Psyllid ID: psy2983

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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
Protein Sequence
MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPAAASALNLAQNAILNSSTPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHGVGASTVCFIYSVIFLKLWSYVQVNLWCRHARKQDNPGHQRRQSMSANATSIEILSSHGLLALVIS
Secondary Structure (PSIPRED)
cccccccccccccccccEEEEEcccccccHHHHHHHHcccccEEEEEEEEEccccccccEEEEEEcccccHHHHHHccccEEccEEEEEccccccccccccccccccccccccccEEEEccccccccHHHHHHHccccccEEEEEEEEcccccccccEEEEEEccHHHHHHHHHHHcccccccccEEEEEcccccccccccccccccHHHHHHccccccccHHHHcccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccccEEEEEEEEEEEEEEcccccEEEEEEEccccccHHHHHHccccccHHHHHHHHHccEEEEEcc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccEEEEEcccccccHHHHHHHHHHcccEEEEEEEEEcccccccEEEEEEEccHHHHHHHHHHccccccccEEEEEcccHHHHHHHHHHHccccccccccEEEEEEcccccccHHHHHHHHHHHccEEEEEccEccccccEccEEEEEEccHHHHHHHHHHHcccEEccEEcEEEEEcccHHHHHHcccccccccHccccccccccHHHHHHHHHHccccccccccccccccccccHcccccccccccccccccccHEEEEcccccccccccccHHHHHHHHHHHHHHHccccccccccEEEEEEccHHHHHHHHHHHHHHHHcccccccccccccHcccHHHHHHcccHHEEEEc
Coil and Loop (DISEMBL)
mrpaysddlspeerDARTIFCMQLSQRIRTRDLEEFFssvgkvrdvrlitcnktrrfkgiayiefkdpesvplamglngqkllgipiivqptqaeknragntlpnlqprgtggpmrlYIGSLHFNITEDMLRGifepfgkidniqlmvdpdtgrskgygfitfhsADDAKKAQEQLNGfelagrpmkvgtvtdrnesvgggpsnldtdemERAGVDLGATGRLQLMFKLAegtglelppaAASALNLAQNAilnsstpqvssstappiatQCFLLanmfdpatetnptwdveIRDDVIEECnkhgvgasTVCFIYSVIFLKLWSYVQVNLWCRharkqdnpghqrrqsmsanATSIEILSSHGLLALVIS
Flexible Loop (DISEMBL)
mrpaysddlspeerdARTIFCMQLSQRIRTRDLEeffssvgkvrdvrlitcnktrrfkgiayiefkdpesvpLAMGLNGQKLLGIPIIVQPTQaeknragntlpnlqprgtgGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGfelagrpmkvgtvtdrnesvgggpsnldtdeMERAGVDLGATGRLQLMFKLAEGTGLELPPAAASALNLAQNAILNSstpqvssstaPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHGVGASTVCFIYSVIFLKLWSYVQVNLWCRHARkqdnpghqrRQSMSANATSIEilsshgllalvis
Low Complexity Region (SEG)
MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPaaasalnlaqnailnssTPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHGVGASTVCFIYSVIFLKLWSYVQVNLWCRHARKQDNPGHQRRQSMSANATSIEILSSHGLLALVIS
Disordered region (IsUnstruct)
*****************TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQ***********************PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS**************************************************DLGATGRLQLMFKLAEGTGLEL*******L**********************IATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHGVGASTVCFIYSVIFLKLWSYVQVNLWCRH***************************HGLLAL***
Disordered Region (DISOPRED)
******************IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIV***************************LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG***************************************************************************************************WDVEIRDDVIEECNKHGVGASTVCFIYSVIFLKLWSYVQVNLWCRHARKQD***********ANATSIEILSSHGLLALVIS
Disordered Region (DISEMBL)
*************RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPAAASALNLAQNAILN***********PPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHGVGASTVCFIYSVIFLKLWSYVQVNLWCRHARK*************ANATSIEILSSHGLLALVIS
Disordered Region (DISPRO)
*****S*******RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNT********TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESV******LDTDE*ERAGVDLGATGRLQLMFKLAEGTGLELPPAAA*********************TAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHGVGASTVCFIYSVIFLKLWSYVQVNLWCRHARKQ*****************IEILSSHGLLALVIS
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPAAASALNLAQNAILNSSTPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHGVGASTVCFIYSVIFLKLWSYVQVNLWCRHARKQDNPGHQRRQSMSANATSIEILSSHGLLALVIS
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	370	2.2.26 [Sep-21-2011]
Q5RC80	524	RNA-binding protein 39 OS	yes	N/A	0.8	0.564	0.651	1e-113
Q14498	530	RNA-binding protein 39 OS	no	N/A	0.802	0.560	0.632	1e-112
Q8VH51	530	RNA-binding protein 39 OS	yes	N/A	0.802	0.560	0.632	1e-112
Q86U06	439	Probable RNA-binding prot	no	N/A	0.732	0.617	0.605	1e-86
O13845	603	RNA-binding protein rsd1	yes	N/A	0.791	0.485	0.357	2e-47
P41891	500	Protein gar2 OS=Schizosac	no	N/A	0.505	0.374	0.339	5e-19
Q5R469	558	Poly(U)-binding-splicing	no	N/A	0.456	0.302	0.280	7e-17
Q9UHX1	559	Poly(U)-binding-splicing	no	N/A	0.456	0.302	0.280	7e-17
Q9WV25	564	Poly(U)-binding-splicing	no	N/A	0.456	0.299	0.280	7e-17
Q3UEB3	564	Poly(U)-binding-splicing	no	N/A	0.456	0.299	0.280	7e-17

>sp|Q5RC80|RBM39_PONAB RNA-binding protein 39 OS=Pongo abelii GN=RBM39 PE=2 SV=1

 Score =  408 bits (1049), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 204/313 (65%), Positives = 246/313 (78%), Gaps = 17/313 (5%)

Query: 7   DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
           D+L+PEERDART+FCMQL+ RIR RDLEEFFS+VGKVRDVR+I+   +RR KGIAY+EF 
Sbjct: 143 DNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFV 202

Query: 67  DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
           D  SVPLA+GL GQ++LG+PIIVQ +QAEKNRA     NLQ +G+ GPMRLY+GSLHFNI
Sbjct: 203 DVSSVPLAIGLTGQRVLGVPIIVQASQAEKNRAAAMANNLQ-KGSAGPMRLYVGSLHFNI 261

Query: 127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
           TEDMLRGIFEPFG+I++IQLM+D +TGRSKGYGFITF  ++ AKKA EQLNGFELAGRPM
Sbjct: 262 TEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM 321

Query: 187 KVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPAAASAL- 245
           KVG VT+R ++     S LD+DE+ER G+DLG TGRLQLM +LAEGTGL++PPAA  AL 
Sbjct: 322 KVGHVTERTDA-SSASSFLDSDELERTGIDLGTTGRLQLMARLAEGTGLQIPPAAQQALQ 380

Query: 246 ---NLAQNAILNSSTPQVSSST----------APPIATQCFLLANMFDPATETNPTWDVE 292
              +LA  A+ +  T ++S  T            P+ATQCF L+NMF+P TE    WD E
Sbjct: 381 MSGSLAFGAVADLQT-RLSQQTEASALAAAASVQPLATQCFQLSNMFNPQTEEEVGWDTE 439

Query: 293 IRDDVIEECNKHG 305
           I+DDVIEECNKHG
Sbjct: 440 IKDDVIEECNKHG 452

Transcriptional coactivator for steroid nuclear receptors ESR1/ER-alpha and ESR2/ER-beta, and JUN/AP-1 (By similarity). May be involved in pre-mRNA splicing process.
Pongo abelii (taxid: 9601)

>sp|Q14498|RBM39_HUMAN RNA-binding protein 39 OS=Homo sapiens GN=RBM39 PE=1 SV=2

 Score =  405 bits (1040), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 201/318 (63%), Positives = 244/318 (76%), Gaps = 21/318 (6%)

Query: 7   DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
           D+L+PEERDART+FCMQL+ RIR RDLEEFFS+VGKVRDVR+I+   +RR KGIAY+EF 
Sbjct: 143 DNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFV 202

Query: 67  DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
           D  SVPLA+GL GQ++LG+PIIVQ +QAEKNRA     NLQ +G+ GPMRLY+GSLHFNI
Sbjct: 203 DVSSVPLAIGLTGQRVLGVPIIVQASQAEKNRAAAMANNLQ-KGSAGPMRLYVGSLHFNI 261

Query: 127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
           TEDMLRGIFEPFG+I++IQLM+D +TGRSKGYGFITF  ++ AKKA EQLNGFELAGRPM
Sbjct: 262 TEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM 321

Query: 187 KVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPAAASALN 246
           KVG VT+R ++     S LD+DE+ER G+DLG TGRLQLM +LAEGTGL++PPAA  AL 
Sbjct: 322 KVGHVTERTDA-SSASSFLDSDELERTGIDLGTTGRLQLMARLAEGTGLQIPPAAQQALQ 380

Query: 247 L---------AQNAILNSSTPQVSSST----------APPIATQCFLLANMFDPATETNP 287
           +         A+ + +     ++S  T            P+ATQCF L+NMF+P TE   
Sbjct: 381 MSGSLAFGAVAEFSFVIDLQTRLSQQTEASALAAAASVQPLATQCFQLSNMFNPQTEEEV 440

Query: 288 TWDVEIRDDVIEECNKHG 305
            WD EI+DDVIEECNKHG
Sbjct: 441 GWDTEIKDDVIEECNKHG 458

Transcriptional coactivator for steroid nuclear receptors ESR1/ER-alpha and ESR2/ER-beta, and JUN/AP-1 (By similarity). May be involved in pre-mRNA splicing process.

Homo sapiens (taxid: 9606)

>sp|Q8VH51|RBM39_MOUSE RNA-binding protein 39 OS=Mus musculus GN=Rbm39 PE=1 SV=2

 Score =  405 bits (1040), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 201/318 (63%), Positives = 244/318 (76%), Gaps = 21/318 (6%)

Query: 7   DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
           D+L+PEERDART+FCMQL+ RIR RDLEEFFS+VGKVRDVR+I+   +RR KGIAY+EF 
Sbjct: 143 DNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFV 202

Query: 67  DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
           D  SVPLA+GL GQ++LG+PIIVQ +QAEKNRA     NLQ +G+ GPMRLY+GSLHFNI
Sbjct: 203 DVSSVPLAIGLTGQRVLGVPIIVQASQAEKNRAAAMANNLQ-KGSAGPMRLYVGSLHFNI 261

Query: 127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
           TEDMLRGIFEPFG+I++IQLM+D +TGRSKGYGFITF  ++ AKKA EQLNGFELAGRPM
Sbjct: 262 TEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM 321

Query: 187 KVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPAAASALN 246
           KVG VT+R ++     S LD+DE+ER G+DLG TGRLQLM +LAEGTGL++PPAA  AL 
Sbjct: 322 KVGHVTERTDA-SSASSFLDSDELERTGIDLGTTGRLQLMARLAEGTGLQIPPAAQQALQ 380

Query: 247 L---------AQNAILNSSTPQVSSST----------APPIATQCFLLANMFDPATETNP 287
           +         A+ + +     ++S  T            P+ATQCF L+NMF+P TE   
Sbjct: 381 MSGSLAFGAVAEFSFVIDLQTRLSQQTEASALAAAASVQPLATQCFQLSNMFNPQTEEEV 440

Query: 288 TWDVEIRDDVIEECNKHG 305
            WD EI+DDVIEECNKHG
Sbjct: 441 GWDTEIKDDVIEECNKHG 458

Transcriptional coactivator for steroid nuclear receptors ESR1/ER-alpha and ESR2/ER-beta, and JUN/AP-1. May be involved in pre-mRNA splicing process.

Mus musculus (taxid: 10090)

>sp|Q86U06|RBM23_HUMAN Probable RNA-binding protein 23 OS=Homo sapiens GN=RBM23 PE=1 SV=1

 Score =  320 bits (819), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 175/289 (60%), Positives = 213/289 (73%), Gaps = 18/289 (6%)

Query: 7   DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
           D+LSPEERDART+FCMQL+ RIR RDLE+FFS+VGKVRDVR+I+   +RR KGIAY+EF 
Sbjct: 156 DNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFC 215

Query: 67  DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
           + +SVPLA+GL GQ+LLG+PIIVQ +QAEKNR      NLQ +G GGPMRLY+GSLHFNI
Sbjct: 216 EIQSVPLAIGLTGQRLLGVPIIVQASQAEKNRLAAMANNLQ-KGNGGPMRLYVGSLHFNI 274

Query: 127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
           TEDMLRGIFEPFGKIDNI LM D DTGRSKGYGFITF  ++ A++A EQLNGFELAGRPM
Sbjct: 275 TEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPM 334

Query: 187 KVGTVTDRNESVGGGPSNLDTDEMERAGVDLG-ATGRLQLMFKLAEGTGLELPPAAASAL 245
           +VG VT+R +  GG        + E   +DLG A GR QLM KLAEG G++LP  AA+A 
Sbjct: 335 RVGHVTERLD--GGTDITFPDGDQE---LDLGSAGGRFQLMAKLAEGAGIQLPSTAAAAA 389

Query: 246 NLAQNAI---------LNSSTPQVSSSTAPP--IATQCFLLANMFDPAT 283
             A  A          L +  P   ++ +P   +A+QCF L+++F P T
Sbjct: 390 AAAAQAAALQLNGAVPLGALNPAALTALSPALNLASQCFQLSSLFTPQT 438

Probable RNA-binding protein. May be involved in pre-mRNA splicing process.

Homo sapiens (taxid: 9606)

>sp|O13845|RSD1_SCHPO RNA-binding protein rsd1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rsd1 PE=1 SV=2

 Score =  190 bits (482), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 125/350 (35%), Positives = 185/350 (52%), Gaps = 57/350 (16%)

Query: 9   LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDP 68
           LS EERD RT+F  QL+ R+ +R+L +FF   G VRD +++    + R KG+AY+EF   
Sbjct: 232 LSEEERDRRTVFVSQLANRLTSRELYDFFEQAGPVRDAQIVRDKISGRSKGVAYVEFCHE 291

Query: 69  ESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGG-PM-RLYIGSLHFNI 126
           +SV  A+ L+G++LLG+P+IVQ T+AEKNR       L    +   P  RL + ++HFN+
Sbjct: 292 DSVQAAIALSGKRLLGLPVIVQLTEAEKNRKAREAAELARAASAEIPFHRLCVSNIHFNL 351

Query: 127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
           T++ ++ IFEPFG I+ + L  D D  RSKG+G+I + +   A+ A E++NGF+LAGR M
Sbjct: 352 TDEDVKAIFEPFGDIEFVHLQRD-DQNRSKGFGYIQYRNPISARNALEKMNGFDLAGRNM 410

Query: 187 KVGTVTDR-------------NESVG-----------GGPSNLDTDEMERAGVDLGAT-- 220
           +V    D+             +E++            GG S  ++ +  R    L  T  
Sbjct: 411 RVCLGNDKFTTETTSSMLKRFDETLARQERSQPSQRNGGSSTYESQDY-REAAPLSPTEE 469

Query: 221 -----GRLQLMFKLAEGTGLELPPAAASALNLAQNAILNSSTPQVSSSTAPPIATQCFLL 275
                 R +LM KLA    +                   S   ++ S   PPI ++C LL
Sbjct: 470 ESRPITRDELMKKLARSEDI-------------------SDNSKLVSEPEPPIRSRCALL 510

Query: 276 ANMFDPATETNPTWDVEIRDDVIEECN-KHG--VGASTVCFIYSVIFLKL 322
            NMF+PA ET+P W  E+  DV EEC+ K+G  V  + V      IF+K 
Sbjct: 511 ENMFNPAEETSPNWVQELEQDVKEECDEKYGKVVHIAVVPNELGQIFVKF 560

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

>sp|P41891|GAR2_SCHPO Protein gar2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=gar2 PE=1 SV=2

 Score = 95.5 bits (236), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 69/203 (33%), Positives = 101/203 (49%), Gaps = 16/203 (7%)

Query: 2   RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIA 61
           RPA     S +  +  T+F  +LS  +  + L + F   G +   R+I   ++ R KG  
Sbjct: 248 RPAKITKPSQDSNETCTVFVGRLSWNVDDQWLGQEFEEYGTIVGARVIMDGQSGRSKGYG 307

Query: 62  YIEFKDPESVPLAMGLNGQKL---------LGIPIIVQPTQAEKNRAGNTLPNL-QPRGT 111
           Y++F+ PE+   A+  NG K          L  P    P    + RAGN    L +P  T
Sbjct: 308 YVDFETPEAAKAAVAANGTKEIDGRMVNLDLSNPRPANPQPYAQQRAGNFGDQLSEPSDT 367

Query: 112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
                +++G+L FN TED L   F   G I +I+L  DP +GR KG+G++TF   D AKK
Sbjct: 368 -----VFVGNLSFNATEDDLSTAFGGCGDIQSIRLPTDPQSGRLKGFGYVTFSDIDSAKK 422

Query: 172 AQEQLNGFELAGRPMKVGTVTDR 194
             E +NG  +AGRP ++   T R
Sbjct: 423 CVE-MNGHFIAGRPCRLDFSTPR 444

Helps the assembly of pre-ribosomal particles containing 18S rRNA.

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

>sp|Q5R469|PUF60_PONAB Poly(U)-binding-splicing factor PUF60 OS=Pongo abelii GN=PUF60 PE=2 SV=1

 Score = 88.6 bits (218), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 59/210 (28%), Positives = 101/210 (48%), Gaps = 41/210 (19%)

Query: 5   YSDDLSP------EERDARTIFCM----QLSQRIRTRDLEEFFSSVGKVRDVRLITCNKT 54
           + D LSP      + + A  I C      +   +    + + F+  G ++ + +   + T
Sbjct: 106 FGDPLSPLQSMAAQRQRALAIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVT 165

Query: 55  RRFKGIAYIEFKDPESVPLAMGLNGQKLLG---------------IPIIVQPTQAEKNRA 99
            + KG A++E++ PE+  LA+      +LG                PII Q   AE+ RA
Sbjct: 166 MKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQ--LAEEARA 223

Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
            N              R+Y+ S+H ++++D ++ +FE FGKI +  L  DP TG+ KGYG
Sbjct: 224 FN--------------RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYG 269

Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVG 189
           FI +  A  ++ A   +N F+L G+ ++VG
Sbjct: 270 FIEYEKAQSSQDAVSSMNLFDLGGQYLRVG 299

DNA- and RNA-binding protein, involved in several nuclear processes such as pre-mRNA splicing, apoptosis and transcription regulation. In association with FUBP1 regulates MYC transcription at the P2 promoter through the core-TFIIH basal transcription factor. Acts as a transcriptional repressor through the core-TFIIH basal transcription factor. Represses FUBP1-induced transcriptional activation but not basal transcription. Decreases ERCC3 helicase activity. Is also involved in pre-mRNA splicing. Promotes splicing of an intron with weak 3'-splice site and pyrimidine tract in a cooperative manner with U2AF2. Involved in apoptosis induction when overexpressed in HeLa cells. Modulates alternative splicing of several mRNAs. Binds to relaxed DNA of active promoter regions. Binds to the pyrimidine tract and 3'-splice site regions of pre-mRNA; binding is enhanced in presence of U2AF2. Binds to Y5 RNA in association with TROVE2. Binds to poly(U) RNA.

Pongo abelii (taxid: 9601)

>sp|Q9UHX1|PUF60_HUMAN Poly(U)-binding-splicing factor PUF60 OS=Homo sapiens GN=PUF60 PE=1 SV=1

 Score = 88.6 bits (218), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 59/210 (28%), Positives = 101/210 (48%), Gaps = 41/210 (19%)

Query: 5   YSDDLSP------EERDARTIFCM----QLSQRIRTRDLEEFFSSVGKVRDVRLITCNKT 54
           + D LSP      + + A  I C      +   +    + + F+  G ++ + +   + T
Sbjct: 107 FGDPLSPLQSMAAQRQRALAIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVT 166

Query: 55  RRFKGIAYIEFKDPESVPLAMGLNGQKLLG---------------IPIIVQPTQAEKNRA 99
            + KG A++E++ PE+  LA+      +LG                PII Q   AE+ RA
Sbjct: 167 MKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQ--LAEEARA 224

Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
            N              R+Y+ S+H ++++D ++ +FE FGKI +  L  DP TG+ KGYG
Sbjct: 225 FN--------------RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYG 270

Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVG 189
           FI +  A  ++ A   +N F+L G+ ++VG
Sbjct: 271 FIEYEKAQSSQDAVSSMNLFDLGGQYLRVG 300

DNA- and RNA-binding protein, involved in several nuclear processes such as pre-mRNA splicing, apoptosis and transcription regulation. In association with FUBP1 regulates MYC transcription at the P2 promoter through the core-TFIIH basal transcription factor. Acts as a transcriptional repressor through the core-TFIIH basal transcription factor. Represses FUBP1-induced transcriptional activation but not basal transcription. Decreases ERCC3 helicase activity. Does not repress TFIIH-mediated transcription in xeroderma pigmentosum complementation group B (XPB) cells. Is also involved in pre-mRNA splicing. Promotes splicing of an intron with weak 3'-splice site and pyrimidine tract in a cooperative manner with U2AF2. Involved in apoptosis induction when overexpressed in HeLa cells. Isoform 6 failed to repress MYC transcription and inhibited FIR-induced apoptosis in colorectal cancer. Isoform 6 may contribute to tumor progression by enabling increased MYC expression and greater resistance to apoptosis in tumors than in normal cells. Modulates alternative splicing of several mRNAs. Binds to relaxed DNA of active promoter regions. Binds to the pyrimidine tract and 3'-splice site regions of pre-mRNA; binding is enhanced in presence of U2AF2. Binds to Y5 RNA in association with TROVE2. Binds to poly(U) RNA.

Homo sapiens (taxid: 9606)

>sp|Q9WV25|PUF60_RAT Poly(U)-binding-splicing factor PUF60 OS=Rattus norvegicus GN=Puf60 PE=2 SV=2

 Score = 88.6 bits (218), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 59/210 (28%), Positives = 101/210 (48%), Gaps = 41/210 (19%)

Query: 5   YSDDLSP------EERDARTIFCM----QLSQRIRTRDLEEFFSSVGKVRDVRLITCNKT 54
           + D LSP      + + A  I C      +   +    + + F+  G ++ + +   + T
Sbjct: 112 FGDPLSPLQSMAAQRQRALAIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVT 171

Query: 55  RRFKGIAYIEFKDPESVPLAMGLNGQKLLG---------------IPIIVQPTQAEKNRA 99
            + KG A++E++ PE+  LA+      +LG                PII Q   AE+ RA
Sbjct: 172 MKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQ--LAEEARA 229

Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
            N              R+Y+ S+H ++++D ++ +FE FGKI +  L  DP TG+ KGYG
Sbjct: 230 FN--------------RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYG 275

Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVG 189
           FI +  A  ++ A   +N F+L G+ ++VG
Sbjct: 276 FIEYEKAQSSQDAVSSMNLFDLGGQYLRVG 305

DNA- and RNA-binding protein, involved in several nuclear processes such as pre-mRNA splicing, apoptosis and transcription regulation. In association with FUBP1 regulates MYC transcription at the P2 promoter through the core-TFIIH basal transcription factor. Acts as a transcriptional repressor through the core-TFIIH basal transcription factor. Represses FUBP1-induced transcriptional activation but not basal transcription. Decreases ERCC3 helicase activity. Is also involved in pre-mRNA splicing. Promotes splicing of an intron with weak 3'-splice site and pyrimidine tract in a cooperative manner with U2AF2. Involved in apoptosis induction when overexpressed in HeLa cells. Modulates alternative splicing of several mRNAs. Binds to relaxed DNA of active promoter regions. Binds to the pyrimidine tract and 3'-splice site regions of pre-mRNA; binding is enhanced in presence of U2AF2. Binds to Y5 RNA in association with TROVE2. Binds to poly(U) RNA.

Rattus norvegicus (taxid: 10116)

>sp|Q3UEB3|PUF60_MOUSE Poly(U)-binding-splicing factor PUF60 OS=Mus musculus GN=Puf60 PE=2 SV=2

 Score = 88.6 bits (218), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 59/210 (28%), Positives = 101/210 (48%), Gaps = 41/210 (19%)

Query: 5   YSDDLSP------EERDARTIFCM----QLSQRIRTRDLEEFFSSVGKVRDVRLITCNKT 54
           + D LSP      + + A  I C      +   +    + + F+  G ++ + +   + T
Sbjct: 112 FGDPLSPLQSMAAQRQRALAIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVT 171

Query: 55  RRFKGIAYIEFKDPESVPLAMGLNGQKLLG---------------IPIIVQPTQAEKNRA 99
            + KG A++E++ PE+  LA+      +LG                PII Q   AE+ RA
Sbjct: 172 MKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQ--LAEEARA 229

Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
            N              R+Y+ S+H ++++D ++ +FE FGKI +  L  DP TG+ KGYG
Sbjct: 230 FN--------------RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYG 275

Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVG 189
           FI +  A  ++ A   +N F+L G+ ++VG
Sbjct: 276 FIEYEKAQSSQDAVSSMNLFDLGGQYLRVG 305

DNA- and RNA-binding protein, involved in several nuclear processes such as pre-mRNA splicing, apoptosis and transcription regulation. In association with FUBP1 regulates MYC transcription at the P2 promoter through the core-TFIIH basal transcription factor. Acts as a transcriptional repressor through the core-TFIIH basal transcription factor. Represses FUBP1-induced transcriptional activation but not basal transcription. Decreases ERCC3 helicase activity. Is also involved in pre-mRNA splicing. Promotes splicing of an intron with weak 3'-splice site and pyrimidine tract in a cooperative manner with U2AF2. Involved in apoptosis induction when overexpressed in HeLa cells. Modulates alternative splicing of several mRNAs. Binds to relaxed DNA of active promoter regions. Binds to the pyrimidine tract and 3'-splice site regions of pre-mRNA; binding is enhanced in presence of U2AF2. Binds to Y5 RNA in association with TROVE2. Binds to poly(U) RNA.

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	370
357612395	536	putative RNA-binding region-containing p	0.789	0.544	0.782	1e-137
215820610	516	RNA binding motif protein 39 [Nasonia vi	0.797	0.571	0.77	1e-135
350410158	532	PREDICTED: RNA-binding protein 39-like i	0.797	0.554	0.79	1e-135
340718898	520	PREDICTED: RNA-binding protein 39-like i	0.797	0.567	0.79	1e-135
350410161	508	PREDICTED: RNA-binding protein 39-like i	0.797	0.580	0.79	1e-134
340718900	508	PREDICTED: RNA-binding protein 39-like i	0.797	0.580	0.79	1e-134
328781105	506	PREDICTED: RNA-binding protein 39-like [	0.797	0.583	0.786	1e-134
383864352	530	PREDICTED: RNA-binding protein 39-like i	0.797	0.556	0.786	1e-134
383864354	507	PREDICTED: RNA-binding protein 39-like i	0.797	0.581	0.786	1e-134
189237575	501	PREDICTED: similar to splicing factor [T	0.8	0.590	0.762	1e-134

>gi|357612395|gb|EHJ67964.1| putative RNA-binding region-containing protein [Danaus plexippus]

 Score =  493 bits (1268), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 234/299 (78%), Positives = 260/299 (86%), Gaps = 7/299 (2%)

Query: 7   DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
           DDL PEERD RT+FCMQLSQRIR +DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK
Sbjct: 172 DDLPPEERDLRTVFCMQLSQRIRAKDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 231

Query: 67  DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
           D ESVPLA+GL GQKLLG+PIIVQ TQAEKNR GNTLPNL P+ + GP RLY+GSLHFNI
Sbjct: 232 DAESVPLALGLTGQKLLGVPIIVQHTQAEKNRVGNTLPNLAPKTSNGPTRLYVGSLHFNI 291

Query: 127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
           TEDMLRGIFEPFGKID+IQLM DPDTG+SKGYGF+TFH A DAKKA EQLNGFELAGRPM
Sbjct: 292 TEDMLRGIFEPFGKIDHIQLMTDPDTGKSKGYGFLTFHHATDAKKAMEQLNGFELAGRPM 351

Query: 187 KVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPAAASALN 246
           KVG VT+R +  GG  +  D DE++RAGVDLGATGRLQLMFKLAEGTGL++PPAAAS L 
Sbjct: 352 KVGNVTERAD--GGSSTRFDADELDRAGVDLGATGRLQLMFKLAEGTGLQIPPAAASVL- 408

Query: 247 LAQNAILNSSTPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
           +   + L +  PQV    APPIATQCF+L NMFDP++E+NP+WD+EIRDDVI ECNKHG
Sbjct: 409 MGAGSTLVAPQPQV----APPIATQCFMLNNMFDPSSESNPSWDIEIRDDVISECNKHG 463

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|215820610|ref|NP_001135964.1| RNA binding motif protein 39 [Nasonia vitripennis]

 Score =  488 bits (1257), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 231/300 (77%), Positives = 266/300 (88%), Gaps = 5/300 (1%)

Query: 6   SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
           SD+L+PEERDARTIFCMQLSQRIR RDLEEFFSSVGKV+DVRLITCNKTRRFKGIAY+EF
Sbjct: 146 SDELTPEERDARTIFCMQLSQRIRARDLEEFFSSVGKVQDVRLITCNKTRRFKGIAYVEF 205

Query: 66  KDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFN 125
           KDPESV LA+GL+GQKLLG+PI+VQ TQAEKNR GN++PNL P+G  GPMRLY+GSL FN
Sbjct: 206 KDPESVTLALGLSGQKLLGVPIVVQHTQAEKNRMGNSMPNLMPKGQTGPMRLYVGSLLFN 265

Query: 126 ITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRP 185
           ITE+ML+GIFEPFGKI+NIQL++DP+TGRSKGYGF+TF +ADDAKKA EQLNGFELAGRP
Sbjct: 266 ITEEMLKGIFEPFGKIENIQLIMDPETGRSKGYGFLTFRNADDAKKALEQLNGFELAGRP 325

Query: 186 MKVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPAAASAL 245
           MKVG VT+R + +  GPS LDTDE++R+G+DLGATGRLQLMFKLAEGTGLE+PPAAA+AL
Sbjct: 326 MKVGNVTERTDLI-QGPSLLDTDELDRSGIDLGATGRLQLMFKLAEGTGLEIPPAAANAL 384

Query: 246 NLAQNAILNSSTPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
           N+        + PQ++  TAPPIATQCF+L+NMFDP  E N  W  EIRDDVIEECNKHG
Sbjct: 385 NMTPVV----TAPQINQQTAPPIATQCFMLSNMFDPQNENNSLWVKEIRDDVIEECNKHG 440

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350410158|ref|XP_003488966.1| PREDICTED: RNA-binding protein 39-like isoform 1 [Bombus impatiens]

 Score =  486 bits (1251), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 237/300 (79%), Positives = 268/300 (89%), Gaps = 5/300 (1%)

Query: 6   SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
           +D+L+PEERDART+FCMQLSQRIR RDLEEFFSSVGKV+DVRLITCNKTRRFKGIAY+EF
Sbjct: 162 NDELTPEERDARTVFCMQLSQRIRARDLEEFFSSVGKVQDVRLITCNKTRRFKGIAYVEF 221

Query: 66  KDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFN 125
           KDPESV LA+GL+GQKLLG+PI+VQ TQAEKNR GN++PNL P+G  GPMRLY+GSLHFN
Sbjct: 222 KDPESVTLALGLSGQKLLGVPIVVQHTQAEKNRMGNSMPNLMPKGQTGPMRLYVGSLHFN 281

Query: 126 ITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRP 185
           ITEDMLRGIFEPFGKIDNIQL++DP+TGRSKGYGF+TF +ADDAKKA EQLNGFELAGRP
Sbjct: 282 ITEDMLRGIFEPFGKIDNIQLIMDPETGRSKGYGFLTFRNADDAKKALEQLNGFELAGRP 341

Query: 186 MKVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPAAASAL 245
           MKVG VT+R + +  GPS LDTDE++R+G+DLGATGRLQLMFKLAEGTGLE+PPAAA+AL
Sbjct: 342 MKVGNVTERTDLI-QGPSLLDTDELDRSGIDLGATGRLQLMFKLAEGTGLEIPPAAANAL 400

Query: 246 NLAQNAILNSSTPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
           N+A       STPQ     APPIATQCF+L+NMFDP  ETNP W  EIRDDVIEECNKHG
Sbjct: 401 NMAPVM----STPQPPPQAAPPIATQCFMLSNMFDPQNETNPNWAKEIRDDVIEECNKHG 456

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340718898|ref|XP_003397899.1| PREDICTED: RNA-binding protein 39-like isoform 1 [Bombus terrestris]

 Score =  486 bits (1250), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 237/300 (79%), Positives = 268/300 (89%), Gaps = 5/300 (1%)

Query: 6   SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
           +D+L+PEERDART+FCMQLSQRIR RDLEEFFSSVGKV+DVRLITCNKTRRFKGIAY+EF
Sbjct: 150 NDELTPEERDARTVFCMQLSQRIRARDLEEFFSSVGKVQDVRLITCNKTRRFKGIAYVEF 209

Query: 66  KDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFN 125
           KDPESV LA+GL+GQKLLG+PI+VQ TQAEKNR GN++PNL P+G  GPMRLY+GSLHFN
Sbjct: 210 KDPESVTLALGLSGQKLLGVPIVVQHTQAEKNRMGNSMPNLMPKGQTGPMRLYVGSLHFN 269

Query: 126 ITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRP 185
           ITEDMLRGIFEPFGKIDNIQL++DP+TGRSKGYGF+TF +ADDAKKA EQLNGFELAGRP
Sbjct: 270 ITEDMLRGIFEPFGKIDNIQLIMDPETGRSKGYGFLTFRNADDAKKALEQLNGFELAGRP 329

Query: 186 MKVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPAAASAL 245
           MKVG VT+R + +  GPS LDTDE++R+G+DLGATGRLQLMFKLAEGTGLE+PPAAA+AL
Sbjct: 330 MKVGNVTERTDLI-QGPSLLDTDELDRSGIDLGATGRLQLMFKLAEGTGLEIPPAAANAL 388

Query: 246 NLAQNAILNSSTPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
           N+A       STPQ     APPIATQCF+L+NMFDP  ETNP W  EIRDDVIEECNKHG
Sbjct: 389 NMAPVM----STPQPPPQAAPPIATQCFMLSNMFDPQNETNPNWAKEIRDDVIEECNKHG 444

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350410161|ref|XP_003488967.1| PREDICTED: RNA-binding protein 39-like isoform 2 [Bombus impatiens]

 Score =  486 bits (1250), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 237/300 (79%), Positives = 268/300 (89%), Gaps = 5/300 (1%)

Query: 6   SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
           +D+L+PEERDART+FCMQLSQRIR RDLEEFFSSVGKV+DVRLITCNKTRRFKGIAY+EF
Sbjct: 138 NDELTPEERDARTVFCMQLSQRIRARDLEEFFSSVGKVQDVRLITCNKTRRFKGIAYVEF 197

Query: 66  KDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFN 125
           KDPESV LA+GL+GQKLLG+PI+VQ TQAEKNR GN++PNL P+G  GPMRLY+GSLHFN
Sbjct: 198 KDPESVTLALGLSGQKLLGVPIVVQHTQAEKNRMGNSMPNLMPKGQTGPMRLYVGSLHFN 257

Query: 126 ITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRP 185
           ITEDMLRGIFEPFGKIDNIQL++DP+TGRSKGYGF+TF +ADDAKKA EQLNGFELAGRP
Sbjct: 258 ITEDMLRGIFEPFGKIDNIQLIMDPETGRSKGYGFLTFRNADDAKKALEQLNGFELAGRP 317

Query: 186 MKVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPAAASAL 245
           MKVG VT+R + +  GPS LDTDE++R+G+DLGATGRLQLMFKLAEGTGLE+PPAAA+AL
Sbjct: 318 MKVGNVTERTDLI-QGPSLLDTDELDRSGIDLGATGRLQLMFKLAEGTGLEIPPAAANAL 376

Query: 246 NLAQNAILNSSTPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
           N+A       STPQ     APPIATQCF+L+NMFDP  ETNP W  EIRDDVIEECNKHG
Sbjct: 377 NMAPVM----STPQPPPQAAPPIATQCFMLSNMFDPQNETNPNWAKEIRDDVIEECNKHG 432

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340718900|ref|XP_003397900.1| PREDICTED: RNA-binding protein 39-like isoform 2 [Bombus terrestris]

 Score =  486 bits (1250), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 237/300 (79%), Positives = 268/300 (89%), Gaps = 5/300 (1%)

Query: 6   SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
           +D+L+PEERDART+FCMQLSQRIR RDLEEFFSSVGKV+DVRLITCNKTRRFKGIAY+EF
Sbjct: 138 NDELTPEERDARTVFCMQLSQRIRARDLEEFFSSVGKVQDVRLITCNKTRRFKGIAYVEF 197

Query: 66  KDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFN 125
           KDPESV LA+GL+GQKLLG+PI+VQ TQAEKNR GN++PNL P+G  GPMRLY+GSLHFN
Sbjct: 198 KDPESVTLALGLSGQKLLGVPIVVQHTQAEKNRMGNSMPNLMPKGQTGPMRLYVGSLHFN 257

Query: 126 ITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRP 185
           ITEDMLRGIFEPFGKIDNIQL++DP+TGRSKGYGF+TF +ADDAKKA EQLNGFELAGRP
Sbjct: 258 ITEDMLRGIFEPFGKIDNIQLIMDPETGRSKGYGFLTFRNADDAKKALEQLNGFELAGRP 317

Query: 186 MKVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPAAASAL 245
           MKVG VT+R + +  GPS LDTDE++R+G+DLGATGRLQLMFKLAEGTGLE+PPAAA+AL
Sbjct: 318 MKVGNVTERTDLI-QGPSLLDTDELDRSGIDLGATGRLQLMFKLAEGTGLEIPPAAANAL 376

Query: 246 NLAQNAILNSSTPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
           N+A       STPQ     APPIATQCF+L+NMFDP  ETNP W  EIRDDVIEECNKHG
Sbjct: 377 NMAPVM----STPQPPPQAAPPIATQCFMLSNMFDPQNETNPNWAKEIRDDVIEECNKHG 432

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328781105|ref|XP_624668.3| PREDICTED: RNA-binding protein 39-like [Apis mellifera]

 Score =  484 bits (1247), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 236/300 (78%), Positives = 268/300 (89%), Gaps = 5/300 (1%)

Query: 6   SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
           +D+L+PEERDART+FCMQLSQRIR RDLEEFFSSVGKV+DVRLITCNKTRRFKGIAY+EF
Sbjct: 136 NDELTPEERDARTVFCMQLSQRIRARDLEEFFSSVGKVQDVRLITCNKTRRFKGIAYVEF 195

Query: 66  KDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFN 125
           KDPESV LA+GL+GQKLLG+PI+VQ TQAEKNR GN++PNL P+G  GPMRLY+GSLHFN
Sbjct: 196 KDPESVTLALGLSGQKLLGVPIVVQHTQAEKNRMGNSMPNLMPKGQTGPMRLYVGSLHFN 255

Query: 126 ITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRP 185
           ITEDMLRGIFEPFGKIDNIQL++DP+TGRSKGYGF+TF +ADDAKKA EQLNGFELAGRP
Sbjct: 256 ITEDMLRGIFEPFGKIDNIQLIMDPETGRSKGYGFLTFRNADDAKKALEQLNGFELAGRP 315

Query: 186 MKVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPAAASAL 245
           MKVG VT+R + +  GPS LDTDE++R+G++LGATGRLQLMFKLAEGTGLE+PPAAA+AL
Sbjct: 316 MKVGNVTERTDLI-QGPSLLDTDELDRSGIELGATGRLQLMFKLAEGTGLEIPPAAANAL 374

Query: 246 NLAQNAILNSSTPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
           N+A       STPQ     APPIATQCF+L+NMFDP  ETNP W  EIRDDVIEECNKHG
Sbjct: 375 NMAPVM----STPQPPPQVAPPIATQCFMLSNMFDPQNETNPNWAKEIRDDVIEECNKHG 430

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383864352|ref|XP_003707643.1| PREDICTED: RNA-binding protein 39-like isoform 1 [Megachile rotundata]

 Score =  484 bits (1246), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 236/300 (78%), Positives = 268/300 (89%), Gaps = 5/300 (1%)

Query: 6   SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
           +D+L+PEERDART+FCMQLSQRIR RDLE+FFSSVGKV+DVRLITCNKTRRFKGIAY+EF
Sbjct: 160 NDELTPEERDARTVFCMQLSQRIRARDLEDFFSSVGKVQDVRLITCNKTRRFKGIAYVEF 219

Query: 66  KDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFN 125
           KDPESV LA+GL+GQKLLG+PI+VQ TQAEKNR GN++PNL P+G  GPMRLY+GSLHFN
Sbjct: 220 KDPESVTLALGLSGQKLLGVPIVVQHTQAEKNRMGNSMPNLMPKGQTGPMRLYVGSLHFN 279

Query: 126 ITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRP 185
           ITEDMLRGIFEPFGKIDNIQL++DP+TGRSKGYGF+TF +ADDAKKA EQLNGFELAGRP
Sbjct: 280 ITEDMLRGIFEPFGKIDNIQLIMDPETGRSKGYGFLTFRNADDAKKALEQLNGFELAGRP 339

Query: 186 MKVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPAAASAL 245
           MKVG VT+R + +  GPS LDTDE++R+G+DLGATGRLQLMFKLAEGTGLE+PPAAA+AL
Sbjct: 340 MKVGNVTERTDLI-QGPSLLDTDELDRSGIDLGATGRLQLMFKLAEGTGLEIPPAAANAL 398

Query: 246 NLAQNAILNSSTPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
           N+A       STPQ     APPIATQCF+L+NMFDP  ETNP W  EIRDDVIEECNKHG
Sbjct: 399 NMAPVM----STPQPPPQAAPPIATQCFMLSNMFDPQNETNPNWAKEIRDDVIEECNKHG 454

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383864354|ref|XP_003707644.1| PREDICTED: RNA-binding protein 39-like isoform 2 [Megachile rotundata]

 Score =  484 bits (1245), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 236/300 (78%), Positives = 268/300 (89%), Gaps = 5/300 (1%)

Query: 6   SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
           +D+L+PEERDART+FCMQLSQRIR RDLE+FFSSVGKV+DVRLITCNKTRRFKGIAY+EF
Sbjct: 137 NDELTPEERDARTVFCMQLSQRIRARDLEDFFSSVGKVQDVRLITCNKTRRFKGIAYVEF 196

Query: 66  KDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFN 125
           KDPESV LA+GL+GQKLLG+PI+VQ TQAEKNR GN++PNL P+G  GPMRLY+GSLHFN
Sbjct: 197 KDPESVTLALGLSGQKLLGVPIVVQHTQAEKNRMGNSMPNLMPKGQTGPMRLYVGSLHFN 256

Query: 126 ITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRP 185
           ITEDMLRGIFEPFGKIDNIQL++DP+TGRSKGYGF+TF +ADDAKKA EQLNGFELAGRP
Sbjct: 257 ITEDMLRGIFEPFGKIDNIQLIMDPETGRSKGYGFLTFRNADDAKKALEQLNGFELAGRP 316

Query: 186 MKVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPAAASAL 245
           MKVG VT+R + +  GPS LDTDE++R+G+DLGATGRLQLMFKLAEGTGLE+PPAAA+AL
Sbjct: 317 MKVGNVTERTDLI-QGPSLLDTDELDRSGIDLGATGRLQLMFKLAEGTGLEIPPAAANAL 375

Query: 246 NLAQNAILNSSTPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
           N+A       STPQ     APPIATQCF+L+NMFDP  ETNP W  EIRDDVIEECNKHG
Sbjct: 376 NMAPVM----STPQPPPQAAPPIATQCFMLSNMFDPQNETNPNWAKEIRDDVIEECNKHG 431

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189237575|ref|XP_974855.2| PREDICTED: similar to splicing factor [Tribolium castaneum]

 Score =  483 bits (1244), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 228/299 (76%), Positives = 262/299 (87%), Gaps = 3/299 (1%)

Query: 7   DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
           ++LSPEERDART+F MQLSQRIR RDLEEFFSSVGKVRDVRLI CNKTRRFKGIAYIEFK
Sbjct: 133 EELSPEERDARTVFVMQLSQRIRARDLEEFFSSVGKVRDVRLIVCNKTRRFKGIAYIEFK 192

Query: 67  DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
           DPESV LA+GL+GQKLLG+PIIVQ TQAEKNR GN++PNL P+   GPMRLY+GSLHFNI
Sbjct: 193 DPESVTLALGLSGQKLLGVPIIVQHTQAEKNRMGNSMPNLMPKNMTGPMRLYVGSLHFNI 252

Query: 127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
           TEDMLR IFEPFGKIDNIQL++DP+TGRSKGYGFI F + +DAKKA EQLNGFELAGRPM
Sbjct: 253 TEDMLRSIFEPFGKIDNIQLIMDPETGRSKGYGFIAFRNCEDAKKALEQLNGFELAGRPM 312

Query: 187 KVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPAAASALN 246
           KVG VT+R +    GPS LD+DE++R+G+DLGATGRLQLMFKLAEG G+++P AAA+AL+
Sbjct: 313 KVGNVTERLDLQQQGPSILDSDELDRSGIDLGATGRLQLMFKLAEGAGMQVPQAAANALS 372

Query: 247 LAQNAILNSSTPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
           +A         PQV +++ PPIATQCF+L+NMFDPATE+  TWDVEIRDDVIEECNKHG
Sbjct: 373 IATG---QPVVPQVQTNSTPPIATQCFMLSNMFDPATESTQTWDVEIRDDVIEECNKHG 428

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

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	370
FB|FBgn0031883	594	CG11266 [Drosophila melanogast	0.786	0.489	0.721	1.8e-112
UNIPROTKB|E1BRU3	529	LOC100858247 "Uncharacterized	0.624	0.436	0.712	1.8e-101
UNIPROTKB|E2R4L0	530	RBM39 "Uncharacterized protein	0.624	0.435	0.712	2.8e-101
UNIPROTKB|Q14498	530	RBM39 "RNA-binding protein 39"	0.624	0.435	0.712	2.8e-101
MGI|MGI:2157953	530	Rbm39 "RNA binding motif prote	0.624	0.435	0.712	2.8e-101
UNIPROTKB|F1MA64	530	Rbm39 "Protein Rbm39" [Rattus	0.624	0.435	0.712	2.8e-101
UNIPROTKB|F6QIA5	525	RBM39 "Uncharacterized protein	0.802	0.565	0.628	8.2e-99
UNIPROTKB|F2Z5I2	525	RBM39 "Uncharacterized protein	0.802	0.565	0.628	8.2e-99
RGD|1310071	524	Rbm39 "RNA binding motif prote	0.802	0.566	0.628	8.2e-99
ZFIN|ZDB-GENE-040426-2852	523	rbm39a "RNA binding motif prot	0.802	0.567	0.631	1.3e-98

FB|FBgn0031883 CG11266 [Drosophila melanogaster (taxid:7227)]

 Score = 1110 (395.8 bits), Expect = 1.8e-112, P = 1.8e-112
 Identities = 215/298 (72%), Positives = 242/298 (81%)

