.79  E-value=2.3e-09  Score=88.06  Aligned_cols=82  Identities=13%  Similarity=0.070  Sum_probs=65.8

Q ss_pred             ccccceeccCc--cccc--------CHHHHHHHhccCCCeeeeEEEeCCC---CCceeEEEEEeCCHHHHHHHHHHhhCC
Q psy93           185 PINAAIKVKNL--TSCV--------TNELLELAFGVFGDIERAIVIVDER---GNSKCEGIVEFARKPAAAQALRRCAEG  251 (503)
Q Consensus       185 ~~~~~L~V~nL--p~~~--------tee~L~~~Fs~~G~V~~~~v~~d~~---g~skg~gfV~F~s~e~A~kAl~~ln~g  251 (503)
                      +|+++|+|.|+  |..+        ..++|++.|++||.|.+|.|+++..   ....+++||+|.+.++|.+|+..|| +
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~-G   80 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLT-G   80 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHS-S
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHC-C
Confidence            46778888998  3332        3367899999999999999987643   2346899999999999999999997 6


Q ss_pred             eeeecCCCCeEEeecCCcc
Q psy93           252 CFFLTQSLRPVIVEPLELT  270 (503)
Q Consensus       252 ~~~~~~~~rpl~V~~~~~~  270 (503)
                      .++   .+|+|.+.+++..
T Consensus        81 r~f---~gR~v~v~f~~~~   96 (104)
T d1o0pa_          81 RKF---ANRVVVTKYCDPD   96 (104)
T ss_dssp             CCS---SSSCCEEEEECHH
T ss_pred             CEE---CCeEEEEEEcCHH
Confidence            666   7999999987643

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.21  E-value=0.00046  Score=53.90  Aligned_cols=63  Identities=13%  Similarity=0.230  Sum_probs=54.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecC--------CCceEEeeCCHHHHHHHHHHhCCccccC
Q psy93           114 CRLYLGNIGGDITENDIIELFKPYGETQELFINKE--------KMFGFIRMDYKHNADKAKAKLDGHVLKG  176 (503)
Q Consensus       114 ~~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~--------kg~aFV~F~~~e~A~~Ai~~l~g~~l~g  176 (503)
                      |+|.|..||+++|++++.+.++..+.+........        -.-|||.|.+.+++....+.++|..+.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            57999999999999999999999999887766432        2479999999999999999999997753

>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=96.76  E-value=0.0019  Score=47.22  Aligned_cols=57  Identities=14%  Similarity=0.220  Sum_probs=50.1

Q ss_pred             HHHHhhccCCCeEEEEEecC---CCceEEeeCCHHHHHHHHHHhCCccccCceEEEEecc
Q psy93           129 DIIELFKPYGETQELFINKE---KMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFAP  185 (503)
Q Consensus       129 ~L~~~F~~~G~V~~v~i~~~---kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a~  185 (503)
                      .|.++|.++++|.++.|...   .-.|-|...+..+|..|+..|+...|..+.|.|.++.
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            45668999999999999543   3479999999999999999999999999999998864

>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=96.47  E-value=0.0018  Score=49.83  Aligned_cols=54  Identities=24%  Similarity=0.346  Sum_probs=47.3

Q ss_pred             HHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhCCccccCceEEEEec
Q psy93           128 NDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLDGHVLKGRSLKIRFA  184 (503)
Q Consensus       128 ~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~g~~l~g~~l~V~~a  184 (503)
                      .+|.+.|..||+|.-|+++.  ....|+|.+-.+|.+|++ ++++++.|+.|+|...
T Consensus        39 ~~Llq~l~~~GeViLvRFv~--d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQ--GQMLVTFADSHSALSVLD-VDGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEET--TEEEEECSCSHHHHHHHH-GGGSEETTEEEEEECC
T ss_pred             HHHHHHHhhCCeEEEEEEeC--CeEEEEECCcHHHHHHhc-cCCeEEcceEEEEecC
Confidence            35778899999999999874  468999999999999996 8999999999999753

>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=96.06  E-value=0.015  Score=45.03  Aligned_cols=71  Identities=13%  Similarity=0.178  Sum_probs=56.3

Q ss_pred             cceeccCcccccCHHHHHHHhccCCCeeeeEEEeCC--C-CCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCC
Q psy93           188 AAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDE--R-GNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSL  259 (503)
Q Consensus       188 ~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~--~-g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~  259 (503)
                      ++|.|..||+.+|++++.+.++..+++........+  . ...-.-|+|.|.+.++...-.+.++ ++.+....+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~-g~~F~D~~g   75 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFD-GYVFLDNKG   75 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHT-TCEEECTTC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcC-CcEEEcCCC
Confidence            578999999999999999999999998887666542  1 1223579999999999999999997 655554444