Query:     8 DLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKD 67
             +LSPEERDART+FC+QLSQR+R RDLEEFFSSVGKVRDVRLITCNKT+RFKGIAYIEF D
Sbjct:   228 ELSPEERDARTVFCIQLSQRVRARDLEEFFSSVGKVRDVRLITCNKTKRFKGIAYIEFDD 287

Query:    68 PESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNIT 127
             PESV LA+GL+GQ+LLG+PI+VQ TQAEKNR  N  P  QP+   GPMRLY+GSLHFNIT
Sbjct:   288 PESVALALGLSGQRLLGVPIMVQHTQAEKNRLQNAAPAFQPKSHTGPMRLYVGSLHFNIT 347

Query:   128 EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMK 187
             EDMLRGIFEPFGKID IQL++D +TGRSKGYGFIT+H+ADDAKKA EQLNGFELAGR MK
Sbjct:   348 EDMLRGIFEPFGKIDAIQLIMDTETGRSKGYGFITYHNADDAKKALEQLNGFELAGRLMK 407

Query:   188 VGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPXXXXXXXX 247
             VG VT+R +      ++LDTDEM+R G+DLGATGRLQLMFKLAEG GL +P         
Sbjct:   408 VGNVTERLDM---NTTSLDTDEMDRTGIDLGATGRLQLMFKLAEGAGLAVPQAAANALLA 464

Query:   248 XXXXXXXXXTPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
                       P      AP IATQCF+L+NMFDP TETNPTWDVEIRDDV+EEC KHG
Sbjct:   465 TAPQPA----PLQQQEVAPSIATQCFILSNMFDPRTETNPTWDVEIRDDVLEECAKHG 518

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0008380 "RNA splicing" evidence=ISS

GO:0003729 "mRNA binding" evidence=ISS

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=IMP

GO:0005634 "nucleus" evidence=IC

GO:0071011 "precatalytic spliceosome" evidence=IDA

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

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

UNIPROTKB|E1BRU3 LOC100858247 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 859 (307.4 bits), Expect = 1.8e-101, Sum P(2) = 1.8e-101
 Identities = 166/233 (71%), Positives = 199/233 (85%)

Query:     7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
             D+L+PEERDART+FCMQL+ RIR RDLEEFFS+VGKVRDVR+I+   +RR KGIAY+EF 
Sbjct:   143 DNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFV 202

Query:    67 DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
             D  SVPLA+GL GQ++LG+PIIVQ +QAEKNRA     NLQ +G+ GPMRLY+GSLHFNI
Sbjct:   203 DVSSVPLAIGLTGQRVLGVPIIVQASQAEKNRAAAMANNLQ-KGSAGPMRLYVGSLHFNI 261

Query:   127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
             TEDMLRGIFEPFG+I++IQLM+D +TGRSKGYGFITF  ++ AKKA EQLNGFELAGRPM
Sbjct:   262 TEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM 321

Query:   187 KVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPP 239
             KVG VT+R ++     S LD+DE+ER G+DLG TGRLQLM +LAEGTGL++PP
Sbjct:   322 KVGHVTERTDA-SSASSFLDSDELERTGIDLGTTGRLQLMARLAEGTGLQIPP 373

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005813 "centrosome" evidence=IEA

UNIPROTKB|E2R4L0 RBM39 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 859 (307.4 bits), Expect = 2.8e-101, Sum P(2) = 2.8e-101
 Identities = 166/233 (71%), Positives = 199/233 (85%)

Query:     7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
             D+L+PEERDART+FCMQL+ RIR RDLEEFFS+VGKVRDVR+I+   +RR KGIAY+EF 
Sbjct:   143 DNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFV 202

Query:    67 DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
             D  SVPLA+GL GQ++LG+PIIVQ +QAEKNRA     NLQ +G+ GPMRLY+GSLHFNI
Sbjct:   203 DVSSVPLAIGLTGQRVLGVPIIVQASQAEKNRAAAMANNLQ-KGSAGPMRLYVGSLHFNI 261

Query:   127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
             TEDMLRGIFEPFG+I++IQLM+D +TGRSKGYGFITF  ++ AKKA EQLNGFELAGRPM
Sbjct:   262 TEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM 321

Query:   187 KVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPP 239
             KVG VT+R ++     S LD+DE+ER G+DLG TGRLQLM +LAEGTGL++PP
Sbjct:   322 KVGHVTERTDA-SSASSFLDSDELERTGIDLGTTGRLQLMARLAEGTGLQIPP 373

GO:0005813 "centrosome" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q14498 RBM39 "RNA-binding protein 39" [Homo sapiens (taxid:9606)]

 Score = 859 (307.4 bits), Expect = 2.8e-101, Sum P(2) = 2.8e-101
 Identities = 166/233 (71%), Positives = 199/233 (85%)

Query:     7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
             D+L+PEERDART+FCMQL+ RIR RDLEEFFS+VGKVRDVR+I+   +RR KGIAY+EF 
Sbjct:   143 DNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFV 202

Query:    67 DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
             D  SVPLA+GL GQ++LG+PIIVQ +QAEKNRA     NLQ +G+ GPMRLY+GSLHFNI
Sbjct:   203 DVSSVPLAIGLTGQRVLGVPIIVQASQAEKNRAAAMANNLQ-KGSAGPMRLYVGSLHFNI 261

Query:   127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
             TEDMLRGIFEPFG+I++IQLM+D +TGRSKGYGFITF  ++ AKKA EQLNGFELAGRPM
Sbjct:   262 TEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM 321

Query:   187 KVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPP 239
             KVG VT+R ++     S LD+DE+ER G+DLG TGRLQLM +LAEGTGL++PP
Sbjct:   322 KVGHVTERTDA-SSASSFLDSDELERTGIDLGTTGRLQLMARLAEGTGLQIPP 373

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:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006396 "RNA processing" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005813 "centrosome" evidence=IDA

GO:0015630 "microtubule cytoskeleton" evidence=IDA

MGI|MGI:2157953 Rbm39 "RNA binding motif protein 39" [Mus musculus (taxid:10090)]

 Score = 859 (307.4 bits), Expect = 2.8e-101, Sum P(2) = 2.8e-101
 Identities = 166/233 (71%), Positives = 199/233 (85%)

Query:     7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
             D+L+PEERDART+FCMQL+ RIR RDLEEFFS+VGKVRDVR+I+   +RR KGIAY+EF 
Sbjct:   143 DNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFV 202

Query:    67 DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
             D  SVPLA+GL GQ++LG+PIIVQ +QAEKNRA     NLQ +G+ GPMRLY+GSLHFNI
Sbjct:   203 DVSSVPLAIGLTGQRVLGVPIIVQASQAEKNRAAAMANNLQ-KGSAGPMRLYVGSLHFNI 261

Query:   127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
             TEDMLRGIFEPFG+I++IQLM+D +TGRSKGYGFITF  ++ AKKA EQLNGFELAGRPM
Sbjct:   262 TEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM 321

Query:   187 KVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPP 239
             KVG VT+R ++     S LD+DE+ER G+DLG TGRLQLM +LAEGTGL++PP
Sbjct:   322 KVGHVTERTDA-SSASSFLDSDELERTGIDLGTTGRLQLMARLAEGTGLQIPP 373

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=TAS

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=TAS

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

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

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

UNIPROTKB|F1MA64 Rbm39 "Protein Rbm39" [Rattus norvegicus (taxid:10116)]

 Score = 859 (307.4 bits), Expect = 2.8e-101, Sum P(2) = 2.8e-101
 Identities = 166/233 (71%), Positives = 199/233 (85%)

Query:     7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
             D+L+PEERDART+FCMQL+ RIR RDLEEFFS+VGKVRDVR+I+   +RR KGIAY+EF 
Sbjct:   143 DNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFV 202

Query:    67 DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
             D  SVPLA+GL GQ++LG+PIIVQ +QAEKNRA     NLQ +G+ GPMRLY+GSLHFNI
Sbjct:   203 DVSSVPLAIGLTGQRVLGVPIIVQASQAEKNRAAAMANNLQ-KGSAGPMRLYVGSLHFNI 261

Query:   127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
             TEDMLRGIFEPFG+I++IQLM+D +TGRSKGYGFITF  ++ AKKA EQLNGFELAGRPM
Sbjct:   262 TEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM 321

Query:   187 KVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPP 239
             KVG VT+R ++     S LD+DE+ER G+DLG TGRLQLM +LAEGTGL++PP
Sbjct:   322 KVGHVTERTDA-SSASSFLDSDELERTGIDLGTTGRLQLMARLAEGTGLQIPP 373

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005813 "centrosome" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

UNIPROTKB|F6QIA5 RBM39 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 981 (350.4 bits), Expect = 8.2e-99, P = 8.2e-99
 Identities = 196/312 (62%), Positives = 236/312 (75%)

Query:     7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
             D+L+PEERDART+FCMQL+ RIR RDLEEFFS+VGKVRDVR+I+   +RR KGIAY+EF 
Sbjct:   143 DNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFV 202

Query:    67 DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
             D  SVPLA+GL GQ++LG+PIIVQ +QAEKNRA     NLQ +G+ GPMRLY+GSLHFNI
Sbjct:   203 DVSSVPLAIGLTGQRVLGVPIIVQASQAEKNRAAAMANNLQ-KGSAGPMRLYVGSLHFNI 261

Query:   127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
             TEDMLRGIFEPFG+I++IQLM+D +TGRSKGYGFITF  ++ AKKA EQLNGFELAGRPM
Sbjct:   262 TEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM 321

Query:   187 KVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPXXXXXXX 246
             KVG VT+R ++     S LD+DE+ER G+DLG TGRLQLM +LAEGTGL++PP       
Sbjct:   322 KVGHVTERTDA-SSASSFLDSDELERTGIDLGTTGRLQLMARLAEGTGLQIPPAAQQALQ 380

Query:   247 XXXXXXXXXX-------TPQVSSS------TAPPIATQCFLLANMFDPATETNPTWDVEI 293
                              + Q  +S      +  P+ATQCF L+NMF+P TE    WD EI
Sbjct:   381 MSGSLAFGAVADLQTRLSQQTEASALAAAASVQPLATQCFQLSNMFNPQTEEEVGWDTEI 440

Query:   294 RDDVIEECNKHG 305
             +DDVIEECNKHG
Sbjct:   441 KDDVIEECNKHG 452

GO:0005813 "centrosome" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F2Z5I2 RBM39 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 981 (350.4 bits), Expect = 8.2e-99, P = 8.2e-99
 Identities = 196/312 (62%), Positives = 236/312 (75%)

Query:     7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
             D+L+PEERDART+FCMQL+ RIR RDLEEFFS+VGKVRDVR+I+   +RR KGIAY+EF 
Sbjct:   143 DNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFV 202

Query:    67 DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
             D  SVPLA+GL GQ++LG+PIIVQ +QAEKNRA     NLQ +G+ GPMRLY+GSLHFNI
Sbjct:   203 DVSSVPLAIGLTGQRVLGVPIIVQASQAEKNRAAAMANNLQ-KGSAGPMRLYVGSLHFNI 261

Query:   127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
             TEDMLRGIFEPFG+I++IQLM+D +TGRSKGYGFITF  ++ AKKA EQLNGFELAGRPM
Sbjct:   262 TEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM 321

Query:   187 KVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPXXXXXXX 246
             KVG VT+R ++     S LD+DE+ER G+DLG TGRLQLM +LAEGTGL++PP       
Sbjct:   322 KVGHVTERTDA-SSASSFLDSDELERTGIDLGTTGRLQLMARLAEGTGLQIPPAAQQALQ 380

Query:   247 XXXXXXXXXX-------TPQVSSS------TAPPIATQCFLLANMFDPATETNPTWDVEI 293
                              + Q  +S      +  P+ATQCF L+NMF+P TE    WD EI
Sbjct:   381 MSGSLAFGAVADLQTRLSQQTEASALAAAASVQPLATQCFQLSNMFNPQTEEEVGWDTEI 440

Query:   294 RDDVIEECNKHG 305
             +DDVIEECNKHG
Sbjct:   441 KDDVIEECNKHG 452

GO:0005813 "centrosome" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

RGD|1310071 Rbm39 "RNA binding motif protein 39" [Rattus norvegicus (taxid:10116)]

 Score = 981 (350.4 bits), Expect = 8.2e-99, P = 8.2e-99
 Identities = 196/312 (62%), Positives = 236/312 (75%)

Query:     7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
             D+L+PEERDART+FCMQL+ RIR RDLEEFFS+VGKVRDVR+I+   +RR KGIAY+EF 
Sbjct:   143 DNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFV 202

Query:    67 DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
             D  SVPLA+GL GQ++LG+PIIVQ +QAEKNRA     NLQ +G+ GPMRLY+GSLHFNI
Sbjct:   203 DVSSVPLAIGLTGQRVLGVPIIVQASQAEKNRAAAMANNLQ-KGSAGPMRLYVGSLHFNI 261

Query:   127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
             TEDMLRGIFEPFG+I++IQLM+D +TGRSKGYGFITF  ++ AKKA EQLNGFELAGRPM
Sbjct:   262 TEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM 321

Query:   187 KVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPXXXXXXX 246
             KVG VT+R ++     S LD+DE+ER G+DLG TGRLQLM +LAEGTGL++PP       
Sbjct:   322 KVGHVTERTDA-SSASSFLDSDELERTGIDLGTTGRLQLMARLAEGTGLQIPPAAQQALQ 380

Query:   247 XXXXXXXXXX-------TPQVSSS------TAPPIATQCFLLANMFDPATETNPTWDVEI 293
                              + Q  +S      +  P+ATQCF L+NMF+P TE    WD EI
Sbjct:   381 MSGSLAFGAVADLQTRLSQQTEASALAAAASVQPLATQCFQLSNMFNPQTEEEVGWDTEI 440

Query:   294 RDDVIEECNKHG 305
             +DDVIEECNKHG
Sbjct:   441 KDDVIEECNKHG 452

GO:0005634 "nucleus" evidence=ISO

GO:0005813 "centrosome" evidence=ISO

GO:0015630 "microtubule cytoskeleton" evidence=ISO

GO:0005730 "nucleolus" evidence=ISO

ZFIN|ZDB-GENE-040426-2852 rbm39a "RNA binding motif protein 39a" [Danio rerio (taxid:7955)]

 Score = 979 (349.7 bits), Expect = 1.3e-98, P = 1.3e-98
 Identities = 199/315 (63%), Positives = 237/315 (75%)

Query:     7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
             D+L+PEERDART+FCMQL+ RIR RDLEEFFS+VGKVRDVR+I+   +RR KGIAYIEF 
Sbjct:   139 DNLTPEERDARTVFCMQLAARIRPRDLEEFFSAVGKVRDVRIISDRNSRRSKGIAYIEFV 198

Query:    67 DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
             D  SVPLA+GL+GQ+LLG+PIIVQ +QAEKNRA     NLQ +G+ GPMRLY+GSLHFNI
Sbjct:   199 DSTSVPLAIGLSGQRLLGVPIIVQASQAEKNRAAALANNLQ-KGSAGPMRLYVGSLHFNI 257

Query:   127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
             TEDMLRGIFEPFG+ID+IQLM+D +TGRSKGYGFITF  A+ AKKA EQLNGFELAGRPM
Sbjct:   258 TEDMLRGIFEPFGRIDSIQLMMDSETGRSKGYGFITFSDAECAKKALEQLNGFELAGRPM 317

Query:   187 KVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPXXXXX-- 244
             KVG VT+R ++     S LD DE+ER G+DLG TGRLQLM +LAEGTGL++PP       
Sbjct:   318 KVGHVTERTDA-STASSFLDNDELERTGIDLGTTGRLQLMARLAEGTGLQIPPAAQQALQ 376

Query:   245 ---XXXXXXXXXXXXTPQVSSS-TAP----------PIATQCFLLANMFDPATETNPTWD 290
                             P +S +   P          PIAT CF L+NMF+P +E +  W+
Sbjct:   377 MSGSMVAMAAATAAMNPGLSFNINVPTNQALNLPSQPIATHCFQLSNMFNPNSENDHGWE 436

Query:   291 VEIRDDVIEECNKHG 305
             +EI+DDVIEECNKHG
Sbjct:   437 IEIQDDVIEECNKHG 451

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5RC80	RBM39_PONAB	No assigned EC number	0.6517	0.8	0.5648	yes	N/A
Q8VH51	RBM39_MOUSE	No assigned EC number	0.6320	0.8027	0.5603	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	370
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-128
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	4e-47
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	4e-44
cd12536	85	cd12536, RRM1_RBM39, RNA recognition motif 1 in ve	5e-39
cd12537	85	cd12537, RRM1_RBM23, RNA recognition motif 1 in ve	6e-38
smart00360	73	smart00360, RRM, RNA recognition motif	4e-29
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-25
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-23
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-23
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-22
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	4e-22
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	5e-21
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	9e-20
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	3e-19
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-18
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	5e-18
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	6e-18
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	7e-18
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	7e-18
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	8e-18
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	9e-18
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-17
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-17
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-17
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	3e-17
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	7e-17
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	9e-17
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-16
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-16
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	2e-16
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	7e-16
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	8e-16
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	1e-15
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-15
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-15
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-15
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	3e-15
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	3e-15
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	3e-15
smart00360	73	smart00360, RRM, RNA recognition motif	7e-15
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-14
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-14
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	2e-14
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	3e-14
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	4e-14
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	6e-14
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-14
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	7e-14
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	8e-14
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	8e-14
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	1e-13
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	1e-13
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-13
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	1e-13
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-13
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	2e-13
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-13
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-13
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	3e-13
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	3e-13
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	3e-13
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	3e-13
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	4e-13
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	5e-13
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	5e-13
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	6e-13
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	7e-13
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	1e-12
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	1e-12
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	2e-12
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-12
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-12
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	2e-12
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	2e-12
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	3e-12
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	3e-12
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	3e-12
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	3e-12
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	3e-12
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	4e-12
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	4e-12
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	5e-12
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	6e-12
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-11
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	1e-11
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	1e-11
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	1e-11
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	1e-11
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-11
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	2e-11
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	3e-11
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	3e-11
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	3e-11
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	4e-11
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	5e-11
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	5e-11
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	5e-11
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	5e-11
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	7e-11
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	8e-11
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	8e-11
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	1e-10
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	1e-10
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	1e-10
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	1e-10
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	1e-10
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	1e-10
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	1e-10
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-10
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	2e-10
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-10
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	2e-10
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	2e-10
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	2e-10
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-10
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	3e-10
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	3e-10
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	3e-10
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	3e-10
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	3e-10
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	4e-10
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	4e-10
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	4e-10
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	5e-10
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	5e-10
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	5e-10
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	5e-10
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	6e-10
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	6e-10
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	8e-10
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	1e-09
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	1e-09
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	2e-09
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	2e-09
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	2e-09
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	2e-09
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-09
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	2e-09
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	2e-09
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	2e-09
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	2e-09
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	2e-09
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	3e-09
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	3e-09
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	3e-09
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	3e-09
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	3e-09
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	3e-09
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	3e-09
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	3e-09
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	4e-09
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	4e-09
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	4e-09
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	5e-09
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	6e-09
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	6e-09
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	6e-09
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	6e-09
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	6e-09
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	7e-09
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	7e-09
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	8e-09
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	1e-08
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	1e-08
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	1e-08
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	1e-08
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	1e-08
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-08
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	2e-08
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	2e-08
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	2e-08
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-08
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	2e-08
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-08
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	3e-08
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	3e-08
cd12303	86	cd12303, RRM_spSet1p_like, RNA recognition motif i	3e-08
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	3e-08
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	3e-08
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	3e-08
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	3e-08
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	3e-08
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	4e-08
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	4e-08
cd12364	81	cd12364, RRM_RDM1, RNA recognition motif of RAD52	4e-08
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	5e-08
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	5e-08
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	5e-08
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	5e-08
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	5e-08
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	6e-08
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	6e-08
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	7e-08
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	7e-08
cd12460	82	cd12460, RRM2_CID8_like, RNA recognition motif 2 i	8e-08
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	8e-08
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	9e-08
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	1e-07
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	1e-07
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	1e-07
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	1e-07
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	1e-07
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	1e-07
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	1e-07
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	1e-07
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-07
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	1e-07
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	1e-07
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	2e-07
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	2e-07
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	2e-07
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	2e-07
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	2e-07
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	2e-07
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	2e-07
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	2e-07
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	2e-07
cd12253	79	cd12253, RRM_PIN4_like, RNA recognition motif in y	2e-07
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	2e-07
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	2e-07
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	2e-07
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	3e-07
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	3e-07
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	3e-07
cd12403	75	cd12403, RRM1_NCL, RNA recognition motif 1 in vert	4e-07
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	4e-07
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	4e-07
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	5e-07
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	5e-07
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	6e-07
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	7e-07
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	7e-07
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	7e-07
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	7e-07
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	8e-07
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	8e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	9e-07
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	9e-07
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	1e-06
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	1e-06
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	1e-06
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	1e-06
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	1e-06
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	2e-06
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	2e-06
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	2e-06
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	2e-06
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	2e-06
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	2e-06
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	2e-06
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	2e-06
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	2e-06
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	2e-06
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	2e-06
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	3e-06
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	3e-06
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	3e-06
cd12657	76	cd12657, RRM1_hnRNPM, RNA recognition motif 1 in v	3e-06
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	3e-06
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	3e-06
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	3e-06
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	4e-06
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	4e-06
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	4e-06
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	4e-06
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	4e-06
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	4e-06
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	4e-06
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	5e-06
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	5e-06
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	5e-06
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	6e-06
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	6e-06
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	7e-06
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	7e-06
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	7e-06
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	7e-06
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	8e-06
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	8e-06
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	1e-05
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	1e-05
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	1e-05
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	1e-05
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	1e-05
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	1e-05
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	1e-05
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-05
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	2e-05
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-05
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-05
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	2e-05
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	2e-05
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	2e-05
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	2e-05
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	2e-05
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	2e-05
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	3e-05
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	3e-05
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	3e-05
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	3e-05
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	3e-05
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	3e-05
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	3e-05
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	3e-05
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	4e-05
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	4e-05
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	4e-05
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	4e-05
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	5e-05
cd12438	98	cd12438, RRM_CNOT4, RNA recognition motif in Eukar	5e-05
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	6e-05
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	6e-05
cd12658	76	cd12658, RRM1_MYEF2, RNA recognition motif 1 in ve	6e-05
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	6e-05
TIGR01649	481	TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus spl	7e-05
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	8e-05
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	9e-05
cd12277	86	cd12277, RRM3_MEI2_EAR1_like, RNA recognition moti	9e-05
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	9e-05
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	9e-05
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-04
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	1e-04
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	1e-04
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	1e-04
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	1e-04
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	1e-04
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	1e-04
cd12262	82	cd12262, RRM2_4_MRN1, RNA recognition motif 2 and	1e-04
cd12274	71	cd12274, RRM2_NEFsp, RNA recognition motif 2 in ve	1e-04
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-04
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-04
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-04
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-04
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	2e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	2e-04
cd12478	91	cd12478, RRM1_U2B, RNA recognition motif 1 in U2 s	2e-04
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	2e-04
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	2e-04
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	2e-04
cd12439	79	cd12439, RRM_TRMT2A, RNA recognition motif in tRNA	2e-04
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	2e-04
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	2e-04
PLN03120	260	PLN03120, PLN03120, nucleic acid binding protein;	2e-04
cd12535	86	cd12535, RRM_FUS_TAF15, RNA recognition motif in v	2e-04
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	3e-04
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-04
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	3e-04
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	3e-04
cd12259	76	cd12259, RRM_SRSF11_SREK1, RNA recognition motif i	3e-04
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	3e-04
cd12269	69	cd12269, RRM_Vip1_like, RNA recognition motif in a	3e-04
cd12360	78	cd12360, RRM_cwf2, RNA recognition motif in yeast	3e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	4e-04
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	4e-04
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	4e-04
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	4e-04
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	4e-04
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	5e-04
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	5e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	5e-04
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	5e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	5e-04
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	5e-04
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	5e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	6e-04
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	6e-04
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	6e-04
cd12403	75	cd12403, RRM1_NCL, RNA recognition motif 1 in vert	6e-04
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	6e-04
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	7e-04
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	7e-04
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	7e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	7e-04
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	7e-04
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	7e-04
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	8e-04
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	8e-04
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	9e-04
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	0.001
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	0.001
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	0.001
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	0.001
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	0.001
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	0.001
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	0.001
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	0.001
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	0.001
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	0.001
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	0.001
cd12356	79	cd12356, RRM_PPARGC1B, RNA recognition motif in pe	0.001
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	0.001
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	0.001
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	0.001
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	0.002
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	0.002
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	0.002
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	0.002
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	0.002
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	0.002
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	0.002
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	0.002
cd12533	84	cd12533, RRM_EWS, RNA recognition motif in vertebr	0.002
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	0.002
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	0.002
cd12331	79	cd12331, RRM_NRD1_SEB1_like, RNA recognition motif	0.002
cd12749	88	cd12749, RRM4_RBM12, RNA recognition motif 4 in RN	0.002
cd12263	98	cd12263, RRM_ABT1_like, RNA recognition motif foun	0.002
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	0.002
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	0.002
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	0.003
cd12299	71	cd12299, RRM4_Prp24, RNA recognition motif 4 in fu	0.003
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	0.003
smart00361	70	smart00361, RRM_1, RNA recognition motif	0.003
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	0.004
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	0.004
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	0.004
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	0.004
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	0.004
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	0.004
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	0.004
cd12535	86	cd12535, RRM_FUS_TAF15, RNA recognition motif in v	0.004
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	0.004
cd12436	76	cd12436, RRM1_2_MATR3_like, RNA recognition motif	0.004
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	0.004
cd12549	93	cd12549, RRM_Set1B, RNA recognition motif in verte	0.004
cd12590	80	cd12590, RRM2_PSF, RNA recognition motif 2 in vert	0.004
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	0.004
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	0.004

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

 Score =  376 bits (967), Expect = e-128
 Identities = 149/319 (46%), Positives = 197/319 (61%), Gaps = 21/319 (6%)

Query: 7   DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
           + L+  ERD RT+F +QL+ + R RDL EFFS VGKVRDV+ I    +RR KG+AY+EF 
Sbjct: 80  EPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFY 139

Query: 67  DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
           D ESV  A+ L GQ LLG PIIVQ +QAEKNRA     +         ++LY+G+LHFNI
Sbjct: 140 DVESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPN-FLKLYVGNLHFNI 198

Query: 127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
           TE  LR IFEPFG I+++QL  DP+TGRSKG+GFI FH A++AK+A E +NGFELAGRP+
Sbjct: 199 TEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPI 258

Query: 187 KVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGT---GLELPPAAAS 243
           KVG   D    +    +  D D+ ++ G +L    R QLM KL       GL +P   + 
Sbjct: 259 KVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSK 318

Query: 244 ALNLA---QNAILNSSTPQVSSSTAPPI--------------ATQCFLLANMFDPATETN 286
              +    ++ I++ + P   ++ A  I              AT C +L+NMFDPATE  
Sbjct: 319 IALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEE 378

Query: 287 PTWDVEIRDDVIEECNKHG 305
           P +D EI DDV EEC+K+G
Sbjct: 379 PNFDNEILDDVKEECSKYG 397

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

 Score =  154 bits (391), Expect = 4e-47
 Identities = 57/73 (78%), Positives = 65/73 (89%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+G+LHFNITED LRGIFEPFG+I+ +QL  DP+TGRSKGYGFI F  A+DAKKA EQL
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 177 NGFELAGRPMKVG 189
           NGFELAGRP+KVG
Sbjct: 61  NGFELAGRPIKVG 73

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

 Score =  146 bits (370), Expect = 4e-44
 Identities = 48/73 (65%), Positives = 58/73 (79%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGL 77
          T+F MQLS ++R RDL EFFS  GKVRDVR+I    +RR KG+AY+EF D ESVPLA+GL
Sbjct: 1  TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGL 60

Query: 78 NGQKLLGIPIIVQ 90
           GQ+LLG PI+VQ
Sbjct: 61 TGQRLLGQPIMVQ 73

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

>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39)

 Score =  134 bits (337), Expect = 5e-39
 Identities = 61/85 (71%), Positives = 73/85 (85%)

Query: 16  ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM 75
           ART+FCMQL+ RIR RDLEEFFS+VGKVRDVR+I+   +RR KGIAY+EF D  SVPLA+
Sbjct: 1   ARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAI 60

Query: 76  GLNGQKLLGIPIIVQPTQAEKNRAG 100
           GL GQ++LG+PIIVQ +QAEKNRA 
Sbjct: 61  GLTGQRVLGVPIIVQASQAEKNRAA 85

This subgroup corresponds to the RRM1 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor 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. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)

 Score =  130 bits (329), Expect = 6e-38
 Identities = 59/84 (70%), Positives = 73/84 (86%)

Query: 16 ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM 75
          ART+FCMQL+ RIR RDLE+FFS+VGKVRDVR+I+   +RR KGIAY+EF + +SVPLA+
Sbjct: 1  ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI 60

Query: 76 GLNGQKLLGIPIIVQPTQAEKNRA 99
          GL GQ+LLG+PIIVQ +QAEKNR 
Sbjct: 61 GLTGQRLLGVPIIVQASQAEKNRL 84

This subgroup corresponds to the RRM1 of RBM23, also termed RNA-binding region-containing protein 4, or splicing factor SF2, which may function as a pre-mRNA splicing factor. It shows high sequence homology to RNA-binding protein 39 (RBM39 or 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). In contrast to RBM39, RBM23 contains only two RRMs. . Length = 85

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

 Score =  107 bits (269), Expect = 4e-29
 Identities = 36/73 (49%), Positives = 55/73 (75%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            L++G+L  + TE+ LR +F  FGK+++++L+ D +TG+SKG+ F+ F S +DA+KA E 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 176 LNGFELAGRPMKV 188
           LNG EL GRP+KV
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 98.1 bits (245), Expect = 1e-25
 Identities = 29/73 (39%), Positives = 52/73 (71%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            LY+G+L +N+TE+ L+ +F  FG++ + +++ D +TGRS+G+GF+   +A++A  A E+
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 176 LNGFELAGRPMKV 188
           LNG +  GR + V
Sbjct: 61  LNGTDFGGRTLTV 73

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 92.3 bits (230), Expect = 2e-23
 Identities = 32/71 (45%), Positives = 50/71 (70%), Gaps = 1/71 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++G+L  + TE+ L+ +F  FG I++I+++ D  TGRSKG+ F+ F   +DA+KA E L
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 177 NGFELAGRPMK 187
           NG EL GR ++
Sbjct: 60  NGKELGGRELR 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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 91.2 bits (227), Expect = 4e-23
 Identities = 34/72 (47%), Positives = 53/72 (73%), Gaps = 1/72 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++G+L  + TE+ LR +F  FG+I++++++ D D G+SKG+ F+ F S +DA+KA E L
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKD-GKSKGFAFVEFESPEDAEKALEAL 59

Query: 177 NGFELAGRPMKV 188
           NG EL GR +KV
Sbjct: 60  NGKELDGRKLKV 71

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

>gnl|CDD|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 = 90.0 bits (224), Expect = 1e-22
 Identities = 33/75 (44%), Positives = 47/75 (62%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
             +L++  L    TE  L  +F  FG+++ + LM DP+TG S+G+GF+TF S +DA  A 
Sbjct: 1   GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAI 60

Query: 174 EQLNGFELAGRPMKV 188
             LNG EL GR +KV
Sbjct: 61  RDLNGKELEGRVIKV 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|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 88.5 bits (220), Expect = 4e-22
 Identities = 31/74 (41%), Positives = 51/74 (68%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           R+Y+ S+H +++ED ++ +FE FGKI +  L  DP+TG+ KGYGFI + +   A+ A   
Sbjct: 2   RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIAS 61

Query: 176 LNGFELAGRPMKVG 189
           +N F+L G+ ++VG
Sbjct: 62  MNLFDLGGQQLRVG 75

This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 77

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

 Score = 85.9 bits (213), Expect = 5e-21
 Identities = 30/73 (41%), Positives = 52/73 (71%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            L++G+L +++ ++ L+  FE FG +   +++ D +TGRS+G+G++ F S +DAKKA E 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 176 LNGFELAGRPMKV 188
           ++G EL GRP+ V
Sbjct: 61  MDGKELDGRPINV 73

This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 76

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

 Score = 82.1 bits (203), Expect = 9e-20
 Identities = 32/74 (43%), Positives = 47/74 (63%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           R+Y+GS+ F + ED +R  F PFG I +I +  DP T + KG+ F+ +   + A+ A EQ
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

Query: 176 LNGFELAGRPMKVG 189
           +NG  L GR +KVG
Sbjct: 62  MNGVMLGGRNIKVG 75

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

 Score = 86.9 bits (214), Expect = 3e-19
 Identities = 37/150 (24%), Positives = 72/150 (48%)

Query: 63  IEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSL 122
            +               ++             E+    +  P  + +       L++G+L
Sbjct: 64  KKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNL 123

Query: 123 HFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELA 182
            +++TE+ LR +F+ FG +  ++L+ D +TG+S+G+ F+ F S + A+KA E+LNG EL 
Sbjct: 124 PYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELE 183

Query: 183 GRPMKVGTVTDRNESVGGGPSNLDTDEMER 212
           GRP++V      ++      +NLD    ++
Sbjct: 184 GRPLRVQKAQPASQPRSELSNNLDASFAKK 213

Length = 306

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

 Score = 79.2 bits (196), Expect = 1e-18
 Identities = 28/73 (38%), Positives = 51/73 (69%), Gaps = 1/73 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +Y+ +L  ++ ++ L+ +F  +GKI + ++M D D G+SKG+GF+ F + + A+KA E+L
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 177 NGFELAGRPMKVG 189
           NG E+ G+ + VG
Sbjct: 63  NGKEVNGKKLYVG 75

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

 Score = 83.5 bits (205), Expect = 5e-18
 Identities = 48/191 (25%), Positives = 79/191 (41%), Gaps = 12/191 (6%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
              + +  T+F   L   +   DL E F   G V+ VRL+   +T + +G A++EF+  E
Sbjct: 109 QKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEE 168

Query: 70  SVPLAMG-LNGQKLLGIPIIVQPTQAEK-----------NRAGNTLPNLQPRGTGGPMRL 117
           S   A+  LNG++L G P+ VQ  Q                    L   +         L
Sbjct: 169 SAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNL 228

Query: 118 YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN 177
           Y+G+L     E+ L  +F+  G I    L    D    K   F+   ++ DA ++  + N
Sbjct: 229 YVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSRGN 288

Query: 178 GFELAGRPMKV 188
             ++ GR  + 
Sbjct: 289 KKKILGRGPRK 299

Length = 306

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

 Score = 77.2 bits (191), Expect = 6e-18
 Identities = 28/72 (38%), Positives = 46/72 (63%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+G LH ++TE ML  IF P G + +I++  D  T RS GY ++ F +  DA++A + L
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 177 NGFELAGRPMKV 188
           N   + G+P+++
Sbjct: 62  NFDVIKGKPIRI 73

This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|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 = 76.8 bits (190), Expect = 7e-18
 Identities = 30/76 (39%), Positives = 49/76 (64%), Gaps = 3/76 (3%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L++G L    TE+ +R +FE +G I+ + ++ D DTG+SKG  F+ F S ++A+KA E 
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 176 LNG---FELAGRPMKV 188
           L+G      A RP++V
Sbjct: 61  LHGKVTMPGASRPLQV 76

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|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 = 77.0 bits (190), Expect = 7e-18
 Identities = 29/69 (42%), Positives = 44/69 (63%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL++ +L F  TE+ LR +FE FG+I  + L +D +T RSKG+ F++F   + A KA  +
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 176 LNGFELAGR 184
           L+G    GR
Sbjct: 61  LDGSIFQGR 69

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

 Score = 76.9 bits (190), Expect = 8e-18
 Identities = 27/72 (37%), Positives = 43/72 (59%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+G L   + E +L   F PFG I +IQ+ +D +T + +G+ F+ F   +DA  A + +
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 177 NGFELAGRPMKV 188
           N  EL GR ++V
Sbjct: 61  NESELFGRTIRV 72

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

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

 Score = 76.6 bits (189), Expect = 9e-18
 Identities = 28/72 (38%), Positives = 49/72 (68%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++G+L F+  ED +   F  +G+I +++L  DPD+GR KG+G++ F S + A+ A + L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 177 NGFELAGRPMKV 188
            G +L GRP+++
Sbjct: 61  GGTDLLGRPVRL 72

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

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

 Score = 83.3 bits (206), Expect = 2e-17
 Identities = 41/168 (24%), Positives = 80/168 (47%), Gaps = 14/168 (8%)

Query: 33  LEEFFSSVGKVRDVRLITC-NKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIP---- 86
           L E F+  G++         + + R +G A++ F+  E    A+  +NG+K+        
Sbjct: 195 LRELFAKFGEI--TSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKK 252

Query: 87  IIVQPTQAEKNRAGNTLPNLQPRGTGGPMR-----LYIGSLHFNITEDMLRGIFEPFGKI 141
           + V   Q    R        +       M+     LY+ +L   +T++ LR +F   G+I
Sbjct: 253 LYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEI 312

Query: 142 DNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
            + ++M+D   G S+G+GF+ F + ++A +A  +++G  L G+P+ V 
Sbjct: 313 TSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVA 359

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

 Score = 75.7 bits (187), Expect = 2e-17
 Identities = 31/67 (46%), Positives = 47/67 (70%)

Query: 122 LHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFEL 181
           L    TE  LR +F  +G I+ +Q++ D  TGRS+G+GF+ F S +DAK+A+E+LNG E+
Sbjct: 7   LSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEI 66

Query: 182 AGRPMKV 188
            GR ++V
Sbjct: 67  DGRRIRV 73

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|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 = 75.4 bits (186), Expect = 2e-17
 Identities = 27/72 (37%), Positives = 43/72 (59%)

Query: 118 YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN 177
           ++G++ ++ TE+ L  IF   G + + +L+ D DTG+ KGYGF  F   + A  A   LN
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 178 GFELAGRPMKVG 189
           G+E  GR ++V 
Sbjct: 62  GYEFNGRALRVD 73

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

 Score = 75.3 bits (186), Expect = 3e-17
 Identities = 22/72 (30%), Positives = 45/72 (62%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++G L  N+ +D L+ IF  +G + ++ L +D +    +GY ++ F S +DA+KA + +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 177 NGFELAGRPMKV 188
           +G ++ G+ + V
Sbjct: 61  DGGQIDGQEVTV 72

This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. . Length = 73

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

 Score = 81.7 bits (201), Expect = 7e-17
 Identities = 65/273 (23%), Positives = 113/273 (41%), Gaps = 35/273 (12%)

Query: 19  IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
           ++   +S  +R   +   F   G ++ + +     T + KG A++E++ PE+  LA+  +
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 78  NGQKLLGIPIIVQPTQAEKNRAGNTLPNLQP------RGTGGPMRLYIGSLHFNITEDML 131
           NGQ L G  I V        R  N +P  QP             R+Y+ S+H +++E  +
Sbjct: 170 NGQMLGGRNIKV-------GRPSN-MPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDI 221

Query: 132 RGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG-T 190
           + +FE FG+I   QL   P     KGYGFI +++     +A   +N F+L G+ ++VG  
Sbjct: 222 KSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC 281

Query: 191 VTDRN-----ESVGGGP-----------SNLDTDEMERAGVDLGATGRLQLMFKLAEGTG 234
           VT  +      +V   P           + +   E       LG   +       +  T 
Sbjct: 282 VTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGAAVLGPRAQSPATPSSSLPTD 341

Query: 235 LELPPAAASALNLAQNAILNSSTPQVSSSTAPP 267
           +      +SA   A+        PQ + +   P
Sbjct: 342 IGNKAVVSSAKKEAE---EVPPLPQAAPAVVKP 371

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

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

 Score = 73.7 bits (182), Expect = 9e-17
 Identities = 27/55 (49%), Positives = 40/55 (72%)

Query: 125 NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF 179
           +  ED LR +F PFG I  + L  D +TG+S+G+ F+TFH+ +DA++A E+LNGF
Sbjct: 10  DADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGF 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 80.6 bits (199), Expect = 1e-16
 Identities = 44/166 (26%), Positives = 79/166 (47%), Gaps = 11/166 (6%)

Query: 19  IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
           IF   L + +  + L + FS  G +   ++   ++  + +G  ++ F+  ES   A+  +
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVA-TDENGKSRGYGFVHFEKEESAKAAIQKV 149

Query: 78  NGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEP 137
           NG  L    + V     +  R    L             LY+ +L  ++ ED LR +F  
Sbjct: 150 NGMLLNDKEVYVGRFIKKHEREAAPLKKF--------TNLYVKNLDPSVNEDKLRELFAK 201

Query: 138 FGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG 183
           FG+I +  +M D  +GRS+G+ F+ F   +DA KA E++NG ++  
Sbjct: 202 FGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGL 246

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

 Score = 73.2 bits (180), Expect = 2e-16
 Identities = 28/71 (39%), Positives = 46/71 (64%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++G L   I  + LR  F PFG+I + +++ D  TG+SKGYGF++F   +DA+ A + +
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 177 NGFELAGRPMK 187
           NG  L GR ++
Sbjct: 62  NGQWLGGRAIR 72

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

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

 Score = 73.0 bits (180), Expect = 2e-16
 Identities = 21/36 (58%), Positives = 28/36 (77%)

Query: 270 TQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
           ++C +L NMFDPA ET   WD EI++DV+EEC+K G
Sbjct: 1   SRCVILKNMFDPAEETEDEWDDEIKEDVLEECSKFG 36

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

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

 Score = 71.0 bits (175), Expect = 7e-16
 Identities = 27/69 (39%), Positives = 46/69 (66%), Gaps = 2/69 (2%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+ +L  ++TE+ LR  F P+GK++ ++L+ + D  R +G+ F+ F S +DA+ A ++L
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58

Query: 177 NGFELAGRP 185
           NG  L GR 
Sbjct: 59  NGLVLDGRT 67

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

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

 Score = 71.5 bits (176), Expect = 8e-16
 Identities = 30/75 (40%), Positives = 46/75 (61%), Gaps = 4/75 (5%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSK---GYGFITFHSADDAKKAQ 173
           +Y+ +L F + ED LRGIF  FG++++I++    D  + +   G+ F+TF  A  A+ A 
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 174 EQLNGFELAGRPMKV 188
            QLNG EL GR + V
Sbjct: 63  -QLNGTELGGRKISV 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|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 70.7 bits (174), Expect = 1e-15
 Identities = 30/75 (40%), Positives = 49/75 (65%), Gaps = 1/75 (1%)

Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           + LY+ +L  +I ++ LR  F PFG I + ++M D + GRSKG+GF+ F S ++A KA  
Sbjct: 2   VNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTD-EKGRSKGFGFVCFSSPEEATKAVT 60

Query: 175 QLNGFELAGRPMKVG 189
           ++NG  + G+P+ V 
Sbjct: 61  EMNGRIIGGKPLYVA 75

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

 Score = 70.3 bits (173), Expect = 2e-15
 Identities = 26/73 (35%), Positives = 47/73 (64%), Gaps = 1/73 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL + +LH+++TE+ L  +F   G++  +++  D  +GRS+G   + F   +DA++A +Q
Sbjct: 2   RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQ 60

Query: 176 LNGFELAGRPMKV 188
            NG  L G+PM+V
Sbjct: 61  FNGVLLDGQPMQV 73

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|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 77.2 bits (190), Expect = 2e-15
 Identities = 52/255 (20%), Positives = 90/255 (35%), Gaps = 37/255 (14%)

Query: 2   RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSV---------GKVRDVRLITCN 52
              Y    +   R AR ++   +        + +FF+ +            + V  +  N
Sbjct: 164 VLPYQQQAT---RQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNIN 220

Query: 53  KTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQ--------------PTQ--AEK 96
           K + F   A++EF+  E    AM L+      + + ++               +Q   + 
Sbjct: 221 KEKNF---AFLEFRTVEEATFAMALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDD 277

Query: 97  NRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSK 156
           N                  R+YIG+L   + ED ++ + E FG +    L+ D  TG SK
Sbjct: 278 NAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSK 337

Query: 157 GYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSNLDTDEMERAGVD 216
           GY F  +        A   LNG +     + V     +   VG   + +DT     A V 
Sbjct: 338 GYAFCEYKDPSVTDVAIAALNGKDTGDNKLHV-----QRACVGANQATIDTSNGM-APVT 391

Query: 217 LGATGRLQLMFKLAE 231
           L A    Q + ++  
Sbjct: 392 LLAKALSQSILQIGG 406

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

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

 Score = 70.0 bits (172), Expect = 2e-15
 Identities = 20/72 (27%), Positives = 40/72 (55%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++ +L ++ T++ L   F   G I    ++ D  + + +G+G++TF   +DAK+A E+ 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 177 NGFELAGRPMKV 188
              +  GR + V
Sbjct: 62  KKTKFGGRKIHV 73

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

 Score = 76.6 bits (188), Expect = 3e-15
 Identities = 33/74 (44%), Positives = 49/74 (66%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           R+Y+GS+ F + ED +R  F+PFG I +I +  DP TG+ KG+ F+ +   + A+ A EQ
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168

Query: 176 LNGFELAGRPMKVG 189
           +NG  L GR +KVG
Sbjct: 169 MNGQMLGGRNIKVG 182

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

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 69.9 bits (171), Expect = 3e-15
 Identities = 29/73 (39%), Positives = 47/73 (64%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L+IG L F+  E  L  +F  +G+I  + ++ D +T RS+G+GF+TF + DDAK A   
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 176 LNGFELAGRPMKV 188
           +NG  + GR ++V
Sbjct: 62  MNGKSVDGRQIRV 74

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

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

 Score = 69.7 bits (171), Expect = 3e-15
 Identities = 23/73 (31%), Positives = 45/73 (61%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL++ +L ++  ED L  +F  FG++  + + +D  +G+SKG+ ++ F   +DA KA ++
Sbjct: 4   RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 176 LNGFELAGRPMKV 188
           L+G    GR + +
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 = 68.8 bits (169), Expect = 7e-15
 Identities = 28/73 (38%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
          T+F   L       +L E FS  GKV  VRL+   +T + KG A++EF+  E    A+  
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 77 LNGQKLLGIPIIV 89
          LNG++L G P+ V
Sbjct: 61 LNGKELDGRPLKV 73

Length = 73

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

 Score = 74.1 bits (182), Expect = 2e-14
 Identities = 46/158 (29%), Positives = 80/158 (50%), Gaps = 13/158 (8%)

Query: 33  LEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQP 91
           L + F   G V  VR+   + TRR  G  Y+ F++P     A+  +N ++L G PI +  
Sbjct: 17  LYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMW 76

Query: 92  TQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPD 151
           +Q +        P+L+  G G    +++ +L  ++    L   F  FG I + ++  D +
Sbjct: 77  SQRD--------PSLRRSGVGN---IFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-E 124

Query: 152 TGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
            G+S+GYGF+ F   + AK A +++NG  L  + + VG
Sbjct: 125 NGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVG 162

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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 68.0 bits (167), Expect = 2e-14
 Identities = 26/72 (36%), Positives = 43/72 (59%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +YIG L + +TE  +  +F  +G+I +I L+ D  TG+SKG+ F+ +        A + L
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 177 NGFELAGRPMKV 188
           NG +L GR ++V
Sbjct: 72  NGIKLLGRTIRV 83

This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well. . Length = 89

>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 67.4 bits (165), Expect = 2e-14
 Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 8/74 (10%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L+IG L +  T+D L+  F  +G+I +  +M DP+T RS+G+GF+TF SA +   A   
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAM-- 58

Query: 176 LNGFELAGRPMKVG 189
                   RP KV 
Sbjct: 59  ------NARPHKVD 66

This subfamily corresponds to the RRM1 in 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 = 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 = 67.0 bits (164), Expect = 3e-14
 Identities = 27/72 (37%), Positives = 43/72 (59%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +Y+ +L F++T + L  IF  +GK+  + ++ D +T +SKG  FI F   +DA K  + L
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 177 NGFELAGRPMKV 188
           N  EL GR +K 
Sbjct: 64  NNKELFGRTLKC 75

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

 Score = 66.6 bits (163), Expect = 4e-14
 Identities = 27/73 (36%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++G L  ++TE+  +  F  FGK+ + QLM D DTGRS+G+GF+TF S    ++    
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 176 LNGFELAGRPMKV 188
               EL G+ ++V
Sbjct: 61  -GMLELGGKQVEV 72

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 75

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

 Score = 66.2 bits (162), Expect = 6e-14
 Identities = 30/73 (41%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKI-DNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           L+IG+L   + E +L   F  FG I    ++M DPDTG SKG+ FI++ S + +  A E 
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 176 LNGFELAGRPMKV 188
           +NG  L  RP+ V
Sbjct: 64  MNGQYLCNRPITV 76

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

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

 Score = 72.5 bits (178), Expect = 7e-14
 Identities = 27/72 (37%), Positives = 47/72 (65%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+G L  ++TE  L  +F+PFG + ++++  D  T RS GYG++ F +  DA++A E +
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 177 NGFELAGRPMKV 188
           N   L G+P+++
Sbjct: 63  NFKRLGGKPIRI 74

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

 Score = 65.6 bits (161), Expect = 7e-14
 Identities = 26/71 (36%), Positives = 45/71 (63%), Gaps = 1/71 (1%)

Query: 118 YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN 177
           ++G+L F+I E+ LR  FE  G ++ ++++ D  TG  KG+G++ F + D    A  +LN
Sbjct: 3   FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KLN 61

Query: 178 GFELAGRPMKV 188
           G +L GR ++V
Sbjct: 62  GIKLKGRKIRV 72

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

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

 Score = 65.9 bits (161), Expect = 8e-14
 Identities = 27/77 (35%), Positives = 51/77 (66%), Gaps = 2/77 (2%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL++ ++ F   +  LR +F  FG I +++++ + + G SKG+GF+TF ++ DA +A+E+
Sbjct: 2   RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFN-ERG-SKGFGFVTFANSADADRAREK 59

Query: 176 LNGFELAGRPMKVGTVT 192
           L+G  + GR ++V   T
Sbjct: 60  LHGTVVEGRKIEVNNAT 76

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|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score = 65.6 bits (160), Expect = 8e-14
 Identities = 26/72 (36%), Positives = 45/72 (62%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++G++ +  TE+ L+ IF   G + + +L+ D +TG+ KGYGF  +   + A  A   L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 177 NGFELAGRPMKV 188
           NG+EL GR ++V
Sbjct: 61  NGYELNGRQLRV 72

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

>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 65.4 bits (160), Expect = 1e-13
 Identities = 27/77 (35%), Positives = 47/77 (61%), Gaps = 1/77 (1%)

Query: 117 LYIGSLHFNITEDMLRGIF-EPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +++G L  ++T+ ML+  F   +  +   ++++DP TGRSKGYGF+ F   D+  +A  +
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 176 LNGFELAGRPMKVGTVT 192
           +NG   + RPM+V   T
Sbjct: 64  MNGVYCSSRPMRVSPAT 80

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

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

 Score = 64.9 bits (159), Expect = 1e-13
 Identities = 27/72 (37%), Positives = 37/72 (51%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +YIG L     E  LR  F  FG +  ++L     TG+SKGY F+ F S + AK   E +
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 177 NGFELAGRPMKV 188
           N + L  R +K 
Sbjct: 62  NNYLLFERLLKC 73

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

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

 Score = 65.0 bits (159), Expect = 1e-13
 Identities = 28/79 (35%), Positives = 50/79 (63%), Gaps = 2/79 (2%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            L++G+L ++  +D L   F+  G++ ++++  D D GRSKG+G + F + + A+KA E 
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQD-DDGRSKGFGHVEFATEEGAQKALE- 58

Query: 176 LNGFELAGRPMKVGTVTDR 194
            +G EL GR ++V   T+R
Sbjct: 59  KSGEELLGREIRVDLATER 77

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

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 65.5 bits (160), Expect = 1e-13
 Identities = 29/78 (37%), Positives = 46/78 (58%), Gaps = 3/78 (3%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
            ++L++G +  N+ E  LR +FE FGKI  + ++ D  TG  KG  F+T+ + + A KAQ
Sbjct: 5   AIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQ 64

Query: 174 EQLNG-FELAG--RPMKV 188
             L+    L G  RP++V
Sbjct: 65  SALHEQKTLPGMNRPIQV 82

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

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

 Score = 64.2 bits (157), Expect = 2e-13
 Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
          +F   L       DL E FS  G++  VR++  +K  + KG A++EF+ PE    A+  L
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVR-DKDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 78 NGQKLLGIPIIVQ 90
          NG++L G  + V 
Sbjct: 60 NGKELDGRKLKVS 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|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 64.8 bits (158), Expect = 2e-13
 Identities = 25/72 (34%), Positives = 42/72 (58%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++G L   +T+  L   F  F    + ++M D  +GRS+GYGF++F S  DA+ A  ++
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 177 NGFELAGRPMKV 188
           NG  L  RP++ 
Sbjct: 62  NGKWLGSRPIRC 73

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

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

 Score = 64.6 bits (158), Expect = 2e-13
 Identities = 29/73 (39%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL + +L F  TE  L+ +F PFG +  + +   PD G+ KG+ F+ F S  DA+KA + 
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPD-GKKKGFAFVQFTSKADAEKAIKG 59

Query: 176 LNGFELAGRPMKV 188
           +NG ++ GRP+ V
Sbjct: 60  VNGKKIKGRPVAV 72

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|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 = 64.2 bits (157), Expect = 2e-13
 Identities = 25/72 (34%), Positives = 47/72 (65%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L+I  L    T+  L  +F PFG + + ++ VD +TG+SK +GF+++ + + A+ A + +
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 177 NGFELAGRPMKV 188
           NGF++ G+ +KV
Sbjct: 61  NGFQVGGKRLKV 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|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 63.9 bits (156), Expect = 3e-13
 Identities = 30/72 (41%), Positives = 46/72 (63%), Gaps = 1/72 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +Y+G + +  TED +R  F   G+I+ + LM  PDTGR +G  FITF + + AK+A   L
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALA-L 59

Query: 177 NGFELAGRPMKV 188
           +G ++ GR +KV
Sbjct: 60  DGEDMGGRFLKV 71

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

>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 64.0 bits (156), Expect = 3e-13
 Identities = 24/59 (40%), Positives = 36/59 (61%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           ++++G L  N TED ++  F  FGK+++  LM D  T R +G+GF+TF S D   K  E
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCE 59

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 63.9 bits (156), Expect = 3e-13
 Identities = 26/64 (40%), Positives = 44/64 (68%)

Query: 125 NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGR 184
           ++T++ LR +FE  G I++ +++ D  TG+S GYGF+ +   +DA+KA   LNGFE+  +
Sbjct: 11  DMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNK 70

Query: 185 PMKV 188
            +KV
Sbjct: 71  RLKV 74

This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 77

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

 Score = 64.3 bits (156), Expect = 3e-13
 Identities = 28/76 (36%), Positives = 47/76 (61%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++G L   IT + ++  F PFGKI + +++ D  TG+SKGYGF++F++  DA+ A   +
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 177 NGFELAGRPMKVGTVT 192
            G  L GR ++    T
Sbjct: 64  GGQWLGGRQIRTNWAT 79

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

 Score = 63.5 bits (155), Expect = 4e-13
 Identities = 24/72 (33%), Positives = 44/72 (61%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L + +L +  T D LR +FE +G++ ++ +  D  T  S+G+ F+ F+   DA+ A + +
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 177 NGFELAGRPMKV 188
           +G EL GR ++V
Sbjct: 61  DGKELDGRELRV 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|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 63.4 bits (155), Expect = 5e-13
 Identities = 27/72 (37%), Positives = 43/72 (59%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L +G+L    T++  R +  PFG ++   L+    TG SKGYGF+ + S   A KA+ QL
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 177 NGFELAGRPMKV 188
           +G ++ GR ++V
Sbjct: 62  DGKQIGGRKLQV 73

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|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 63.6 bits (155), Expect = 5e-13
 Identities = 26/64 (40%), Positives = 42/64 (65%)

Query: 125 NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGR 184
           N+T+D +R +F   G+I++ +L+ D  TG+S GYGF+ +   +DA+KA   LNG  L  +
Sbjct: 12  NMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNK 71

Query: 185 PMKV 188
            +KV
Sbjct: 72  TIKV 75

This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

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

 Score = 63.0 bits (154), Expect = 6e-13
 Identities = 23/59 (38%), Positives = 35/59 (59%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           L+IG L ++ TE+ LR  F  +G++ +  +M DP TGRS+G+GF+TF       K    
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAA 59

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

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

 Score = 63.1 bits (154), Expect = 7e-13
 Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 3/72 (4%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLM---VDPDTGRSKGYGFITFHSADDAKKA 172
           RL+IG+L   +TE  L  +F  +GKI     +     P  G+ +GY F+TF + ++A+KA
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 173 QEQLNGFELAGR 184
            + LNG    G+
Sbjct: 61  LKSLNGKTALGK 72

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

 Score = 62.3 bits (152), Expect = 1e-12
 Identities = 26/72 (36%), Positives = 45/72 (62%), Gaps = 1/72 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++ +L F++T   L+ +F   G +    +  D D GRSKG+G + F S +DA++A E  
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEMF 59

Query: 177 NGFELAGRPMKV 188
           NG++L GR ++V
Sbjct: 60  NGYDLEGRELEV 71

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

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

 Score = 62.4 bits (151), Expect = 1e-12
 Identities = 29/76 (38%), Positives = 48/76 (63%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++G L   IT D ++  F PFG+I + +++ D  TG+SKGYGF++F +  DA+ A +Q+
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 177 NGFELAGRPMKVGTVT 192
            G  L GR ++    T
Sbjct: 64  GGQWLGGRQIRTNWAT 79

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

 Score = 62.1 bits (151), Expect = 2e-12
 Identities = 27/59 (45%), Positives = 41/59 (69%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           +L++G L+   ++  LR  F  +GK+    +MVDP+T RS+G+GFITF SAD+A +A E
Sbjct: 4   KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAME 62

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

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

 Score = 62.0 bits (151), Expect = 2e-12
 Identities = 21/54 (38%), Positives = 31/54 (57%)

Query: 122 LHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           L +  TE  L+  F  FG++  +Q+  DP TG+SKG+GF+ F   +D  K   Q
Sbjct: 7   LPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ 60

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

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

 Score = 61.8 bits (151), Expect = 2e-12
 Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 5/77 (6%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           ++I +L F+ TE+ L+ +F  FG++   +++ D  TG SKG  F+ F + + A+K  E  
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 177 N-----GFELAGRPMKV 188
           +     G  L GR + V
Sbjct: 63  DNAEDSGLSLDGRRLIV 79

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

>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 61.9 bits (151), Expect = 2e-12
 Identities = 24/73 (32%), Positives = 39/73 (53%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +++IG L   ++ED ++ + E FGK+    L+ D  TG SKGY F  +       +A   
Sbjct: 2   KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61

Query: 176 LNGFELAGRPMKV 188
           LNG +L  + + V
Sbjct: 62  LNGMQLGDKKLTV 74

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

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

 Score = 61.5 bits (150), Expect = 2e-12
 Identities = 18/57 (31%), Positives = 37/57 (64%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
           +L++G L  ++TE+ LR  F  +G +++++++ D +TG+ +G+ F+TF   D   K 
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKI 57

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

 Score = 61.5 bits (150), Expect = 3e-12
 Identities = 23/62 (37%), Positives = 41/62 (66%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++G L ++ T+D LR  F  FG+I+   ++ D  TG+S+GYGF+TF   + A++A + 
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 176 LN 177
            N
Sbjct: 62  PN 63

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

 Score = 63.5 bits (154), Expect = 3e-12
 Identities = 29/79 (36%), Positives = 48/79 (60%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L+IG L +   +  LR  F  FG + + +++VD +TGRS+G+GF+ F+    A  A  +
Sbjct: 36  KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95

Query: 176 LNGFELAGRPMKVGTVTDR 194
           ++G EL GR ++V    DR
Sbjct: 96  MDGKELNGRHIRVNPANDR 114

Length = 144

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

 Score = 61.1 bits (149), Expect = 3e-12
 Identities = 26/72 (36%), Positives = 43/72 (59%), Gaps = 8/72 (11%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+ +L  + TE+ LR +F  +G+++ ++ + D        Y F+ F   DDA KA E++
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55

Query: 177 NGFELAGRPMKV 188
           NG EL G P++V
Sbjct: 56  NGKELEGSPIEV 67

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

 Score = 61.6 bits (150), Expect = 3e-12
 Identities = 25/72 (34%), Positives = 45/72 (62%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++ +L  +  E +L  +F PFG + N++++ D  T + KGYGF+T  + ++A  A   L
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 177 NGFELAGRPMKV 188
           NG+ L GR ++V
Sbjct: 64  NGYRLGGRVLQV 75

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

>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 61.6 bits (150), Expect = 3e-12
 Identities = 28/66 (42%), Positives = 41/66 (62%), Gaps = 2/66 (3%)

Query: 125 NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG- 183
           ++TED LR  F PFG+I +I ++ D  T  SKG  ++ F  A  A +A E++NG  L G 
Sbjct: 13  SVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGD 72

Query: 184 -RPMKV 188
            +P+KV
Sbjct: 73  TKPLKV 78

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

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

 Score = 60.7 bits (148), Expect = 4e-12
 Identities = 27/62 (43%), Positives = 39/62 (62%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +YI  L  N T++ L  + +PFGKI + + ++D  T + KGYGF+ F S + A KA E L
Sbjct: 3   VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGL 62

Query: 177 NG 178
           NG
Sbjct: 63  NG 64

This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 71

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

 Score = 60.6 bits (148), Expect = 4e-12
 Identities = 21/74 (28%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA-KKAQE 174
           RL++G L  ++TE  L   F  FG + +++++   D G  +G+ +I   +++   KK + 
Sbjct: 1   RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKS 60

Query: 175 QLNGFELAGRPMKV 188
            LNG +  G  +K+
Sbjct: 61  TLNGTKWKGSVLKI 74

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

 Score = 60.8 bits (148), Expect = 5e-12
 Identities = 29/77 (37%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGL 77
          T+F   LS      DLEEFF   G+V DVR I  +   R KG  ++EF   E    A+  
Sbjct: 1  TLFVGNLSWSAEQDDLEEFFKECGEVVDVR-IAQDDDGRSKGFGHVEFATEEGAQKALEK 59

Query: 78 NGQKLLGIPIIVQPTQA 94
          +G++LLG  I V     
Sbjct: 60 SGEELLGREIRVDLATE 76

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

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

 Score = 60.4 bits (147), Expect = 6e-12
 Identities = 26/76 (34%), Positives = 45/76 (59%), Gaps = 2/76 (2%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
           P R+++G +  + TE+ LR  F  FG + +++++ D   G SKGYGF+TF + +DA+K  
Sbjct: 2   PNRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRA-GVSKGYGFVTFETQEDAEKIL 60

Query: 174 EQLNGFELAGRPMKVG 189
              N     G+ + +G
Sbjct: 61  AMGN-LNFRGKKLNIG 75

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

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

 Score = 59.9 bits (145), Expect = 1e-11
 Identities = 26/78 (33%), Positives = 47/78 (60%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++ +L F++T++ L   F     I +  ++ DP+TG S+GYGF+TF   +DA++A  +L
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 177 NGFELAGRPMKVGTVTDR 194
              +L GR +++     R
Sbjct: 62  KNKKLHGRILRLDIAERR 79

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

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

 Score = 60.0 bits (146), Expect = 1e-11
 Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L + +L F +++D ++ +F  FG +    +  D  +GRS G   + F    DA KA +Q
Sbjct: 2   KLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYD-RSGRSLGTADVVFERRADALKAMKQ 60

Query: 176 LNGFELAGRPMKV 188
            NG  L GRPMK+
Sbjct: 61  YNGVPLDGRPMKI 73

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

 Score = 59.8 bits (145), Expect = 1e-11
 Identities = 25/72 (34%), Positives = 39/72 (54%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +YIG L     E  L+  F  FG + N+++     TG SK YGFI F + + A  A + +
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 177 NGFELAGRPMKV 188
           N + L G+ ++V
Sbjct: 62  NNYLLMGKVLQV 73

This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

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

 Score = 59.6 bits (145), Expect = 1e-11
 Identities = 26/75 (34%), Positives = 37/75 (49%), Gaps = 4/75 (5%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITC-NKTRRFKGIAYIEFKDPESVPLAM 75
          RTI+   L        L EFFS  G+V+ VR+     +  R+   A++EF +  SV  A+
Sbjct: 5  RTIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTRY---AFVEFAEQTSVINAL 61

Query: 76 GLNGQKLLGIPIIVQ 90
           LNG    G P+ V 
Sbjct: 62 KLNGAMFGGRPLKVN 76

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

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

 Score = 60.0 bits (146), Expect = 1e-11
 Identities = 23/58 (39%), Positives = 38/58 (65%), Gaps = 1/58 (1%)

Query: 131 LRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
           LR +F   GK    QL + P+ G+ +G+ F+ + +A+DA++AQ+ LNG  L G P++V
Sbjct: 20  LRKLFSQVGKPTFCQLAIAPN-GQPRGFAFVEYATAEDAEEAQQALNGHSLQGSPIRV 76

This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 92

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

 Score = 59.3 bits (144), Expect = 1e-11
 Identities = 26/72 (36%), Positives = 43/72 (59%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L I  L   +T++  R +F   G + N +++ D  TG S G+GF+ + SA+DA++A   L
Sbjct: 3   LIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTL 62

Query: 177 NGFELAGRPMKV 188
           NG +L  + +KV
Sbjct: 63  NGLQLQNKRIKV 74

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

>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 58.7 bits (142), Expect = 2e-11
 Identities = 25/65 (38%), Positives = 41/65 (63%), Gaps = 3/65 (4%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFH---SADDAKKAQ 173
           ++IG L++  T+D LR  F  FG++ +  +M D  TGRS+G+GF+TF    S ++  K +
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 174 EQLNG 178
             L+G
Sbjct: 61  HILDG 65

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 76

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

 Score = 57.9 bits (141), Expect = 3e-11
 Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 5/58 (8%)

Query: 131 LRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
           L  +F PFG ++ I+L+         G+ F+ F + + A+KA + LNG    GRP++V
Sbjct: 1   LYKLFSPFGNVEKIKLLKK-----KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRV 53

(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|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 59.2 bits (144), Expect = 3e-11
 Identities = 27/72 (37%), Positives = 42/72 (58%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++  L+++ TE  LR  FE +G I  I+L+ D  TG+ +GY FI F    D K A +  
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 177 NGFELAGRPMKV 188
           +G ++ GR + V
Sbjct: 64  DGKKIDGRRVLV 75

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

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

 Score = 58.8 bits (143), Expect = 3e-11
 Identities = 24/73 (32%), Positives = 45/73 (61%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           R+++G L   +T+++L   F  +      +++ D  TG+SKGYGF++F   +D  KA ++
Sbjct: 8   RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKE 67

Query: 176 LNGFELAGRPMKV 188
           +NG  +  RP+K+
Sbjct: 68  MNGKYVGNRPIKL 80

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

>gnl|CDD|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 = 58.0 bits (141), Expect = 4e-11
 Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 6/73 (8%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +Y+G+L   +TE+ L+  F PFG I+ ++  V  D    KGY F+ F + + A  A   +
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVR--VFKD----KGYAFVRFDTHEAAATAIVAV 56

Query: 177 NGFELAGRPMKVG 189
           NG  + G+ +K  
Sbjct: 57  NGTSINGQTVKCS 69

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

 Score = 57.9 bits (141), Expect = 5e-11
 Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
           G   ++I +L  +I    L   F  FG I + ++  D + G SKGYGF+ F + + A +A
Sbjct: 1   GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVATD-ENGGSKGYGFVHFETEEAAVRA 59

Query: 173 QEQLNGFELAGRPMKVG 189
            E++NG  L  + + VG
Sbjct: 60  IEKVNGMLLNDKKVFVG 76

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

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

 Score = 58.0 bits (141), Expect = 5e-11
 Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 3/68 (4%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+ +L F I+ + L  +F  +G I  I++    +T   +G  F+ +    DAK A + L
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNACDHL 61

Query: 177 NGFELAGR 184
           +GF +A R
Sbjct: 62  SGFNVANR 69

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

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

 Score = 63.0 bits (153), Expect = 5e-11
 Identities = 45/156 (28%), Positives = 73/156 (46%), Gaps = 14/156 (8%)

Query: 24  LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL 82
           L Q +   ++   F+S+G++   +L+    T +  G  ++ +  PE    A+  LNG +L
Sbjct: 11  LPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRL 70

Query: 83  LGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKID 142
               I V   +           +   +G      LY+  L   +T+  L  IF PFG+I 
Sbjct: 71  QNKTIKVSYARPS---------SDSIKGAN----LYVSGLPKTMTQHELESIFSPFGQII 117

Query: 143 NIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNG 178
             +++ D  TG SKG GFI F   D+A +A + LNG
Sbjct: 118 TSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNG 153

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

 Score = 57.7 bits (139), Expect = 5e-11
 Identities = 27/67 (40%), Positives = 40/67 (59%)

Query: 122 LHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFEL 181
           L    TE  LR +F  +G +  + ++ D  TGRS+G+ F+ F   DD+K+A E  NG EL
Sbjct: 7   LSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMEL 66

Query: 182 AGRPMKV 188
            GR ++V
Sbjct: 67  DGRRIRV 73

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

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

 Score = 57.3 bits (139), Expect = 7e-11
 Identities = 26/72 (36%), Positives = 42/72 (58%), Gaps = 1/72 (1%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGL 77
          T+F   L   +   +L + FS  G++ DVRL+  N   + KG AY+EF++ ESV  A+ L
Sbjct: 1  TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVK-NYKGKSKGYAYVEFENEESVQEALKL 59

Query: 78 NGQKLLGIPIIV 89
          + + + G P+ V
Sbjct: 60 DRELIKGRPMFV 71

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

>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 57.5 bits (139), Expect = 8e-11
 Identities = 26/77 (33%), Positives = 44/77 (57%), Gaps = 1/77 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFE-PFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +++G L   + E  L  +F+  F    + ++M DP TG S+GYGF+ F   +D ++A  +
Sbjct: 4   IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63

Query: 176 LNGFELAGRPMKVGTVT 192
           + G    GRPM++ T T
Sbjct: 64  MQGVYCGGRPMRISTAT 80

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

>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 57.6 bits (140), Expect = 8e-11
 Identities = 25/72 (34%), Positives = 40/72 (55%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++  +H    E+ +   F  FG+I N+ L +D  TG  KGY  I + +  +A+ A E L
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 177 NGFELAGRPMKV 188
           NG EL G+ + V
Sbjct: 69  NGKELLGQTISV 80

This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). . Length = 88

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

 Score = 57.3 bits (139), Expect = 1e-10
 Identities = 23/76 (30%), Positives = 49/76 (64%), Gaps = 3/76 (3%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLM---VDPDTGRSKGYGFITFHSADDAKKAQ 173
           LY+G+L+  +TE++L   F  FG + ++++M    + +  R++  GF+ F +  DA++A 
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 174 EQLNGFELAGRPMKVG 189
           ++L+G ++ G  +K+G
Sbjct: 64  DELDGKDVMGYELKLG 79

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

 Score = 56.7 bits (137), Expect = 1e-10
 Identities = 27/72 (37%), Positives = 41/72 (56%), Gaps = 3/72 (4%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++G+L F  TED LR  F   G+I  +++M   D+G+ KG+ F+ F   + A  A   L
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNA---L 57

Query: 177 NGFELAGRPMKV 188
            G  L GR ++V
Sbjct: 58  KGKHLNGRALRV 69

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

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

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 3/73 (4%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+G+L   +TED+L  +F   G I + +L+ +     +  Y F+ ++    A  A + +
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREH---GNDPYAFVEYYDHRSAAAALQTM 57

Query: 177 NGFELAGRPMKVG 189
           NG  + G+ +KV 
Sbjct: 58  NGRLILGQEIKVN 70

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

 Score = 57.4 bits (138), Expect = 1e-10
 Identities = 27/67 (40%), Positives = 43/67 (64%)

Query: 122 LHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFEL 181
           L    TE  LR +F  +G I ++ ++ D  + RS+G+ F+ F + DDAK+A+E+ NG EL
Sbjct: 17  LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 76

Query: 182 AGRPMKV 188
            GR ++V
Sbjct: 77  DGRRIRV 83

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 56.6 bits (136), Expect = 1e-10
 Identities = 24/59 (40%), Positives = 37/59 (62%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           ++++G L  N T + ++  FE FGK+D+  LM D  T R +G+GF+TF S D  +K  E
Sbjct: 1   KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 56.8 bits (138), Expect = 1e-10
 Identities = 31/82 (37%), Positives = 42/82 (51%), Gaps = 12/82 (14%)

Query: 115 MRLYIGSLHFNITEDMLRGIF--------EPFGKIDNIQLMVDPDTGRSKGYGFITFHSA 166
            RLY+ +L   +TE+ L  IF        E     D I+LM     GR KG  F+TF S 
Sbjct: 2   KRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFD-IRLM---TEGRMKGQAFVTFPSE 57

Query: 167 DDAKKAQEQLNGFELAGRPMKV 188
           + A KA   +NG+ L G+PM +
Sbjct: 58  EIATKALNLVNGYVLKGKPMVI 79

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

 Score = 57.0 bits (137), Expect = 1e-10
 Identities = 29/85 (34%), Positives = 52/85 (61%), Gaps = 2/85 (2%)

Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           GTG  + +Y  +L  +  E +L  +F PFG ++N++++ D +T + KG+GF+T  + D+A
Sbjct: 1   GTGWCIFVY--NLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEA 58

Query: 170 KKAQEQLNGFELAGRPMKVGTVTDR 194
             A   LNG+ L  R ++V   T++
Sbjct: 59  AMAIASLNGYRLGDRVLQVSFKTNK 83

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 56.1 bits (136), Expect = 2e-10
 Identities = 23/70 (32%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
          +F   L       DL++ FS  G +  +R++  ++T R KG A++EF+D E    A+  L
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVR-DETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 78 NGQKLLGIPI 87
          NG++L G  +
Sbjct: 60 NGKELGGREL 69

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

 Score = 56.2 bits (136), Expect = 2e-10
 Identities = 26/72 (36%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGL 77
          T++   L+  I   D+ EFF    ++  VRL T  +T  FKG  +++F D ES+  A+ L
Sbjct: 1  TVYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALKL 59

Query: 78 NGQKLLGIPIIV 89
          +G  L G PI +
Sbjct: 60 DGTVLCGRPIRI 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|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 56.1 bits (136), Expect = 2e-10
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 118 YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN 177
           ++G++ +  T + L+  F+  G I+ I ++ D  TG+ KG+ +I F      + A   LN
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LLN 61

Query: 178 GFELAGRPMKV 188
             E  GR +KV
Sbjct: 62  ESEFRGRQIKV 72

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

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

 Score = 56.2 bits (136), Expect = 2e-10
 Identities = 24/67 (35%), Positives = 38/67 (56%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+  L   +T+  L  +F P+G+I   +++ D  TG S+G GFI F    +A++A + L
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 177 NGFELAG 183
           NG    G
Sbjct: 63  NGTIPPG 69

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

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

 Score = 55.8 bits (135), Expect = 2e-10
 Identities = 24/72 (33%), Positives = 42/72 (58%), Gaps = 1/72 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++G+L ++ T + L   F+  G   +++L+ D  TG+SKG  F+ F +A+   KA  +L
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKAL-KL 61

Query: 177 NGFELAGRPMKV 188
           +   L GR + V
Sbjct: 62  HHTLLKGRKINV 73

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

>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 55.8 bits (135), Expect = 2e-10
 Identities = 22/66 (33%), Positives = 41/66 (62%), Gaps = 1/66 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL++  +  ++T++ L  +F+    ++   L  DP TG+SKG+ ++T+ +   A  A+E+
Sbjct: 2   RLFV-VVSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEK 60

Query: 176 LNGFEL 181
           LNGFE 
Sbjct: 61  LNGFEY 66

This subfamily corresponds to the RRM3 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 = 75

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

 Score = 60.7 bits (147), Expect = 3e-10
 Identities = 32/102 (31%), Positives = 54/102 (52%), Gaps = 7/102 (6%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L +  L   +T++ +R +F   G+I++ +L+ D  TG+S GYGF+ +   +DA+KA   L
Sbjct: 6   LIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSL 65

Query: 177 NGFELAGRPMKVG-------TVTDRNESVGGGPSNLDTDEME 211
           NG  L  + +KV        ++   N  V G P  +   E+E
Sbjct: 66  NGLRLQNKTIKVSYARPSSDSIKGANLYVSGLPKTMTQHELE 107

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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 55.8 bits (134), Expect = 3e-10
 Identities = 27/73 (36%), Positives = 43/73 (58%), Gaps = 8/73 (10%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L+IG L F  T++ LR  FE +G + +  +M DP+T RS+G+GF+T+ S ++   A   
Sbjct: 4   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAA--- 60

Query: 176 LNGFELAGRPMKV 188
                +  RP KV
Sbjct: 61  -----MNARPHKV 68

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 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. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 55.6 bits (134), Expect = 3e-10
 Identities = 24/72 (33%), Positives = 46/72 (63%), Gaps = 1/72 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+G+L   +TED+L+ IF+  G + N++++ D +  +   YGF+ +H + DA+ A + L
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNN-KGVNYGFVEYHQSHDAEIALQTL 59

Query: 177 NGFELAGRPMKV 188
           NG ++    ++V
Sbjct: 60  NGRQIENNEIRV 71

This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 55.9 bits (134), Expect = 3e-10
 Identities = 27/72 (37%), Positives = 44/72 (61%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L +  L  N+T+D LR +F   G++++ +L+ D   G S GYGF+ + +A DA++A   L
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 177 NGFELAGRPMKV 188
           NG  L  + +KV
Sbjct: 64  NGLRLQSKTIKV 75

This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a 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. Meanwhile, 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 = 81

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

 Score = 55.8 bits (135), Expect = 3e-10
 Identities = 23/63 (36%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL + +L   I ED LR +FE FG I ++QL    D G+ + +GF+ + + ++A+KA + 
Sbjct: 2   RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKD-GKFRKFGFVGYKTEEEAQKALKH 60

Query: 176 LNG 178
            N 
Sbjct: 61  FNN 63

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

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

 Score = 55.7 bits (135), Expect = 3e-10
 Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 5/74 (6%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGR-----SKGYGFITFHSADDAKK 171
           L++ +L+F  TE+ L+  FE  G + ++ +    D        S GYGF+ F S + A+K
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 172 AQEQLNGFELAGRP 185
           A ++L G  L G  
Sbjct: 63  ALKRLQGTVLDGHA 76

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

>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 55.5 bits (133), Expect = 4e-10
 Identities = 30/84 (35%), Positives = 47/84 (55%), Gaps = 9/84 (10%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L+IG L F  T+D LR  FE +G + +  +M DP T RS+G+GF+T+   ++   A   
Sbjct: 4   KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA--- 60

Query: 176 LNGFELAGRPMKV-GTVTDRNESV 198
                ++ RP KV G V +   +V
Sbjct: 61  -----MSARPHKVDGRVVEPKRAV 79

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 55.4 bits (134), Expect = 4e-10
 Identities = 21/57 (36%), Positives = 33/57 (57%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
           ++++G L  N+TE  LR  F  FG +  + +M D +  R +G+GFITF S D   + 
Sbjct: 4   KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV 60

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 55.5 bits (133), Expect = 4e-10
 Identities = 29/85 (34%), Positives = 47/85 (55%), Gaps = 9/85 (10%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L+IG L F  TE+ LR  +E +GK+ +  +M DP + RS+G+GF+TF   ++   A   
Sbjct: 4   KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAA--- 60

Query: 176 LNGFELAGRPMKV-GTVTDRNESVG 199
                +A RP  + G V +   +V 
Sbjct: 61  -----MAARPHTIDGRVVEPKRAVA 80

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which 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 A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 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 = 81

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

 Score = 55.3 bits (134), Expect = 5e-10
 Identities = 23/73 (31%), Positives = 47/73 (64%), Gaps = 2/73 (2%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++G +  ++ ED L  +FE  G I  ++LM+D   G ++GY F+T+ + + A++A +QL
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFS-GLNRGYAFVTYTNKEAAQRAVKQL 62

Query: 177 NGFEL-AGRPMKV 188
           + +E+  G+ + V
Sbjct: 63  HNYEIRPGKRLGV 75

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

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

 Score = 55.5 bits (133), Expect = 5e-10
 Identities = 29/85 (34%), Positives = 51/85 (60%), Gaps = 2/85 (2%)

Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           GTG  + +Y  +L  +  E +L  +F PFG + N++++ D +T + KG+GF+T  + D+A
Sbjct: 1   GTGWCIFVY--NLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEA 58

Query: 170 KKAQEQLNGFELAGRPMKVGTVTDR 194
             A   LNG+ L  R ++V   T++
Sbjct: 59  AMAIASLNGYRLGDRVLQVSFKTNK 83

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

 Score = 55.0 bits (133), Expect = 5e-10
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKID--NIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           LY+G+L +  T++ L G     G +D  +I+       G+SKG+ ++ F S   A   +E
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 175 QLNGFELAGRPMKV 188
           +L G E  G+   V
Sbjct: 61  KLEGREFNGKKCVV 74

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

>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 55.3 bits (134), Expect = 5e-10
 Identities = 25/53 (47%), Positives = 37/53 (69%), Gaps = 3/53 (5%)

Query: 131 LRGIFEPFG--KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFEL 181
           LR IF  FG  KI  I + VD +TG++KGY F+ F + ++AK+A + LNG++L
Sbjct: 24  LRKIFSKFGVGKIVGIYMPVD-ETGKTKGYAFVEFATPEEAKEAVKALNGYKL 75

This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain. . Length = 84

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

 Score = 59.6 bits (144), Expect = 6e-10
 Identities = 28/97 (28%), Positives = 51/97 (52%), Gaps = 4/97 (4%)

Query: 99  AGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGY 158
           AG  +        G    +++ +L  +  E +L  +F PFG + N++++ D  T + KGY
Sbjct: 258 AGAQIAAS----DGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGY 313

Query: 159 GFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRN 195
           GF++  + D+A  A   LNG+ L  R ++V   T++ 
Sbjct: 314 GFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKA 350

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

 Score = 54.6 bits (132), Expect = 6e-10
 Identities = 22/58 (37%), Positives = 31/58 (53%)

Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIV 89
          +L+E F S G +  + ++    T + KG AYIEF D  SV  A+ LN  +  G  I V
Sbjct: 15 ELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLNESEFRGRQIKV 72

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

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

 Score = 54.7 bits (132), Expect = 8e-10
 Identities = 23/73 (31%), Positives = 41/73 (56%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL+I +L +  TE+ L  +F  +G +  + L +D  T + KG+ F+T+   + A KA  +
Sbjct: 4   RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63

Query: 176 LNGFELAGRPMKV 188
           L+G    GR + +
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|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 53.7 bits (130), Expect = 1e-09
 Identities = 25/59 (42%), Positives = 33/59 (55%)

Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQ 90
          +L + F   G V  VR++   KT   KG  Y+ FK  +SV LA+ LNG KL G  I V+
Sbjct: 15 ELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNGIKLKGRKIRVK 73

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

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

 Score = 54.4 bits (130), Expect = 1e-09
 Identities = 26/72 (36%), Positives = 44/72 (61%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L +  L  N+T++  + +F   G+I++ +L+ D  TG+S GYGF+ +   +DA KA   L
Sbjct: 6   LIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTL 65

Query: 177 NGFELAGRPMKV 188
           NG +L  + +KV
Sbjct: 66  NGLKLQTKTIKV 77

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

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

 Score = 53.2 bits (128), Expect = 2e-09
 Identities = 26/74 (35%), Positives = 45/74 (60%), Gaps = 2/74 (2%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            +YIG+L ++ITED +R  F+   +I +++L  D +TG  KG+G + F   +    A + 
Sbjct: 1   TVYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALK- 58

Query: 176 LNGFELAGRPMKVG 189
           L+G  L GRP+++ 
Sbjct: 59  LDGTVLCGRPIRIA 72

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

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

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 23/74 (31%), Positives = 43/74 (58%)

Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
             +++G++   +++D +R + E  GK+ + + + DP TG+ K +GF  F   + A +A  
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 175 QLNGFELAGRPMKV 188
            LNG EL G+ + V
Sbjct: 61  LLNGLELGGKKLLV 74

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

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

 Score = 53.5 bits (128), Expect = 2e-09
 Identities = 24/66 (36%), Positives = 40/66 (60%), Gaps = 4/66 (6%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ- 175
           ++IG L ++ T+  L+  F  FG++ +  L +DP TGRS+G+GF+ F  ++   K  +Q 
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 176 ---LNG 178
              LNG
Sbjct: 61  EHKLNG 66

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

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

 Score = 53.9 bits (129), Expect = 2e-09
 Identities = 25/78 (32%), Positives = 45/78 (57%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++ +L     E +L  +F PFG + N++++ D  T + KG+GF+T  + D+A  A   L
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 177 NGFELAGRPMKVGTVTDR 194
           NG+ L  R ++V   T +
Sbjct: 64  NGYRLGDRVLQVSFKTSK 81

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

 Score = 53.4 bits (128), Expect = 2e-09
 Identities = 26/70 (37%), Positives = 37/70 (52%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+ +L   +TED LR IFE +G I    L+ D  TG  +G  F+ +   ++A+ A   L
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 177 NGFELAGRPM 186
           NG    G  M
Sbjct: 63  NGTIPPGSTM 72

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

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 23/73 (31%), Positives = 44/73 (60%), Gaps = 6/73 (8%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL++G+L  +ITE+  + +F  +G++  + L       + KG+GFI   +  +A+KA+ +
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGEVSEVFL------NKEKGFGFIRLDTRTNAEKAKAE 56

Query: 176 LNGFELAGRPMKV 188
           L+G    GR ++V
Sbjct: 57  LDGIMRKGRQLRV 69

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

>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 53.5 bits (128), Expect = 2e-09
 Identities = 23/60 (38%), Positives = 38/60 (63%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++G L+   TE+ +R  F  FG+I+ I+L +DP T + +G+ FITF   D  KK  E+
Sbjct: 6   KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLEK 65

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 80

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 53.4 bits (128), Expect = 2e-09
 Identities = 28/73 (38%), Positives = 47/73 (64%), Gaps = 2/73 (2%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           ++IG L  ++ ED L  + E  GKI  +++M+D + G ++GY F+TF +  +AK A +QL
Sbjct: 4   IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFN-GNNRGYAFVTFSNKQEAKNAIKQL 62

Query: 177 NGFELA-GRPMKV 188
           N +E+  GR + V
Sbjct: 63  NNYEIRNGRLLGV 75

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

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

 Score = 53.1 bits (128), Expect = 2e-09
 Identities = 22/72 (30%), Positives = 42/72 (58%), Gaps = 1/72 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++G+L   +TE++L  +F   G ++ +++  DP+ G+ K + F+TF        A + L
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVPYAIQLL 62

Query: 177 NGFELAGRPMKV 188
           NG  L GR +++
Sbjct: 63  NGIRLFGRELRI 74

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

 Score = 53.1 bits (127), Expect = 2e-09
 Identities = 24/79 (30%), Positives = 48/79 (60%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           ++I +L  +  E +L  +F PFG + N++++ D +T + KG+GF+T  + ++A  A   L
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 177 NGFELAGRPMKVGTVTDRN 195
           NG+ L  + ++V   T ++
Sbjct: 64  NGYRLGDKILQVSFKTSKS 82

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|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 = 53.0 bits (128), Expect = 3e-09
 Identities = 23/59 (38%), Positives = 31/59 (52%), Gaps = 1/59 (1%)

Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIV 89
           L E FS VG V   RL+T   T + KG  + EF+D E+   A+  LNG +  G  + V
Sbjct: 14 QLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGYEFNGRALRV 72

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

 Score = 52.7 bits (127), Expect = 3e-09
 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 2/75 (2%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
          RT+F   L  R+    L E F   G +  V+ I  +   + K  A++ FK   SVP A+ 
Sbjct: 2  RTLFVGNLDARVTEEILYELFLQAGPLEGVK-IPKDPNGKPKSFAFVTFKHEVSVPYAIQ 60

Query: 77 L-NGQKLLGIPIIVQ 90
          L NG +L G  + ++
Sbjct: 61 LLNGIRLFGRELRIK 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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 53.2 bits (127), Expect = 3e-09
 Identities = 27/72 (37%), Positives = 43/72 (59%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L +  L  N+T++  R +F   G+I++ +L+ D  TG+S GYGF+ +    DA+KA   L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 177 NGFELAGRPMKV 188
           NG  L  + +KV
Sbjct: 65  NGLRLQTKTIKV 76

This subgroup corresponds to the RRM1 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, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

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

 Score = 53.4 bits (129), Expect = 3e-09
 Identities = 23/68 (33%), Positives = 36/68 (52%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++G L    TE+ LR +F  +G I  ++L+ D  TG SKGY F+ +    DA +A    
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 177 NGFELAGR 184
           +   + G 
Sbjct: 66  HKLVIDGS 73

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

>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 52.8 bits (127), Expect = 3e-09
 Identities = 23/59 (38%), Positives = 32/59 (54%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++IG L +  T + LR  F  FG+I    +M DP T RS+G+GF+TF       K   Q
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQ 59

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 52.9 bits (127), Expect = 3e-09
 Identities = 22/58 (37%), Positives = 37/58 (63%), Gaps = 1/58 (1%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
           P R+++G + F   E+ LR  F  +G +  ++++ D   G SKGYGF+TF + +DA+K
Sbjct: 2   PNRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQK 58

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

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

 Score = 53.0 bits (127), Expect = 3e-09
 Identities = 24/69 (34%), Positives = 45/69 (65%), Gaps = 3/69 (4%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++G +  ++ ED L  +FE  G+I  ++LM+D D G+++GY F+ +    +AK+A  +L
Sbjct: 4   VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFD-GKNRGYAFVMYTQKHEAKRAVREL 62

Query: 177 NGFELAGRP 185
           N +E+  RP
Sbjct: 63  NNYEI--RP 69

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

>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 52.7 bits (126), Expect = 3e-09
 Identities = 19/56 (33%), Positives = 34/56 (60%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
           ++++G +  +  E  LR  FE +GKI+ I++M D  +G+ +G+ F+TF   D   K
Sbjct: 2   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 57

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 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. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 77

>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 52.6 bits (127), Expect = 4e-09
 Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 5/64 (7%)

Query: 126 ITEDMLRGIFEPFGK--IDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNG---FE 180
            TE+ +           I +++L+ D  TG S+G+ F+ F S +DA +  + LN    F 
Sbjct: 14  TTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNNLDPFV 73

Query: 181 LAGR 184
           + GR
Sbjct: 74  IDGR 77

This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 84

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

 Score = 52.3 bits (126), Expect = 4e-09
 Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++G L  ++T++ L   F   GKI  + L+   +   +  + FI F     A +A E  
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNA--FAFIKFEREQAAARAVESE 63

Query: 177 NGFELAGRPMKV 188
           N   L  + M V
Sbjct: 64  NHSMLKNKTMHV 75

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|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 52.4 bits (126), Expect = 4e-09
 Identities = 22/58 (37%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 131 LRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
           L   F   G+I  + +  D +TG SKG+ +I F S D  +KA E L+G +L G  + V
Sbjct: 20  LTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALE-LDGSDLGGGNLVV 76

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 52.2 bits (126), Expect = 5e-09
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
           ++   L   +   DL++ F   G+V   R+IT  +T R +G  ++E +  E    A+  
Sbjct: 1  NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 77 LNGQKLLGIPIIV 89
          LNG    G  + V
Sbjct: 61 LNGTDFGGRTLTV 73

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|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 51.9 bits (124), Expect = 6e-09
 Identities = 21/60 (35%), Positives = 39/60 (65%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++G L ++ ++  L+  F  FG++ +  + +DP+TGRS+G+GFI F  A   +K  EQ
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 51.9 bits (125), Expect = 6e-09
 Identities = 21/60 (35%), Positives = 37/60 (61%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L++G+L + +    L+  F  FGK+ +  +  D +TG SKGYGF++F S D  + A ++
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities. . Length = 73

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

 Score = 51.7 bits (124), Expect = 6e-09
 Identities = 18/73 (24%), Positives = 37/73 (50%), Gaps = 8/73 (10%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RLY+     + +E  +R IF P+G +  ++++          + F+ F S + A +A++ 
Sbjct: 1   RLYVRPFPPDTSESAIREIFSPYGAVKEVKMI--------SNFAFVEFESLESAIRAKDS 52

Query: 176 LNGFELAGRPMKV 188
           ++G  L   P+ V
Sbjct: 53  VHGKVLNNNPLYV 65

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

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

 Score = 52.2 bits (125), Expect = 6e-09
 Identities = 20/63 (31%), Positives = 40/63 (63%), Gaps = 1/63 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L++G L+   TE  +  +F P+G++++I +M D +  +S+G  F+ + S + A+ A + 
Sbjct: 1   KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKEMAQAAIKA 59

Query: 176 LNG 178
           LNG
Sbjct: 60  LNG 62

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

>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 51.8 bits (124), Expect = 6e-09
 Identities = 26/72 (36%), Positives = 44/72 (61%), Gaps = 5/72 (6%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L + +L ++ +ED L+ +FE   K  +I+  +  + GR KGY F+ F SA+DAK+A    
Sbjct: 4   LVVNNLSYSASEDSLQEVFE---KATSIR--IPQNNGRPKGYAFVEFESAEDAKEALNSC 58

Query: 177 NGFELAGRPMKV 188
           N  E+ GR +++
Sbjct: 59  NNTEIEGRSIRL 70

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 52.0 bits (124), Expect = 7e-09
 Identities = 21/56 (37%), Positives = 35/56 (62%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
           +L++G +  +  E  LR  FE +GKID I+++ D  +G+ +G+GF+TF   D   K
Sbjct: 2   KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDK 57

This subgroup corresponds to the RRM2 of hnRNP A2/B1, 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 A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 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|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 51.5 bits (124), Expect = 7e-09
 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++Y+G+L    T+  L   FE +G + ++ +  +P      G+ F+ F    DA+ A   
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRA 55

Query: 176 LNGFELAGRPMKV 188
           L+G  + G  ++V
Sbjct: 56  LDGRRICGNRVRV 68

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

 Score = 51.5 bits (124), Expect = 8e-09
 Identities = 22/72 (30%), Positives = 46/72 (63%), Gaps = 2/72 (2%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++ +L +++ ED LR +F   G+I +++L+ +   G+SKGY ++ F + +  ++A + L
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKN-YKGKSKGYAYVEFENEESVQEALK-L 59