>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=94.17  E-value=0.077  Score=41.09  Aligned_cols=54  Identities=15%  Similarity=0.281  Sum_probs=46.3

Q ss_pred             EEEEcCCCCCCCHHHHHHhhccCCCeEEEEEecCCCceEEeeCCHHHHHHHHHHhC
Q psy93           115 RLYLGNIGGDITENDIIELFKPYGETQELFINKEKMFGFIRMDYKHNADKAKAKLD  170 (503)
Q Consensus       115 ~l~V~nLp~~~te~~L~~~F~~~G~V~~v~i~~~kg~aFV~F~~~e~A~~Ai~~l~  170 (503)
                      .||.-..|..+...||.++|++||.|.--.|  +-.-|||...+.++|..++..+.
T Consensus        17 HVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI--ddTSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          17 HVLHVTFPKEWKTSDLYQLFSAFGNIQISWI--DDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEEECCTTCCHHHHHHHHTTTCSCCCEEE--ETTEEEEECSCHHHHHHHHHHHH
T ss_pred             eeEEEeCCcccchhHHHHHhcCCCceEEEEe--cCceEEEEecCHHHHHHHHHHhc
Confidence            4888899999999999999999999876666  34579999999999998887544

>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=93.69  E-value=0.046  Score=41.77  Aligned_cols=53  Identities=23%  Similarity=0.250  Sum_probs=43.5

Q ss_pred             HHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeec
Q psy93           202 ELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEP  266 (503)
Q Consensus       202 e~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~  266 (503)
                      .+|.+.|..||+|.-++++.+       ...|+|.+-.+|.+|+..  ++..+   .++.+.+..
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d-------~mwVTF~dG~SAL~al~l--~g~~v---~G~~l~It~   91 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG-------QMLVTFADSHSALSVLDV--DGMKV---KGRAVKISG   91 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT-------EEEEECSCSHHHHHHHHG--GGSEE---TTEEEEEEC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC-------eEEEEECCcHHHHHHhcc--CCeEE---cceEEEEec
Confidence            467788999999999999877       689999999999999985  36555   577777754

>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=92.18  E-value=0.2  Score=36.22  Aligned_cols=61  Identities=15%  Similarity=0.182  Sum_probs=48.3

Q ss_pred             HHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhhCCeeeecCCCCeEEeecC
Q psy93           201 NELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCAEGCFFLTQSLRPVIVEPL  267 (503)
Q Consensus       201 ee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln~g~~~~~~~~rpl~V~~~  267 (503)
                      .+.|.+.|.+++.|.++.+....++..  .|.|...+..+|..|+..|+ ...+   ..+.+.|...
T Consensus        10 qq~L~~~f~~h~~V~sv~l~~~~dg~~--~A~V~v~~~q~A~~~v~~Lh-R~Ki---G~KRI~Vs~~   70 (73)
T d2dgxa1          10 QQLLQEAFARHGKVKSVELSPHTDYQL--KAVVQMENLQDAIGAVNSLH-RYKI---GSKKILVSLA   70 (73)
T ss_dssp             HHHHHHHHHHHSCEEEEEECSCCSTTC--CEEEEESSHHHHHHHHHHHT-TEEE---TTEEEEEEEC
T ss_pred             HHHHHHHHHhheeEEEEEEEeccCCcE--EEEEEcCCHHHHHHHHHHHH-HHhc---CCeEEEEEEe
Confidence            356778899999999998877655543  69999999999999999996 6666   4666666553

>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=86.28  E-value=0.92  Score=34.82  Aligned_cols=57  Identities=14%  Similarity=0.166  Sum_probs=45.8

Q ss_pred             cccceeccCcccccCHHHHHHHhccCCCeeeeEEEeCCCCCceeEEEEEeCCHHHHHHHHHHhh
Q psy93           186 INAAIKVKNLTSCVTNELLELAFGVFGDIERAIVIVDERGNSKCEGIVEFARKPAAAQALRRCA  249 (503)
Q Consensus       186 ~~~~L~V~nLp~~~tee~L~~~Fs~~G~V~~~~v~~d~~g~skg~gfV~F~s~e~A~kAl~~ln  249 (503)
                      ....||.-..|......+|.++|+.||.|.-..| .| +     .|||...+.+.|..++..++
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-dd-T-----Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DD-T-----SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ET-T-----EEEEECSCHHHHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cC-c-----eEEEEecCHHHHHHHHHHhc
Confidence            3456788889999999999999999998764333 33 2     79999999999998887765