Query: 177 NGFELAGRPMKV 188
           +   + GRPM V
Sbjct: 60  DRELIKGRPMFV 71

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

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

 Score = 51.2 bits (123), Expect = 1e-08
 Identities = 24/73 (32%), Positives = 35/73 (47%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGL 77
           +F   L       DL   F + G    VRL+T  KT + KG A++EF   E++  A+ L
Sbjct: 2  ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKL 61

Query: 78 NGQKLLGIPIIVQ 90
          +   L G  I V+
Sbjct: 62 HHTLLKGRKINVE 74

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

>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 51.3 bits (123), Expect = 1e-08
 Identities = 26/63 (41%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L++G L    TED +R +FEPFG I+   ++  PD G SKG  F+ F S  +A+ A   
Sbjct: 3   KLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPD-GNSKGCAFVKFSSHAEAQAAINA 61

Query: 176 LNG 178
           L+G
Sbjct: 62  LHG 64

This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 81

>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 51.3 bits (122), Expect = 1e-08
 Identities = 27/72 (37%), Positives = 44/72 (61%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L +  L  N+T++ L+ +F   G+I++ +L+ D  TG+S GYGF+ +    DA+KA   L
Sbjct: 7   LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 66

Query: 177 NGFELAGRPMKV 188
           NG  L  + +KV
Sbjct: 67  NGLRLQTKTIKV 78

This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

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

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 8/75 (10%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++G L    +   L   F+ FG I  I      D    + Y +I + S + A+ A+E L
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRI------DYDPGRNYAYIEYESIEAAQAAKEAL 54

Query: 177 NGFEL--AGRPMKVG 189
            GF L   GR ++V 
Sbjct: 55  RGFPLGGPGRRLRVD 69

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|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 50.7 bits (122), Expect = 1e-08
 Identities = 25/72 (34%), Positives = 44/72 (61%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +Y+G+L   +TE++L  +F   G + N+ +  D  T   +GYGF+ F S +DA  A + +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 177 NGFELAGRPMKV 188
           N  +L G+P++V
Sbjct: 61  NMIKLYGKPIRV 72

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

>gnl|CDD|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 = 50.7 bits (122), Expect = 2e-08
 Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
           +F   LS R   ++LE  FS  G+V +V L+   +T   +G  ++ F+  E    A+  
Sbjct: 3  KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 77 LNGQKLLGIPIIVQ 90
          LNG++L G  I V+
Sbjct: 63 LNGKELEGRVIKVE 76

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|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 50.9 bits (122), Expect = 2e-08
 Identities = 25/61 (40%), Positives = 34/61 (55%)

Query: 31 RDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQ 90
          R L E FSS G++  V + T  +T   KG AYIEFK  + V  A+ L+G  L G  ++V 
Sbjct: 18 RSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALELDGSDLGGGNLVVD 77

Query: 91 P 91
           
Sbjct: 78 E 78

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 50.8 bits (122), Expect = 2e-08
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++ +L + +    L+ +F+  GK+    +  D + G+S+G G + F    +A +A    
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQFEHPIEAVQAISMF 59

Query: 177 NGFELAGRPMKV 188
           NG  L  RPM+V
Sbjct: 60  NGQMLFDRPMRV 71

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

>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 50.7 bits (121), Expect = 2e-08
 Identities = 25/71 (35%), Positives = 47/71 (66%), Gaps = 2/71 (2%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++G +  ++ ED L  +FE  G I +++LM+DP +G+++GY FITF   + A++A +  
Sbjct: 4   VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKLC 63

Query: 177 NGFELAGRPMK 187
           + +E+  RP K
Sbjct: 64  DNYEI--RPGK 72

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains. . Length = 79

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

 Score = 50.4 bits (121), Expect = 2e-08
 Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 6/69 (8%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++G L   +TED LR +F PFG+I  +++         KG GF+ F     A+ A +QL
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPP------GKGCGFVQFVHRAAAEAAIQQL 57

Query: 177 NGFELAGRP 185
            G  + G  
Sbjct: 58  QGTIIGGSR 66

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

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

 Score = 50.2 bits (120), Expect = 2e-08
 Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 4/72 (5%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++ +L +NIT D L+ +FE    I     +     G SKG  +I F +  +A+KA E+ 
Sbjct: 6   LFVKNLPYNITVDELKEVFEDAVDIR----LPSGKDGSSKGIAYIEFKTEAEAEKALEEK 61

Query: 177 NGFELAGRPMKV 188
            G E+ GR + V
Sbjct: 62  QGAEVDGRSIVV 73

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

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

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 19/62 (30%), Positives = 38/62 (61%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++G L   + E  +   F   G++ +++++ +  TG+S GYGF+ F + + A++A + L
Sbjct: 2   LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61

Query: 177 NG 178
           NG
Sbjct: 62  NG 63

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

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

 Score = 49.9 bits (120), Expect = 3e-08
 Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 2/66 (3%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLN 78
          ++   L   +   DL EFFS  GKV  VRL+      R +G A++EF  PE    A+   
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLV--RNKDRPRGFAFVEFASPEDAEAALKKL 58

Query: 79 GQKLLG 84
             +L 
Sbjct: 59 NGLVLD 64

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

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

 Score = 50.0 bits (120), Expect = 3e-08
 Identities = 26/78 (33%), Positives = 38/78 (48%), Gaps = 5/78 (6%)

Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLIT-CNKTRRFKGIAYIEFKDPESVPL 73
          D  +IF  QLS  +   +L E FS  GK+ +V LI   N T  F   A+I+F+  ++   
Sbjct: 2  DKYSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAF---AFIKFEREQAAAR 58

Query: 74 AM-GLNGQKLLGIPIIVQ 90
          A+   N   L    + VQ
Sbjct: 59 AVESENHSMLKNKTMHVQ 76

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|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast Schizosaccharomyces pombe SET domain-containing protein 1 (spSet1p) and similar proteins

 Score = 50.4 bits (121), Expect = 3e-08
 Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 8/70 (11%)

Query: 127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITF--------HSADDAKKAQEQLNG 178
           T   +R  F PFG+I+  +L +DP TG+S G   +TF         + + AK A + LNG
Sbjct: 11  TPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPLRPSAAHEAAKAAVDGLNG 70

Query: 179 FELAGRPMKV 188
             + G+ ++V
Sbjct: 71  RRIGGKRVRV 80

This subfamily corresponds to the RRM of spSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, or Set1 complex component, is encoded by SET1 from the fission yeast S. pombe. It is essential for the H3 lysine-4 methylation. in vivo, and plays an important role in telomere maintenance and DNA repair in an ATM kinase Rad3-dependent pathway. spSet1p is the homology counterpart of Saccharomyces cerevisiae Set1p (scSet1p). However, it is more closely related to Set1 found in mammalian. Moreover, unlike scSet1p, spSet1p is not required for heterochromatin assembly in fission yeast. spSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 86

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

 Score = 50.1 bits (120), Expect = 3e-08
 Identities = 20/61 (32%), Positives = 34/61 (55%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +Y+  L  N T + L+ +F  +G +  + L     TG  KG+ FI F + ++A+KA + L
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 177 N 177
           N
Sbjct: 62  N 62

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 50.1 bits (119), Expect = 3e-08
 Identities = 21/48 (43%), Positives = 31/48 (64%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITF 163
           +++IG L +  + D LR  F  FG+I    +M DP T RS+G+GF+TF
Sbjct: 1   KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTF 48

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

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

 Score = 50.3 bits (120), Expect = 3e-08
 Identities = 19/57 (33%), Positives = 34/57 (59%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
           +L++G L  ++ E  L   F  FG ++  +++ D  TG+ +G+GF+ F + D A KA
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA 57

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|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 49.9 bits (119), Expect = 3e-08
 Identities = 20/59 (33%), Positives = 37/59 (62%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +++G L ++ T+  L+  F  FG++ +  + +DP TGRS+G+GF+ F  A   +K  +Q
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQ 59

This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 54.6 bits (131), Expect = 3e-08
 Identities = 33/96 (34%), Positives = 56/96 (58%), Gaps = 3/96 (3%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++G +  ++ ED L  +FE  G I  ++LM+D   G+++GY F+TF   ++AK+A + L
Sbjct: 61  VFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFS-GQNRGYAFVTFCGKEEAKEAVKLL 119

Query: 177 NGFEL-AGRPMKVGTVTDRNE-SVGGGPSNLDTDEM 210
           N +E+  GR + V    D     VGG P N   +E+
Sbjct: 120 NNYEIRPGRLLGVCISVDNCRLFVGGIPKNKKREEI 155

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

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

 Score = 49.5 bits (119), Expect = 4e-08
 Identities = 22/63 (34%), Positives = 40/63 (63%), Gaps = 1/63 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           R+ + +L   +TED LR  FE  G++ ++++M   D G+S+ +GF+ F S +DA++A + 
Sbjct: 2   RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRD-GKSRRFGFVGFKSEEDAQQAVKY 60

Query: 176 LNG 178
            N 
Sbjct: 61  FNK 63

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 49.6 bits (119), Expect = 4e-08
 Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 31 RDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIV 89
           DL+  F  +  V+ VRL+   +T +FKG  Y+EF+D ES+  A+  +G       + V
Sbjct: 16 GDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALEYDGALFDDRSLRV 73

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

>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing protein 1 (RDM1) and similar proteins

 Score = 49.7 bits (119), Expect = 4e-08
 Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 3/60 (5%)

Query: 131 LRGIFEPFGKIDNIQLMVDPDTGRSKG-YGFITFHSADDAKKAQEQLNGFEL-AGRPMKV 188
           L   F  FG + ++++        + G Y F+ F+SA  A +AQ+  NG  L  G P+KV
Sbjct: 21  LCSAFSQFGLLYSVKVF-PNAAVATPGFYAFVKFYSARAASRAQKACNGKWLFQGSPLKV 79

This subfamily corresponds to the RRM of RDM1, also termed RAD52 homolog B, a novel factor involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. RDM1 contains a small RD motif that shares with the recombination and repair protein RAD52, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RD motif is responsible for the acidic pH-dependent DNA-binding properties of RDM1. It interacts with ss- and dsDNA, and may act as a DNA-damage recognition factor by recognizing the distortions of the double helix caused by cisplatin-DNA adducts in vitro. In addition, due to the presence of RRM, RDM1 can bind to RNA as well as DNA. . Length = 81

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

 Score = 49.3 bits (118), Expect = 5e-08
 Identities = 24/70 (34%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-L 77
          +F   LS       + E F   G++  VRL T   + R KG  Y+EF   E+   A+  L
Sbjct: 1  LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 78 NGQKLLGIPI 87
           G  LLG P+
Sbjct: 61 GGTDLLGRPV 70

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

>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 49.3 bits (118), Expect = 5e-08
 Identities = 17/75 (22%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
             +L++  L F++T++ L  +F+  G + +++L V   +G+ KG  ++ + +   A +A 
Sbjct: 2   KHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRL-VTNRSGKPKGLAYVEYENESSASQAV 60

Query: 174 EQLNGFELAGRPMKV 188
            +++G E+  + + V
Sbjct: 61  LKMDGTEIKEKTISV 75

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 49.7 bits (118), Expect = 5e-08
 Identities = 21/59 (35%), Positives = 36/59 (61%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           ++++G L  N   + ++  FE FGK+++  LM D  T R +G+GF+TF + D  +K  E
Sbjct: 5   KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCE 63

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 49.6 bits (119), Expect = 5e-08
 Identities = 24/61 (39%), Positives = 35/61 (57%), Gaps = 3/61 (4%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +Y+G +  + T   LR  F+PFG+I+ I L    D G +  YGF+T+  A DA +A E  
Sbjct: 5   IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDD-GDN--YGFVTYRYACDAFRAIEHG 61

Query: 177 N 177
           N
Sbjct: 62  N 62

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 49.7 bits (119), Expect = 5e-08
 Identities = 19/72 (26%), Positives = 37/72 (51%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+ ++      D LR +F  +G I ++ + +D  T R +G+ ++ F    DA+ A   L
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 177 NGFELAGRPMKV 188
           +     GR +++
Sbjct: 63  DRTRFLGREIEI 74

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 49.6 bits (118), Expect = 6e-08
 Identities = 23/73 (31%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L+IG+L  N++E  LR  F+ +G I+ + ++  P  G+   Y F+ F + D A +A+  +
Sbjct: 11  LFIGNLDHNVSEVELRRAFDKYGIIEEV-VIKRPARGQGGAYAFLKFQNLDMAHRAKVAM 69

Query: 177 NGFELAGRPMKVG 189
           +G  +   P+K+G
Sbjct: 70  SGRVIGRNPIKIG 82

This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 85

>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 49.4 bits (118), Expect = 6e-08
 Identities = 28/91 (30%), Positives = 42/91 (46%), Gaps = 25/91 (27%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L++G L +  T++ LR  F  +G++ +  +M D  T RS+G+GF+ F   D        
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKF--KD-------- 50

Query: 176 LNGFELAGRPMKVGTVTDRNESVGGGPSNLD 206
                    P  VGTV        GGP  LD
Sbjct: 51  ---------PNCVGTVLA------GGPHTLD 66

This subfamily corresponds to the RRM1 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated form is predominantly nuclear and the nonacetylated form is in cytoplasm. It also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 82

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 49.2 bits (117), Expect = 7e-08
 Identities = 26/71 (36%), Positives = 46/71 (64%), Gaps = 2/71 (2%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++G +  ++ ED L  +FE  G I +++LM+DP TG ++GY F+TF + + A++A +  
Sbjct: 4   IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKLY 63

Query: 177 NGFELAGRPMK 187
           N  E+  RP K
Sbjct: 64  NNHEI--RPGK 72

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

>gnl|CDD|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 = 48.8 bits (117), Expect = 7e-08
 Identities = 22/69 (31%), Positives = 39/69 (56%), Gaps = 1/69 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L + ++ F  T+  LR +F PFG++ +++L    D G  +G+ F+ F +  +A+ A E 
Sbjct: 2   KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFD-GSHRGFAFVEFVTKQEAQNAMEA 60

Query: 176 LNGFELAGR 184
           L    L GR
Sbjct: 61  LKSTHLYGR 69

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|240906 cd12460, RRM2_CID8_like, RNA recognition motif 2 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 49.0 bits (117), Expect = 8e-08
 Identities = 29/85 (34%), Positives = 48/85 (56%), Gaps = 7/85 (8%)

Query: 13 ERDARTIFCMQLSQRIRTRDLEEFFSSV-GKVRDVRLI--TCNKTRRFKGIAYIEFKDPE 69
          E  ARTI+C  + +++   D++ FF S+ G+V  +RL+    + TR    IA++EF   E
Sbjct: 1  EMCARTIYCTNIDKKVTQSDVKLFFESLCGEVSRLRLLGDYHHSTR----IAFVEFAMAE 56

Query: 70 SVPLAMGLNGQKLLGIPIIVQPTQA 94
          S   A+  +G  L  +PI V P++ 
Sbjct: 57 SAIAALNCSGAVLGSLPIRVSPSKT 81

This subgroup corresponds to the RRM2 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 82

>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 = 48.4 bits (116), Expect = 8e-08
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 8/73 (10%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L++G+L    T + LR +FE +G +       + D    K YGF+     +DA+ A + 
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTV------TECD--VVKNYGFVHMEEEEDAEDAIKA 52

Query: 176 LNGFELAGRPMKV 188
           LNG+E  G+ + V
Sbjct: 53  LNGYEFMGKRINV 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|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 48.4 bits (116), Expect = 9e-08
 Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 6/65 (9%)

Query: 124 FNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG 183
           + +TE++L+  F PFG I NI +  +      K  GF+TF   + A +A  +LNG  + G
Sbjct: 12  YGLTEEILKKAFSPFGNIINISMEKE------KNCGFVTFEKMESADRAIAELNGTTVQG 65

Query: 184 RPMKV 188
             +KV
Sbjct: 66  VQLKV 70

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

 Score = 48.1 bits (115), Expect = 1e-07
 Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
           P   ++G+L FN  +  L  IF+    + +++L+ D +T + KG+ ++ F   +  K+A 
Sbjct: 1   PFTAFVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEAL 59

Query: 174 EQLNGFELAGRPMKV 188
           E  +G     R ++V
Sbjct: 60  E-YDGALFDDRSLRV 73

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

>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 48.4 bits (115), Expect = 1e-07
 Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 8/68 (11%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           R+YIG L +++ E  ++  F  +GK+  I L          GYGF+ F  + DA  A  +
Sbjct: 1   RVYIGRLSYHVREKDIQRFFGGYGKLLEIDL--------KNGYGFVEFEDSRDADDAVYE 52

Query: 176 LNGFELAG 183
           LNG +L G
Sbjct: 53  LNGKDLCG 60

This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 48.5 bits (115), Expect = 1e-07
 Identities = 20/48 (41%), Positives = 32/48 (66%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITF 163
           +++IG L +  T++ LR  F  FG++    +M DP T RS+G+GF+TF
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

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

 Score = 48.4 bits (115), Expect = 1e-07
 Identities = 26/67 (38%), Positives = 41/67 (61%), Gaps = 3/67 (4%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++  L  + TE+ L+  F+  G I   +++ D DTG SKG+GF+ F S +DAK A+E +
Sbjct: 3   LFVKGLSEDTTEETLKESFD--GSI-AARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

Query: 177 NGFELAG 183
              E+ G
Sbjct: 60  EDGEIDG 66

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

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

 Score = 48.3 bits (116), Expect = 1e-07
 Identities = 24/72 (33%), Positives = 42/72 (58%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+G+L F  TE+ +  +F   G I  I + +D  T    G+ F+ +++ +DA+ A + L
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 177 NGFELAGRPMKV 188
           NG +L  R ++V
Sbjct: 61  NGTKLDDRIIRV 72

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

>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 47.9 bits (114), Expect = 1e-07
 Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 8/73 (10%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++G++    T D LRG+FE FG++      V+ D    K Y F+     ++A  A E 
Sbjct: 2   KIFVGNVSATCTSDELRGLFEEFGRV------VECDK--VKDYAFVHMEREEEALAAIEA 53

Query: 176 LNGFELAGRPMKV 188
           LNG E+ GR + V
Sbjct: 54  LNGKEVKGRRINV 66

This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 68

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

 Score = 48.2 bits (115), Expect = 1e-07
 Identities = 20/48 (41%), Positives = 30/48 (62%)

Query: 127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           TE+ LR  F+ FG I+ + ++ D +TG SKG+G++ FH    A  A E
Sbjct: 13  TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALE 60

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|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 48.1 bits (114), Expect = 1e-07
 Identities = 23/72 (31%), Positives = 42/72 (58%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L+I  L    T+  L   F PFG + + ++ +D  T  SK +GF+++ + D A+ A + +
Sbjct: 7   LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66

Query: 177 NGFELAGRPMKV 188
           NGF++  + +KV
Sbjct: 67  NGFQIGTKRLKV 78

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

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

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 20/56 (35%), Positives = 33/56 (58%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
           L++  L+   T++ L  IF  FGKI + +++ D  TG S  Y FI F + +D ++A
Sbjct: 6   LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 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|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in azoospermia-like (DAZL) proteins

 Score = 48.3 bits (115), Expect = 1e-07
 Identities = 23/76 (30%), Positives = 42/76 (55%), Gaps = 3/76 (3%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
           P  +++G +   + E  +R  F  +G +  ++++ D  TG SKGYGF++F+   D +K  
Sbjct: 5   PNTVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSFYDDVDVQKIV 63

Query: 174 EQLNGFELAGRPMKVG 189
           E    F   G+ +K+G
Sbjct: 64  ESQINFH--GKKLKLG 77

This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 82

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

 Score = 48.0 bits (114), Expect = 1e-07
 Identities = 24/72 (33%), Positives = 36/72 (50%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L I +L    T+     +  PFG ++   L+    TG SKGYGF+ +   D A +A+  L
Sbjct: 2   LCIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDL 61

Query: 177 NGFELAGRPMKV 188
            G +L  R + V
Sbjct: 62  LGKQLGSRTLYV 73

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

>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 20/66 (30%), Positives = 38/66 (57%), Gaps = 2/66 (3%)

Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
          +   +F   L   +   +LE+ F   G V+ VRL+T N++ + KG+AY+E+++  S   A
Sbjct: 1  EKHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVT-NRSGKPKGLAYVEYENESSASQA 59

Query: 75 -MGLNG 79
           + ++G
Sbjct: 60 VLKMDG 65

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

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

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 22/74 (29%), Positives = 44/74 (59%), Gaps = 2/74 (2%)

Query: 116 RLYIGSLHFNITEDMLRGIF-EPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           R++I ++ +++    L+ +F E  G++  ++L  D + G+S+G G + F   +  +KA E
Sbjct: 1   RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKD-EEGKSRGCGVVEFKDKESVQKALE 59

Query: 175 QLNGFELAGRPMKV 188
            +N +EL GR + V
Sbjct: 60  TMNRYELKGRKLVV 73

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 48.2 bits (115), Expect = 2e-07
 Identities = 22/73 (30%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++G+L   ITE+ LR  FE +G ++++ +   P  G+   Y F+ F + D A +A+  +
Sbjct: 5   LFVGNLEITITEEELRRAFERYGVVEDVDIK-RPPRGQGNAYAFVKFLNLDMAHRAKVAM 63

Query: 177 NGFELAGRPMKVG 189
           +G  +    +K+G
Sbjct: 64  SGQYIGRNQIKIG 76

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

>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQ 90
          D++EFF   GKV ++R+   +  ++FKG  ++EFK  E     +     K     + V 
Sbjct: 15 DIQEFFEKFGKVNNIRMRR-DLDKKFKGSVFVEFKTEEDAKKFLEKEKLKYKEKELTVM 72

This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 72

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

 Score = 47.7 bits (113), Expect = 2e-07
 Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++G+L   + E++L  +F   G +  + +  D + G+ K +GF+ F  ++    A   L
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAIALL 62

Query: 177 NGFELAGRPMKV 188
           NG  L GRP+KV
Sbjct: 63  NGIRLYGRPIKV 74

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

>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 48.1 bits (114), Expect = 2e-07
 Identities = 20/60 (33%), Positives = 35/60 (58%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++G +  +  E  LR  FE +GKI+ I++M D  +G+ +G+ F+TF   D   K   Q
Sbjct: 2   KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQ 61

This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 47.9 bits (115), Expect = 2e-07
 Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 7/76 (9%)

Query: 117 LYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
           LYI +L+  I +D L+     +F  FG + +I       T + +G  F+ F   + A  A
Sbjct: 2   LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVAS---KTLKMRGQAFVVFKDVESATNA 58

Query: 173 QEQLNGFELAGRPMKV 188
              L GF    +PM++
Sbjct: 59  LRALQGFPFYDKPMRI 74

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 22/60 (36%), Positives = 34/60 (56%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++G L    TE+ +R  F  FG I  I+L +D  T + +G+ FITF S +  KK  E 
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 24/68 (35%), Positives = 33/68 (48%), Gaps = 8/68 (11%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           R+YIG L +   E  +   F+ +G+I  I L          G+GF+ F    DA  A  +
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDPRDADDAVYE 52

Query: 176 LNGFELAG 183
           LNG EL G
Sbjct: 53  LNGKELCG 60

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|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast RNA-binding protein PIN4, fission yeast RNA-binding post-transcriptional regulators cip1, cip2 and similar proteins

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 22/75 (29%), Positives = 38/75 (50%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
           P  + I ++ F++ ++ L  I E  G           D G  +G  F  F S ++A+   
Sbjct: 1   PTAIVIKNIPFSLRKEQLLDIIEDLGIPLPYAFNYHFDNGVFRGLAFANFRSPEEAQTVV 60

Query: 174 EQLNGFELAGRPMKV 188
           E LNG+E++GR ++V
Sbjct: 61  EALNGYEISGRRLRV 75

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

>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 47.9 bits (114), Expect = 2e-07
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITF---HSADDAKKA 172
           +L++G L     E+ +R +F PFG I+   ++ D + G+S+G  F+TF     A +A KA
Sbjct: 3   KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQN-GQSRGCAFVTFASRQCALNAIKA 61

Query: 173 QEQLNGFELAGRPMKV 188
                  E    P+ V
Sbjct: 62  MHHSQTMEGCSSPLVV 77

This subgroup corresponds to the RRM2 of Bruno, 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 = 81

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

 Score = 47.4 bits (112), Expect = 2e-07
 Identities = 25/71 (35%), Positives = 40/71 (56%), Gaps = 6/71 (8%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +Y G +   +TE ++R  F PFG+I  +++ V PD    KGY F+ F+S + A  A   +
Sbjct: 3   VYCGGVTSGLTEQLMRQTFSPFGQI--MEVRVFPD----KGYSFVRFNSHESAAHAIVSV 56

Query: 177 NGFELAGRPMK 187
           NG  + G  +K
Sbjct: 57  NGTTIEGHVVK 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|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 47.6 bits (113), Expect = 2e-07
 Identities = 22/62 (35%), Positives = 36/62 (58%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+  L   +T+  L  +F  +G+I   +++ D  TG S+G GFI F    +A++A + L
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 177 NG 178
           NG
Sbjct: 63  NG 64

This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

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

 Score = 47.1 bits (112), Expect = 3e-07
 Identities = 24/53 (45%), Positives = 29/53 (54%), Gaps = 4/53 (7%)

Query: 14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
          RDART+F   L   I   +L+E F       D+RL +  K    KGIAYIEFK
Sbjct: 1  RDARTLFVKNLPYNITVDELKEVFED---AVDIRLPS-GKDGSSKGIAYIEFK 49

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 47.6 bits (113), Expect = 3e-07
 Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 2/81 (2%)

Query: 116 RLYIGSLHFNITE-DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           +L I +L ++I +   L+ IF  +GK+    +      G+  G+ F+T     +A+ A E
Sbjct: 2   KLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRG-GKLCGFAFVTMKKRKNAEIALE 60

Query: 175 QLNGFELAGRPMKVGTVTDRN 195
             NG E+ GRP+ V     +N
Sbjct: 61  NTNGLEIDGRPVAVDWAVQKN 81

This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

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

 Score = 47.5 bits (113), Expect = 3e-07
 Identities = 23/72 (31%), Positives = 42/72 (58%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L+I  L     +  L  +F PFG + + ++ VD  T +SK +GF++F +   A+ A + +
Sbjct: 7   LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66

Query: 177 NGFELAGRPMKV 188
           NGF++  + +KV
Sbjct: 67  NGFQIGMKRLKV 78

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

>gnl|CDD|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin

 Score = 46.7 bits (111), Expect = 4e-07
 Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 4/73 (5%)

Query: 117 LYIGSLHFNITEDMLR-GIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           L++G+L+ N   D L+  I E F K  N+ +  D   G SK +G++ F SA+D +KA E 
Sbjct: 3   LFVGNLNPNKDFDELKTAISEFFSK-KNLAV-QDVRIGSSKKFGYVDFESAEDLEKALE- 59

Query: 176 LNGFELAGRPMKV 188
           L G +L G  +K+
Sbjct: 60  LTGKKLLGNEIKL 72

This subfamily corresponds to the RRM1 of ubiquitously expressed protein nucleolin, also termed protein C23. Nucleolin is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. RRM1, together with RRM2, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 75

>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 46.5 bits (110), Expect = 4e-07
 Identities = 19/60 (31%), Positives = 37/60 (61%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++G L  +  E+ +R  F  FG++++I+L +D  T + +G+ FITF   +  KK  E+
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 75

>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 46.4 bits (111), Expect = 4e-07
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 3/73 (4%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFG-KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           + +  L F+ TE+ +R  F       D I ++ D D GR  G  ++ F S +DA++A  +
Sbjct: 2   VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDD-GRPTGEAYVEFASPEDARRA-LR 59

Query: 176 LNGFELAGRPMKV 188
            +  ++ GR ++V
Sbjct: 60  KHNNKMGGRYIEV 72

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 46.3 bits (109), Expect = 5e-07
 Identities = 23/56 (41%), Positives = 34/56 (60%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
           LYI  LH   T+  L  + +P+GKI + + ++D  T + KGYGF+ F S   A+KA
Sbjct: 4   LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 59

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has 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. MSSP-2 contains 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 as well as induction of apoptosis. . Length = 75

>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 46.5 bits (110), Expect = 5e-07
 Identities = 27/82 (32%), Positives = 43/82 (52%), Gaps = 2/82 (2%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LYI  L   +T+  +  +F  FG+I N +++VD  TG S+G  FI F    +A++A    
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 177 NGFELAG--RPMKVGTVTDRNE 196
           NG +  G   P+ V    + N+
Sbjct: 63  NGHKPPGSSEPITVKFAANPNQ 84

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

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

 Score = 46.4 bits (111), Expect = 6e-07
 Identities = 16/44 (36%), Positives = 25/44 (56%)

Query: 31 RDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
           +L ++FS  G V  +RL    KT + KG A++EF+ PE   + 
Sbjct: 14 PELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIV 57

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

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

 Score = 46.1 bits (110), Expect = 7e-07
 Identities = 18/72 (25%), Positives = 40/72 (55%), Gaps = 5/72 (6%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++ +++ N+ ++ LR +FE FG I  +         + +G+  ++++    A++A+  L
Sbjct: 4   LFVRNINSNVEDEELRALFEQFGDIRTLY-----TACKHRGFIMVSYYDIRAARRAKRAL 58

Query: 177 NGFELAGRPMKV 188
            G EL GR + +
Sbjct: 59  QGTELGGRKLDI 70

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

>gnl|CDD|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 = 46.2 bits (110), Expect = 7e-07
 Identities = 22/72 (30%), Positives = 42/72 (58%), Gaps = 6/72 (8%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L+IG L   +TE+ L+ +FE +G+I +I ++        +G  ++   +  DA +A ++L
Sbjct: 5   LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP------PRGCAYVCMETRQDAHRALQKL 58

Query: 177 NGFELAGRPMKV 188
              +LAG+ +KV
Sbjct: 59  RNVKLAGKKIKV 70

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

 Score = 46.2 bits (110), Expect = 7e-07
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 8/70 (11%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++G+L  +ITED L+  F+ FG +  +++      GR   +GF+ F   +  +K     
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKI---- 61

Query: 177 NGFELAGRPM 186
               LA +P+
Sbjct: 62  ----LANKPI 67

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

 Score = 46.1 bits (109), Expect = 7e-07
 Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 6/73 (8%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL++G+L  +ITED  + +F  +G+   + +       + KG+GFI   S   A+ A+ +
Sbjct: 3   RLFVGNLPADITEDEFKKLFAKYGEPGEVFI------NKGKGFGFIKLESRALAEIAKAE 56

Query: 176 LNGFELAGRPMKV 188
           L+   + GR ++V
Sbjct: 57  LDDTPMRGRQLRV 69

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

>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 45.8 bits (109), Expect = 8e-07
 Identities = 20/59 (33%), Positives = 37/59 (62%)

Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQ 90
          ++  +FS  G++ ++ L+T   T RF+GIA+I FK  E+   A+ L+G+ + G  + V+
Sbjct: 14 EIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALALDGEDMGGRFLKVE 72

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

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

 Score = 45.8 bits (109), Expect = 8e-07
 Identities = 29/75 (38%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
          RTI    +   +   DL+EFFS+ G+V  VRL  C   +     A++EF D ES   A+ 
Sbjct: 1  RTIHVGGIDGSLSEDDLKEFFSNCGEVTRVRL--CGDRQHSARFAFVEFADAESALSALN 58

Query: 77 LNGQKLLGIPIIVQP 91
          L+G  L G P+ V P
Sbjct: 59 LSGTLLGGHPLRVSP 73

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

>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 46.2 bits (110), Expect = 9e-07
 Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 1/80 (1%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG- 76
          +++   ++   R  DL   F   G + DV +     TRR +G AY++F+D      A+  
Sbjct: 2  SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 77 LNGQKLLGIPIIVQPTQAEK 96
          L+  + LG  I +Q  Q ++
Sbjct: 62 LDRTRFLGREIEIQFAQGDR 81

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 45.6 bits (109), Expect = 9e-07
 Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 8/78 (10%)

Query: 18 TIFCMQLSQRIR----TRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
          T++   L+++I+     R L   FS  G V D+     +KT + +G A++ FKD ES   
Sbjct: 1  TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIV---ASKTLKMRGQAFVVFKDVESATN 57

Query: 74 AM-GLNGQKLLGIPIIVQ 90
          A+  L G      P+ +Q
Sbjct: 58 ALRALQGFPFYDKPMRIQ 75

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 25/94 (26%), Positives = 45/94 (47%), Gaps = 7/94 (7%)

Query: 17  RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
           +T+F  +L+       L   F   G ++ +RL+   KT + +G A+IEF+    +  A  
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 76  GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPR 109
             +G+K+ G  ++V     E+ R   T+    PR
Sbjct: 62  YADGKKIDGRRVLV---DVERGR---TVKGWLPR 89

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

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

 Score = 45.3 bits (107), Expect = 1e-06
 Identities = 29/75 (38%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
          RT+F   L  R+R   L E F   G +  V  I  +K  + K   ++ FK  ESVP A+ 
Sbjct: 2  RTLFVGNLECRVREEILYELFLQAGPLTKVT-ICKDKEGKPKSFGFVCFKHSESVPYAIA 60

Query: 77 -LNGQKLLGIPIIVQ 90
           LNG +L G PI V 
Sbjct: 61 LLNGIRLYGRPIKVH 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|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 45.8 bits (108), Expect = 1e-06
 Identities = 18/59 (30%), Positives = 36/59 (61%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           ++++G L  + TE+ ++  F  FG+I+NI+L +D  T   +G+ F+T+   +  +K  E
Sbjct: 1   KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLE 59

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 45.4 bits (107), Expect = 1e-06
 Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 4/76 (5%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS---ADDAKKA 172
           +L+IG +     E+ +R +F PFG+I+  +++  PD G S+G  F+TF +   A  A KA
Sbjct: 3   KLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKA 61

Query: 173 QEQLNGFELAGRPMKV 188
             Q    E    P+ V
Sbjct: 62  MHQAQTMEGCSSPIVV 77

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 81

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

 Score = 45.0 bits (106), Expect = 1e-06
 Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 6/71 (8%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +Y G +   +TE ++R  F PFG+I  +++ V P+    KGY FI F + + A  A   +
Sbjct: 3   VYCGGIASGLTEQLMRQTFSPFGQI--MEIRVFPE----KGYSFIRFSTHESAAHAIVSV 56

Query: 177 NGFELAGRPMK 187
           NG  + G  +K
Sbjct: 57  NGTTIEGHVVK 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|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 9/77 (11%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
          ++  +L  R R RD+E FF   G++R++ L          G  ++EF+DP     A+  L
Sbjct: 2  VYIGRLPYRARERDVERFFKGYGRIREINLK--------NGFGFVEFEDPRDADDAVYEL 53

Query: 78 NGQKLLGIPIIVQPTQA 94
          NG++L G  +IV+  + 
Sbjct: 54 NGKELCGERVIVEHARG 70

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

>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 45.3 bits (107), Expect = 2e-06
 Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++G+L   +TE  LR  F+ FG I  + +   P  G++  YGF+ F + D A +A+  +
Sbjct: 10  LFLGNLDITVTETDLRRAFDRFGVITEVDIK-RPGRGQTSTYGFLKFENLDMAHRAKLAM 68

Query: 177 NGFELAGRPMKVG 189
           +G  L   P+K+G
Sbjct: 69  SGKVLRRNPIKIG 81

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 45.1 bits (107), Expect = 2e-06
 Identities = 27/80 (33%), Positives = 41/80 (51%), Gaps = 8/80 (10%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITC---NKTRRFKGIAYIEFKDPESVPL 73
          RT++   + Q++    L   FS+ G+V D R+  C   N   RF   A+IEF D E    
Sbjct: 3  RTVYVSDIDQQVTEEQLAALFSNCGQVVDCRV--CGDPNSVLRF---AFIEFTDEEGARA 57

Query: 74 AMGLNGQKLLGIPIIVQPTQ 93
          A+ L+G  L   P+ V P++
Sbjct: 58 ALSLSGTMLGFYPVRVLPSK 77

This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 80

>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 44.8 bits (106), Expect = 2e-06
 Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 3/73 (4%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            +Y+G+L  +I E  +  +F  +G I +I L + P   R  GY FI F  A DA+ A   
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPP---RPPGYAFIEFEDARDAEDAIRG 57

Query: 176 LNGFELAGRPMKV 188
            +G++  G+ ++V
Sbjct: 58  RDGYDFDGQRLRV 70

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

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

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 1/67 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LYI +L  ++ E  L  + +P+G++ + +++ D   G+S+G GF    S +  +    + 
Sbjct: 3   LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSK-GQSRGVGFARMESREKCEDIISKF 61

Query: 177 NGFELAG 183
           NG  L G
Sbjct: 62  NGKYLKG 68

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

 Score = 48.9 bits (116), Expect = 2e-06
 Identities = 43/167 (25%), Positives = 75/167 (44%), Gaps = 14/167 (8%)

Query: 24  LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLL 83
           L Q +  R+L   F ++G +   R++   KT    G A+++F        A+    + L 
Sbjct: 115 LPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAI----KNLN 170

Query: 84  GIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDN 143
           GI +  +  +    R G        + T     LY+ +L   IT+D L  IF  +G+I  
Sbjct: 171 GITVRNKRLKVSYARPGGE----SIKDTN----LYVTNLPRTITDDQLDTIFGKYGQIVQ 222

Query: 144 IQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF--ELAGRPMKV 188
             ++ D  TG  +G  F+ F+  ++A++A   LN    E   +P+ V
Sbjct: 223 KNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTV 269

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

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 45.0 bits (106), Expect = 2e-06
 Identities = 19/62 (30%), Positives = 36/62 (58%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L++GS+   ITE  +R +FE  G +  + ++ D  TG  +G  F+ + + D+A +A   
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60

Query: 176 LN 177
           L+
Sbjct: 61  LH 62

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. 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|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 44.7 bits (106), Expect = 2e-06
 Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 6/60 (10%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +YIG+L  + +E+ LR   E FG ID I+++      + K   F+ F S  +A K    L
Sbjct: 6   VYIGNLPESYSEEELREDLEKFGPIDQIKIV------KEKNIAFVHFLSIANAIKVVTTL 59

This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 78

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 44.6 bits (105), Expect = 2e-06
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 8/72 (11%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++ +L   +TE++L   F  FGK++ ++ + D        Y FI F   D A KA E++
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 55

Query: 177 NGFELAGRPMKV 188
           NG EL G  +++
Sbjct: 56  NGKELEGENIEI 67

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

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

 Score = 44.5 bits (105), Expect = 2e-06
 Identities = 23/73 (31%), Positives = 43/73 (58%), Gaps = 6/73 (8%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL++G+L  +ITE+  + +FE +G+   + +       R +G+GFI   S   A+ A+ +
Sbjct: 3   RLFVGNLPTDITEEDFKKLFEKYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 56

Query: 176 LNGFELAGRPMKV 188
           L+G  L  RP+++
Sbjct: 57  LDGTILKNRPLRI 69

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

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

 Score = 44.4 bits (105), Expect = 2e-06
 Identities = 19/74 (25%), Positives = 41/74 (55%), Gaps = 8/74 (10%)

Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           +++++G++  + +++ LR +FE +G + +  +M        + + F+       A +A E
Sbjct: 1   VKIFVGNVDEDTSQEELRALFEAYGAVLSCAVM--------RQFAFVHLRGEAAADRAIE 52

Query: 175 QLNGFELAGRPMKV 188
           +LNG EL GR + V
Sbjct: 53  ELNGRELHGRKLVV 66

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

 Score = 44.8 bits (106), Expect = 3e-06
 Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGR-----SKGYGFITFHSADDAKK 171
           L++ +L+F+ T   L   F+        ++   PD  R     S G+GF+ F + + A+ 
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 172 AQEQLNGFELAGRPMKV 188
           A + ++GF L G  + V
Sbjct: 63  ALKAMDGFVLDGHTLVV 79

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

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

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 7/73 (9%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+G L   +TE  LR  F  FG+I +I ++        +   F+TF + + A+KA E+L
Sbjct: 4   LYVGGLGERVTEKDLRDHFYQFGEIRSITVV------PRQQCAFVTFTTREAAEKAAERL 57

Query: 177 -NGFELAGRPMKV 188
            N   + GR +K+
Sbjct: 58  FNKLIINGRRLKL 70

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

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

 Score = 44.4 bits (105), Expect = 3e-06
 Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 8/78 (10%)

Query: 118 YIGSL-HFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           Y+G++  +    D++  +F+ FG I   +   D      +G+ F+   + + A  A  QL
Sbjct: 4   YVGNIPPYTTQADLIP-LFQNFGYILEFRHQPD------RGFAFVKLDTHEQAAMAIVQL 56

Query: 177 NGFELAGRPMKVGTVTDR 194
            GF + GRP++ G   DR
Sbjct: 57  QGFPVHGRPLRCGWGKDR 74

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

 Score = 44.6 bits (105), Expect = 3e-06
 Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 2/74 (2%)

Query: 116 RLYIGSLHFNITEDMLRGIF-EPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           R +I ++ F++    L+ +  E  G++  ++L++D   G+S+G   + F   +  KKA E
Sbjct: 1   RAFISNIPFDVKWQSLKDLVKEKVGEVTYVELLMD-AEGKSRGCAVVEFKMEESMKKAVE 59

Query: 175 QLNGFELAGRPMKV 188
            LN   L GRP+KV
Sbjct: 60  VLNKHVLNGRPLKV 73

This subgroup corresponds to the RRM1 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 44.5 bits (105), Expect = 3e-06
 Identities = 23/71 (32%), Positives = 44/71 (61%), Gaps = 3/71 (4%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++G +  ++ ED L  +FE  GKI   +LM++  +G ++GY F+ + + ++A+ A   L
Sbjct: 4   VFVGKIPRDMYEDELVPLFERAGKIYEFRLMME-FSGENRGYAFVMYTTKEEAQLAIRIL 62

Query: 177 NGFELAGRPMK 187
           N +E+  RP K
Sbjct: 63  NNYEI--RPGK 71

This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins

 Score = 44.3 bits (105), Expect = 3e-06
 Identities = 25/66 (37%), Positives = 33/66 (50%), Gaps = 3/66 (4%)

Query: 125 NITEDMLRGIF-EPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG 183
           ++TE  +R  F    G I  + L  +   G+S G   ITF  A DA KA ++ NG    G
Sbjct: 10  DVTEAQIREYFVSQIGPIKRVLLSYNE-GGKSTGIANITFKRAGDATKAYDKFNGRIDDG 68

Query: 184 -RPMKV 188
            R MKV
Sbjct: 69  NRKMKV 74

This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p. . Length = 77

>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 44.3 bits (104), Expect = 3e-06
 Identities = 24/67 (35%), Positives = 40/67 (59%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+  L   +T+  L  +F  +G+I   +++VD  TG S+G GFI F    +A++A + L
Sbjct: 5   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64

Query: 177 NGFELAG 183
           NG + +G
Sbjct: 65  NGQKPSG 71

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 44.2 bits (105), Expect = 4e-06
 Identities = 18/59 (30%), Positives = 34/59 (57%), Gaps = 1/59 (1%)

Query: 25 SQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKL 82
           + +   DL E F+  G+++D+ ++   +T+  KG+AY++F    S   AM  +NG+ L
Sbjct: 11 GKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCL 69

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

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

 Score = 44.1 bits (104), Expect = 4e-06
 Identities = 25/73 (34%), Positives = 43/73 (58%), Gaps = 6/73 (8%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL++G+L  +ITE+ +R +FE +GK   I +  D      KG+GFI   +   A+ A+ +
Sbjct: 3   RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAEIAKAE 56

Query: 176 LNGFELAGRPMKV 188
           L+   L G+ ++V
Sbjct: 57  LDNMPLRGKQLRV 69

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

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

 Score = 44.0 bits (104), Expect = 4e-06
 Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 5/74 (6%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
          T++           D++  F + G VR V ++    +R  +  A+I F++ E+  LA+  
Sbjct: 1  TVYAGPFPTSFCLSDVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQLAIET 56

Query: 77 LNGQKLLGIPIIVQ 90
          LNG  + G  I VQ
Sbjct: 57 LNGASVDGNCIKVQ 70

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

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

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 9/75 (12%)

Query: 115 MRLYIGSLH-FNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
            R+++G+L+   ++++ L  IF  +GKI  I L         KGYGF+ F + +DA+ A 
Sbjct: 1   SRVFVGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAV 52

Query: 174 EQLNGFELAGRPMKV 188
              NG E+AG+ + +
Sbjct: 53  AGENGREIAGQKLDI 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|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 43.7 bits (103), Expect = 4e-06
 Identities = 28/75 (37%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
          RT+F   L  ++    + E F   G V  V+ I  +K  + K  A++ FK   SVP AM 
Sbjct: 2  RTLFVGNLDPKVTEELIFELFLQAGPVIKVK-IPKDKDGKPKQFAFVNFKHEVSVPYAMN 60

Query: 77 -LNGQKLLGIPIIVQ 90
           LNG KL G P+ +Q
Sbjct: 61 LLNGIKLYGRPLNIQ 75

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 44.0 bits (104), Expect = 4e-06
 Identities = 19/64 (29%), Positives = 36/64 (56%), Gaps = 2/64 (3%)

Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGR--SKGYGFITFHSADDAKKA 172
           +++++G +  + +E  LR +FE +G +  I ++ D       SKG  F+TF++   A +A
Sbjct: 2   IKMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 61

Query: 173 QEQL 176
           Q  L
Sbjct: 62  QNAL 65

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. 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 = 84

>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 43.9 bits (103), Expect = 4e-06
 Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 8/72 (11%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++ +L   +TE++L   F  FGK++ ++ + D        Y F+ F   D A +A +++
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEERDAAVRAMDEM 55

Query: 177 NGFELAGRPMKV 188
           NG E+ G  +++
Sbjct: 56  NGKEIEGEEIEI 67

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. . Length = 72

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 43.7 bits (103), Expect = 5e-06
 Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++G+L   +TE+++  +F   G +  +++  D D G+ K + F+ F        A   L
Sbjct: 4   LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKD-GKPKQFAFVNFKHEVSVPYAMNLL 62

Query: 177 NGFELAGRPMKV 188
           NG +L GRP+ +
Sbjct: 63  NGIKLYGRPLNI 74

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 43.6 bits (103), Expect = 5e-06
 Identities = 26/61 (42%), Positives = 31/61 (50%), Gaps = 2/61 (3%)

Query: 32 DLEEFFSSVGKVRDVRLITCNK-TRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQ 90
          +LE  F   G V  V  I C+K +   KG AYIEF D ESV  A+ L+     G  I V 
Sbjct: 15 ELEAHFHGCGSVNRVT-ILCDKFSGHPKGFAYIEFSDKESVRTALALDESLFRGRQIKVM 73

Query: 91 P 91
          P
Sbjct: 74 P 74

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 43.8 bits (103), Expect = 5e-06
 Identities = 19/59 (32%), Positives = 33/59 (55%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           +++IG L ++ ++  L      FG++ +  +  DP TGRS+G+GF+ F  A    K  E
Sbjct: 1   KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLE 59

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 43.2 bits (102), Expect = 6e-06
 Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 11/69 (15%)

Query: 123 HFN---ITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF 179
            F+     E+ +  +FEPFG +    +         K + F+ F  ++DA KA E L+G 
Sbjct: 6   GFDPGTTREEDIEKLFEPFGPLVRCDI--------RKTFAFVEFEDSEDATKALEALHGS 57

Query: 180 ELAGRPMKV 188
            + G  + V
Sbjct: 58  RIDGSVLTV 66

This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus. Length = 70

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 43.4 bits (103), Expect = 6e-06
 Identities = 20/75 (26%), Positives = 42/75 (56%), Gaps = 2/75 (2%)

Query: 115 MRLYIGSLHFNITEDMLRGIF-EPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
            RL + +L  ++TE  L+  F +  G+I +++L+   D G+S+   FI + + ++A+KA+
Sbjct: 1   SRLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTED-GKSRRIAFIGYKTEEEAQKAK 59

Query: 174 EQLNGFELAGRPMKV 188
           +  N   +    + V
Sbjct: 60  DYFNNTYINTSKISV 74

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

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

 Score = 43.0 bits (102), Expect = 7e-06
 Identities = 25/67 (37%), Positives = 33/67 (49%), Gaps = 1/67 (1%)

Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKL 82
          L   I   DL   F   G++  V+L    +T R KG  +I+F D E    A+  LNG +L
Sbjct: 6  LHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFEL 65

Query: 83 LGIPIIV 89
           G PI V
Sbjct: 66 AGRPIKV 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|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 43.4 bits (102), Expect = 7e-06
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 9/79 (11%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
          ++  +LS + R RD+E FF   GK+ +V L          G  ++EF D      A+  L
Sbjct: 2  VYIGRLSYQARERDVERFFKGYGKILEVDLKN--------GYGFVEFDDLRDADDAVYEL 53

Query: 78 NGQKLLGIPIIVQPTQAEK 96
          NG+ L G  +IV+  +  +
Sbjct: 54 NGKDLCGERVIVEHARGPR 72

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 43.1 bits (101), Expect = 7e-06
 Identities = 24/68 (35%), Positives = 33/68 (48%), Gaps = 8/68 (11%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           R+YIG L +   E  +   F+ +GKI  + L          GYGF+ F    DA  A  +
Sbjct: 1   RVYIGRLSYQARERDVERFFKGYGKILEVDL--------KNGYGFVEFDDLRDADDAVYE 52

Query: 176 LNGFELAG 183
           LNG +L G
Sbjct: 53  LNGKDLCG 60

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins

 Score = 43.4 bits (103), Expect = 7e-06
 Identities = 18/56 (32%), Positives = 33/56 (58%), Gaps = 6/56 (10%)

Query: 126 ITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFEL 181
           ++ + L  +FE +G ++++ +M  P     K Y F+++ S +DA  A + LNG EL
Sbjct: 15  VSREELLRVFEKYGTVEDL-VMP-PG----KPYCFVSYSSIEDAAAAYDALNGKEL 64

This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain. . 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 = 43.3 bits (103), Expect = 8e-06
 Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 5/54 (9%)

Query: 31 RDLEEFFSSVGKVRDVRL--ITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKL 82
           D+ + F   G++  +R   +  NKTRRF    Y++F  PES   A+ L   KL
Sbjct: 15 SDIRDLFEQYGEILSIRFPSLRFNKTRRF---CYVQFTSPESAAAAVALLNGKL 65

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

 Score = 43.5 bits (102), Expect = 8e-06
 Identities = 21/70 (30%), Positives = 44/70 (62%), Gaps = 1/70 (1%)

Query: 128 EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMK 187
           +D+L+ +F PFG + + ++ +D  T  SK +GF+++ +   A+ A + +NGF++  + +K
Sbjct: 22  QDLLQ-MFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAMNGFQIGMKRLK 80

Query: 188 VGTVTDRNES 197
           V     +N+S
Sbjct: 81  VQLKRSKNDS 90

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

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

 Score = 42.9 bits (102), Expect = 1e-05
 Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 1/64 (1%)

Query: 31 RDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIV 89
            L E FS  G V  +R+     TRR  G AY+ F++P     A+  LN   + G PI +
Sbjct: 14 AMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLNFDVIKGKPIRI 73

Query: 90 QPTQ 93
            +Q
Sbjct: 74 MWSQ 77

This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 46.5 bits (110), Expect = 1e-05
 Identities = 29/102 (28%), Positives = 51/102 (50%), Gaps = 7/102 (6%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L +  L  ++T+  L  +F   G I+  ++M D  TG S GY F+ F S  D+++A + L
Sbjct: 110 LIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNL 169

Query: 177 NGFELAGRPMKVG-------TVTDRNESVGGGPSNLDTDEME 211
           NG  +  + +KV        ++ D N  V   P  +  D+++
Sbjct: 170 NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLD 211

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

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

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 4/73 (5%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            +Y G    +     ++ +FE  G +  + ++    +   + + FITF + + A+ A E 
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQLAIET 56

Query: 176 LNGFELAGRPMKV 188
           LNG  + G  +KV
Sbjct: 57  LNGASVDGNCIKV 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|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 7/73 (9%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL + +LH ++TED +  +F   G +   +L+         G   + +   DDA  A ++
Sbjct: 2   RLVVSNLHPSVTEDDIVELFSAIGALKRARLV-------RPGVAEVVYVRKDDALTAIDK 54

Query: 176 LNGFELAGRPMKV 188
            N  EL G+PMK 
Sbjct: 55  YNNRELDGQPMKC 67

This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. 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. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Length = 69

>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 43.2 bits (101), Expect = 1e-05
 Identities = 23/62 (37%), Positives = 37/62 (59%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+  L   +T+  L  +F  +G+I   +++VD  TG S+G GFI F    +A++A + L
Sbjct: 8   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67

Query: 177 NG 178
           NG
Sbjct: 68  NG 69

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

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

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 3/76 (3%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDP-DTGRSKGYGFITFHSADDAKKA 172
           P   Y+G+L +++TE+ ++  F     + +++L  +P D GR +G+G+  F   D   +A
Sbjct: 1   PYTAYLGNLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQA 59

Query: 173 QEQLNGFELAGRPMKV 188
              LN   L  R ++V
Sbjct: 60  L-SLNDESLKNRRIRV 74

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

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 1/54 (1%)

Query: 124 FNITEDMLRGIFEPFGKIDNIQLMVDP-DTGRSKGYGFITFHSADDAKKAQEQL 176
           F  T   LR +F  FG++  ++L      TG  +G+GF+ F +  DAK+A + L
Sbjct: 10  FEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKAL 63

This subgroup corresponds to the RRM6 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|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 18/60 (30%), Positives = 34/60 (56%), Gaps = 4/60 (6%)

Query: 132 RGIFEPF---GKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
           R ++E F   GK+ +++++ D ++ RSKG  ++ F+  +    A   L G  L G+P+ V
Sbjct: 14  RDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG-LTGQRLLGQPIMV 72

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

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

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE-SVPLAMGL 77
          +F   L    +  DLE+ FS  G++ +V +    K+ + KG AY+ F DPE +V     L
Sbjct: 5  LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 78 NGQKLLGIPIIVQP 91
          +G+   G  I + P
Sbjct: 65 DGKVFQGRLIHILP 78

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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
          +D+  I+   L   +   D+   FS  G++ D+ L+   KT + KG A++ ++D  S  L
Sbjct: 7  KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTIL 66

Query: 74 AM-GLNGQKLLGIPIIV 89
          A+  LNG KLLG  I V
Sbjct: 67 AVDNLNGIKLLGRTIRV 83

This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well. . Length = 89

>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG- 76
           I+   L      ++L+++FS  G V++VR+    KT   K   +I+F +PE   +A   
Sbjct: 1  VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 77 LNGQKLLG 84
          +N   L+G
Sbjct: 61 MNNYLLMG 68

This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 42.5 bits (99), Expect = 2e-05
 Identities = 24/60 (40%), Positives = 35/60 (58%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LYI  L  N T+  L  + +P+GKI + + ++D  T + KGYGF+ F S   A+KA   L
Sbjct: 10  LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSAL 69

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has 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. MSSP-1 contains 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 as well as induction of apoptosis. . Length = 86

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

 Score = 41.8 bits (98), Expect = 2e-05
 Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 8/74 (10%)

Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           ++L++G+L    TE  +R +FE +GK+    ++        K YGF+       A +A  
Sbjct: 1   VKLFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIR 52

Query: 175 QLNGFELAGRPMKV 188
            L+ ++L G  + V
Sbjct: 53  NLHHYKLHGVAINV 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|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 25/80 (31%), Positives = 45/80 (56%), Gaps = 4/80 (5%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++ +L F+ T  ML+  F   G +  +   +  + G+SKG G + F S + A++A   
Sbjct: 1   QIFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVRFESPEVAERACRM 58

Query: 176 LNGFELAGRPMKVGTVTDRN 195
           +NG++L GR + V    DRN
Sbjct: 59  MNGYKLNGREIDVR--IDRN 76

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

>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 42.1 bits (99), Expect = 2e-05
 Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 5/72 (6%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L + +L  +++ D L  IF  +G+I  I+     +T   + + FI F+    A+ A + L
Sbjct: 4   LVVFNLDPSVSNDDLHQIFGAYGEIKEIR-----ETPNKRHHKFIEFYDVRSAEAALKAL 58

Query: 177 NGFELAGRPMKV 188
           N  E+AG+ +K+
Sbjct: 59  NRSEIAGKRIKL 70

This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 42.1 bits (98), Expect = 2e-05
 Identities = 23/60 (38%), Positives = 35/60 (58%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LYI  L    T+  L  + +P+GKI + + ++D +T + KGYGF+ F S   A+KA   L
Sbjct: 7   LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVASL 66

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It 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. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 41.9 bits (98), Expect = 2e-05
 Identities = 21/62 (33%), Positives = 37/62 (59%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+  L   +++  +  +F  +G+I   +++VD  TG S+G GFI F    +A++A + L
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63

Query: 177 NG 178
           NG
Sbjct: 64  NG 65

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|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 = 41.5 bits (98), Expect = 3e-05
 Identities = 15/44 (34%), Positives = 24/44 (54%)

Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM 75
          +L E F + G++ +V L    +T+R KG A++ F  PE    A 
Sbjct: 15 ELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAY 58

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

 Score = 41.4 bits (98), Expect = 3e-05
 Identities = 18/57 (31%), Positives = 27/57 (47%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM 75
          +F   LS       L E+FS  G+V D  ++    T R +G  ++ F DP SV   +
Sbjct: 1  LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVL 57

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

>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 41.4 bits (98), Expect = 3e-05
 Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 2/68 (2%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVG-KVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
           +    L       D+ +FFS +      + ++  +   R  G AY+EF  PE    A+ 
Sbjct: 1  VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIV-YDDDGRPTGEAYVEFASPEDARRALR 59

Query: 77 LNGQKLLG 84
           +  K+ G
Sbjct: 60 KHNNKMGG 67

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 41.6 bits (98), Expect = 3e-05
 Identities = 18/57 (31%), Positives = 28/57 (49%)

Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
          D+  +F   L   I   +L+EFF   G V +VR+ +     R     ++ F DPE+V
Sbjct: 2  DSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAV 58

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|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 19/72 (26%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+G+L  ++TE ++  +F   G   + ++++  DT  +  Y F+ F     A  +   +
Sbjct: 2   LYVGNLSRDVTEALILQLFSQIGPCKSCKMIM--DTAGNDPYCFVEFFEHRHAAASLAAM 59

Query: 177 NGFELAGRPMKV 188
           NG ++ G+ +KV
Sbjct: 60  NGRKIMGKEVKV 71

This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal EAR1-like proteins

 Score = 41.3 bits (97), Expect = 3e-05
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L I +L   ++ + LR IF+ +G +  ++     +T   +   F+ F    DA KA   +
Sbjct: 4   LVIFNLDPTVSSETLRSIFQVYGDVKELR-----ETPCKREQRFVEFFDVRDAAKALRAM 58

Query: 177 NGFELAGRPMKV 188
           NG E++G+P+ +
Sbjct: 59  NGKEISGKPVVI 70

This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 71

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

 Score = 41.4 bits (97), Expect = 3e-05
 Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 4/54 (7%)

Query: 32 DLEE----FFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQK 81
          D+EE     F   G +  VR++   KT   KG AY++FKD  +V  A+ LN +K
Sbjct: 11 DVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLNEKK 64

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

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

 Score = 41.2 bits (97), Expect = 3e-05
 Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 6/72 (8%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LYIG+L  ++ E  LR +FE      +  L+         GY F+       A KA E+L
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVK------KGGYAFVDCPDQSWADKAIEKL 54

Query: 177 NGFELAGRPMKV 188
           NG  L G+ ++V
Sbjct: 55  NGKILQGKVIEV 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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 41.2 bits (97), Expect = 4e-05
 Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
          T+F   LS  +    L+  F   G V   R+IT  +T R +G  Y++F+ PE    A+  
Sbjct: 1  TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 77 LNGQKLLGIPI 87
          ++G++L G PI
Sbjct: 61 MDGKELDGRPI 71

This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 76

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

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 3/78 (3%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFK---GIAYIEFKDPESVPL 73
          R I+   L  ++   DL   FS  G+V  +R+      ++ +   G A++ FKD  S   
Sbjct: 1  REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

Query: 74 AMGLNGQKLLGIPIIVQP 91
          A+ LNG +L G  I V  
Sbjct: 61 ALQLNGTELGGRKISVSL 78

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate RNA-binding protein 47 (RBM47)

 Score = 41.2 bits (96), Expect = 4e-05
 Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 10/74 (13%)

Query: 117 LYIGSLHFNITEDMLRGIFEPF--GKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           LY+ +L    +ED ++  F  F  G ++ ++ + D        Y F+ F S +DA  A  
Sbjct: 4   LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRD--------YAFVHFTSREDAVHAMN 55

Query: 175 QLNGFELAGRPMKV 188
            LNG EL G  ++V
Sbjct: 56  NLNGTELEGSCIEV 69

This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 41.2 bits (97), Expect = 4e-05
 Identities = 18/79 (22%), Positives = 38/79 (48%), Gaps = 5/79 (6%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNI-QLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           ++ I ++  ++  + L  +   +G + N  Q+    +T        +T+ S + A++A  
Sbjct: 2   KIQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATVN----VTYESPEQAQQAVN 57

Query: 175 QLNGFELAGRPMKVGTVTD 193
           +LNG E  G  +KV  + D
Sbjct: 58  KLNGHEYEGSKLKVSYIPD 76

This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. . Length = 76

>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 41.4 bits (98), Expect = 5e-05
 Identities = 27/90 (30%), Positives = 39/90 (43%), Gaps = 19/90 (21%)

Query: 115 MRLYIGSLHFNITEDMLRGIFEPF---------GKIDNIQLMVDPD------TGRSKGYG 159
            RL I +L  ++ E  L+ +F             KI  +++M D         G+SKGYG
Sbjct: 1   TRLSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYG 60

Query: 160 FITFHSADDAKKAQEQLNG----FELAGRP 185
           F+ F + + A KA   LN     F    RP
Sbjct: 61  FVEFTNHEHALKALRALNNNPEIFGPDKRP 90

This subfamily corresponds to the RRM4 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 = 98

>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins

 Score = 41.4 bits (98), Expect = 5e-05
 Identities = 19/72 (26%), Positives = 39/72 (54%), Gaps = 9/72 (12%)

Query: 127 TEDMLRGIFEPFGKIDNIQ-LMVDPDTGRSKGYG-----FITFHSADDAKKAQEQLNGFE 180
            E++L+   E FG+   I+ ++++ +T  +   G     ++T+   +DA +  + ++GF 
Sbjct: 19  DEEVLKK-PEYFGQYGKIKKIVINRNTSYNGSQGPSASAYVTYSRKEDALRCIQAVDGFY 77

Query: 181 LAGRPMKV--GT 190
           L GR +K   GT
Sbjct: 78  LDGRLLKASFGT 89

This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T. Length = 98

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

 Score = 40.6 bits (95), Expect = 6e-05
 Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 1/68 (1%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG- 76
          T+F   L+  +   DL +FFS V  ++   ++T  +T   +G  ++ F   E    A+  
Sbjct: 1  TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 77 LNGQKLLG 84
          L  +KL G
Sbjct: 61 LKNKKLHG 68

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

>gnl|CDD|240868 cd12422, RRM2_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 = 41.0 bits (97), Expect = 6e-05
 Identities = 16/58 (27%), Positives = 31/58 (53%), Gaps = 6/58 (10%)

Query: 122 LHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGY-GFITFHSADDAKKAQEQLNG 178
           L + +T D+L  +F P+G ++ I +       ++ G    + F S + A+ A++ LNG
Sbjct: 9   LLYPVTVDVLHQVFSPYGAVEKILIFE-----KNTGVQALVQFDSVESAENAKKALNG 61

This subfamily corresponds to the RRM2 of 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, and RRM3 of PTBPH1 and PTBPH2. 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. This 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. . Length = 85

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

 Score = 40.8 bits (95), Expect = 6e-05
 Identities = 22/77 (28%), Positives = 46/77 (59%), Gaps = 8/77 (10%)

Query: 116 RLYIGSLHFNIT----EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
           R++I ++ +++     +D++R   E  G++  ++L  D + G+S+G G + F   +  KK
Sbjct: 1   RVFISNIPYDMKWQAIKDLMR---EKVGEVTYVELFKDAE-GKSRGCGVVEFKDEEFVKK 56

Query: 172 AQEQLNGFELAGRPMKV 188
           A E +N ++L GRP+ +
Sbjct: 57  ALEVMNKYDLNGRPLNI 73

This subgroup corresponds to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 40.8 bits (96), Expect = 6e-05
 Identities = 20/80 (25%), Positives = 41/80 (51%), Gaps = 3/80 (3%)

Query: 117 LYIGSLHFNITEDMLRGIF-EPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           L++G L  ++ +  L   F + +      ++++D   G S+GYGF+ F    + K+A  +
Sbjct: 4   LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQ-NGNSRGYGFVRFSDESEQKRALTE 62

Query: 176 LNGFE-LAGRPMKVGTVTDR 194
           + G   L G+P++V     +
Sbjct: 63  MQGASGLGGKPIRVSLAIPK 82

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

>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor family

 Score = 44.0 bits (104), Expect = 7e-05
 Identities = 39/151 (25%), Positives = 61/151 (40%), Gaps = 16/151 (10%)

Query: 32  DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA---MGLNGQKLLGIPII 88
           DL E     G V  V ++        K  A +EF+D ES              + G P  
Sbjct: 18  DLVEALIPFGPVSYVMML------PGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAF 71

Query: 89  VQ-PTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLM 147
               T  E  R GN+  +    G    +R+ + +  + IT D+L  IF P+GK+  I   
Sbjct: 72  FNYSTSQEIKRDGNS--DFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTF 129

Query: 148 VDPDTGRSKGYGFITFHSADDAKKAQEQLNG 178
              +  ++     + F S + A+ A+  LNG
Sbjct: 130 TKNNVFQA----LVEFESVNSAQHAKAALNG 156

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). Length = 481

>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases

 Score = 40.7 bits (96), Expect = 8e-05
 Identities = 18/64 (28%), Positives = 35/64 (54%)

Query: 125 NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGR 184
           NI E  L+ + + +G+++ +++   P T +  G   + F S   AK+  E+LN   + G+
Sbjct: 13  NIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKLNQTSVMGK 72

Query: 185 PMKV 188
            +KV
Sbjct: 73  IIKV 76

This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo. . Length = 93

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

 Score = 39.9 bits (94), Expect = 9e-05
 Identities = 15/40 (37%), Positives = 24/40 (60%)

Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
          DL E+FS  G V  V ++T  +T + +G A++ F D + V
Sbjct: 15 DLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPV 54

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|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 40.3 bits (95), Expect = 9e-05
 Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 8/79 (10%)

Query: 125 NI----TEDMLRGIFEPFGK---IDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN 177
           NI    T++ML  + +  GK    D + L +D     + GY FI F + + A+K  +  N
Sbjct: 5   NIPNKYTQEMLLQLLDEHGKGGAYDFLYLPIDFKNKCNVGYAFINFVNPEYAEKFYKAFN 64

Query: 178 GFELAGRP-MKVGTVTDRN 195
           G +       KV  +T   
Sbjct: 65  GKKWKNFKSKKVCDITYAR 83

This subfamily corresponds to the RRM3 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 86

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

 Score = 40.1 bits (94), Expect = 9e-05
 Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 9/76 (11%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKG---YGFITFHSADDAKKAQ 173
           L+IG+L    T   LR  FE FG+I      +D D  +  G   Y FI +       KA 
Sbjct: 5   LFIGNLEKTTTYSDLREAFERFGEI------IDIDIKKQGGNPAYAFIQYADIASVVKAM 58

Query: 174 EQLNGFELAGRPMKVG 189
            +++G  L    +K+G
Sbjct: 59  RKMDGEYLGNNRVKLG 74

This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 40.3 bits (94), Expect = 9e-05
 Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 5/70 (7%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L + +L  + T +    +   +G I+   L+    TG SKGYGF+ +   D A KA+   
Sbjct: 2   LCVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKAR--- 58

Query: 177 NGFELAGRPM 186
              EL G+ +
Sbjct: 59  --LELLGKQL 66

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct 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. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

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

 Score = 39.8 bits (94), Expect = 1e-04
 Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
          TI    LS+     DL E F   G +  V L    +T + +G A++ F   E    A+  
Sbjct: 1  TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 77 LNG 79
          LNG
Sbjct: 61 LNG 63

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|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 43.7 bits (103), Expect = 1e-04
 Identities = 44/206 (21%), Positives = 75/206 (36%), Gaps = 35/206 (16%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
             + +D   I+   L   +    ++E   S G ++   LI    T   KG A+ E+KDP 
Sbjct: 291 VLDSKD--RIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPS 348

Query: 70  SVPLAM-GLNGQKLLGIPIIVQ-------PTQAEKNRAGNTLPNLQPRGT--------GG 113
              +A+  LNG+      + VQ           + +  G     L  +          G 
Sbjct: 349 VTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSN-GMAPVTLLAKALSQSILQIGGK 407

Query: 114 PMR------------LYIGSLHFNITEDMLRGIFEPFGKIDNIQL---MVDPDTGRSKGY 158
           P +            L     +  I ED+ +  F  +G + NI +     D ++    G 
Sbjct: 408 PTKVVQLTNLVTGDDLMDDEEYEEIYEDV-KTEFSKYGPLINIVIPRPNGDRNSTPGVGK 466

Query: 159 GFITFHSADDAKKAQEQLNGFELAGR 184
            F+ +     A+KA E +NG +   R
Sbjct: 467 VFLEYADVRSAEKAMEGMNGRKFNDR 492

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 15/53 (28%), Positives = 23/53 (43%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
          IF   LS       + E+F   G + ++ L    KT + +G  +I F   E V
Sbjct: 2  IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPV 54

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 41.1 bits (96), Expect = 1e-04
 Identities = 17/59 (28%), Positives = 29/59 (49%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           L++ +L ++ TE+ L   F  FG +     ++D  TGR+KG GF+ F          + 
Sbjct: 4   LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKN 62

This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 107

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

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           R+Y+G+L  +I E  +  +F  +G I  I L       R   + F+ F    DA+ A   
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRR---RGPPFAFVEFEDPRDAEDAVRG 57

Query: 176 LNGFELAGRPMKV 188
            +G++  G  ++V
Sbjct: 58  RDGYDFDGYRLRV 70

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|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 = 1e-04
 Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 3/51 (5%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDP 68
           I+   L   IR RD+E+ F   G ++ + L      RR    A++EF+DP
Sbjct: 1  RIYVGNLPGDIRERDIEDLFYKYGPIKAIDL---KNRRRGPPFAFVEFEDP 48

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

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 20/50 (40%), Positives = 29/50 (58%), Gaps = 4/50 (8%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDP 68
          I+   L   IRT+D+E+ F   G +RD+ L    K RR    A++EF+DP
Sbjct: 2  IYVGNLPPDIRTKDIEDLFYKYGAIRDIDL----KNRRGPPFAFVEFEDP 47

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|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 17/68 (25%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFG-KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           L++G L   + E+ ++  F   G  + +++++ +  TG   GY F+ F     A++   +
Sbjct: 2   LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61

Query: 176 LNGFELAG 183
           LNG  + G
Sbjct: 62  LNGKPIPG 69

This subgroup corresponds to the RRM1 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 84

>gnl|CDD|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding protein MRN1 and similar proteins

 Score = 39.9 bits (93), Expect = 1e-04
 Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 11/83 (13%)

Query: 117 LYIGSLHF-----NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
           +YIG++       N+ E  LR   E +G+I++I+++      R K   FI F +  +A  
Sbjct: 5   VYIGNVSDVGDERNLPEKELRKECEKYGEIESIRIL------REKACAFINFMNIPNAIA 58

Query: 172 AQEQLNGFELAGRPMKVGTVTDR 194
           A + LNG +     +++    DR
Sbjct: 59  ALQTLNGKKPYDTIVRINYGKDR 81

This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an 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 = 82

>gnl|CDD|240720 cd12274, RRM2_NEFsp, RNA recognition motif 2 in vertebrate putative RNA exonuclease NEF-sp

 Score = 39.5 bits (92), Expect = 1e-04
 Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +Y+     ++TE+ L+  F     ++ I L  D  +G+   Y F+ F  +  A  A + +
Sbjct: 1   IYVSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAALDHI 60

Query: 177 NG-FELAGR 184
            G +EL GR
Sbjct: 61  TGEWELKGR 69

This subfamily corresponds to the RRM2 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 = 39.5 bits (93), Expect = 2e-04
 Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 1/67 (1%)

Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL 82
          LS     RDL E FS  G +  V+++   KT R +G  ++ F+  E    A   LNG ++
Sbjct: 7  LSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEI 66

Query: 83 LGIPIIV 89
           G  I V
Sbjct: 67 DGRRIRV 73

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

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL 82
          L++ +    L+E FS+ G V+DV L    +    +G AY+EF+ PE    A+  ++G ++
Sbjct: 6  LTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDGGQI 65

Query: 83 LGIPIIVQ 90
           G  + V+
Sbjct: 66 DGQEVTVE 73

This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. . Length = 73

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

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 2/60 (3%)

Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ 90
          DLEE F  VG+V+ V+ I  +++ R +G A + F+  E    A+   NG  L G P+ V+
Sbjct: 16 DLEELFGRVGEVKKVK-INYDRSGRSEGTADVVFEKREDAERAIKQFNGVLLDGQPMQVE 74

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|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 33 LEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIV 89
          L++ FS VG V   RL+   +T + KG  + E+KD E+   AM  LNG +L G  + V
Sbjct: 15 LKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNGYELNGRQLRV 72

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

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

 Score = 38.6 bits (91), Expect = 2e-04
 Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 6/58 (10%)

Query: 35 EFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP 91
          + FS  G V  ++L+         G A++EF   E+   A+  LNG    G P+ V  
Sbjct: 3  KLFSPFGNVEKIKLLKKKP-----GFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

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

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 17/57 (29%), Positives = 31/57 (54%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM 75
          +F   LS      +L   F  VG++R VR++T   + + KG A+++F++ E    A+
Sbjct: 1  LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 57

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

>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 39.5 bits (92), Expect = 2e-04
 Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 2/76 (2%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLN 78
          +F   LS     +DL+E+FS  G+V D  +     T R +G  ++ FKD  SV   +   
Sbjct: 1  MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 79 GQKLLGIPIIVQPTQA 94
            KL G   ++ P +A
Sbjct: 61 EHKLDG--RVIDPKRA 74

This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

>gnl|CDD|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B" (U2B") and similar proteins

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 117 LYIGSLHFNIT-EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +YI +L+  I  E++ R ++  F +  ++  +V   T + +G  F+ F     A  A  Q
Sbjct: 4   IYINNLNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELSSATNALRQ 63

Query: 176 LNGFELAGRPMKV 188
           L GF   G+PM++
Sbjct: 64  LQGFPFYGKPMRI 76

This subgroup corresponds to the RRM1 of U2B" (also termed U2 snRNP B") a unique protein that comprises the U2 snRNP. It was initially identified as binding to stem-loop IV (SLIV) at the 3' end of U2 snRNA. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA. In addition, the nuclear transport of U2B" is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus. . Length = 91

>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 5/64 (7%)

Query: 125 NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGR 184
            I++  LR +F  FG++ +I+    P     K   F+ F+    A+ A + LNG    G 
Sbjct: 12  PISDQELRSLFSQFGEVKDIRE--TPLRPSQK---FVEFYDIRAAEAALDALNGRPFLGG 66

Query: 185 PMKV 188
            +KV
Sbjct: 67  RLKV 70

This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++ +L F +    L+ +F   G +    +  D D G+S+G G +TF    +A +A    
Sbjct: 3   IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKD-GKSRGMGTVTFEQPIEAVQAISMF 61

Query: 177 NGFELAGRPMKV 188
           NG  L  RPM V
Sbjct: 62  NGQFLFDRPMHV 73

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

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 22/85 (25%), Positives = 34/85 (40%), Gaps = 17/85 (20%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRL----ITCNKTRRFKGI------------ 60
          RT+F   L    + +DL++ F   G +  VR     +   K  +                
Sbjct: 1  RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNV 60

Query: 61 -AYIEFKDPESVPLAMGLNGQKLLG 84
           AY+ FK+ ES   A+ LNG +  G
Sbjct: 61 NAYVVFKEEESAEKALKLNGTEFEG 85

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

>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 12/35 (34%), Positives = 22/35 (62%)

Query: 154 RSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
           + + + F+TF S ++ +KA E L+GF+  GR +  
Sbjct: 40  KRQDFAFVTFRSEEERQKALEILDGFKWKGRVLSA 74

This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases. . Length = 79

>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 4/66 (6%)

Query: 126 ITEDMLRGIFEPFGKIDNIQL-MVDPDTGRSKGYG--FITFHSADDAKKAQEQLNGFELA 182
           I ED+ +     +GK+ ++ +   + +     G G  F+ F   +DA+KAQ  L G +  
Sbjct: 24  ILEDV-KEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFD 82

Query: 183 GRPMKV 188
           GR +  
Sbjct: 83  GRTVVA 88

This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 89

>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 39.1 bits (91), Expect = 2e-04
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +Y+G++ +  T + L   F   G I+ + ++ D  +G  KGY +I F + D  + A   L
Sbjct: 2   VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVA-L 60

Query: 177 NGFELAGRPMKV 188
           +     GR +KV
Sbjct: 61  DESSFRGRVIKV 72

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

>gnl|CDD|215588 PLN03120, PLN03120, nucleic acid binding protein; Provisional

 Score = 42.0 bits (99), Expect = 2e-04
 Identities = 22/89 (24%), Positives = 40/89 (44%), Gaps = 4/89 (4%)

Query: 31  RDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQ 90
           RD++EFFS  G +  V + + N+  +   IAY+ FKDP+    A+ L+G  ++   + + 
Sbjct: 19  RDIKEFFSFSGDIEYVEMQSENERSQ---IAYVTFKDPQGAETALLLSGATIVDQSVTIT 75

Query: 91  PTQAEKNRAGNTLPNLQPRGTGGPMRLYI 119
           P +  +      L  L            +
Sbjct: 76  PAEDYQLPPEA-LAPLSSNSPASGAESAV 103

Length = 260

>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused in Ewing's sarcoma protein (FUS), TATA-binding protein-associated factor 15 (TAF15) and similar proteins

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 8/80 (10%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDN--------IQLMVDPDTGRSKGYGFITFHSADD 168
           +++  L  ++T + +   F+  G I          I L  D +TG+ KG   ++F     
Sbjct: 5   IFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 64

Query: 169 AKKAQEQLNGFELAGRPMKV 188
           AK A +  +G E +G P+KV
Sbjct: 65  AKAAIDWFDGKEFSGNPIKV 84

This subgroup corresponds to the RRM of FUS and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed 75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS (Translocated in liposarcoma), is a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multi-functional protein and has been implicated in pre-mRNA splicing, chromosome stability, cell spreading, and transcription. FUS was originally identified in human myxoid and round cell liposarcomas as an oncogenic fusion with the stress-induced DNA-binding transcription factor CHOP (CCAAT enhancer-binding homologous protein) and later as hnRNP P2, a component of hnRNP H complex assembled on pre-mRNA. It can form ternary complexes with hnRNP A1 and hnRNP C1/C2. Additional research indicates that FUS binds preferentially to GGUG-containing RNAs. In the presence of Mg2+, it can bind both single- and double-stranded DNA (ssDNA/dsDNA) and promote ATP-independent annealing of complementary ssDNA and D-loop formation in superhelical dsDNA. FUS has been shown to be recruited by single stranded noncoding RNAs to the regulatory regions of target genes such as cyclin D1, where it represses transcription by disrupting complex formation. TAF15 (TAFII68), also termed TATA-binding protein-associated factor 2N (TAF2N), or RNA-binding protein 56 (RBP56), originally identified as a TAF in the general transcription initiation TFIID complex, is a novel RNA/ssDNA-binding protein with homology to the proto-oncoproteins FUS and EWS (also termed EWSR1), belonging to the FET family as well. TAF15 likely functions in RNA polymerase II (RNAP II) transcription by interacting with TFIID and subunits of RNAP II itself. TAF15 is also associated with U1 snRNA, chromatin and RNA, in a complex distinct from the Sm-containing U1 snRNP that functions in splicing. Like other members in the FET family, both FUS and TAF15 contain an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. . Length = 86

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

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 3/80 (3%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG- 76
          T+F   L        LEEFFS VG ++   ++    +++ +G  Y+ F   E    A+  
Sbjct: 1  TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 77 LNGQKLLGIPIIVQPTQAEK 96
              K  G  I V    A+K
Sbjct: 61 KKKTKFGGRKIHV--EFAKK 78

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

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

 Score = 38.7 bits (91), Expect = 3e-04
 Identities = 19/55 (34%), Positives = 29/55 (52%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
          RT+F   L       +L+E FS  G+V+  R++    T   KG A+++FK  ES 
Sbjct: 1  RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESA 55

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

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

 Score = 39.2 bits (92), Expect = 3e-04
 Identities = 17/51 (33%), Positives = 27/51 (52%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKD 67
           T+F  +LS +     L E FS  G +R +RL+    T   KG A++E++ 
Sbjct: 4  LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEH 54

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

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLN 78
          +F   LS     +DL E+ S  G+V D  + T   T R +G  ++ FKD  SV   + L 
Sbjct: 2  MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELK 61

Query: 79 GQKLLGIPIIVQPTQAE 95
            KL G   ++ P +A+
Sbjct: 62 EHKLDG--KLIDPKRAK 76

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

>gnl|CDD|240705 cd12259, RRM_SRSF11_SREK1, RNA recognition motif in serine/arginine-rich splicing factor 11 (SRSF11), splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 4/71 (5%)

Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTR---RFKGIAYIEFKDPESVPLAMGLNGQ 80
          +S +     +   F  +GK+ ++RL   +        K + +++++DPE V +A+ L   
Sbjct: 7  VSPQATEEQMRTLFGFLGKIEELRLYPSDDDLAPVLSK-VCFVKYEDPEDVGVALHLTNT 65

Query: 81 KLLGIPIIVQP 91
            +   +IV P
Sbjct: 66 VFIDRALIVVP 76

This subfamily corresponds to the RRM domain of SRSF11 (SRp54 or p54), SREK1 ( SFRS12 or SRrp86) and similar proteins, a group of proteins containing regions rich in serine-arginine dipeptides (SR protein family). These are involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SR proteins have been identified as crucial regulators of alternative splicing. Different SR proteins display different substrate specificity, have distinct functions in alternative splicing of different pre-mRNAs, and can even negatively regulate splicing. All SR family members are characterized by the presence of one or two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and the C-terminal regions rich in serine and arginine dipeptides (SR domains). The RRM domain is responsible for RNA binding and specificity in both alternative and constitutive splicing. In contrast, SR domains are thought to be protein-protein interaction domains that are often interchangeable. . Length = 76

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

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 13/56 (23%), Positives = 30/56 (53%), Gaps = 5/56 (8%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
           ++++G L  ++TE+ LR  F  FG++ ++ +         + + F+TF   + A+ 
Sbjct: 2   KVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPF-----RAFAFVTFADPEVAQS 52

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|240715 cd12269, RRM_Vip1_like, RNA recognition motif in a group of uncharacterized plant proteins similar to fission yeast Vip1

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 22 MQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQK 81
            LS +   RD+ +FFS  G +  V +    +  +    AY+ FKDP++   A+ L+G  
Sbjct: 4  TNLSPKATERDIYDFFSFSGDIEYVEIQRSGEQSQ---TAYVTFKDPQAQETALLLSGAT 60

Query: 82 LL 83
          ++
Sbjct: 61 IV 62

This subfamily corresponds to the Vip1-like, uncharacterized proteins found in plants. Although their biological roles remain unclear, these proteins show high sequence similarity to the fission yeast Vip1. Like Vip1 protein, members in this family contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 69

>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing factor Cwc2 and similar proteins

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 13/63 (20%)

Query: 117 LYIGSLHFNI----TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFH---SADDA 169
           LY+G +         E++LR  F  +G I++I+++       SKG  F+ +    SA+ A
Sbjct: 4   LYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVL------PSKGIAFVRYKYRASAEFA 57

Query: 170 KKA 172
           K+A
Sbjct: 58  KEA 60

This subfamily corresponds to the RRM of yeast protein Cwc2, also termed Complexed with CEF1 protein 2, or PRP19-associated complex protein 40 (Ntc40), or synthetic lethal with CLF1 protein 3, one of the components of the Prp19-associated complex [nineteen complex (NTC)] that can bind to RNA. NTC is composed of the scaffold protein Prp19 and a number of associated splicing factors, and plays a crucial role in intron removal during premature mRNA splicing in eukaryotes. Cwc2 functions as an RNA-binding protein that can bind both small nuclear RNAs (snRNAs) and pre-mRNA in vitro. It interacts directly with the U6 snRNA to link the NTC to the spliceosome during pre-mRNA splicing. In the N-terminal half, Cwc2 contains a CCCH-type zinc finger (ZnF domain), a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an intervening loop, also termed RNA-binding loop or RB loop, between ZnF and RRM, all of which are necessary and sufficient for RNA binding. The ZnF is also responsible for mediating protein-protein interaction. The C-terminal flexible region of Cwc2 interacts with the WD40 domain of Prp19. Length = 78

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

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 6/68 (8%)

Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKL 82
          L  R   R+LE+ F   G +R V +      R   G A++EF+DP     A+  L+G+++
Sbjct: 7  LGPRATKRELEDEFEKYGPLRSVWV-----ARNPPGFAFVEFEDPRDAEDAVRALDGRRI 61

Query: 83 LGIPIIVQ 90
           G  + V+
Sbjct: 62 CGNRVRVE 69

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|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 38.3 bits (90), Expect = 4e-04
 Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 2/62 (3%)

Query: 127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
           T D ++  FE FGK++NI++  D D  + KG  F+ F + +DAKK  E     +   + +
Sbjct: 12  TLDDIQEFFEKFGKVNNIRMRRDLD-KKFKGSVFVEFKTEEDAKKFLE-KEKLKYKEKEL 69

Query: 187 KV 188
            V
Sbjct: 70  TV 71

This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 72

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

 Score = 38.7 bits (90), Expect = 4e-04
 Identities = 16/56 (28%), Positives = 32/56 (57%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
           +++G+L F   E+ L  +F   G I+ ++++ DP T   KG+ ++ F   +  +KA
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKA 57

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

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

 Score = 38.5 bits (89), Expect = 4e-04
 Identities = 24/80 (30%), Positives = 45/80 (56%), Gaps = 4/80 (5%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++ +L F++T   L+  F   G +   ++ ++   G+SKG G + F S + A+KA   
Sbjct: 1   QIFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKME--NGKSKGCGTVRFDSPESAEKACRL 58

Query: 176 LNGFELAGRPMKVGTVTDRN 195
           +NG ++ GR + V    DRN
Sbjct: 59  MNGIKINGREIDVR--LDRN 76

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

>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 11/33 (33%), Positives = 18/33 (54%)

Query: 152 TGRSKGYGFITFHSADDAKKAQEQLNGFELAGR 184
               +G G + F S +D ++A  +L+G E  GR
Sbjct: 33  DRDQEGEGVVEFTSQEDMERALRKLDGTEFRGR 65

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C) and plant pre-mRNA-splicing factor SF2 (SR1). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

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

 Score = 38.1 bits (89), Expect = 5e-04
 Identities = 23/70 (32%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
          IF   LS  I T  L   F+  G++ D R++   +T + KG  ++ F   E    A+  +
Sbjct: 2  IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 78 NGQKLLGIPI 87
          NGQ L G  I
Sbjct: 62 NGQWLGGRAI 71

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

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

 Score = 38.1 bits (89), Expect = 5e-04
 Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 1/54 (1%)

Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLG 84
          DL + FS  GKV  V ++   +TR+ KG+A+I F D E     +  LN ++L G
Sbjct: 17 DLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNNKELFG 70

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

 Score = 37.9 bits (89), Expect = 5e-04
 Identities = 18/46 (39%), Positives = 23/46 (50%)

Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
          LS  +   DLEE FS  G V DV +I        +G AYI+ +  E
Sbjct: 7  LSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSE 52

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|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 37.6 bits (87), Expect = 5e-04
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 9/73 (12%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
          ++  +LS  +R +D++ FF   GK+ ++ L          G  ++EF+D      A+  L
Sbjct: 2  VYIGRLSYHVREKDIQRFFGGYGKLLEIDLKN--------GYGFVEFEDSRDADDAVYEL 53

Query: 78 NGQKLLGIPIIVQ 90
          NG+ L G  +IV+
Sbjct: 54 NGKDLCGERVIVE 66

This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 70

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

 Score = 38.1 bits (89), Expect = 5e-04
 Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 118 YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN 177
           ++G +  +++ED L+  F   G++  ++L  D     S  + F+ F  A+ A  A   L+
Sbjct: 4   HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQH--SARFAFVEFADAESALSALN-LS 60

Query: 178 GFELAGRPMKV 188
           G  L G P++V
Sbjct: 61  GTLLGGHPLRV 71

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

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

 Score = 38.0 bits (88), Expect = 5e-04
 Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 9/77 (11%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
          +F  +L+   R +D+E FF   G++RD+ L         +G  ++EF DP     A+  L
Sbjct: 2  VFIGRLNPAAREKDVERFFKGYGRIRDIDLK--------RGFGFVEFDDPRDADDAVYEL 53

Query: 78 NGQKLLGIPIIVQPTQA 94
          +G++L    + ++  +A
Sbjct: 54 DGKELCNERVTIEHARA 70

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

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

 Score = 38.2 bits (89), Expect = 5e-04
 Identities = 18/65 (27%), Positives = 35/65 (53%), Gaps = 6/65 (9%)

Query: 112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
           G    +YIG++  ++TE+ LR  F  +G+I+++  +      R K   F+ F +  +A K
Sbjct: 1   GASRNVYIGNIDDSLTEEKLRNDFSQYGEIESVNYL------REKNCAFVNFTNISNAIK 54

Query: 172 AQEQL 176
           A + +
Sbjct: 55  AIDGV 59

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

 Score = 37.6 bits (88), Expect = 6e-04
 Identities = 17/58 (29%), Positives = 28/58 (48%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
            IF   L        L ++FS  G++ +  +IT  +T + +G  ++ FKD ES   A
Sbjct: 1  TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERA 58

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

 Score = 38.0 bits (89), Expect = 6e-04
 Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 6/70 (8%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVP--LAM 75
           IF   +       +L +FFS  G V+DV++I  ++    KG  ++ F+  E     LAM
Sbjct: 4  RIFVGGIPPDTTEEELRDFFSRFGSVKDVKII-TDRAGVSKGYGFVTFETQEDAEKILAM 62

Query: 76 G---LNGQKL 82
          G     G+KL
Sbjct: 63 GNLNFRGKKL 72

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

>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 37.7 bits (88), Expect = 6e-04
 Identities = 18/73 (24%), Positives = 34/73 (46%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGL 77
           +F   L   + +++L+E+FS  GKV+   +    +T   KG  ++ F   + +  A+  
Sbjct: 1  KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 78 NGQKLLGIPIIVQ 90
              L G  + VQ
Sbjct: 61 QKHILEGNKLQVQ 73

This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities. . Length = 73

>gnl|CDD|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin

 Score = 37.9 bits (88), Expect = 6e-04
 Identities = 20/56 (35%), Positives = 32/56 (57%), Gaps = 7/56 (12%)

Query: 33 LEEFFSSVG-KVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPI 87
          + EFFS     V+DVR+     +++F    Y++F+  E +  A+ L G+KLLG  I
Sbjct: 21 ISEFFSKKNLAVQDVRI---GSSKKF---GYVDFESAEDLEKALELTGKKLLGNEI 70

This subfamily corresponds to the RRM1 of ubiquitously expressed protein nucleolin, also termed protein C23. Nucleolin is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. RRM1, together with RRM2, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 75

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

 Score = 37.8 bits (87), Expect = 6e-04
 Identities = 20/76 (26%), Positives = 41/76 (53%), Gaps = 2/76 (2%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+G+L  ++TE ++  +F   G   + +++ +  +  +  Y F+ F+   DA  A   +
Sbjct: 2   LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAM 59

Query: 177 NGFELAGRPMKVGTVT 192
           NG ++ G+ +KV   T
Sbjct: 60  NGRKILGKEVKVNWAT 75

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|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 37.4 bits (87), Expect = 7e-04
 Identities = 17/53 (32%), Positives = 28/53 (52%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
          IF   LS      D++++FS  GKV D  L+   +T R +G  ++ F+  + V
Sbjct: 2  IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVV 54

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 37.7 bits (88), Expect = 7e-04
 Identities = 12/62 (19%), Positives = 28/62 (45%), Gaps = 1/62 (1%)

Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKL 82
          L Q +   +L   F ++G +   +++    T +  G  ++++ D      A+  LNG ++
Sbjct: 8  LPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEI 67

Query: 83 LG 84
            
Sbjct: 68 RN 69

This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 77

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 37.7 bits (87), Expect = 7e-04
 Identities = 18/53 (33%), Positives = 28/53 (52%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
          +F   LS     +DL+++F+  G+V D  +     T R +G  +I FKD  SV
Sbjct: 2  MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSV 54

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 41.1 bits (96), Expect = 7e-04
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 10/74 (13%)

Query: 117 LYIGSLHFNITEDMLRGIFEPF--GKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           LY+ +L    TE+++   F  F  GK++ ++ + D        Y F+ F   +DA KA +
Sbjct: 236 LYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD--------YAFVHFEDREDAVKAMD 287

Query: 175 QLNGFELAGRPMKV 188
           +LNG EL G  ++V
Sbjct: 288 ELNGKELEGSEIEV 301

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

>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 38.2 bits (88), Expect = 7e-04
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
           P  LYI +L  ++ E  L  + +PFG + + +++ D + G S+G GF    S +  +   
Sbjct: 1   PTNLYISNLPVSMDEQELENMLKPFGHVISTRILRDAN-GVSRGVGFARMESTEKCEVVI 59

Query: 174 EQLNGFELAGRP 185
           +  NG  L   P
Sbjct: 60  QHFNGKYLKTPP 71

This subgroup corresponds to the RRM2 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It 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. RBMS3 contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 88

>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 37.8 bits (88), Expect = 7e-04
 Identities = 26/80 (32%), Positives = 34/80 (42%), Gaps = 8/80 (10%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFG--KIDN------IQLMVDPDTGRSKGYGFITFHSADD 168
           +++ +L  N TE  L   F   G  KID       I L  D DTG  KG   +T+     
Sbjct: 1   VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 169 AKKAQEQLNGFELAGRPMKV 188
           A  A E  N  +  G  +KV
Sbjct: 61  ASAAIEWFNNKDFMGNTIKV 80

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

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

 Score = 37.6 bits (88), Expect = 8e-04
 Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 6/57 (10%)

Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG------LNGQKL 82
          D++  F + GK++   L    +T + KG  +IE+++P+S   A+       L GQ+L
Sbjct: 16 DIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASMNLFDLGGQQL 72

This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 77

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

 Score = 37.3 bits (87), Expect = 8e-04
 Identities = 15/64 (23%), Positives = 25/64 (39%), Gaps = 3/64 (4%)

Query: 31 RDLEEFFSSVGK--VRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPI 87
           DLE   +  G   V+ ++        + KG AY+EF    +       L G++  G   
Sbjct: 13 EDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKEKLEGREFNGKKC 72

Query: 88 IVQP 91
          +V  
Sbjct: 73 VVTY 76

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

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

 Score = 37.3 bits (87), Expect = 9e-04
 Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L + +L   ++ ++L   F  FG+++   ++VD D GRS G G + F     A+ A ++ 
Sbjct: 2   LRVKNLSPFVSNELLEQAFSQFGEVERAVVIVD-DRGRSTGEGIVEFSRKPGAQAAIKRC 60

Query: 177 N 177
           +
Sbjct: 61  S 61

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA-MGL 77
          IF   L   +    ++E   S GK++   L+  + T   KG A+ E+ DP     A  GL
Sbjct: 3  IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 78 NGQKLLGIPIIVQ 90
          NG +L    + VQ
Sbjct: 63 NGMQLGDKKLTVQ 75

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

>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 22/62 (35%), Positives = 36/62 (58%), Gaps = 7/62 (11%)

Query: 32 DLEEFFSSVGKVRDVRLITCNKTRR---FKGIAYIEFKDPESVPLAM-GLNGQKLLGIPI 87
          D+ + F+  G+++++ L   N  RR    KG A IE++  +    A+ GLNG++LLG  I
Sbjct: 22 DVHDKFAEFGEIKNLHL---NLDRRTGFVKGYALIEYETKKEAQAAIEGLNGKELLGQTI 78

Query: 88 IV 89
           V
Sbjct: 79 SV 80

This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). . Length = 88

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 27/75 (36%), Positives = 37/75 (49%), Gaps = 11/75 (14%)

Query: 24 LSQRIRTRDLEEFF------SSVGKVR-DVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
          LS+R+   DL   F      SS  K   D+RL+T     R KG A++ F   E    A+ 
Sbjct: 9  LSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMT---EGRMKGQAFVTFPSEEIATKALN 65

Query: 77 L-NGQKLLGIPIIVQ 90
          L NG  L G P+++Q
Sbjct: 66 LVNGYVLKGKPMVIQ 80

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|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 16/58 (27%), Positives = 30/58 (51%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
          +F   LS +     L ++FS  G++R+  ++    T+R +G  ++ F DP SV   + 
Sbjct: 2  MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLA 59

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 3/75 (4%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF-KDPESVPLAMGL 77
          ++   L + +  +++E+ FS  G++   R++    T   +G+ +I F K  E+     GL
Sbjct: 4  LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63

Query: 78 NGQKLLGI--PIIVQ 90
          NGQK LG   PI V+
Sbjct: 64 NGQKPLGAAEPITVK 78

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 37.2 bits (86), Expect = 0.001
 Identities = 24/61 (39%), Positives = 31/61 (50%), Gaps = 2/61 (3%)

Query: 32 DLEEFFSSVGKVRDVRLITCNK-TRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQ 90
          +LE  FS  G +  V  I C+K +   KG AYIEF   +SV  A+ L+     G  I V 
Sbjct: 15 ELEAHFSGCGPINRVT-ILCDKFSGHPKGYAYIEFATRDSVEAAVALDESSFRGRVIKVL 73

Query: 91 P 91
          P
Sbjct: 74 P 74

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

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

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 8/66 (12%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           R++IG L+    E  +   F+ +G+I +I L         +G+GF+ F    DA  A  +
Sbjct: 1   RVFIGRLNPAAREKDVERFFKGYGRIRDIDL--------KRGFGFVEFDDPRDADDAVYE 52

Query: 176 LNGFEL 181
           L+G EL
Sbjct: 53  LDGKEL 58

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

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

 Score = 37.1 bits (86), Expect = 0.001
 Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 4/62 (6%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
          I+   L   +R +DLE+ F   G++RD+ L        F   A++ F+DP     A+ G 
Sbjct: 2  IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPF---AFVRFEDPRDAEDAVFGR 58

Query: 78 NG 79
          NG
Sbjct: 59 NG 60

This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

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

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++ +L + +    L+ +F   G +    ++ D D G+S+G G +TF    +A +A    
Sbjct: 3   VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKD-GKSRGIGTVTFEQPIEAVQAISMF 61

Query: 177 NGFELAGRPMKV 188
           NG  L  RPM V
Sbjct: 62  NGQLLFDRPMHV 73

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

>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 25/80 (31%), Positives = 37/80 (46%), Gaps = 9/80 (11%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKID--------NIQLMVDPDTGRSKGYGFITFHSADD 168
           +YI  L  ++TED L  +F   G I          I++  D +T   KG   +T+     
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKET-EPKGEATVTYDDPSA 59

Query: 169 AKKAQEQLNGFELAGRPMKV 188
           A+ A E  NG+E  G  +KV
Sbjct: 60  AQAAIEWFNGYEFRGNKIKV 79

This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15. . Length = 81

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

 Score = 37.1 bits (86), Expect = 0.001
 Identities = 17/69 (24%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++ + +L F  T+  +R +F  +G++ ++++    D   ++G+ F+ F +A +A  A   
Sbjct: 2   KILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQS-ARGFAFVEFSTAKEALNAMNA 60

Query: 176 LNGFELAGR 184
           L    L GR
Sbjct: 61  LKDTHLLGR 69

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

>gnl|CDD|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator 1-beta (PGC-1-beta) and similar proteins

 Score = 37.1 bits (86), Expect = 0.001
 Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 11/62 (17%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKG--YGFITF----HSADDAK 170
           +YI +L  +++   L+  FE FG+I+  ++++     +S+G  YGFIT+    H+A    
Sbjct: 5   IYIRNLSSSMSSTELKKRFEVFGEIEECKVLI-----KSRGEKYGFITYRHSEHAALSLG 59

Query: 171 KA 172
           K 
Sbjct: 60  KG 61

This subfamily corresponds to the RRM of PGC-1beta, also termed PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or PGC-1-related estrogen receptor alpha coactivator, which is one of the members of PGC-1 transcriptional coactivators family, including PGC-1alpha and PGC-1-related coactivator (PRC). PGC-1beta plays a nonredundant role in controlling mitochondrial oxidative energy metabolism and affects both, insulin sensitivity and mitochondrial biogenesis, and functions in a number of oxidative tissues. It is involved in maintaining baseline mitochondrial function and cardiac contractile function following pressure overload hypertrophy by preserving glucose metabolism and preventing oxidative stress. PGC-1beta induces hypertriglyceridemia in response to dietary fats through activating hepatic lipogenesis and lipoprotein secretion. It can stimulate apolipoprotein C3 (APOC3) expression, further mediating hypolipidemic effect of nicotinic acid. PGC-1beta also drives nuclear respiratory factor 1 (NRF-1) target gene expression and NRF-1 and estrogen related receptor alpha (ERRalpha)-dependent mitochondrial biogenesis. The modulation of the expression of PGC-1beta can trigger ERRalpha-induced adipogenesis. PGC-1beta is also a potent regulator inducing angiogenesis in skeletal muscle. The transcriptional activity of PGC-1beta can be increased through binding to host cell factor (HCF), a cellular protein involved in herpes simplex virus (HSV) infection and cell cycle regulation. PGC-1beta is a multi-domain protein containing an N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, two glutamic/aspartic acid-rich acidic domains, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha, PGC-1beta lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 79

>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 6/46 (13%)

Query: 127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
               L   F  FG I NIQ  V+ +   +     + F ++++AKKA
Sbjct: 15  NITKLNEHFSKFGTIVNIQ--VNYNPESA----LVQFSTSEEAKKA 54

This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear. . Length = 72

>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 16/61 (26%), Positives = 31/61 (50%), Gaps = 6/61 (9%)

Query: 128 EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMK 187
           + +L  +F  FG + ++ L+        K YG+  +   + A++A   L+G E+ G  +K
Sbjct: 13  DYILEDVFCRFGGLIDVYLV------PGKNYGYAKYADRESAERAITTLHGKEVNGVKLK 66

Query: 188 V 188
           V
Sbjct: 67  V 67

This subfamily corresponds to the RRM4 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 = 68

>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 7/76 (9%)

Query: 117 LYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
           +YI +L+  I +D L+     IF  FG+I +I +     + + +G  F+ F     A  A
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVIFKEVSSATNA 62

Query: 173 QEQLNGFELAGRPMKV 188
              + GF    +PM++
Sbjct: 63  LRSMQGFPFYDKPMRI 78

This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 89

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

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 6/65 (9%)

Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA------MGL 77
          LS     RDL E FS  G + DV ++   ++RR +G A++ F++ +    A      M L
Sbjct: 17 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 76

Query: 78 NGQKL 82
          +G+++
Sbjct: 77 DGRRI 81

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

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

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 1/67 (1%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-L 77
          +F   L+      DLE+ FS  G + +V L     T++ KG A++ +  PE    A   L
Sbjct: 5  LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 78 NGQKLLG 84
          +G    G
Sbjct: 65 DGTVFQG 71

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

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 2/76 (2%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLN 78
          +F   LS     +DL+++FS  G+V D  L     T R +G  ++ FK+ ESV   M   
Sbjct: 1  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 79 GQKLLGIPIIVQPTQA 94
            KL G   ++ P +A
Sbjct: 61 EHKLNG--KVIDPKRA 74

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

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

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 19/57 (33%), Positives = 25/57 (43%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
          T++   L +      L+  FS  G V  V L     T   KG A+IEF+ PE    A
Sbjct: 1  TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKA 57

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

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

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 9/58 (15%)

Query: 31 RDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPI 87
           DLEE FS  GK+  + L         KG  +++F + E    A+ G NG+++ G  +
Sbjct: 16 EDLEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVAGENGREIAGQKL 65

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

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

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 2/73 (2%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCN-KTRRFKGIAYIEFKDPESVPLAMG 76
          T +   L   +   D++EFF  +  V  VRL        R +G  Y EF+D +S+  A+ 
Sbjct: 3  TAYLGNLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALS 61

Query: 77 LNGQKLLGIPIIV 89
          LN + L    I V
Sbjct: 62 LNDESLKNRRIRV 74

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

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

 Score = 36.7 bits (85), Expect = 0.002
 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 3/73 (4%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           R+Y+G+L  ++ E  L  +F  +G+I +I+L    +      + F+ F    DA+ A   
Sbjct: 1   RIYVGNLPSDVREKDLEDLFYKYGRIRDIEL---KNRRGLVPFAFVRFEDPRDAEDAVFG 57

Query: 176 LNGFELAGRPMKV 188
            NG++     ++V
Sbjct: 58  RNGYDFGQCRLRV 70

This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 36.8 bits (85), Expect = 0.002
 Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 7/77 (9%)

Query: 117 LYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
           +YI +L+  + ++ L+     IF  FG+I +I  +    T + +G  F+ F     A  A
Sbjct: 2   IYINNLNEKVKKEELKKSLYAIFSQFGQILDIVAL---KTLKMRGQAFVVFKDISSATNA 58

Query: 173 QEQLNGFELAGRPMKVG 189
              + GF    +PM++ 
Sbjct: 59  LRSMQGFPFYDKPMRIA 75

This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. . Length = 78

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

 Score = 36.8 bits (85), Expect = 0.002
 Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 8/80 (10%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFG--KIDN------IQLMVDPDTGRSKGYGFITFHSADD 168
           +Y+  L+ N+T + L   F+  G  KI+       + +  D +TG+ KG   +++     
Sbjct: 3   IYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPPS 62

Query: 169 AKKAQEQLNGFELAGRPMKV 188
           AK A E  +G +  G  +KV
Sbjct: 63  AKAAVEWFDGKDFQGSKLKV 82

This subgroup corresponds to the RRM of EWS, also termed Ewing sarcoma breakpoint region 1 protein, a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multifunctional protein and may play roles in transcription and RNA processing. EWS is involved in transcriptional regulation by interacting with the preinitiation complex TFIID and the RNA polymerase II (RNAPII) complexes. It is also associated with splicing factors, such as the U1 snRNP protein U1C, suggesting its implication in pre-mRNA splicing. Additionally, EWS has been shown to regulate DNA damage-induced alternative splicing (AS). Like other members in the FET family, EWS contains an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. EWS specifically binds to poly G and poly U RNA. It also binds to the proximal-element DNA of the macrophage-specific promoter of the CSF-1 receptor gene. . Length = 84

>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 36.6 bits (84), Expect = 0.002
 Identities = 16/58 (27%), Positives = 34/58 (58%)

Query: 131 LRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
           L+ +F  +GK+   +++ +  +  ++ YGF+T  ++++A K    L+  EL GR + V
Sbjct: 18  LKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHLHRTELHGRMISV 75

This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1. Length = 76

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 18/85 (21%)

Query: 116 RLYIGSLHFNITEDMLRGIF-----------EPFGKIDNIQLMVDPDTGRSKGYGFITFH 164
           RLY+G+L   ITE+ L   F            P   + ++Q+         K + F+ F 
Sbjct: 3   RLYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQI------NPEKNFAFVEFR 56

Query: 165 SADDAKKAQEQLNGFELAGRPMKVG 189
           + ++A  A   L+G    G+P+K+ 
Sbjct: 57  TVEEATAAL-ALDGIIFKGQPLKIR 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|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in Saccharomyces cerevisiae protein Nrd1, Schizosaccharomyces pombe Rpb7-binding protein seb1 and similar proteins

 Score = 36.4 bits (84), Expect = 0.002
 Identities = 17/71 (23%), Positives = 34/71 (47%), Gaps = 6/71 (8%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L+ G + FN+ E  LR  F  FG++ +  L         K + F+  ++  DA+ A+E +
Sbjct: 6   LFPGGVTFNMIEYDLRSGFGRFGEVQSCIL------NNDKRHAFVKMYNRRDAENAREAM 59

Query: 177 NGFELAGRPMK 187
             ++     ++
Sbjct: 60  EQYKSGDMQLR 70

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|241193 cd12749, RRM4_RBM12, RNA recognition motif 4 in RNA-binding protein 12 (RBM12) and similar proteins

 Score = 36.4 bits (84), Expect = 0.002
 Identities = 24/82 (29%), Positives = 47/82 (57%), Gaps = 5/82 (6%)

Query: 118 YIGSLHFNITEDMLRGIFEPFGKIDN-IQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +I ++ ++IT+  +    E  G  +N +Q++VD + G+  G   + F S DDA+K+ E+L
Sbjct: 3   HISNIPYSITKKDILQFLEGIGVDENSVQVLVD-NNGQGLGQALVQFKSEDDARKS-ERL 60

Query: 177 NGFELAGRPMKVGTVT--DRNE 196
           +  +L GR + +  VT  +  +
Sbjct: 61  HRKKLNGRDVFLHLVTAEEMRD 82

This subgroup corresponds to the RRM4 of RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), which is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. The biological role of RBM12 remains unclear. . Length = 88

>gnl|CDD|240709 cd12263, RRM_ABT1_like, RNA recognition motif found in activator of basal transcription 1 (ABT1) and similar proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 16/79 (20%), Positives = 30/79 (37%), Gaps = 12/79 (15%)

Query: 118 YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGR----------SKGY--GFITFHS 165
           Y+  +   +    LR +   +G++  I L  +    R           K +  G++ F  
Sbjct: 4   YLSRIPPRMNPAKLRQLLSQYGEVGRIYLQPEDPAKRKRRKKKGGNKKKKFTEGWVEFED 63

Query: 166 ADDAKKAQEQLNGFELAGR 184
              AK+  E LN   + G+
Sbjct: 64  KKVAKRVAESLNNTPIGGK 82

This subfamily corresponds to the RRM of novel nuclear proteins termed ABT1 and its homologous counterpart, pre-rRNA-processing protein ESF2 (eighteen S factor 2), from yeast. ABT1 associates with the TATA-binding protein (TBP) and enhances basal transcription activity of class II promoters. Meanwhile, ABT1 could be a transcription cofactor that can bind to DNA in a sequence-independent manner. The yeast ABT1 homolog, ESF2, is a component of 90S preribosomes and 5' ETS-based RNPs. It is previously identified as a putative partner of the TATA-element binding protein. However, it is primarily localized to the nucleolus and physically associates with pre-rRNA processing factors. ESF2 may play a role in ribosome biogenesis. It is required for normal pre-rRNA processing, as well as for SSU processome assembly and function. Both ABT1 and ESF2 contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 98

>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 3/51 (5%)

Query: 126 ITEDMLRGIFEPFG--KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           +TE+ +R      G    D ++LM    TG S+G+ F+ F S ++A +  E
Sbjct: 14  VTEEDIRNALVSHGVEPKD-VRLMRRKTTGASRGFAFVEFMSLEEATRWME 63

This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 81

>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 7/62 (11%)

Query: 127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
           +ED LR IF  +G + +  ++V     + KG   + F S   A+ A E   G  L   P+
Sbjct: 17  SEDELRKIFSKYGDVSD--VVVSS---KKKGSAIVEFASKKAAEAAVENECG--LPSNPL 69

Query: 187 KV 188
            V
Sbjct: 70  LV 71

The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding. . Length = 74

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

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 4/58 (6%)

Query: 33 LEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIV 89
          L E FS +G ++  +LI  +    +   A++E+ D  S   A+  +NG+ +LG  I V
Sbjct: 15 LAELFSQIGPIKSCKLIREHGNDPY---AFVEYYDHRSAAAALQTMNGRLILGQEIKV 69

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

>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 7/67 (10%)

Query: 125 NITEDMLRGIFEPFG-KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG 183
            + E+ ++  FE  G  +  I+L  D           + F S  DA KA   LNG +  G
Sbjct: 11  TVNEEQIKAFFEKIGPDVRKIELFPD------HEGALVEFESPSDAGKASLSLNGSQFGG 64

Query: 184 RPMKVGT 190
           + +K+GT
Sbjct: 65  KTIKIGT 71

This subfamily corresponds to the RRM4 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 71

>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 15/54 (27%), Positives = 29/54 (53%), Gaps = 8/54 (14%)

Query: 135 FEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
           FEP+GK+ N+++         + + F+ + + +DA KA E  N  ++  R + V
Sbjct: 21  FEPYGKLVNVRI--------RRNFAFVQYETQEDATKALESTNMSKVLDRVISV 66

This subgroup corresponds to the RRM2 in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 70

>gnl|CDD|214637 smart00361, RRM_1, RNA recognition motif

 Score = 35.5 bits (82), Expect = 0.003
 Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 3/63 (4%)

Query: 128 EDMLRGIFEPFGKIDNIQLMVDPDTGR---SKGYGFITFHSADDAKKAQEQLNGFELAGR 184
           E  L+   E FG++  I  +   D G     +G  +ITF  ++DA +A   LNG    GR
Sbjct: 6   ERELKEEEEYFGEVGKINKIYIDDVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGR 65

Query: 185 PMK 187
            +K
Sbjct: 66  LVK 68

Length = 70

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 35.6 bits (82), Expect = 0.004
 Identities = 18/58 (31%), Positives = 35/58 (60%), Gaps = 1/58 (1%)

Query: 33 LEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIV 89
          LE+ FS  G++ +V ++   +T+R +G  ++ F++P+    AM  +NG+ + G  I V
Sbjct: 17 LEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDGRQIRV 74

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

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

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 19/73 (26%), Positives = 33/73 (45%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLN 78
          IF   L   +   + +E+FS  GKV D +L+  + T R +G  ++ F    +V       
Sbjct: 2  IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAG 61

Query: 79 GQKLLGIPIIVQP 91
            +L G  + V+ 
Sbjct: 62 MLELGGKQVEVKR 74

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 75

>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 15/48 (31%), Positives = 27/48 (56%)

Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
          LS +     L E+FS  G++++  ++    T+R +G  ++ F DP SV
Sbjct: 6  LSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASV 53

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

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

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 2/73 (2%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDP-ESVPLAMGL 77
          IF   L  ++  + L+E F   GKV    +   +K  + +G+  ++F+ P E+V      
Sbjct: 1  IFVANLDYKVGWKKLKEVFKLAGKVVRADIKE-DKEGKSRGMGVVQFEHPIEAVQAISMF 59

Query: 78 NGQKLLGIPIIVQ 90
          NGQ L   P+ V+
Sbjct: 60 NGQMLFDRPMRVK 72

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|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 3/51 (5%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDP 68
          T++   L   IR R++E+ F   G + D+ L       R  G A+IEF+D 
Sbjct: 1  TVYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDA 48

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 35.9 bits (82), Expect = 0.004
 Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 4/80 (5%)

Query: 14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF-KDPESVP 72
          RDA  ++   L + +  ++LE+ FS  G++   R++    T   +G+ +I F K  E+  
Sbjct: 1  RDA-NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEE 59

Query: 73 LAMGLNGQKLLGI--PIIVQ 90
             GLNGQK  G   PI V+
Sbjct: 60 AIKGLNGQKPSGAAEPITVK 79

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +Y+G++ +  T + L   F   G ++ + ++ D  +G  KG+ +I F   +  + A   L
Sbjct: 2   VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALA-L 60

Query: 177 NGFELAGRPMKV 188
           +     GR +KV
Sbjct: 61  DESLFRGRQIKV 72

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused in Ewing's sarcoma protein (FUS), TATA-binding protein-associated factor 15 (TAF15) and similar proteins

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 9/84 (10%)

Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRD--------VRLITCNKTRRFKGIAYIEFK 66
          D  TIF   L + +    + ++F  +G ++         + L T  +T + KG A + F 
Sbjct: 1  DNNTIFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 60

Query: 67 DPESVPLAMG-LNGQKLLGIPIIV 89
          DP S   A+   +G++  G PI V
Sbjct: 61 DPPSAKAAIDWFDGKEFSGNPIKV 84

This subgroup corresponds to the RRM of FUS and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed 75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS (Translocated in liposarcoma), is a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multi-functional protein and has been implicated in pre-mRNA splicing, chromosome stability, cell spreading, and transcription. FUS was originally identified in human myxoid and round cell liposarcomas as an oncogenic fusion with the stress-induced DNA-binding transcription factor CHOP (CCAAT enhancer-binding homologous protein) and later as hnRNP P2, a component of hnRNP H complex assembled on pre-mRNA. It can form ternary complexes with hnRNP A1 and hnRNP C1/C2. Additional research indicates that FUS binds preferentially to GGUG-containing RNAs. In the presence of Mg2+, it can bind both single- and double-stranded DNA (ssDNA/dsDNA) and promote ATP-independent annealing of complementary ssDNA and D-loop formation in superhelical dsDNA. FUS has been shown to be recruited by single stranded noncoding RNAs to the regulatory regions of target genes such as cyclin D1, where it represses transcription by disrupting complex formation. TAF15 (TAFII68), also termed TATA-binding protein-associated factor 2N (TAF2N), or RNA-binding protein 56 (RBP56), originally identified as a TAF in the general transcription initiation TFIID complex, is a novel RNA/ssDNA-binding protein with homology to the proto-oncoproteins FUS and EWS (also termed EWSR1), belonging to the FET family as well. TAF15 likely functions in RNA polymerase II (RNAP II) transcription by interacting with TFIID and subunits of RNAP II itself. TAF15 is also associated with U1 snRNA, chromatin and RNA, in a complex distinct from the Sm-containing U1 snRNP that functions in splicing. Like other members in the FET family, both FUS and TAF15 contain an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. . Length = 86

>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 16/58 (27%), Positives = 34/58 (58%)

Query: 131 LRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
           L+ +F  +GK+   +++ +  +  ++ +GF+T  S ++A K  + L+  EL GR + V
Sbjct: 16  LKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHLHRTELHGRVISV 73

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

>gnl|CDD|240882 cd12436, RRM1_2_MATR3_like, RNA recognition motif 1 and 2 in the matrin 3 family of nuclear proteins

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 8/64 (12%)

Query: 127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE--QLNGFELAGR 184
           TE  L  + EPFGK+D+   +       ++   FI   S +DA+      +     + G+
Sbjct: 14  TEAELLKLAEPFGKVDHYIFL------PNRNKAFIEMESPEDAQALVSFYKTYPLTIGGK 67

Query: 185 PMKV 188
            +KV
Sbjct: 68  SIKV 71

This subfamily corresponds to the RRM of the matrin 3 family of nuclear proteins consisting of Matrin 3 (MATR3), nuclear protein 220 (NP220) and similar proteins. MATR3 is a highly conserved inner nuclear matrix protein that has been implicated in various biological processes. NP220 is a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). Both, Matrin 3 and NP220, contain two RNA recognition motif (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Cys2-His2 zinc finger-like motif at the C-terminal region. . Length = 76

>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 35.8 bits (82), Expect = 0.004
 Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LYI +L  ++ E  L  + +PFG++ + +++ D  +G S+G GF    S +  +      
Sbjct: 3   LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVISHF 61

Query: 177 NG 178
           NG
Sbjct: 62  NG 63

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has 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. MSSP-1 contains 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 as well as induction of apoptosis. . Length = 85

>gnl|CDD|240993 cd12549, RRM_Set1B, RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B)

 Score = 35.8 bits (82), Expect = 0.004
 Identities = 15/70 (21%), Positives = 36/70 (51%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
           P ++    L+ NI E+ L  + + +G+++ ++++ +P   +  G   + F +   AK A 
Sbjct: 2   PKQVTFAKLNDNIRENFLTDMCKKYGEVEEVEILYNPKNKKHLGIAKVVFATVKGAKDAV 61

Query: 174 EQLNGFELAG 183
           + L+   + G
Sbjct: 62  QHLHNTSVMG 71

This subgroup corresponds to the RRM of Setd1B, also termed SET domain-containing protein 1B (Set1B), or lysine N-methyltransferase 2G, a ubiquitously expressed vertebrates histone methyltransferase that exhibits high homology to yeast Set1. Set1B is localized to euchromatic nuclear speckles and associates with a complex containing six human homologs of the yeast Set1/COMPASS complex, including CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). Set1B complex is a histone methyltransferase that produces trimethylated histone H3 at Lys4. Set1B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. . Length = 93

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

 Score = 35.5 bits (81), Expect = 0.004
 Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 3/65 (4%)

Query: 126 ITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNG--FELAG 183
           ++ ++L   F  FG ++   ++VD D GRS G G + F S   A+KA E+     F L  
Sbjct: 11  VSNELLEEAFSQFGPVERAVVIVD-DRGRSTGKGIVEFASKPAARKAFERCTEGVFLLTT 69

Query: 184 RPMKV 188
            P  V
Sbjct: 70  TPRPV 74

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

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 1/80 (1%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
          ++F   ++   R+ DL   F   G + DV +     TRR +G AY++F+D      A+  
Sbjct: 2  SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61

Query: 77 LNGQKLLGIPIIVQPTQAEK 96
          L+ + + G  I +Q  Q ++
Sbjct: 62 LDRKWICGRQIEIQFAQGDR 81

This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 35.8 bits (82), Expect = 0.004
 Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LYI +L  ++ E  L  + +PFG++ + +++ D  +G S+G GF    S +  +      
Sbjct: 3   LYISNLPLSMDEQELESMLKPFGQVISTRILRDA-SGTSRGVGFARMESTEKCEAIITHF 61

Query: 177 NG 178
           NG
Sbjct: 62  NG 63

This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has 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. MSSP-2 contains 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 as well as induction of apoptosis. . Length = 86

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	370
KOG0147|consensus	549		100.0
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
KOG0124|consensus	544		100.0
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.97
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.96
KOG0148|consensus	321		99.96
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.96
KOG0145|consensus	360		99.96
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.95
KOG0144|consensus	510		99.95
KOG0120|consensus	500		99.95
KOG0117|consensus	506		99.94
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.94
KOG0131|consensus	203		99.94
KOG0123|consensus	369		99.93
KOG0127|consensus	678		99.93
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.92
KOG0148|consensus	321		99.92
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.9
KOG0145|consensus	360		99.9
KOG0123|consensus	369		99.9
KOG0109|consensus	346		99.9
KOG0117|consensus	506		99.89
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.89
KOG0127|consensus	678		99.88
KOG0110|consensus	725		99.84
KOG4205|consensus	311		99.84
KOG0146|consensus	371		99.8
KOG0144|consensus	510		99.79
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.77
KOG4206|consensus	221		99.77
KOG0110|consensus	725		99.75
KOG1548|consensus	382		99.75
KOG0105|consensus	241		99.74
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.72
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.68
KOG4211|consensus	510		99.67
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.65
KOG0147|consensus	549		99.65
KOG4212|consensus	608		99.64
KOG1548|consensus	382		99.6
KOG0106|consensus	216		99.58
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.57
KOG0131|consensus	203		99.57
KOG1457|consensus	284		99.55
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.55
KOG1190|consensus	492		99.55
KOG0124|consensus	544		99.54
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.53
KOG0120|consensus	500		99.51
KOG0122|consensus	270		99.51
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.5
KOG0125|consensus	376		99.5
PLN03120	260	nucleic acid binding protein; Provisional	99.49
KOG0122|consensus	270		99.49
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.48
KOG0121|consensus	153		99.45
KOG0107|consensus	195		99.44
KOG0149|consensus	247		99.43
KOG0125|consensus	376		99.43
PLN03121	243	nucleic acid binding protein; Provisional	99.43
KOG1190|consensus	492		99.42
KOG0126|consensus	219		99.42
KOG0126|consensus	219		99.41
KOG0111|consensus	298		99.41
KOG0149|consensus	247		99.4
PLN03120	260	nucleic acid binding protein; Provisional	99.4
PLN03213	759	repressor of silencing 3; Provisional	99.4
KOG0107|consensus	195		99.38
KOG0113|consensus	335		99.37
KOG0121|consensus	153		99.37
KOG0109|consensus	346		99.36
smart00362	72	RRM_2 RNA recognition motif.	99.35
KOG0113|consensus	335		99.34
KOG4207|consensus	256		99.34
KOG0114|consensus	124		99.34
PLN03213	759	repressor of silencing 3; Provisional	99.33
smart00362	72	RRM_2 RNA recognition motif.	99.33
smart00360	71	RRM RNA recognition motif.	99.33
KOG0130|consensus	170		99.32
KOG0130|consensus	170		99.3
PLN03121	243	nucleic acid binding protein; Provisional	99.3
KOG0108|consensus	435		99.29
KOG4207|consensus	256		99.28
KOG1456|consensus	494		99.28
smart00360	71	RRM RNA recognition motif.	99.27
KOG0114|consensus	124		99.27
KOG0111|consensus	298		99.27
KOG0108|consensus	435		99.26
KOG1365|consensus	508		99.25
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.22
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.21
KOG4212|consensus	608		99.2
KOG4206|consensus	221		99.2
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.2
KOG4205|consensus	311		99.18
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.16
KOG0105|consensus	241		99.16
smart00361	70	RRM_1 RNA recognition motif.	99.16
KOG0129|consensus	520		99.15
KOG4454|consensus	267		99.1
KOG4210|consensus	285		99.08
KOG1456|consensus	494		99.06
smart00361	70	RRM_1 RNA recognition motif.	99.04
PF15519	73	RBM39linker: linker between RRM2 and RRM3 domains	99.02
KOG0128|consensus	881		99.01
KOG4208|consensus	214		99.01
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.99
KOG4211|consensus	510		98.98
KOG0415|consensus	479		98.96
KOG4208|consensus	214		98.91
KOG0415|consensus	479		98.88
KOG0153|consensus	377		98.86
KOG1365|consensus	508		98.85
KOG0112|consensus	975		98.79
KOG0226|consensus	290		98.76
KOG0146|consensus	371		98.71
KOG0132|consensus	894		98.7
KOG0153|consensus	377		98.69
KOG4660|consensus	549		98.66
KOG4661|consensus	940		98.65
KOG0132|consensus	894		98.63
KOG0533|consensus	243		98.63
KOG4307|consensus	944		98.59
KOG0116|consensus	419		98.57
KOG1457|consensus	284		98.56
KOG4209|consensus	231		98.51
KOG4661|consensus	940		98.36
KOG0226|consensus	290		98.36
KOG0128|consensus	881		98.35
KOG4676|consensus	479		98.35
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.34
KOG4209|consensus	231		98.33
KOG0116|consensus	419		98.33
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.31
KOG0533|consensus	243		98.31
KOG4454|consensus	267		98.31
KOG4660|consensus	549		98.24
KOG0151|consensus	877		98.09
KOG2193|consensus	584		98.02
KOG0106|consensus	216		98.01
KOG0151|consensus	877		98.01
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.82
KOG1995|consensus	351		97.77
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.72
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.56
KOG1995|consensus	351		97.49
KOG4676|consensus	479		97.36
KOG4307|consensus	944		97.35
KOG4849|consensus	498		97.3
KOG4210|consensus	285		97.29
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.23
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.22
KOG1996|consensus	378		97.22
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.21
KOG2314|consensus	698		97.21
KOG3152|consensus	278		97.15
KOG1855|consensus	484		96.94
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.88
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.87
KOG0115|consensus	275		96.82
KOG0129|consensus	520		96.74
KOG3152|consensus	278		96.64
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.63
KOG1996|consensus	378		96.59
KOG2314|consensus	698		96.55
KOG4849|consensus	498		96.44
KOG1855|consensus	484		96.44
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.34
KOG0112|consensus	975		96.07
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.05
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.04
KOG2416|consensus	718		96.0
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	95.93
KOG2193|consensus	584		95.77
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.55
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.39
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.05
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.81
KOG2202|consensus	260		94.8
KOG0804|consensus	493		94.47
KOG2416|consensus	718		94.22
KOG2202|consensus	260		93.89
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	93.41
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	93.29
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	92.83
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	92.73
KOG0115|consensus	275		91.97
KOG2135|consensus	526		91.46
KOG4285|consensus	350		91.39
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	91.36
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	90.5
KOG2253|consensus	668		89.02
KOG2068|consensus	327		88.64
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	88.59
KOG4574|consensus	1007		88.48
KOG2591|consensus	684		87.83
KOG2068|consensus	327		87.73
KOG2135|consensus	526		85.74
KOG0804|consensus	493		83.52
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	82.19
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	81.73
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	81.58
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	80.16
KOG2318|consensus	650		80.08

>KOG0147|consensus

Probab=100.00  E-value=2.6e-45  Score=347.21  Aligned_cols=308  Identities=62%  Similarity=0.974  Sum_probs=260.0

Q ss_pred             CCCCCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCC
Q psy2983           5 YSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLG   84 (370)
Q Consensus         5 ~~~~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g   84 (370)
                      .+..+.+.+|+.||||+..|+..++..+|.+||+.+|+|.+|+++.|+.+++++|.|||||.+.+.+..|+.|.|+.+.|
T Consensus       168 ~~~~l~~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg  247 (549)
T KOG0147|consen  168 ASRILSPEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLG  247 (549)
T ss_pred             ccccCCchHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccC
Confidence            34667788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEecccccccccCCCCCCCCCCCCCCCce-EEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEE
Q psy2983          85 IPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITF  163 (370)
Q Consensus        85 ~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~-l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f  163 (370)
                      .+|.|+.+..++++.....+.........+.. ||||||.+++++++|+.+|++||.|..|.+++|.++|.++||||++|
T Consensus       248 ~pv~vq~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f  327 (549)
T KOG0147|consen  248 VPVIVQLSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITF  327 (549)
T ss_pred             ceeEecccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEE
Confidence            99999999999888655555445444444444 99999999999999999999999999999999988999999999999


Q ss_pred             CCHHHHHHHHHHhCCceeCCeeEEEEEeecCCCCcCCCCCCCCHHHHHHhcccCCceeeeeeeeccccCCCCCChHHHHH
Q psy2983         164 HSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPAAAS  243 (370)
Q Consensus       164 ~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~~~~~~~~~~~~a~~  243 (370)
                      .+.++|.+|+..|||.++.|+.|+|.....+...........+.+.....+..+|..+..|+|.++..+.+.+.+..+..
T Consensus       328 ~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~  407 (549)
T KOG0147|consen  328 VNKEDARKALEQLNGFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAIS  407 (549)
T ss_pred             ecHHHHHHHHHHhccceecCceEEEEEeeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhh
Confidence            99999999999999999999999999988776654333344445555667778888888999999999999888877766


Q ss_pred             HHhhhcccccCC---------CCCCCCCCCCCCCCCceEEeecCCCCCCCCCchhhHHhHHHHHHHHhhcCceeeEEEEE
Q psy2983         244 ALNLAQNAILNS---------STPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHGVGASTVCFI  314 (370)
Q Consensus       244 a~~~~~~~~~~p---------~~~~~~~~~~~~~ps~vl~L~Nm~~~~~l~~d~~~~ei~eDv~~Ec~kyG~~~~~~~~~  314 (370)
                      ++.+........         ...++...+....||+|++|.|||||.+++.+.|..||+|||.|||.|||.    +|.|
T Consensus       408 ~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~----v~hi  483 (549)
T KOG0147|consen  408 ALLLLAKLASAAQFNGVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGK----VCHI  483 (549)
T ss_pred             HHHhccccchHHhhcCCcCccccCccccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCC----eeEE
Confidence            665432211111         111111123334899999999999999999999999999999999999996    5777


Q ss_pred             EE
Q psy2983         315 YS  316 (370)
Q Consensus       315 y~  316 (370)
                      ||
T Consensus       484 ~v  485 (549)
T KOG0147|consen  484 FV  485 (549)
T ss_pred             EE
Confidence            76

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

Probab=100.00  E-value=1.1e-42  Score=345.72  Aligned_cols=301  Identities=49%  Similarity=0.747  Sum_probs=213.4

Q ss_pred             CCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEE
Q psy2983           9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPII   88 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~   88 (370)
                      .++.+++.++|||+|||..+++++|+++|+.||.|.+|.+++|+.+++++|||||+|.+.++|.+|++++|..+.|++|.
T Consensus        82 ~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~  161 (457)
T TIGR01622        82 LTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPII  161 (457)
T ss_pred             cCccccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeE
Confidence            34567789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHH
Q psy2983          89 VQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADD  168 (370)
Q Consensus        89 v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~  168 (370)
                      |+.+..+............ .......+|||+|||..+++++|+++|++||.|..+.++.+..+|.++|||||+|.+.++
T Consensus       162 v~~~~~~~~~~~~~~~~~~-~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~  240 (457)
T TIGR01622       162 VQSSQAEKNRAAKAATHQP-GDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEE  240 (457)
T ss_pred             EeecchhhhhhhhcccccC-CCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHH
Confidence            9987655443322111111 111236899999999999999999999999999999999999889999999999999999


Q ss_pred             HHHHHHHhCCceeCCeeEEEEEeecCCCCcCCCCCCCCHHHHHHhcccCCceeeeeeeeccccCC---CCCChHHHHHHH
Q psy2983         169 AKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGT---GLELPPAAASAL  245 (370)
Q Consensus       169 a~~A~~~l~g~~i~g~~l~V~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~~~~~---~~~~~~~a~~a~  245 (370)
                      |.+|+..|+|..+.|++|+|.++.+...............................++..+....   +...++....+.
T Consensus       241 A~~A~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  320 (457)
T TIGR01622       241 AKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIA  320 (457)
T ss_pred             HHHHHHhcCCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhh
Confidence            99999999999999999999998643222111000000000000000001111111111111111   111111111111


Q ss_pred             hhhcc---c--------------ccCCCCCCCCCCCCCCCCCceEEeecCCCCCCCCCchhhHHhHHHHHHHHhhcCcee
Q psy2983         246 NLAQN---A--------------ILNSSTPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHGVGA  308 (370)
Q Consensus       246 ~~~~~---~--------------~~~p~~~~~~~~~~~~~ps~vl~L~Nm~~~~~l~~d~~~~ei~eDv~~Ec~kyG~~~  308 (370)
                      .|...   .              .+....+...+....+.+++||+|.|||++.++.++.||+||++||++||++||.+.
T Consensus       321 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~  400 (457)
T TIGR01622       321 LMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVV  400 (457)
T ss_pred             hhccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCee
Confidence            11100   0              000001111112224578999999999999999999999999999999999999875


Q ss_pred             eE
Q psy2983         309 ST  310 (370)
Q Consensus       309 ~~  310 (370)
                      .+
T Consensus       401 ~v  402 (457)
T TIGR01622       401 HI  402 (457)
T ss_pred             EE
Confidence            43

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.

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

Probab=100.00  E-value=7.7e-40  Score=324.95  Aligned_cols=182  Identities=25%  Similarity=0.446  Sum_probs=158.7

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      .....++|||+|||.++++++|+++|+.||+|.+|++++|+.+++++|||||+|.+.++|.+|++ ++|..+.|++|+|.
T Consensus       103 a~~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~  182 (612)
T TIGR01645       103 ALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG  182 (612)
T ss_pred             hhcCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeec
Confidence            34567899999999999999999999999999999999999999999999999999999999995 99999999999998


Q ss_pred             cccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHH
Q psy2983          91 PTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAK  170 (370)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~  170 (370)
                      ++........  ............++|||+|||+++++++|+++|+.||.|.++++.+++.+|+++|||||+|.+.++|.
T Consensus       183 rp~~~p~a~~--~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~  260 (612)
T TIGR01645       183 RPSNMPQAQP--IIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQS  260 (612)
T ss_pred             cccccccccc--ccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHH
Confidence            7543221110  00011111234578999999999999999999999999999999999989999999999999999999


Q ss_pred             HHHHHhCCceeCCeeEEEEEeecCC
Q psy2983         171 KAQEQLNGFELAGRPMKVGTVTDRN  195 (370)
Q Consensus       171 ~A~~~l~g~~i~g~~l~V~~~~~~~  195 (370)
                      +|+..||+..++|+.|+|.++..+.
T Consensus       261 kAI~amNg~elgGr~LrV~kAi~pP  285 (612)
T TIGR01645       261 EAIASMNLFDLGGQYLRVGKCVTPP  285 (612)
T ss_pred             HHHHHhCCCeeCCeEEEEEecCCCc
Confidence            9999999999999999999987543

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.

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

Probab=100.00  E-value=9.2e-37  Score=307.18  Aligned_cols=255  Identities=22%  Similarity=0.314  Sum_probs=193.4

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcC------------CCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhc
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSV------------GKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGL   77 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~------------G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l   77 (370)
                      ++.++..|+|||+|||+.+|+++|+++|+.+            +.|..+.+      ++.+|||||+|.+.++|..||+|
T Consensus       169 ~~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al~l  242 (509)
T TIGR01642       169 QQATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAMAL  242 (509)
T ss_pred             ccCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhhcC
Confidence            4567889999999999999999999999974            34555544      34589999999999999999999


Q ss_pred             cCCccCCeeEEEecccccccccCCC------CC----------CCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCce
Q psy2983          78 NGQKLLGIPIIVQPTQAEKNRAGNT------LP----------NLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKI  141 (370)
Q Consensus        78 ~g~~i~g~~l~v~~~~~~~~~~~~~------~~----------~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i  141 (370)
                      +|..|.|++|+|.++..........      .+          ..........++|||+|||..+++++|+++|+.||.|
T Consensus       243 ~g~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i  322 (509)
T TIGR01642       243 DSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDL  322 (509)
T ss_pred             CCeEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCe
Confidence            9999999999998765433111000      00          0011123345799999999999999999999999999


Q ss_pred             eeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecCCCCcCCCCCCCCHHHHHHhcccCCcee
Q psy2983         142 DNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATG  221 (370)
Q Consensus       142 ~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  221 (370)
                      ..+.++++..+|.++|||||+|.+.++|..|+..|+|..|+|+.|.|.++........     .+...      ....+.
T Consensus       323 ~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~-----~~~~~------~~~~~~  391 (509)
T TIGR01642       323 KAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQAT-----IDTSN------GMAPVT  391 (509)
T ss_pred             eEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCC-----ccccc------cccccc
Confidence            9999999988999999999999999999999999999999999999999764332211     00000      000000


Q ss_pred             eeeeeeccccCCCCCChHHHHHHHhhhcccccCCCCCCCCCCCCCCCCCceEEeecCCCCCCCCCchhhHHhHHHHHHHH
Q psy2983         222 RLQLMFKLAEGTGLELPPAAASALNLAQNAILNSSTPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEEC  301 (370)
Q Consensus       222 ~~~l~~~~~~~~~~~~~~~a~~a~~~~~~~~~~p~~~~~~~~~~~~~ps~vl~L~Nm~~~~~l~~d~~~~ei~eDv~~Ec  301 (370)
                         ..                           .+...+.. ......|++||+|.||+++++|.+|++|++|.+||++||
T Consensus       392 ---~~---------------------------~~~~~~~~-~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f  440 (509)
T TIGR01642       392 ---LL---------------------------AKALSQSI-LQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEF  440 (509)
T ss_pred             ---cc---------------------------cccchhhh-ccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHH
Confidence               00                           00000000 012345799999999999999999999999999999999


Q ss_pred             hhcCceeeEEE
Q psy2983         302 NKHGVGASTVC  312 (370)
Q Consensus       302 ~kyG~~~~~~~  312 (370)
                      ++||.+..+.+
T Consensus       441 ~~~G~v~~v~i  451 (509)
T TIGR01642       441 SKYGPLINIVI  451 (509)
T ss_pred             HhcCCeeEEEe
Confidence            99999776544

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

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

Probab=100.00  E-value=3.5e-33  Score=284.12  Aligned_cols=274  Identities=23%  Similarity=0.349  Sum_probs=217.2

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecccccc
Q psy2983          18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQAEK   96 (370)
Q Consensus        18 ~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~~~   96 (370)
                      +|||+|||.++||++|+++|++||+|.+|++.+|..+++++|||||+|.+.++|.+|++ +++..+.|++|+|.++....
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            69999999999999999999999999999999999999999999999999999999995 99999999999999876432


Q ss_pred             cccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHh
Q psy2983          97 NRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL  176 (370)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l  176 (370)
                      ...           ..+..+|||+|||.++++++|+++|+.||.|.+|++..+. +|+++|||||+|.+.++|.+|++.|
T Consensus        82 ~~~-----------~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~-~g~skg~afV~F~~~e~A~~Ai~~l  149 (562)
T TIGR01628        82 SLR-----------RSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKV  149 (562)
T ss_pred             ccc-----------ccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC-CCCcccEEEEEECCHHHHHHHHHHh
Confidence            111           1223579999999999999999999999999999999885 8999999999999999999999999


Q ss_pred             CCceeCCeeEEEEEeecCCC------------CcCCCCCCCCHHHHHHhcccCCceeeeeeeecc---ccCCC---CCCh
Q psy2983         177 NGFELAGRPMKVGTVTDRNE------------SVGGGPSNLDTDEMERAGVDLGATGRLQLMFKL---AEGTG---LELP  238 (370)
Q Consensus       177 ~g~~i~g~~l~V~~~~~~~~------------~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~---~~~~~---~~~~  238 (370)
                      +|..+.|+.|.|.....+..            .+++++..++++++++.|..||.+.++.++.+.   .+|++   |..+
T Consensus       150 ng~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~  229 (562)
T TIGR01628       150 NGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKH  229 (562)
T ss_pred             cccEecCceEEEeccccccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCH
Confidence            99999999999976543222            257889999999999999999999999998763   23444   5677


Q ss_pred             HHHHHHHh-hhccccc----CCCCC----CCC---------------CCCCCCCCCceEEeecCCCCCCCCCchhhHHhH
Q psy2983         239 PAAASALN-LAQNAIL----NSSTP----QVS---------------SSTAPPIATQCFLLANMFDPATETNPTWDVEIR  294 (370)
Q Consensus       239 ~~a~~a~~-~~~~~~~----~p~~~----~~~---------------~~~~~~~ps~vl~L~Nm~~~~~l~~d~~~~ei~  294 (370)
                      ..|..|+. +.+....    .....    +..               ........+..|.+.|+  +.+++        .
T Consensus       230 e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl--~~~~~--------~  299 (562)
T TIGR01628       230 EDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNL--DDTVT--------D  299 (562)
T ss_pred             HHHHHHHHHhCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCC--CCccC--------H
Confidence            77777765 2222211    00000    000               00011234566888888  22222        3


Q ss_pred             HHHHHHHhhcCceeeEEEE
Q psy2983         295 DDVIEECNKHGVGASTVCF  313 (370)
Q Consensus       295 eDv~~Ec~kyG~~~~~~~~  313 (370)
                      +|+++.|++||.+....++
T Consensus       300 ~~L~~~F~~~G~i~~~~i~  318 (562)
T TIGR01628       300 EKLRELFSECGEITSAKVM  318 (562)
T ss_pred             HHHHHHHHhcCCeEEEEEE
Confidence            6788999999998665543

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=4e-33  Score=268.03  Aligned_cols=219  Identities=26%  Similarity=0.410  Sum_probs=191.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      +..+|||+|||.++++++|+++|+.||+|.+|+|++|+.+|+++|||||+|.+.++|.+|++ |+|..+.|++|.|.++.
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            46789999999999999999999999999999999999999999999999999999999995 99999999999998875


Q ss_pred             ccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHH
Q psy2983          94 AEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ  173 (370)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~  173 (370)
                      ....             .....+|||+|||..+++++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|..|+
T Consensus        82 ~~~~-------------~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai  148 (352)
T TIGR01661        82 PSSD-------------SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAI  148 (352)
T ss_pred             cccc-------------ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHH
Confidence            4321             112357999999999999999999999999999999998878999999999999999999999


Q ss_pred             HHhCCceeCC--eeEEEEEeecCC--------------------------------------------------------
Q psy2983         174 EQLNGFELAG--RPMKVGTVTDRN--------------------------------------------------------  195 (370)
Q Consensus       174 ~~l~g~~i~g--~~l~V~~~~~~~--------------------------------------------------------  195 (370)
                      +.|||..+.|  ++|.|.++..+.                                                        
T Consensus       149 ~~l~g~~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  228 (352)
T TIGR01661       149 KTLNGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAH  228 (352)
T ss_pred             HHhCCCccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhh
Confidence            9999999876  677887764221                                                        


Q ss_pred             -------------------------------------------CCcCCCCCCCCHHHHHHhcccCCceeeeeeeecc---
Q psy2983         196 -------------------------------------------ESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKL---  229 (370)
Q Consensus       196 -------------------------------------------~~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~---  229 (370)
                                                                 ..+++++..+++++|...|..||.+.++.++.+.   
T Consensus       229 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~  308 (352)
T TIGR01661       229 QQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTN  308 (352)
T ss_pred             hhhhcccccccccccCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCC
Confidence                                                       2245677889999999999999999999999774   


Q ss_pred             -ccCCC---CCChHHHHHHHh
Q psy2983         230 -AEGTG---LELPPAAASALN  246 (370)
Q Consensus       230 -~~~~~---~~~~~~a~~a~~  246 (370)
                       ++|+|   |..+.+|..|+.
T Consensus       309 ~skG~aFV~F~~~~~A~~Ai~  329 (352)
T TIGR01661       309 QCKGYGFVSMTNYDEAAMAIL  329 (352)
T ss_pred             CccceEEEEECCHHHHHHHHH
Confidence             55666   567777777765

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

>KOG0124|consensus

Probab=100.00  E-value=3.6e-34  Score=258.33  Aligned_cols=178  Identities=26%  Similarity=0.479  Sum_probs=155.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccccc
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQAE   95 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~~   95 (370)
                      ++||||.+.+.+.|+.|+..|.+||+|.+|.+.+|+.|+++||||||||+-+|.|..|++ +||..+.||.|+|.++..-
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNm  193 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM  193 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCC
Confidence            689999999999999999999999999999999999999999999999999999999996 9999999999999876532


Q ss_pred             ccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHH
Q psy2983          96 KNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ  175 (370)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~  175 (370)
                      ....  ...+.........++|||..+.++++++||+.+|+.||+|.+|.+-+++..+.++||+|++|.+..+...|+..
T Consensus       194 pQAQ--piID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAias  271 (544)
T KOG0124|consen  194 PQAQ--PIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS  271 (544)
T ss_pred             cccc--hHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhh
Confidence            1100  00000111122347899999999999999999999999999999999998899999999999999999999999


Q ss_pred             hCCceeCCeeEEEEEeecCCC
Q psy2983         176 LNGFELAGRPMKVGTVTDRNE  196 (370)
Q Consensus       176 l~g~~i~g~~l~V~~~~~~~~  196 (370)
                      ||=+.++|+-|+|..+..+..
T Consensus       272 MNlFDLGGQyLRVGk~vTPP~  292 (544)
T KOG0124|consen  272 MNLFDLGGQYLRVGKCVTPPD  292 (544)
T ss_pred             cchhhcccceEecccccCCCc
Confidence            999999999999998755433

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=9.9e-32  Score=254.49  Aligned_cols=172  Identities=24%  Similarity=0.408  Sum_probs=156.0

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      .....++|||+|||.++|+++|+++|+.||+|.+|+|++|..+++++|||||+|.++++|.+|++ |++..+.+++|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            44567899999999999999999999999999999999999999999999999999999999995 99999999999998


Q ss_pred             cccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHH
Q psy2983          91 PTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAK  170 (370)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~  170 (370)
                      ++.....             .....+|||+|||..+++++|+++|++||.|..++++.++.+|+++|||||+|.+.++|.
T Consensus       183 ~a~p~~~-------------~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~  249 (346)
T TIGR01659       183 YARPGGE-------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQ  249 (346)
T ss_pred             ccccccc-------------ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHH
Confidence            8754321             112357999999999999999999999999999999999889999999999999999999


Q ss_pred             HHHHHhCCceeCC--eeEEEEEeecCCC
Q psy2983         171 KAQEQLNGFELAG--RPMKVGTVTDRNE  196 (370)
Q Consensus       171 ~A~~~l~g~~i~g--~~l~V~~~~~~~~  196 (370)
                      +|++.||+..+.+  ++|+|.++.....
T Consensus       250 ~Ai~~lng~~~~g~~~~l~V~~a~~~~~  277 (346)
T TIGR01659       250 EAISALNNVIPEGGSQPLTVRLAEEHGK  277 (346)
T ss_pred             HHHHHhCCCccCCCceeEEEEECCcccc
Confidence            9999999998875  7899998876543

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).

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

Probab=99.97  E-value=1.2e-28  Score=245.56  Aligned_cols=220  Identities=22%  Similarity=0.310  Sum_probs=175.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh---ccCCccCCeeEEEec
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG---LNGQKLLGIPIIVQP   91 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~---l~g~~i~g~~l~v~~   91 (370)
                      ++|+|||+|||.++++++|+++|++||+|.++.++++      +|||||+|.+.++|.+|++   +++..+.|++|+|++
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~   74 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNY   74 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEe
Confidence            5799999999999999999999999999999998853      6899999999999999996   588999999999999


Q ss_pred             ccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHH
Q psy2983          92 TQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK  171 (370)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~  171 (370)
                      +.......... ............+|||+||++.+++++|+++|++||.|.+|.++++..    .|+|||+|.+.++|.+
T Consensus        75 s~~~~~~~~~~-~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~----~~~afVef~~~~~A~~  149 (481)
T TIGR01649        75 STSQEIKRDGN-SDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNN----VFQALVEFESVNSAQH  149 (481)
T ss_pred             cCCcccccCCC-CcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCC----ceEEEEEECCHHHHHH
Confidence            86543211110 000111122345799999999999999999999999999999987632    4789999999999999


Q ss_pred             HHHHhCCceeCC--eeEEEEEeecCCC-----------------------------------------------------
Q psy2983         172 AQEQLNGFELAG--RPMKVGTVTDRNE-----------------------------------------------------  196 (370)
Q Consensus       172 A~~~l~g~~i~g--~~l~V~~~~~~~~-----------------------------------------------------  196 (370)
                      |++.|||..+.|  ..|+|.+++....                                                     
T Consensus       150 A~~~Lng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  229 (481)
T TIGR01649       150 AKAALNGADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHG  229 (481)
T ss_pred             HHHHhcCCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCC
Confidence            999999999975  4777777542110                                                     


Q ss_pred             -------------------------------------------------CcCCCCC-CCCHHHHHHhcccCCceeeeeee
Q psy2983         197 -------------------------------------------------SVGGGPS-NLDTDEMERAGVDLGATGRLQLM  226 (370)
Q Consensus       197 -------------------------------------------------~~~~~~~-~~~~~~l~~~~~~~g~~~~~~l~  226 (370)
                                                                       .+++++. .++++.|...|..||.+.++.++
T Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~  309 (481)
T TIGR01649       230 GPLAPLAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFM  309 (481)
T ss_pred             CCCCcccccccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEE
Confidence                                                             0123444 58899999999999999999998


Q ss_pred             eccccCCC---CCChHHHHHHHh
Q psy2983         227 FKLAEGTG---LELPPAAASALN  246 (370)
Q Consensus       227 ~~~~~~~~---~~~~~~a~~a~~  246 (370)
                      .. .++++   |..+.+|..|+.
T Consensus       310 ~~-~~g~afV~f~~~~~A~~Ai~  331 (481)
T TIGR01649       310 KN-KKETALIEMADPYQAQLALT  331 (481)
T ss_pred             eC-CCCEEEEEECCHHHHHHHHH
Confidence            76 34666   667888888875

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

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

Probab=99.96  E-value=8e-29  Score=252.16  Aligned_cols=222  Identities=25%  Similarity=0.437  Sum_probs=190.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      ..++|||+|||.++++++|+++|+.||.|.++++..+. +++++|||||+|.+.++|.+|++ ++|..+.|+.|.|....
T Consensus        87 ~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~-~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~  165 (562)
T TIGR01628        87 GVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFI  165 (562)
T ss_pred             CCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC-CCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEeccc
Confidence            45689999999999999999999999999999999875 57889999999999999999995 99999999999997655


Q ss_pred             ccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHH
Q psy2983          94 AEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ  173 (370)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~  173 (370)
                      ....+.        .......++|||+|||.++++++|+++|+.||.|.++.+..+. +|.++|||||+|.+.++|.+|+
T Consensus       166 ~~~~~~--------~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~-~g~~~G~afV~F~~~e~A~~Av  236 (562)
T TIGR01628       166 KKHERE--------AAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAV  236 (562)
T ss_pred             cccccc--------cccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHH
Confidence            433221        1112334679999999999999999999999999999999985 7999999999999999999999


Q ss_pred             HHhCCceeC----CeeEEEEEeecCC-------------------------CCcCCCCCCCCHHHHHHhcccCCceeeee
Q psy2983         174 EQLNGFELA----GRPMKVGTVTDRN-------------------------ESVGGGPSNLDTDEMERAGVDLGATGRLQ  224 (370)
Q Consensus       174 ~~l~g~~i~----g~~l~V~~~~~~~-------------------------~~~~~~~~~~~~~~l~~~~~~~g~~~~~~  224 (370)
                      +.|+|..+.    |+.+.|.++..+.                         ..+++++..+++++|++.|..||.+.++.
T Consensus       237 ~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~  316 (562)
T TIGR01628       237 EEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAK  316 (562)
T ss_pred             HHhCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEE
Confidence            999999999    9999998764332                         22668899999999999999999999999


Q ss_pred             eeecc---ccCCC---CCChHHHHHHHh
Q psy2983         225 LMFKL---AEGTG---LELPPAAASALN  246 (370)
Q Consensus       225 l~~~~---~~~~~---~~~~~~a~~a~~  246 (370)
                      ++.+.   +++++   |..++.|..|+.
T Consensus       317 i~~d~~g~~~g~gfV~f~~~~~A~~A~~  344 (562)
T TIGR01628       317 VMLDEKGVSRGFGFVCFSNPEEANRAVT  344 (562)
T ss_pred             EEECCCCCcCCeEEEEeCCHHHHHHHHH
Confidence            99873   34555   567777766654

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

>KOG0148|consensus

Probab=99.96  E-value=5.6e-29  Score=217.04  Aligned_cols=179  Identities=25%  Similarity=0.456  Sum_probs=157.1

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      .+..-.|||+.|.+.++.++|++.|.+||+|.+.++++|..|+++|||+||.|.+.++|++|++ ++|+-|.+|.|+-.|
T Consensus        59 ~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNW  138 (321)
T KOG0148|consen   59 SNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNW  138 (321)
T ss_pred             cccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccc
Confidence            3445679999999999999999999999999999999999999999999999999999999995 999999999999999


Q ss_pred             ccccccccCC---CCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHH
Q psy2983          92 TQAEKNRAGN---TLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADD  168 (370)
Q Consensus        92 ~~~~~~~~~~---~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~  168 (370)
                      +..+......   .....-......+++||+||++..+++++|++.|++||+|.+|++.++      +|||||.|.+.|+
T Consensus       139 ATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEa  212 (321)
T KOG0148|consen  139 ATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEA  212 (321)
T ss_pred             cccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhh
Confidence            8755422211   111222334556789999999999999999999999999999999998      7899999999999


Q ss_pred             HHHHHHHhCCceeCCeeEEEEEeecCCCC
Q psy2983         169 AKKAQEQLNGFELAGRPMKVGTVTDRNES  197 (370)
Q Consensus       169 a~~A~~~l~g~~i~g~~l~V~~~~~~~~~  197 (370)
                      |..||..+||.++.|+.+++.|.+.....
T Consensus       213 AahAIv~mNntei~G~~VkCsWGKe~~~~  241 (321)
T KOG0148|consen  213 AAHAIVQMNNTEIGGQLVRCSWGKEGDDG  241 (321)
T ss_pred             HHHHHHHhcCceeCceEEEEeccccCCCC
Confidence            99999999999999999999998765443

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.96  E-value=1.5e-28  Score=236.32  Aligned_cols=181  Identities=26%  Similarity=0.478  Sum_probs=152.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCC--eeEEEec
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLG--IPIIVQP   91 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g--~~l~v~~   91 (370)
                      ..++|||+|||..+++++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|..|++ |+|..+.|  .+|.|.+
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            46789999999999999999999999999999999998889999999999999999999995 99999877  5677776


Q ss_pred             ccccccccCCC--------------C------------------------------------------------CCC---
Q psy2983          92 TQAEKNRAGNT--------------L------------------------------------------------PNL---  106 (370)
Q Consensus        92 ~~~~~~~~~~~--------------~------------------------------------------------~~~---  106 (370)
                      +..........              .                                                ...   
T Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (352)
T TIGR01661       168 ANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPP  247 (352)
T ss_pred             CCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCc
Confidence            54322000000              0                                                000   


Q ss_pred             --------------CCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHH
Q psy2983         107 --------------QPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA  172 (370)
Q Consensus       107 --------------~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A  172 (370)
                                    .+.....+.+|||+|||+.+++++|+++|++||.|.++++++|+.+|.++|||||+|.+.++|.+|
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                          000011234699999999999999999999999999999999998999999999999999999999


Q ss_pred             HHHhCCceeCCeeEEEEEeecCC
Q psy2983         173 QEQLNGFELAGRPMKVGTVTDRN  195 (370)
Q Consensus       173 ~~~l~g~~i~g~~l~V~~~~~~~  195 (370)
                      +..|||..+.|+.|+|.+...+.
T Consensus       328 i~~lnG~~~~gr~i~V~~~~~~~  350 (352)
T TIGR01661       328 ILSLNGYTLGNRVLQVSFKTNKA  350 (352)
T ss_pred             HHHhCCCEECCeEEEEEEccCCC
Confidence            99999999999999999987654

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

>KOG0145|consensus

Probab=99.96  E-value=6.8e-28  Score=209.00  Aligned_cols=208  Identities=25%  Similarity=0.428  Sum_probs=182.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecccc
Q psy2983          16 ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQA   94 (370)
Q Consensus        16 ~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~   94 (370)
                      ...|.|.-||..+|+++++.+|...|+|++++++||+.+|.+-||+||.|.+++||++|+. |+|..+..+.|+|.++++
T Consensus        41 kTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARP  120 (360)
T KOG0145|consen   41 KTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARP  120 (360)
T ss_pred             cceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccC
Confidence            3459999999999999999999999999999999999999999999999999999999995 999999999999999876


Q ss_pred             cccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHH
Q psy2983          95 EKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE  174 (370)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~  174 (370)
                      ......             ...|||++||..+|..+|.++|++||.|..-+++.|.-+|.++|.+||.|....+|+.|+.
T Consensus       121 Ss~~Ik-------------~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk  187 (360)
T KOG0145|consen  121 SSDSIK-------------DANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIK  187 (360)
T ss_pred             Chhhhc-------------ccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHH
Confidence            543322             3469999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhCCceeCC--eeEEEEEeecCCCC-------------------------------------------------------
Q psy2983         175 QLNGFELAG--RPMKVGTVTDRNES-------------------------------------------------------  197 (370)
Q Consensus       175 ~l~g~~i~g--~~l~V~~~~~~~~~-------------------------------------------------------  197 (370)
                      .|||+.=.|  .+|.|+++..+...                                                       
T Consensus       188 ~lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~  267 (360)
T KOG0145|consen  188 GLNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLA  267 (360)
T ss_pred             hccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceee
Confidence            999987654  58899887533221                                                       


Q ss_pred             ---------------cCCCCCCCCHHHHHHhcccCCceeeeeeeeccc----cCCCCC
Q psy2983         198 ---------------VGGGPSNLDTDEMERAGVDLGATGRLQLMFKLA----EGTGLE  236 (370)
Q Consensus       198 ---------------~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~~----~~~~~~  236 (370)
                                     +-++.++.++.-|.+.|.+||.+.++++.+++.    .|+||.
T Consensus       268 ~~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFV  325 (360)
T KOG0145|consen  268 GVNLPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFV  325 (360)
T ss_pred             eeccCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEE
Confidence                           113556778888999999999999999999854    467754

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

Probab=99.95  E-value=3e-27  Score=235.02  Aligned_cols=208  Identities=18%  Similarity=0.298  Sum_probs=174.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccC-CeeEEEecc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLL-GIPIIVQPT   92 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~-g~~l~v~~~   92 (370)
                      ..++|||+|||.+++|++|+++|++||.|.+++|++| .+++++|||||+|.+.++|.+|++ |++..+. |+.|.|..+
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence            4589999999999999999999999999999999999 789999999999999999999996 9998885 777766544


Q ss_pred             cccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCc-eeeEEE-eecCCCCCcccEEEEEECCHHHHH
Q psy2983          93 QAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGK-IDNIQL-MVDPDTGRSKGYGFITFHSADDAK  170 (370)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~-i~~v~~-~~~~~~g~~~g~afV~f~~~~~a~  170 (370)
                      .                   ..++|||+|||..+++++|.+.|++++. +..+.+ ..+.+.++++|||||+|.+.++|.
T Consensus       136 ~-------------------~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa  196 (578)
T TIGR01648       136 V-------------------DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAA  196 (578)
T ss_pred             c-------------------cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHH
Confidence            2                   1368999999999999999999999863 434333 333346788999999999999999


Q ss_pred             HHHHHhCC--ceeCCeeEEEEEeecCCC------------CcCCCCCCCCHHHHHHhcccC--CceeeeeeeeccccCCC
Q psy2983         171 KAQEQLNG--FELAGRPMKVGTVTDRNE------------SVGGGPSNLDTDEMERAGVDL--GATGRLQLMFKLAEGTG  234 (370)
Q Consensus       171 ~A~~~l~g--~~i~g~~l~V~~~~~~~~------------~~~~~~~~~~~~~l~~~~~~~--g~~~~~~l~~~~~~~~~  234 (370)
                      .|+..|+.  ..+.|+.|.|.++.+...            .+++++..+++++|++.|..|  |.+.++.+++    +++
T Consensus       197 ~AirkL~~gki~l~Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r----gfA  272 (578)
T TIGR01648       197 MARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR----DYA  272 (578)
T ss_pred             HHHHHhhccceEecCceEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec----CeE
Confidence            99998864  467899999999865432            367899999999999999999  9998887654    355


Q ss_pred             ---CCChHHHHHHHh
Q psy2983         235 ---LELPPAAASALN  246 (370)
Q Consensus       235 ---~~~~~~a~~a~~  246 (370)
                         |..+++|..|+.
T Consensus       273 FVeF~s~e~A~kAi~  287 (578)
T TIGR01648       273 FVHFEDREDAVKAMD  287 (578)
T ss_pred             EEEeCCHHHHHHHHH
Confidence               677788887775

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.

>KOG0144|consensus

Probab=99.95  E-value=7.4e-28  Score=222.03  Aligned_cols=179  Identities=27%  Similarity=0.491  Sum_probs=157.4

Q ss_pred             CCCCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCC-ccC
Q psy2983           6 SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQ-KLL   83 (370)
Q Consensus         6 ~~~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~-~i~   83 (370)
                      .+..+..+.+.-++||+.+|..++|.||+++|++||.|.+|.+++|+.++.++|||||.|.+.++|.+|+. |+.+ .+.
T Consensus        24 ~~~~d~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlp  103 (510)
T KOG0144|consen   24 LDHTDNPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLP  103 (510)
T ss_pred             CCCCCCCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccC
Confidence            34455566778899999999999999999999999999999999999999999999999999999999995 6555 454


Q ss_pred             C--eeEEEecccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEE
Q psy2983          84 G--IPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFI  161 (370)
Q Consensus        84 g--~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV  161 (370)
                      |  .+|.|+++..+..+.            ...++||||-|+..+||.+++++|++||.|++|.|++|. .|.++|||||
T Consensus       104 G~~~pvqvk~Ad~E~er~------------~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV  170 (510)
T KOG0144|consen  104 GMHHPVQVKYADGERERI------------VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFV  170 (510)
T ss_pred             CCCcceeecccchhhhcc------------ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEE
Confidence            4  588998888776554            223689999999999999999999999999999999996 8999999999


Q ss_pred             EECCHHHHHHHHHHhCCce-eC--CeeEEEEEeecCCCC
Q psy2983         162 TFHSADDAKKAQEQLNGFE-LA--GRPMKVGTVTDRNES  197 (370)
Q Consensus       162 ~f~~~~~a~~A~~~l~g~~-i~--g~~l~V~~~~~~~~~  197 (370)
                      .|.+.+.|..|++.|||.. +.  ..+|.|+|+..++..
T Consensus       171 ~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk  209 (510)
T KOG0144|consen  171 KFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDK  209 (510)
T ss_pred             EEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCc
Confidence            9999999999999999954 44  579999999876665

>KOG0120|consensus

Probab=99.95  E-value=1.3e-27  Score=230.01  Aligned_cols=253  Identities=25%  Similarity=0.384  Sum_probs=198.7

Q ss_pred             CCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcC-----------C-CeeEEEEeeeCCCCCeecEEEEEecCCCChHHHh
Q psy2983           8 DLSPEERDARTIFCMQLSQRIRTRDLEEFFSSV-----------G-KVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM   75 (370)
Q Consensus         8 ~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~-----------G-~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al   75 (370)
                      -.++.++..+++||+++|+.++++....+|..-           | .+..+.+      +..+++||++|.+.++|..|+
T Consensus       167 ~~~~~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~------n~~~nfa~ie~~s~~~at~~~  240 (500)
T KOG0120|consen  167 MDSQATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQL------NLEKNFAFIEFRSISEATEAM  240 (500)
T ss_pred             cCcchhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeee------cccccceeEEecCCCchhhhh
Confidence            345678899999999999999999999999863           2 2566655      345789999999999999999


Q ss_pred             hccCCccCCeeEEEecccccccccCCC----------CCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEE
Q psy2983          76 GLNGQKLLGIPIIVQPTQAEKNRAGNT----------LPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQ  145 (370)
Q Consensus        76 ~l~g~~i~g~~l~v~~~~~~~~~~~~~----------~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~  145 (370)
                      .+++..+.|+++++.....+.......          ...........+++++|++||..+++.++++++..||++....
T Consensus       241 ~~~~~~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~  320 (500)
T KOG0120|consen  241 ALDGIIFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFR  320 (500)
T ss_pred             cccchhhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhhe
Confidence            999999999999997765443322211          1122334455678999999999999999999999999999999


Q ss_pred             EeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecCCCCcCCCCCCCCHHHHHHhcccCCceeeeee
Q psy2983         146 LMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQL  225 (370)
Q Consensus       146 ~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~l  225 (370)
                      +..+..+|.++||||++|.++..+..|+..|||+.+++++|.|+.+............ ++..               + 
T Consensus       321 lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~-~~~~---------------~-  383 (500)
T KOG0120|consen  321 LVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFN-ISQS---------------Q-  383 (500)
T ss_pred             eecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCC-cccc---------------c-
Confidence            9999999999999999999999999999999999999999999987654443210000 0000               0 


Q ss_pred             eeccccCCCCCChHHHHHHHhhhcccccCCCCCCCCCCCCCCCCCceEEeecCCCCCCCCCchhhHHhHHHHHHHHhhcC
Q psy2983         226 MFKLAEGTGLELPPAAASALNLAQNAILNSSTPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG  305 (370)
Q Consensus       226 ~~~~~~~~~~~~~~~a~~a~~~~~~~~~~p~~~~~~~~~~~~~ps~vl~L~Nm~~~~~l~~d~~~~ei~eDv~~Ec~kyG  305 (370)
                                                  .+.++.. .......|++||+|+||++++||.+|++|+||+|||+.||.|||
T Consensus       384 ----------------------------~~~i~~~-~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g  434 (500)
T KOG0120|consen  384 ----------------------------VPGIPLL-MTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFG  434 (500)
T ss_pred             ----------------------------cccchhh-hcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccC
Confidence                                        0000000 00124568999999999999999999999999999999999999


Q ss_pred             ceeeEEE
Q psy2983         306 VGASTVC  312 (370)
Q Consensus       306 ~~~~~~~  312 (370)
                      ++.++..
T Consensus       435 ~v~~v~i  441 (500)
T KOG0120|consen  435 AVRSVEI  441 (500)
T ss_pred             ceeEEec
Confidence            9766554

>KOG0117|consensus

Probab=99.94  E-value=2.9e-26  Score=212.49  Aligned_cols=196  Identities=18%  Similarity=0.311  Sum_probs=174.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCcc-CCeeEEEec
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL-LGIPIIVQP   91 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i-~g~~l~v~~   91 (370)
                      ...+.|||+.||.++.|++|.-+|++.|+|-+++|+.|+.+|.++|||||.|.+.++|++|++ ||+..| .|+.|.|..
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            566889999999999999999999999999999999999999999999999999999999995 999988 589999887


Q ss_pred             ccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCc-eeeEEEeecCC-CCCcccEEEEEECCHHHH
Q psy2983          92 TQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGK-IDNIQLMVDPD-TGRSKGYGFITFHSADDA  169 (370)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~-i~~v~~~~~~~-~g~~~g~afV~f~~~~~a  169 (370)
                      +..                   +++|||||||...++++|.+.+++.++ |..|.+++.+. ..+++|||||+|.+...|
T Consensus       161 Sva-------------------n~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~A  221 (506)
T KOG0117|consen  161 SVA-------------------NCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAA  221 (506)
T ss_pred             eee-------------------cceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhH
Confidence            654                   378999999999999999999999874 66777776654 468999999999999999


Q ss_pred             HHHHHHhCC--ceeCCeeEEEEEeecCCCC------------cCCCCCCCCHHHHHHhcccCCceeeeeeeec
Q psy2983         170 KKAQEQLNG--FELAGRPMKVGTVTDRNES------------VGGGPSNLDTDEMERAGVDLGATGRLQLMFK  228 (370)
Q Consensus       170 ~~A~~~l~g--~~i~g~~l~V~~~~~~~~~------------~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~  228 (370)
                      ..|...|-.  ..+.|+.+.|.|+.+....            +.+++..++++.|++.|..||.+.+++..++
T Consensus       222 a~aRrKl~~g~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD  294 (506)
T KOG0117|consen  222 AMARRKLMPGKIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD  294 (506)
T ss_pred             HHHHhhccCCceeecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc
Confidence            999988754  4567999999999877654            6789999999999999999999998877654

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

Probab=99.94  E-value=3.6e-25  Score=220.59  Aligned_cols=221  Identities=22%  Similarity=0.313  Sum_probs=172.0

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCC--eeEEEeccc
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLG--IPIIVQPTQ   93 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g--~~l~v~~~~   93 (370)
                      .+|||+||+..+|+++|+++|+.||.|.+|.+.++..    +++|||+|.+.++|.+|++ |+|..|.|  +.|+|.+++
T Consensus        97 ~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~----~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk  172 (481)
T TIGR01649        97 LRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNN----VFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAK  172 (481)
T ss_pred             EEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCC----ceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEec
Confidence            4799999999999999999999999999999887542    4689999999999999996 99999965  477777665


Q ss_pred             ccccc------cC-C-----C---------------CCC-----------------------------------------
Q psy2983          94 AEKNR------AG-N-----T---------------LPN-----------------------------------------  105 (370)
Q Consensus        94 ~~~~~------~~-~-----~---------------~~~-----------------------------------------  105 (370)
                      ...-.      .. +     .               .+.                                         
T Consensus       173 ~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~  252 (481)
T TIGR01649       173 PTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGPLAPLAGGDRMGPPHGPPSRYR  252 (481)
T ss_pred             CCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCCCCCCcccccccCCCcccCCCCCc
Confidence            31100      00 0     0               000                                         


Q ss_pred             ------C--------CCCCCCCCceEEEecCCC-CCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHH
Q psy2983         106 ------L--------QPRGTGGPMRLYIGSLHF-NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAK  170 (370)
Q Consensus       106 ------~--------~~~~~~~~~~l~V~nlp~-~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~  170 (370)
                            .        .+....+..+|||+|||+ .+++++|+++|+.||.|.+|++++++     +|+|||+|.+.++|.
T Consensus       253 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~  327 (481)
T TIGR01649       253 PAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQ  327 (481)
T ss_pred             ccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHH
Confidence                  0        000012346899999998 69999999999999999999999874     799999999999999


Q ss_pred             HHHHHhCCceeCCeeEEEEEeecCC--------------------------------------------CCcCCCCCCCC
Q psy2983         171 KAQEQLNGFELAGRPMKVGTVTDRN--------------------------------------------ESVGGGPSNLD  206 (370)
Q Consensus       171 ~A~~~l~g~~i~g~~l~V~~~~~~~--------------------------------------------~~~~~~~~~~~  206 (370)
                      .|+..|||..+.|++|+|.+++...                                            ..+.+++..++
T Consensus       328 ~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~t  407 (481)
T TIGR01649       328 LALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVS  407 (481)
T ss_pred             HHHHHhCCCEECCceEEEEEcccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCC
Confidence            9999999999999999999864210                                            01446778899


Q ss_pred             HHHHHHhcccCCc--eeeeeeeecc--ccCCC---CCChHHHHHHHh
Q psy2983         207 TDEMERAGVDLGA--TGRLQLMFKL--AEGTG---LELPPAAASALN  246 (370)
Q Consensus       207 ~~~l~~~~~~~g~--~~~~~l~~~~--~~~~~---~~~~~~a~~a~~  246 (370)
                      +++|+++|..+|.  +..+.++...  .+++|   |...++|..|+.
T Consensus       408 ee~L~~lF~~~G~~~i~~ik~~~~~~~~~~~gfVeF~~~e~A~~Al~  454 (481)
T TIGR01649       408 EEDLKELFAENGVHKVKKFKFFPKDNERSKMGLLEWESVEDAVEALI  454 (481)
T ss_pred             HHHHHHHHHhcCCccceEEEEecCCCCcceeEEEEcCCHHHHHHHHH
Confidence            9999999999998  7777776443  12444   667777777766

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=99.94  E-value=1.1e-26  Score=191.83  Aligned_cols=171  Identities=29%  Similarity=0.504  Sum_probs=153.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      ....||||+||+..++++-|+++|-+.|+|.++.+.+|+-+...+||||+||.+.|+|+-|++ ++...+.|++|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            356799999999999999999999999999999999999999999999999999999999998 9999999999999887


Q ss_pred             cccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceee-EEEeecCCCCCcccEEEEEECCHHHHHH
Q psy2983          93 QAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDN-IQLMVDPDTGRSKGYGFITFHSADDAKK  171 (370)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~-v~~~~~~~~g~~~g~afV~f~~~~~a~~  171 (370)
                      .....            ......+|||+||.+.+++..|.+.|+.||.+.. -++++++++|.++|+||+.|.+.+.+.+
T Consensus        87 s~~~~------------nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~  154 (203)
T KOG0131|consen   87 SAHQK------------NLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDA  154 (203)
T ss_pred             ccccc------------cccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHH
Confidence            62211            1122368999999999999999999999998765 4788999999999999999999999999


Q ss_pred             HHHHhCCceeCCeeEEEEEeecCCC
Q psy2983         172 AQEQLNGFELAGRPMKVGTVTDRNE  196 (370)
Q Consensus       172 A~~~l~g~~i~g~~l~V~~~~~~~~  196 (370)
                      |+..++|+.+.++++.|.++..+..
T Consensus       155 ai~s~ngq~l~nr~itv~ya~k~~~  179 (203)
T KOG0131|consen  155 AIGSMNGQYLCNRPITVSYAFKKDT  179 (203)
T ss_pred             HHHHhccchhcCCceEEEEEEecCC
Confidence            9999999999999999999866544

>KOG0123|consensus

Probab=99.93  E-value=3.2e-24  Score=204.39  Aligned_cols=202  Identities=29%  Similarity=0.450  Sum_probs=176.3

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecccccc
Q psy2983          18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQAEK   96 (370)
Q Consensus        18 ~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~~~   96 (370)
                      .||||   +++|+..|.++|+++|+|.++++.+|. |  +-|||||.|.++++|.+|++ ++...++|+++++-|+....
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~   76 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP   76 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC
Confidence            58999   999999999999999999999999998 6  89999999999999999995 99999999999999987542


Q ss_pred             cccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHh
Q psy2983          97 NRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL  176 (370)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l  176 (370)
                      .                  .+||.||+++++...|.++|+.||.|.+|++..+. .| ++|| ||+|.++++|.+|+..+
T Consensus        77 ~------------------~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~  135 (369)
T KOG0123|consen   77 S------------------LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKL  135 (369)
T ss_pred             c------------------eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHh
Confidence            1                  29999999999999999999999999999999995 56 9999 99999999999999999


Q ss_pred             CCceeCCeeEEEEEeecCCCC---------------cCCCCCCCCHHHHHHhcccCCceeeeeeeecc---ccCCCC---
Q psy2983         177 NGFELAGRPMKVGTVTDRNES---------------VGGGPSNLDTDEMERAGVDLGATGRLQLMFKL---AEGTGL---  235 (370)
Q Consensus       177 ~g~~i~g~~l~V~~~~~~~~~---------------~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~---~~~~~~---  235 (370)
                      ||..+.|+.|.|.....+...               +.+.+...+++.+...|..+|.+.+..+|.+.   +++++|   
T Consensus       136 ng~ll~~kki~vg~~~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f  215 (369)
T KOG0123|consen  136 NGMLLNGKKIYVGLFERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNF  215 (369)
T ss_pred             cCcccCCCeeEEeeccchhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceee
Confidence            999999999999876554332               33455677888999999999999999999873   345653   


Q ss_pred             CChHHHHHHHh
Q psy2983         236 ELPPAAASALN  246 (370)
Q Consensus       236 ~~~~~a~~a~~  246 (370)
                      ..+..+..++.
T Consensus       216 ~~~e~a~~av~  226 (369)
T KOG0123|consen  216 ENPEDAKKAVE  226 (369)
T ss_pred             cChhHHHHHHH
Confidence            44566655554

>KOG0127|consensus

Probab=99.93  E-value=1.8e-24  Score=204.76  Aligned_cols=233  Identities=25%  Similarity=0.390  Sum_probs=188.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecccc
Q psy2983          16 ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQA   94 (370)
Q Consensus        16 ~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~   94 (370)
                      ..||||++||+.++.++|.++|+.+|+|..+.++.+..++.++||+||.|.-.|++++|++ ..+..|+|+.|.|..+..
T Consensus         5 g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~   84 (678)
T KOG0127|consen    5 GATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKK   84 (678)
T ss_pred             CceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccc
Confidence            3799999999999999999999999999999999999999999999999999999999995 899999999999977654


Q ss_pred             cccccC--CCCC--------CCC---CCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEE
Q psy2983          95 EKNRAG--NTLP--------NLQ---PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFI  161 (370)
Q Consensus        95 ~~~~~~--~~~~--------~~~---~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV  161 (370)
                      ......  ....        +..   .....+.-+|.|+|||+.+...+|+.+|+.||.|..|.|++..+ |+-.|||||
T Consensus        85 R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~d-gklcGFaFV  163 (678)
T KOG0127|consen   85 RARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKD-GKLCGFAFV  163 (678)
T ss_pred             cccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCC-CCccceEEE
Confidence            322110  0000        000   00111245899999999999999999999999999999998764 555599999


Q ss_pred             EECCHHHHHHHHHHhCCceeCCeeEEEEEeecCCCC--------------------------------------------
Q psy2983         162 TFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNES--------------------------------------------  197 (370)
Q Consensus       162 ~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~~~~--------------------------------------------  197 (370)
                      .|....+|..|++.+|+..|.||+|-|.|+.++...                                            
T Consensus       164 ~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeE  243 (678)
T KOG0127|consen  164 QFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEE  243 (678)
T ss_pred             EEeeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccc
Confidence            999999999999999999999999999998543322                                            


Q ss_pred             -----------------------------------------------------cCCCCCCCCHHHHHHhcccCCceeeee
Q psy2983         198 -----------------------------------------------------VGGGPSNLDTDEMERAGVDLGATGRLQ  224 (370)
Q Consensus       198 -----------------------------------------------------~~~~~~~~~~~~l~~~~~~~g~~~~~~  224 (370)
                                                                           +.+++-..+++.+...|..||.+..+.
T Consensus       244 e~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~  323 (678)
T KOG0127|consen  244 ETDGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAI  323 (678)
T ss_pred             cccccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEE
Confidence                                                                 123555677889999999999999888


Q ss_pred             eeecc----ccCCC---CCChHHHHHHHhhhc
Q psy2983         225 LMFKL----AEGTG---LELPPAAASALNLAQ  249 (370)
Q Consensus       225 l~~~~----~~~~~---~~~~~~a~~a~~~~~  249 (370)
                      +....    +.|.+   |-++.+++..+.++.
T Consensus       324 iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~As  355 (678)
T KOG0127|consen  324 IVKDKDTGHSKGTAFVKFKTQIAAQNCIEAAS  355 (678)
T ss_pred             EEeccCCCCcccceEEEeccHHHHHHHHHhcC
Confidence            87663    33444   567777777776553

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

Probab=99.92  E-value=2.8e-24  Score=216.51  Aligned_cols=180  Identities=21%  Similarity=0.286  Sum_probs=147.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      ...++|||+|||..+++++|+++|+.||.|..+.++++..+|.++|||||+|.+.++|..|++ |+|..|.|+.|.|.++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            456899999999999999999999999999999999999999999999999999999999995 9999999999999887


Q ss_pred             cccccccCCCCC----------C-----CCCCCCCCCceEEEecCCCC--C--------CHHHHHhcccCCCceeeEEEe
Q psy2983          93 QAEKNRAGNTLP----------N-----LQPRGTGGPMRLYIGSLHFN--I--------TEDMLRGIFEPFGKIDNIQLM  147 (370)
Q Consensus        93 ~~~~~~~~~~~~----------~-----~~~~~~~~~~~l~V~nlp~~--~--------t~e~l~~~f~~~G~i~~v~~~  147 (370)
                      ............          .     .......+..+|+|.|+...  +        ..++|+++|++||.|..|.|+
T Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~  452 (509)
T TIGR01642       373 CVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIP  452 (509)
T ss_pred             ccCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEee
Confidence            543221110000          0     00111234578999999642  1        236899999999999999998


Q ss_pred             ecC---CCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         148 VDP---DTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       148 ~~~---~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      ++.   .++.+.|+|||+|.+.++|.+|+..|||..|.|+.|.|.+...
T Consensus       453 ~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       453 RPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             ccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCH
Confidence            652   3456789999999999999999999999999999999998543

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

>KOG0148|consensus

Probab=99.92  E-value=1.4e-24  Score=189.65  Aligned_cols=191  Identities=26%  Similarity=0.448  Sum_probs=157.6

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecc
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPT   92 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~   92 (370)
                      +.+.|||||+||+..+||+-|..+|++.|+|.+++++.|                                  .++|.++
T Consensus         3 ~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~----------------------------------e~~v~wa   48 (321)
T KOG0148|consen    3 SDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD----------------------------------ELKVNWA   48 (321)
T ss_pred             CCCCceEEeeccChhhHHHHHHHHHHhccccccceeehh----------------------------------hhccccc
Confidence            456799999999999999999999999999999999876                                  3445444


Q ss_pred             cccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHH
Q psy2983          93 QAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA  172 (370)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A  172 (370)
                      ....+...        ........+||+.|...++-++|++.|.+||+|..+++++|..|+++|||+||.|.+.++|+.|
T Consensus        49 ~~p~nQsk--------~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnA  120 (321)
T KOG0148|consen   49 TAPGNQSK--------PTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENA  120 (321)
T ss_pred             cCcccCCC--------CccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHH
Confidence            43311111        1122246799999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhCCceeCCeeEEEEEeecCCCC-----------------------cCCCCCCCCHHHHHHhcccCCceeeeeeeecc
Q psy2983         173 QEQLNGFELAGRPMKVGTVTDRNES-----------------------VGGGPSNLDTDEMERAGVDLGATGRLQLMFKL  229 (370)
Q Consensus       173 ~~~l~g~~i~g~~l~V~~~~~~~~~-----------------------~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~  229 (370)
                      |..|||+-|++|.|+-.|+..+...                       .+++++.++++.+++.|+.||.|..+.+.++.
T Consensus       121 I~~MnGqWlG~R~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q  200 (321)
T KOG0148|consen  121 IQQMNGQWLGRRTIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ  200 (321)
T ss_pred             HHHhCCeeeccceeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEeccc
Confidence            9999999999999999998655432                       45677889999999999999999999887763


Q ss_pred             ccCC-CCCChHHHHHHH
Q psy2983         230 AEGT-GLELPPAAASAL  245 (370)
Q Consensus       230 ~~~~-~~~~~~~a~~a~  245 (370)
                      .-.| -|...++|+.|+
T Consensus       201 GYaFVrF~tkEaAahAI  217 (321)
T KOG0148|consen  201 GYAFVRFETKEAAAHAI  217 (321)
T ss_pred             ceEEEEecchhhHHHHH
Confidence            3332 266777666553

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

Probab=99.90  E-value=5.4e-23  Score=204.67  Aligned_cols=166  Identities=25%  Similarity=0.436  Sum_probs=136.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCC-eeEEEEe-eeCCCCCeecEEEEEecCCCChHHHhh-cc--CCccCCeeEEE
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGK-VRDVRLI-TCNKTRRFKGIAYIEFKDPESVPLAMG-LN--GQKLLGIPIIV   89 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~-v~~v~i~-~d~~~~~~kg~afVeF~~~e~A~~Al~-l~--g~~i~g~~l~v   89 (370)
                      +.++|||+|||.++++++|.+.|++++. +.++.+. .....++++|||||+|.+.++|..|+. ++  ...+.|+.|.|
T Consensus       137 ~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~V  216 (578)
T TIGR01648       137 DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAV  216 (578)
T ss_pred             cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEE
Confidence            4689999999999999999999999864 4444333 333456789999999999999999995 43  34688999999


Q ss_pred             ecccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCC--CceeeEEEeecCCCCCcccEEEEEECCHH
Q psy2983          90 QPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPF--GKIDNIQLMVDPDTGRSKGYGFITFHSAD  167 (370)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~--G~i~~v~~~~~~~~g~~~g~afV~f~~~~  167 (370)
                      .++.+.....        .......++|||+|||.++++++|+++|++|  |.|.+|.++        ++||||+|.+.+
T Consensus       217 dwA~p~~~~d--------~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e  280 (578)
T TIGR01648       217 DWAEPEEEVD--------EDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDRE  280 (578)
T ss_pred             Eeeccccccc--------ccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHH
Confidence            9886543211        1112234689999999999999999999999  999999876        459999999999


Q ss_pred             HHHHHHHHhCCceeCCeeEEEEEeecCCC
Q psy2983         168 DAKKAQEQLNGFELAGRPMKVGTVTDRNE  196 (370)
Q Consensus       168 ~a~~A~~~l~g~~i~g~~l~V~~~~~~~~  196 (370)
                      +|.+|++.|||..|.|+.|+|.++++...
T Consensus       281 ~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       281 DAVKAMDELNGKELEGSEIEVTLAKPVDK  309 (578)
T ss_pred             HHHHHHHHhCCCEECCEEEEEEEccCCCc
Confidence            99999999999999999999999976543

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

>KOG0145|consensus

Probab=99.90  E-value=8.1e-23  Score=177.55  Aligned_cols=179  Identities=28%  Similarity=0.532  Sum_probs=151.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCe--eEEEec
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGI--PIIVQP   91 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~--~l~v~~   91 (370)
                      ..-.|||.+||..+|..||+++|++||.|..-+|+.|.-+|.++|.+||.|...++|+.|+. |+|..-.|.  +|.|++
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            34569999999999999999999999999888999999999999999999999999999996 999987664  788876


Q ss_pred             ccccccccCCC----------------C-------------------CC---------------CCCCCCCCCceEEEec
Q psy2983          92 TQAEKNRAGNT----------------L-------------------PN---------------LQPRGTGGPMRLYIGS  121 (370)
Q Consensus        92 ~~~~~~~~~~~----------------~-------------------~~---------------~~~~~~~~~~~l~V~n  121 (370)
                      +..........                .                   ..               ..+......-+|||.|
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            65322111100                0                   00               0011222346899999


Q ss_pred             CCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         122 LHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       122 lp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      |.++.+|.-|.++|.+||.|..+++++|..+.++||||||.+.+-++|..|+..|||..++++.|.|.+...
T Consensus       286 Lspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtn  357 (360)
T KOG0145|consen  286 LSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTN  357 (360)
T ss_pred             cCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecC
Confidence            999999999999999999999999999998999999999999999999999999999999999999998654

>KOG0123|consensus

Probab=99.90  E-value=1.2e-22  Score=193.64  Aligned_cols=225  Identities=27%  Similarity=0.463  Sum_probs=190.3

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      .|+...|||.||++.++.++|.++|+.||.|.++++..+...  ++|| ||+|.+.++|.+|++ +||..+.|++|.|..
T Consensus        73 ~rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g--~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~  149 (369)
T KOG0123|consen   73 QRDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG--SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGL  149 (369)
T ss_pred             ccCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC--ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEee
Confidence            345555999999999999999999999999999999998764  8999 999999999999996 999999999999988


Q ss_pred             ccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHH
Q psy2983          92 TQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK  171 (370)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~  171 (370)
                      ...+..+......     ....-..+++.+++.+.+++.|..+|..+|.|..+.++.+. .|+++||+||+|.+.+.|..
T Consensus       150 ~~~~~er~~~~~~-----~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~-~g~~~~~gfv~f~~~e~a~~  223 (369)
T KOG0123|consen  150 FERKEEREAPLGE-----YKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDS-IGKSKGFGFVNFENPEDAKK  223 (369)
T ss_pred             ccchhhhcccccc-----hhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecC-CCCCCCccceeecChhHHHH
Confidence            7765554432221     11223568999999999999999999999999999999995 78899999999999999999


Q ss_pred             HHHHhCCceeCCeeEEEEEeecCCCC-------------------------cCCCCCCCCHHHHHHhcccCCceeeeeee
Q psy2983         172 AQEQLNGFELAGRPMKVGTVTDRNES-------------------------VGGGPSNLDTDEMERAGVDLGATGRLQLM  226 (370)
Q Consensus       172 A~~~l~g~~i~g~~l~V~~~~~~~~~-------------------------~~~~~~~~~~~~l~~~~~~~g~~~~~~l~  226 (370)
                      |+..|++..+.+..+.|..+..+...                         +.+++..++.+.++..|..+|.+.+..+|
T Consensus       224 av~~l~~~~~~~~~~~V~~aqkk~e~~~~l~~~~~~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~  303 (369)
T KOG0123|consen  224 AVETLNGKIFGDKELYVGRAQKKSEREAELKRKFEQEFAKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVM  303 (369)
T ss_pred             HHHhccCCcCCccceeecccccchhhHHHHhhhhHhhhhhccccccccccccccCccccchhHHHHHHhcccceeeEEEE
Confidence            99999999999999999887542111                         44567788999999999999999999998


Q ss_pred             ec---cccCCC---CCChHHHHHHHh
Q psy2983         227 FK---LAEGTG---LELPPAAASALN  246 (370)
Q Consensus       227 ~~---~~~~~~---~~~~~~a~~a~~  246 (370)
                      ..   .+.|+|   |+.++.|..|+.
T Consensus       304 ~~~~g~skG~gfV~fs~~eeA~~A~~  329 (369)
T KOG0123|consen  304 VDENGKSKGFGFVEFSSPEEAKKAMT  329 (369)
T ss_pred             eccCCCccceEEEEcCCHHHHHHHHH
Confidence            86   344555   678888877755

>KOG0109|consensus

Probab=99.90  E-value=3.1e-23  Score=182.90  Aligned_cols=149  Identities=26%  Similarity=0.479  Sum_probs=137.5

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecccccc
Q psy2983          18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQAEK   96 (370)
Q Consensus        18 ~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~~~   96 (370)
                      +|||||||.++++.+|+.+|++||+|.++.|++        .||||+.++...|+.|+. |+|..|+|..|.|+.++.+.
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvK--------NYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDIVK--------NYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeeeec--------ccceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence            589999999999999999999999999999985        599999999999999997 99999999999999887552


Q ss_pred             cccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHh
Q psy2983          97 NRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL  176 (370)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l  176 (370)
                                     ....+|+|+|+.+.++.++++..|++||+|.++++.+|        |+||.|...++|..|+..|
T Consensus        76 ---------------k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l  132 (346)
T KOG0109|consen   76 ---------------KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGL  132 (346)
T ss_pred             ---------------CCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcc
Confidence                           22368999999999999999999999999999999855        9999999999999999999


Q ss_pred             CCceeCCeeEEEEEeecCCCC
Q psy2983         177 NGFELAGRPMKVGTVTDRNES  197 (370)
Q Consensus       177 ~g~~i~g~~l~V~~~~~~~~~  197 (370)
                      +|.+|.|++++|+.+..+-..
T Consensus       133 ~~~~~~gk~m~vq~stsrlrt  153 (346)
T KOG0109|consen  133 DNTEFQGKRMHVQLSTSRLRT  153 (346)
T ss_pred             cccccccceeeeeeecccccc
Confidence            999999999999998776554

>KOG0117|consensus

Probab=99.89  E-value=1.4e-22  Score=188.20  Aligned_cols=168  Identities=25%  Similarity=0.424  Sum_probs=143.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCC-eeEEEEeeeCC-CCCeecEEEEEecCCCChHHHhh--ccC-CccCCeeEE
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGK-VRDVRLITCNK-TRRFKGIAYIEFKDPESVPLAMG--LNG-QKLLGIPII   88 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~-v~~v~i~~d~~-~~~~kg~afVeF~~~e~A~~Al~--l~g-~~i~g~~l~   88 (370)
                      .+.++|||+|+|.+.++++|.+-+++.++ |.+|.+..++. ..+.+|||||+|.+...|..|-.  ++| ..+.|+.+.
T Consensus       162 van~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~t  241 (506)
T KOG0117|consen  162 VANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAIT  241 (506)
T ss_pred             eecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcce
Confidence            46789999999999999999999999887 77777765543 35789999999999999999985  444 478999999


Q ss_pred             EecccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHH
Q psy2983          89 VQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADD  168 (370)
Q Consensus        89 v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~  168 (370)
                      |.|+.++......        ....-..|||+||+.++|+|.|+++|++||.|++|+.++|        ||||.|.+.++
T Consensus       242 VdWAep~~e~ded--------~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~d  305 (506)
T KOG0117|consen  242 VDWAEPEEEPDED--------TMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAERED  305 (506)
T ss_pred             eeccCcccCCChh--------hhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHH
Confidence            9999876433221        1223357999999999999999999999999999998866        99999999999


Q ss_pred             HHHHHHHhCCceeCCeeEEEEEeecCCCC
Q psy2983         169 AKKAQEQLNGFELAGRPMKVGTVTDRNES  197 (370)
Q Consensus       169 a~~A~~~l~g~~i~g~~l~V~~~~~~~~~  197 (370)
                      |.+|++.+||++|.|..|.|..+++....
T Consensus       306 avkAm~~~ngkeldG~~iEvtLAKP~~k~  334 (506)
T KOG0117|consen  306 AVKAMKETNGKELDGSPIEVTLAKPVDKK  334 (506)
T ss_pred             HHHHHHHhcCceecCceEEEEecCChhhh
Confidence            99999999999999999999999876543

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

Probab=99.89  E-value=8.7e-22  Score=195.87  Aligned_cols=175  Identities=26%  Similarity=0.376  Sum_probs=142.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      ..++|||+|||..+++++|+++|+.||.|..|.++++..+|+++|||||+|.+.++|..|++ |+|..+.|++|.|.++.
T Consensus       185 ~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            47899999999999999999999999999999999999999999999999999999999995 99999999999999854


Q ss_pred             ccccccCC--------------------------------C------CC-------------------------------
Q psy2983          94 AEKNRAGN--------------------------------T------LP-------------------------------  104 (370)
Q Consensus        94 ~~~~~~~~--------------------------------~------~~-------------------------------  104 (370)
                      ........                                .      .+                               
T Consensus       265 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  344 (457)
T TIGR01622       265 DSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGAL  344 (457)
T ss_pred             CCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhcccccccccccccccccccccc
Confidence            21100000                                0      00                               


Q ss_pred             ------CCCCC--CCCCCceEEEecCCCCCC----------HHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCH
Q psy2983         105 ------NLQPR--GTGGPMRLYIGSLHFNIT----------EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA  166 (370)
Q Consensus       105 ------~~~~~--~~~~~~~l~V~nlp~~~t----------~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~  166 (370)
                            ...+.  ......+|+|.|+....+          .++|++.|++||.|..+.+.    .+...|++||+|.+.
T Consensus       345 ~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~----~~~~~G~~fV~F~~~  420 (457)
T TIGR01622       345 AIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVD----TKNSAGKIYLKFSSV  420 (457)
T ss_pred             ccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEe----CCCCceeEEEEECCH
Confidence                  00000  112346789999954443          36899999999999999886    344579999999999


Q ss_pred             HHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         167 DDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       167 ~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      ++|.+|++.|||..|+|+.|.+.+...
T Consensus       421 e~A~~A~~~lnGr~f~gr~i~~~~~~~  447 (457)
T TIGR01622       421 DAALAAFQALNGRYFGGKMITAAFVVN  447 (457)
T ss_pred             HHHHHHHHHhcCcccCCeEEEEEEEcH
Confidence            999999999999999999999998643

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.

>KOG0127|consensus

Probab=99.88  E-value=4.7e-22  Score=188.53  Aligned_cols=180  Identities=26%  Similarity=0.436  Sum_probs=148.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecccc
Q psy2983          16 ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQA   94 (370)
Q Consensus        16 ~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~   94 (370)
                      .-+|.|+|||..+...+|+.+|+.||.|..|.|.+...++.. |||||.|....+|..|++ ++|..|.||+|-|.|+-.
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklc-GFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~  195 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLC-GFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVD  195 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCcc-ceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecc
Confidence            568999999999999999999999999999999976665555 999999999999999997 999999999999987642


Q ss_pred             cccccCCC---------------------------------------C--C--------------------CCC------
Q psy2983          95 EKNRAGNT---------------------------------------L--P--------------------NLQ------  107 (370)
Q Consensus        95 ~~~~~~~~---------------------------------------~--~--------------------~~~------  107 (370)
                      ...-....                                       .  .                    +..      
T Consensus       196 Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~  275 (678)
T KOG0127|consen  196 KDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKE  275 (678)
T ss_pred             cccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccCc
Confidence            11000000                                       0  0                    000      


Q ss_pred             ----------CCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHh-
Q psy2983         108 ----------PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL-  176 (370)
Q Consensus       108 ----------~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l-  176 (370)
                                .....-..+|||+|||+++|+++|.+.|++||.|..+.++.++.||.++|.|||.|.+...|+.||.+. 
T Consensus       276 ~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~As  355 (678)
T KOG0127|consen  276 SDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAAS  355 (678)
T ss_pred             ccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcC
Confidence                      000011258999999999999999999999999999999999999999999999999999999999976 


Q ss_pred             ----CC-ceeCCeeEEEEEeecCCC
Q psy2983         177 ----NG-FELAGRPMKVGTVTDRNE  196 (370)
Q Consensus       177 ----~g-~~i~g~~l~V~~~~~~~~  196 (370)
                          .| ..+.||.|+|..+..+..
T Consensus       356 pa~e~g~~ll~GR~Lkv~~Av~Rke  380 (678)
T KOG0127|consen  356 PASEDGSVLLDGRLLKVTLAVTRKE  380 (678)
T ss_pred             ccCCCceEEEeccEEeeeeccchHH
Confidence                34 678899999999876554

>KOG0110|consensus

Probab=99.84  E-value=5.4e-21  Score=186.82  Aligned_cols=173  Identities=23%  Similarity=0.429  Sum_probs=146.4

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCC---CCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKT---RRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        18 ~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~---~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      +|||.||+...|.++|...|...|.|.++.|..-+..   ..|.|||||+|.++++|+.|+. |+|..+.|+.|.++.+.
T Consensus       517 ~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  517 KLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             hhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            3999999999999999999999999999988653321   2467999999999999999996 99999999999999887


Q ss_pred             ccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHH
Q psy2983          94 AEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ  173 (370)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~  173 (370)
                      ....   .......+ ......+|+|.|||+..+..+++++|..||.+.++++++....+.++|||||+|-++.+|.+|+
T Consensus       597 ~k~~---~~~gK~~~-~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~  672 (725)
T KOG0110|consen  597 NKPA---STVGKKKS-KKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAF  672 (725)
T ss_pred             Cccc---cccccccc-cccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHH
Confidence            2211   11111111 1122578999999999999999999999999999999987667788999999999999999999


Q ss_pred             HHhCCceeCCeeEEEEEeecC
Q psy2983         174 EQLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       174 ~~l~g~~i~g~~l~V~~~~~~  194 (370)
                      .+|.+..++||.|.+.|+...
T Consensus       673 ~al~STHlyGRrLVLEwA~~d  693 (725)
T KOG0110|consen  673 DALGSTHLYGRRLVLEWAKSD  693 (725)
T ss_pred             Hhhcccceechhhheehhccc
Confidence            999999999999999998664

>KOG4205|consensus

Probab=99.84  E-value=1.7e-20  Score=173.00  Aligned_cols=175  Identities=25%  Similarity=0.452  Sum_probs=155.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecccc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQA   94 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~~~   94 (370)
                      +..++||++|+..++++.|+++|.+||+|.++.+++|+.+++++||+||+|.+++.+..++......|.|+.|.+.++.+
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~   84 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVS   84 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccC
Confidence            78999999999999999999999999999999999999999999999999999999999998888889999998877654


Q ss_pred             cccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHH
Q psy2983          95 EKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE  174 (370)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~  174 (370)
                      ......       ........++||++||.+++++++++.|++||.|..+.++.|..+..++||+||.|.+++++.+++.
T Consensus        85 r~~~~~-------~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~  157 (311)
T KOG4205|consen   85 REDQTK-------VGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL  157 (311)
T ss_pred             cccccc-------cccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc
Confidence            432221       1111145689999999999999999999999999999999999999999999999999999999988


Q ss_pred             HhCCceeCCeeEEEEEeecCCCC
Q psy2983         175 QLNGFELAGRPMKVGTVTDRNES  197 (370)
Q Consensus       175 ~l~g~~i~g~~l~V~~~~~~~~~  197 (370)
                       .+-+.|.++.+.|+.+.++...
T Consensus       158 -~~f~~~~gk~vevkrA~pk~~~  179 (311)
T KOG4205|consen  158 -QKFHDFNGKKVEVKRAIPKEVM  179 (311)
T ss_pred             -cceeeecCceeeEeeccchhhc
Confidence             7889999999999999776554

>KOG0146|consensus

Probab=99.80  E-value=1.5e-19  Score=157.87  Aligned_cols=180  Identities=25%  Similarity=0.467  Sum_probs=146.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCc-cCC--eeEEEe
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQK-LLG--IPIIVQ   90 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~-i~g--~~l~v~   90 (370)
                      +.|+||||-|...-+|+|++.+|..||.|.++.+.+... |.+||+|||.|.+.-+|..|+. |+|.. +-|  ..|.|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~d-g~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPD-GNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCC-CCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            679999999999999999999999999999999988764 8899999999999999999995 88874 333  245554


Q ss_pred             cccccccccCCC--------------------------------------------------------------------
Q psy2983          91 PTQAEKNRAGNT--------------------------------------------------------------------  102 (370)
Q Consensus        91 ~~~~~~~~~~~~--------------------------------------------------------------------  102 (370)
                      +...++++....                                                                    
T Consensus        97 ~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl~A  176 (371)
T KOG0146|consen   97 FADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGLAA  176 (371)
T ss_pred             eccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhccccc
Confidence            433322211100                                                                    


Q ss_pred             ----------CCC-------------------------------------------------------------------
Q psy2983         103 ----------LPN-------------------------------------------------------------------  105 (370)
Q Consensus       103 ----------~~~-------------------------------------------------------------------  105 (370)
                                .+.                                                                   
T Consensus       177 ~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~Aa  256 (371)
T KOG0146|consen  177 APVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYAAA  256 (371)
T ss_pred             CCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHhhh
Confidence                      000                                                                   


Q ss_pred             --------------------CCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECC
Q psy2983         106 --------------------LQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS  165 (370)
Q Consensus       106 --------------------~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~  165 (370)
                                          ...+.....+.|||.+||.+..+.+|.+.|-+||.|.+.+++.|+-|+.+|.|+||.|.+
T Consensus       257 ypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDN  336 (371)
T KOG0146|consen  257 YPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDN  336 (371)
T ss_pred             cchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCC
Confidence                                000122233679999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhCCceeCCeeEEEEEeecCC
Q psy2983         166 ADDAKKAQEQLNGFELAGRPMKVGTVTDRN  195 (370)
Q Consensus       166 ~~~a~~A~~~l~g~~i~g~~l~V~~~~~~~  195 (370)
                      +.+|+.||.+|||+.|+=++|+|....++.
T Consensus       337 p~SaQaAIqAMNGFQIGMKRLKVQLKRPkd  366 (371)
T KOG0146|consen  337 PASAQAAIQAMNGFQIGMKRLKVQLKRPKD  366 (371)
T ss_pred             chhHHHHHHHhcchhhhhhhhhhhhcCccc
Confidence            999999999999999999999998766554

>KOG0144|consensus

Probab=99.79  E-value=2.5e-19  Score=165.87  Aligned_cols=182  Identities=26%  Similarity=0.477  Sum_probs=150.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCC-ccCC--eeEEE
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQ-KLLG--IPIIV   89 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~-~i~g--~~l~v   89 (370)
                      -+.|+|||+-|+..+||.+++++|.+||.|+++.|++|.. +.+||||||.|.+.|.|..|++ +||. .+.|  .+|.|
T Consensus       122 ~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~-~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVV  200 (510)
T KOG0144|consen  122 VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPD-GLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVV  200 (510)
T ss_pred             ccchhhhhhhccccccHHHHHHHHHhhCccchhhheeccc-ccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEE
Confidence            3479999999999999999999999999999999999875 8899999999999999999996 8887 4555  48888


Q ss_pred             ecccccccccCCCC------------------------------------------------------------------
Q psy2983          90 QPTQAEKNRAGNTL------------------------------------------------------------------  103 (370)
Q Consensus        90 ~~~~~~~~~~~~~~------------------------------------------------------------------  103 (370)
                      +++..++.+.....                                                                  
T Consensus       201 kFADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~L~~l~a~~~qq~~~~  280 (510)
T KOG0144|consen  201 KFADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLPPLGPLNATQLQQAAAL  280 (510)
T ss_pred             EecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccccCCCCcchhHHHHHHHh
Confidence            66654332221000                                                                  


Q ss_pred             -------------CCC------------------------C---------------------------------------
Q psy2983         104 -------------PNL------------------------Q---------------------------------------  107 (370)
Q Consensus       104 -------------~~~------------------------~---------------------------------------  107 (370)
                                   ...                        .                                       
T Consensus       281 ~~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~~n~~~~~a~a~~~sp~  360 (510)
T KOG0144|consen  281 AAAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPANYNLAGGMAGAGTTSPV  360 (510)
T ss_pred             hhhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchhcccccccccccccCcc
Confidence                         000                        0                                       


Q ss_pred             ---------------------------------------------------------CCCCCCCceEEEecCCCCCCHHH
Q psy2983         108 ---------------------------------------------------------PRGTGGPMRLYIGSLHFNITEDM  130 (370)
Q Consensus       108 ---------------------------------------------------------~~~~~~~~~l~V~nlp~~~t~e~  130 (370)
                                                                               .........|||.+||.+.-+.+
T Consensus       361 aa~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpeGanlfiyhlPqefgdq~  440 (510)
T KOG0144|consen  361 AASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPEGANLFIYHLPQEFGDQD  440 (510)
T ss_pred             cccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCCccceeeeeCchhhhhHH
Confidence                                                                     00001113499999999999999


Q ss_pred             HHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecCCC
Q psy2983         131 LRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNE  196 (370)
Q Consensus       131 l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~~~  196 (370)
                      |-..|.+||.|.+.++..|+.+|.++.|+||.|++..+|..||..|||..++.++++|....++..
T Consensus       441 l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~~~n  506 (510)
T KOG0144|consen  441 LIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRDRNN  506 (510)
T ss_pred             HHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeeccCC
Confidence            999999999999999999999999999999999999999999999999999999999998776554

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.77  E-value=5.2e-18  Score=161.00  Aligned_cols=136  Identities=24%  Similarity=0.371  Sum_probs=119.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||+++++++|+++|+.||.|.+|++++|..+++++|||||+|.++++|.+|++.|++..+.+++|+|.+
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~  183 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSY  183 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeec
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             eecC-------CCCcCCCCCCCCHHHHHHhcccCCceeeeeeeeccc----cCCC---CCChHHHHHHHh
Q psy2983         191 VTDR-------NESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLA----EGTG---LELPPAAASALN  246 (370)
Q Consensus       191 ~~~~-------~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~~----~~~~---~~~~~~a~~a~~  246 (370)
                      +.+.       ...+.+++..+++++|++.|..+|.+..+.++.+..    ++++   |...+.|..|+.
T Consensus       184 a~p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~  253 (346)
T TIGR01659       184 ARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAIS  253 (346)
T ss_pred             ccccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHH
Confidence            7543       234778999999999999999999999999887632    2444   667788877766

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).

>KOG4206|consensus

Probab=99.77  E-value=1.1e-17  Score=144.06  Aligned_cols=173  Identities=23%  Similarity=0.445  Sum_probs=142.2

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHH----HhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCee
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEE----FFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIP   86 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~----~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~   86 (370)
                      ...+..||||.||+..+..++|+.    +|++||.|.+|...+   +.+.+|.|||.|.+.+.|..|+. |+|..+.|++
T Consensus         5 ~~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~   81 (221)
T KOG4206|consen    5 SVNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKP   81 (221)
T ss_pred             ccCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCch
Confidence            344556999999999999999988    999999999987764   46789999999999999999995 9999999999


Q ss_pred             EEEecccccccccCCCC-------------------C-----------------C-CCCCCCCCCceEEEecCCCCCCHH
Q psy2983          87 IIVQPTQAEKNRAGNTL-------------------P-----------------N-LQPRGTGGPMRLYIGSLHFNITED  129 (370)
Q Consensus        87 l~v~~~~~~~~~~~~~~-------------------~-----------------~-~~~~~~~~~~~l~V~nlp~~~t~e  129 (370)
                      ++|+++...........                   +                 . .......+...+++.|||..++.+
T Consensus        82 mriqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e  161 (221)
T KOG4206|consen   82 MRIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESE  161 (221)
T ss_pred             hheecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHH
Confidence            99998875433222100                   0                 0 001113345689999999999999


Q ss_pred             HHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeC-CeeEEEEEee
Q psy2983         130 MLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELA-GRPMKVGTVT  192 (370)
Q Consensus       130 ~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~-g~~l~V~~~~  192 (370)
                      .+..+|++|...+.++++...     .+.|||+|.+...|..|...|.|..+. ...++|.++.
T Consensus       162 ~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  162 MLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            999999999999999988654     779999999999999999999999887 8888887753

>KOG0110|consensus

Probab=99.75  E-value=2.1e-17  Score=161.86  Aligned_cols=231  Identities=21%  Similarity=0.323  Sum_probs=176.6

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPII   88 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~   88 (370)
                      ++..+..+.++|+|||..+..++|...|..||+|..+.+.+   .|.   -|+|+|.++.+|..|+. +....+...+++
T Consensus       379 ~~~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~---~G~---~aiv~fl~p~eAr~Afrklaysr~k~~ply  452 (725)
T KOG0110|consen  379 SQAERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPP---GGT---GAIVEFLNPLEARKAFRKLAYSRFKSAPLY  452 (725)
T ss_pred             hhhhhhcceeeeccCccccccHHHHHHhhcccccceeecCc---ccc---eeeeeecCccchHHHHHHhchhhhccCccc
Confidence            44678889999999999999999999999999999995542   222   39999999999999996 888888888888


Q ss_pred             EecccccccccC---------CCCC------------------CCC----C------CCCCCCceEEEecCCCCCCHHHH
Q psy2983          89 VQPTQAEKNRAG---------NTLP------------------NLQ----P------RGTGGPMRLYIGSLHFNITEDML  131 (370)
Q Consensus        89 v~~~~~~~~~~~---------~~~~------------------~~~----~------~~~~~~~~l~V~nlp~~~t~e~l  131 (370)
                      +.|.....-...         ....                  +..    .      .......+|||.||+++.+.+++
T Consensus       453 le~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l  532 (725)
T KOG0110|consen  453 LEWAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDL  532 (725)
T ss_pred             cccChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHH
Confidence            766543211100         0000                  000    0      00111234999999999999999


Q ss_pred             HhcccCCCceeeEEEeecCCCC---CcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecCC-------------
Q psy2983         132 RGIFEPFGKIDNIQLMVDPDTG---RSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRN-------------  195 (370)
Q Consensus       132 ~~~f~~~G~i~~v~~~~~~~~g---~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~~-------------  195 (370)
                      ..+|...|.|.++.|.+.++..   .+.|||||+|.++++|+.|+..|+|..++|+.|.|+++....             
T Consensus       533 ~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~gK~~~~kk~  612 (725)
T KOG0110|consen  533 EDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTVGKKKSKKKK  612 (725)
T ss_pred             HHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccccccccccccccc
Confidence            9999999999999887665321   355999999999999999999999999999999999886111             


Q ss_pred             ---CCcCCCCCCCCHHHHHHhcccCCceeeeeeeecc----ccCCC---CCChHHHHHHHh
Q psy2983         196 ---ESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKL----AEGTG---LELPPAAASALN  246 (370)
Q Consensus       196 ---~~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~----~~~~~---~~~~~~a~~a~~  246 (370)
                         ..+.++|-..+..+++..|..||.+.++.+..+.    .+||+   |..|..+..|+.
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~  673 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFD  673 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHH
Confidence               1145677778888999999999999999998873    35566   456666666654

>KOG1548|consensus

Probab=99.75  E-value=2.3e-17  Score=149.30  Aligned_cols=164  Identities=21%  Similarity=0.334  Sum_probs=120.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceee--------EEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeC
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDN--------IQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELA  182 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~--------v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~  182 (370)
                      ...+..|||+|||.++|.+++.++|+++|.|..        |+++++. .|..+|-|+|.|...+++..|++.|++..+.
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCccccc
Confidence            334567999999999999999999999998763        8999995 6999999999999999999999999999999


Q ss_pred             CeeEEEEEeecCCCCcCCCCCC-----CCHHHHHHhcccCCceeeeeeeeccccCCCCCChHHHHHHHhhhcccccCCCC
Q psy2983         183 GRPMKVGTVTDRNESVGGGPSN-----LDTDEMERAGVDLGATGRLQLMFKLAEGTGLELPPAAASALNLAQNAILNSST  257 (370)
Q Consensus       183 g~~l~V~~~~~~~~~~~~~~~~-----~~~~~l~~~~~~~g~~~~~~l~~~~~~~~~~~~~~~a~~a~~~~~~~~~~p~~  257 (370)
                      |+.|+|..|+-....-......     .....+.....               ..++- .|.                  
T Consensus       210 g~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~---------------k~~dw-~pd------------------  255 (382)
T KOG1548|consen  210 GKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQ---------------KLLDW-RPD------------------  255 (382)
T ss_pred             CcEEEEehhhhhhccCcCcccccccccccHHHHHHHHH---------------hhccc-CCC------------------
Confidence            9999999986544332111111     01111110000               00000 000                  


Q ss_pred             CCCCCCCCCCCCCceEEeecCCCCCCC-CCchhhHHhHHHHHHHHhhcCceeeEEE
Q psy2983         258 PQVSSSTAPPIATQCFLLANMFDPATE-TNPTWDVEIRDDVIEECNKHGVGASTVC  312 (370)
Q Consensus       258 ~~~~~~~~~~~ps~vl~L~Nm~~~~~l-~~d~~~~ei~eDv~~Ec~kyG~~~~~~~  312 (370)
                         -..+......++|+|+|||+|+++ .+++...||+||+++||+|||.+-.+++
T Consensus       256 ---~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv  308 (382)
T KOG1548|consen  256 ---RDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVV  308 (382)
T ss_pred             ---ccccccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEE
Confidence               001223456788999999999998 4559999999999999999999877665

>KOG0105|consensus

Probab=99.74  E-value=6.9e-17  Score=134.11  Aligned_cols=167  Identities=19%  Similarity=0.308  Sum_probs=132.8

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      .+.+++|||+|||.++.+.+|+++|-+||.|..|.+...+   ....||||+|+++.+|+.|+. -+|..+.|..|.|..
T Consensus         3 gr~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEf   79 (241)
T KOG0105|consen    3 GRNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEF   79 (241)
T ss_pred             CcccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEEe
Confidence            4678999999999999999999999999999999885432   235799999999999999995 999999999999998


Q ss_pred             ccccccccCCCC-------------CCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccE
Q psy2983          92 TQAEKNRAGNTL-------------PNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGY  158 (370)
Q Consensus        92 ~~~~~~~~~~~~-------------~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~  158 (370)
                      +..........-             ....+...-...++.|++||++-+.++|+++..+.|.|-...+.+|.       +
T Consensus        80 prggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rDg-------~  152 (241)
T KOG0105|consen   80 PRGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRDG-------V  152 (241)
T ss_pred             ccCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeeccc-------c
Confidence            865431111000             00011111223579999999999999999999999999998888773       8


Q ss_pred             EEEEECCHHHHHHHHHHhCCceeC--CeeEEEE
Q psy2983         159 GFITFHSADDAKKAQEQLNGFELA--GRPMKVG  189 (370)
Q Consensus       159 afV~f~~~~~a~~A~~~l~g~~i~--g~~l~V~  189 (370)
                      +.|+|...++..-|+..|+.+.+.  |-...+.
T Consensus       153 GvV~~~r~eDMkYAvr~ld~~~~~seGe~~yir  185 (241)
T KOG0105|consen  153 GVVEYLRKEDMKYAVRKLDDQKFRSEGETAYIR  185 (241)
T ss_pred             eeeeeeehhhHHHHHHhhccccccCcCcEeeEE
Confidence            999999999999999999987765  4444443

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

Probab=99.72  E-value=4.4e-17  Score=162.87  Aligned_cols=133  Identities=31%  Similarity=0.528  Sum_probs=115.4

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ..++|||+|||+.+++++|+++|++||.|.+++++.|+.+|+++|||||+|.+.++|.+|+..|||..+.|+.|+|.+..
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999998643


Q ss_pred             cC------------------CCCcCCCCCCCCHHHHHHhcccCCceeeeeeeecc----ccCCC---CCChHHHHHHH
Q psy2983         193 DR------------------NESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKL----AEGTG---LELPPAAASAL  245 (370)
Q Consensus       193 ~~------------------~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~----~~~~~---~~~~~~a~~a~  245 (370)
                      ..                  ...+++++..+++++|+..|..||.+.++.++.+.    .+|+|   |....++..|+
T Consensus       186 ~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI  263 (612)
T TIGR01645       186 NMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAI  263 (612)
T ss_pred             cccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHH
Confidence            21                  12367899999999999999999999999998763    45565   45566665554

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.

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

Probab=99.68  E-value=3.1e-16  Score=130.80  Aligned_cols=85  Identities=34%  Similarity=0.679  Sum_probs=79.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ...++|||+|||+.+++++|+++|++||.|.++.++.|+.+++++|||||+|.+.++|+.|++.||+..|.|+.|+|.++
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            34578999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ecCCC
Q psy2983         192 TDRNE  196 (370)
Q Consensus       192 ~~~~~  196 (370)
                      .++..
T Consensus       112 ~~~~~  116 (144)
T PLN03134        112 NDRPS  116 (144)
T ss_pred             CcCCC
Confidence            76544

>KOG4211|consensus

Probab=99.67  E-value=1.2e-15  Score=144.15  Aligned_cols=173  Identities=21%  Similarity=0.272  Sum_probs=138.6

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEec
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQP   91 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~   91 (370)
                      +-.....|-+++||.++|++||.+||+.+ .|.++.+.+  .+|+..|-|||||.+.|++.+|++.+...+..+.|.|..
T Consensus         6 e~~~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~   82 (510)
T KOG4211|consen    6 EGSTAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPR--RNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFT   82 (510)
T ss_pred             CCCcceEEEecCCCccccHHHHHHHHhcC-ceeEEEEec--cCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEc
Confidence            44566779999999999999999999999 588866555  458889999999999999999999999999999999987


Q ss_pred             ccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceee-EEEeecCCCCCcccEEEEEECCHHHHH
Q psy2983          92 TQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDN-IQLMVDPDTGRSKGYGFITFHSADDAK  170 (370)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~-v~~~~~~~~g~~~g~afV~f~~~~~a~  170 (370)
                      +.......  ......+....+...|.+++||+.+|++||.++|+..-.+.. +-++.+ ..+++.|-|||+|++.+.|+
T Consensus        83 ~~~~e~d~--~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d-~rgR~tGEAfVqF~sqe~ae  159 (510)
T KOG4211|consen   83 AGGAEADW--VMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMD-QRGRPTGEAFVQFESQESAE  159 (510)
T ss_pred             cCCccccc--cccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeecc-CCCCcccceEEEecCHHHHH
Confidence            75433211  111222222244568999999999999999999998766665 445555 47889999999999999999


Q ss_pred             HHHHHhCCceeCCeeEEEEEe
Q psy2983         171 KAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       171 ~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      +|+. -|...|+-|-|.|-.+
T Consensus       160 ~Al~-rhre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  160 IALG-RHRENIGHRYIEVFRS  179 (510)
T ss_pred             HHHH-HHHHhhccceEEeehh
Confidence            9999 5777888888888554

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

Probab=99.65  E-value=4.8e-16  Score=129.63  Aligned_cols=83  Identities=25%  Similarity=0.434  Sum_probs=77.9

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      ...+++|||+|||..+++++|+++|++||.|.++.++.|..+++++|||||+|.+.++|+.|++ +++..|.|++|+|.+
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            3457889999999999999999999999999999999999999999999999999999999996 999999999999998


Q ss_pred             cccc
Q psy2983          92 TQAE   95 (370)
Q Consensus        92 ~~~~   95 (370)
                      +...
T Consensus       111 a~~~  114 (144)
T PLN03134        111 ANDR  114 (144)
T ss_pred             CCcC
Confidence            7654

>KOG0147|consensus

Probab=99.65  E-value=4.1e-16  Score=149.11  Aligned_cols=175  Identities=24%  Similarity=0.278  Sum_probs=132.8

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      +.+-++|||+||-.++++++|+..|++||+|..|.+.+|..+|+++||+||+|.+.++|.+|++ |||..+-|+.|+|..
T Consensus       275 ~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~  354 (549)
T KOG0147|consen  275 TGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSV  354 (549)
T ss_pred             ccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEE
Confidence            3455569999999999999999999999999999999999999999999999999999999985 999999999999854


Q ss_pred             ccccccccCC---C----------C------------------C-----------------------C-----CCCCCC-
Q psy2983          92 TQAEKNRAGN---T----------L------------------P-----------------------N-----LQPRGT-  111 (370)
Q Consensus        92 ~~~~~~~~~~---~----------~------------------~-----------------------~-----~~~~~~-  111 (370)
                      ..........   .          .                  .                       .     ...... 
T Consensus       355 v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~  434 (549)
T KOG0147|consen  355 VTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPAD  434 (549)
T ss_pred             eeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCccc
Confidence            3211110000   0          0                  0                       0     000000 


Q ss_pred             ------CCCceEEEecCCC--CCC--------HHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHH
Q psy2983         112 ------GGPMRLYIGSLHF--NIT--------EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ  175 (370)
Q Consensus       112 ------~~~~~l~V~nlp~--~~t--------~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~  175 (370)
                            .+..++.+.|+=.  ..|        .+++.+-+.+||.|..|.+-++     +.|+.||.|.+.+.|..|+.+
T Consensus       435 ~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~n-----s~g~VYvrc~s~~~A~~a~~a  509 (549)
T KOG0147|consen  435 ASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKN-----SAGCVYVRCPSAEAAGTAVKA  509 (549)
T ss_pred             cccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccC-----CCceEEEecCcHHHHHHHHHH
Confidence                  1223455555521  111        2788888999999977666333     349999999999999999999


Q ss_pred             hCCceeCCeeEEEEEee
Q psy2983         176 LNGFELAGRPMKVGTVT  192 (370)
Q Consensus       176 l~g~~i~g~~l~V~~~~  192 (370)
                      |||.-|.|+.|+..+..
T Consensus       510 lhgrWF~gr~Ita~~~~  526 (549)
T KOG0147|consen  510 LHGRWFAGRMITAKYLP  526 (549)
T ss_pred             HhhhhhccceeEEEEee
Confidence            99999999999998853

>KOG4212|consensus

Probab=99.64  E-value=4.9e-15  Score=137.69  Aligned_cols=177  Identities=25%  Similarity=0.423  Sum_probs=144.6

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhc-CCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSS-VGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~-~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      +...|.+||.|||+++..++|+++|.. .|+|..|.++.|.. ++++|+|.|||+++|.+++|++ |+...+.|++|.|+
T Consensus        41 ~~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~-GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vK  119 (608)
T KOG4212|consen   41 AARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDES-GKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVK  119 (608)
T ss_pred             ccccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccC-CCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEe
Confidence            345577999999999999999999985 89999999999864 8999999999999999999997 99999999999996


Q ss_pred             cccccccc-cCCC-----------------------------------CCC-----------------------------
Q psy2983          91 PTQAEKNR-AGNT-----------------------------------LPN-----------------------------  105 (370)
Q Consensus        91 ~~~~~~~~-~~~~-----------------------------------~~~-----------------------------  105 (370)
                      ....+... ....                                   ...                             
T Consensus       120 Ed~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl  199 (608)
T KOG4212|consen  120 EDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGL  199 (608)
T ss_pred             ccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccc
Confidence            44321100 0000                                   000                             


Q ss_pred             -------CCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCC
Q psy2983         106 -------LQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNG  178 (370)
Q Consensus       106 -------~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g  178 (370)
                             ...-.++-..++||.||.+.+..+.|++.|.-.|.++.+.+-.|+ .|.++|+|.++|.++-.|..|+.+|++
T Consensus       200 ~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idK-eG~s~G~~vi~y~hpveavqaIsml~~  278 (608)
T KOG4212|consen  200 SASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDK-EGNSRGFAVIEYDHPVEAVQAISMLDR  278 (608)
T ss_pred             hhhhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeecc-ccccCCeeEEEecchHHHHHHHHhhcc
Confidence                   000012223579999999999999999999999999999999997 679999999999999999999999999


Q ss_pred             ceeCCeeEEEEEe
Q psy2983         179 FELAGRPMKVGTV  191 (370)
Q Consensus       179 ~~i~g~~l~V~~~  191 (370)
                      .-+.+++..++..
T Consensus       279 ~g~~~~~~~~Rl~  291 (608)
T KOG4212|consen  279 QGLFDRRMTVRLD  291 (608)
T ss_pred             CCCccccceeecc
Confidence            8888888877763

>KOG1548|consensus

Probab=99.60  E-value=8.9e-14  Score=126.16  Aligned_cols=180  Identities=18%  Similarity=0.304  Sum_probs=141.0

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCee--------EEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccC
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVR--------DVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLL   83 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~--------~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~   83 (370)
                      ......|||.|||.++|.+++.++|+.||-|.        .|++.++.. |..||=|++.|-..|++..|+. |++..+.
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCccccc
Confidence            44556699999999999999999999999764        367777765 8999999999999999999997 9999999


Q ss_pred             CeeEEEecccccccccCCCC------------------------C-CCCCCCCCCCceEEEecCCC----CCC-------
Q psy2983          84 GIPIIVQPTQAEKNRAGNTL------------------------P-NLQPRGTGGPMRLYIGSLHF----NIT-------  127 (370)
Q Consensus        84 g~~l~v~~~~~~~~~~~~~~------------------------~-~~~~~~~~~~~~l~V~nlp~----~~t-------  127 (370)
                      |+.|+|++++.+........                        + ...+......++|.+.|+=.    ..+       
T Consensus       210 g~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dl  289 (382)
T KOG1548|consen  210 GKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDL  289 (382)
T ss_pred             CcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHH
Confidence            99999998875432111110                        0 01122233456888888731    122       


Q ss_pred             HHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecCCCC
Q psy2983         128 EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNES  197 (370)
Q Consensus       128 ~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~~~~  197 (370)
                      .++|++-+++||.|.+|.+.    ...+.|.+-|.|.+.+.|..|++.|+|.-|.||.|....-......
T Consensus       290 kedl~eec~K~G~v~~vvv~----d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~t~~  355 (382)
T KOG1548|consen  290 KEDLTEECEKFGQVRKVVVY----DRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGKTKF  355 (382)
T ss_pred             HHHHHHHHHHhCCcceEEEe----ccCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCccee
Confidence            36788889999999999886    3446889999999999999999999999999999998876554443

>KOG0106|consensus

Probab=99.58  E-value=4.1e-15  Score=129.42  Aligned_cols=156  Identities=28%  Similarity=0.555  Sum_probs=128.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHh-hccCCccCCeeEEEeccccc
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAE   95 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~i~g~~l~v~~~~~~   95 (370)
                      .+|||++||+.+.+.+|..||..||.+.++.+.        .||+||+|.+..+|..|+ .+++..+.|..+.+.++...
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            469999999999999999999999999999774        379999999999999999 69999999999888887743


Q ss_pred             ccccCCCC-------CCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHH
Q psy2983          96 KNRAGNTL-------PNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADD  168 (370)
Q Consensus        96 ~~~~~~~~-------~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~  168 (370)
                      ........       ...-....-....+.+.+++..+...+|.+.|.++|.+.....        ..+++||+|.+.++
T Consensus        74 ~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~d  145 (216)
T KOG0106|consen   74 RRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQED  145 (216)
T ss_pred             ccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhh
Confidence            22111110       0111112234567999999999999999999999999854433        36689999999999


Q ss_pred             HHHHHHHhCCceeCCeeEEE
Q psy2983         169 AKKAQEQLNGFELAGRPMKV  188 (370)
Q Consensus       169 a~~A~~~l~g~~i~g~~l~V  188 (370)
                      +.+|+..|+|..+.++.|.+
T Consensus       146 a~ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen  146 AKRALEKLDGKKLNGRRISV  165 (216)
T ss_pred             hhhcchhccchhhcCceeee
Confidence            99999999999999999999

>PF00076 RRM_1: RNA recognition motif

Probab=99.57  E-value=1.3e-14  Score=105.45  Aligned_cols=70  Identities=47%  Similarity=0.899  Sum_probs=67.4

Q ss_pred             EEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEE
Q psy2983         117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMK  187 (370)
Q Consensus       117 l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~  187 (370)
                      |||+|||.++++++|+++|++||.|..+.+..+ .++.++|+|||+|.+.++|.+|++.|+|..+.|+.|+
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 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999998 5899999999999999999999999999999999885

(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 ....

>KOG0131|consensus

Probab=99.57  E-value=8.6e-15  Score=121.62  Aligned_cols=118  Identities=26%  Similarity=0.423  Sum_probs=105.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      +...+|||+||+..++++.|.++|-+.|+|..+++.+|..++..+||||++|.++++|.-|++.||...++|++|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            44579999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ecCCC--------CcCCCCCCCCHHHHHHhcccCCceee-eeeeecc
Q psy2983         192 TDRNE--------SVGGGPSNLDTDEMERAGVDLGATGR-LQLMFKL  229 (370)
Q Consensus       192 ~~~~~--------~~~~~~~~~~~~~l~~~~~~~g~~~~-~~l~~~~  229 (370)
                      .....        .++++...+++..|-..|+.||.+.+ .++|+..
T Consensus        87 s~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~  133 (203)
T KOG0131|consen   87 SAHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDP  133 (203)
T ss_pred             ccccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccc
Confidence            73322        26678889999999999999999865 4666663

>KOG1457|consensus

Probab=99.55  E-value=5.6e-14  Score=120.22  Aligned_cols=166  Identities=21%  Similarity=0.315  Sum_probs=119.0

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEee-eCCCCCeecEEEEEecCCCChHHHh-hccCCccC---CeeE
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLIT-CNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLL---GIPI   87 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~-d~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~i~---g~~l   87 (370)
                      ...-|||||.+||.++...+|+.+|..|--.+...+.. ++.....+-+|||.|.+..+|..|+ +|+|..|+   +..|
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stL  110 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTL  110 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCcee
Confidence            34579999999999999999999999985555554433 2222335689999999999999999 49999985   6677


Q ss_pred             EEecccccccccC----CCCCC-------------C-------------------------C------------------
Q psy2983          88 IVQPTQAEKNRAG----NTLPN-------------L-------------------------Q------------------  107 (370)
Q Consensus        88 ~v~~~~~~~~~~~----~~~~~-------------~-------------------------~------------------  107 (370)
                      ++..++....+..    ..+.+             .                         .                  
T Consensus       111 hiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~  190 (284)
T KOG1457|consen  111 HIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKA  190 (284)
T ss_pred             EeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcC
Confidence            7765543221111    00000             0                         0                  


Q ss_pred             -------------CCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHH
Q psy2983         108 -------------PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE  174 (370)
Q Consensus       108 -------------~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~  174 (370)
                                   ......+.+|||.||..+++|++|+.+|+.|.-...+++...  .|  ...||++|++.+.|..|+.
T Consensus       191 P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~g--~~vaf~~~~~~~~at~am~  266 (284)
T KOG1457|consen  191 PSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--GG--MPVAFADFEEIEQATDAMN  266 (284)
T ss_pred             CcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--CC--cceEeecHHHHHHHHHHHH
Confidence                         000011247999999999999999999999976555555422  23  3479999999999999999


Q ss_pred             HhCCceeC
Q psy2983         175 QLNGFELA  182 (370)
Q Consensus       175 ~l~g~~i~  182 (370)
                      .|.|..+-
T Consensus       267 ~lqg~~~s  274 (284)
T KOG1457|consen  267 HLQGNLLS  274 (284)
T ss_pred             Hhhcceec
Confidence            99997764

>PF00076 RRM_1: RNA recognition motif

Probab=99.55  E-value=1.2e-14  Score=105.79  Aligned_cols=69  Identities=29%  Similarity=0.592  Sum_probs=65.8

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEE
Q psy2983          19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPII   88 (370)
Q Consensus        19 v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~   88 (370)
                      |||+|||.++|+++|+++|++||.|..+.+..+ .++..+|||||+|.+.++|..|++ ++|..+.|++|+
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 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999998 678899999999999999999997 999999999885

(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 ....

>KOG1190|consensus

Probab=99.55  E-value=4.1e-14  Score=130.72  Aligned_cols=168  Identities=19%  Similarity=0.345  Sum_probs=124.6

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh---ccCCccCCeeEEE
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG---LNGQKLLGIPIIV   89 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~---l~g~~i~g~~l~v   89 (370)
                      ..+++.|+++|||.+++|+||.+++.+||.|..+.+++.      +..||+||.+.++|..-+.   --.-.+.|++|+|
T Consensus        25 ~~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkG------knQAflem~d~~sAvtmv~~y~~~~p~lr~~~~yi   98 (492)
T KOG1190|consen   25 AEPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKG------KNQAFLEMADEESAVTMVNYYTSVTPVLRGQPIYI   98 (492)
T ss_pred             cCCcceeEeccCCccccHHHHHHhcccccceeeeeeecc------chhhhhhhcchhhhhheeecccccCccccCcceee
Confidence            458899999999999999999999999999999988663      4489999999999887543   2333567889999


Q ss_pred             ecccccccccCCCC--------------------CC----C---CCCCCCCCceEEEecCCCCCCHHHHHhcccCCCcee
Q psy2983          90 QPTQAEKNRAGNTL--------------------PN----L---QPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKID  142 (370)
Q Consensus        90 ~~~~~~~~~~~~~~--------------------~~----~---~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~  142 (370)
                      +++....-......                    +.    .   ....+..-.++.|+|+-+.++-+-|+++|++||.|.
T Consensus        99 q~sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~Vl  178 (492)
T KOG1190|consen   99 QYSNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVL  178 (492)
T ss_pred             hhhhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeE
Confidence            87753221111100                    00    0   001111224688899999999999999999999998


Q ss_pred             eEEEeecCCCCCcccE-EEEEECCHHHHHHHHHHhCCceeCCe--eEEEEEe
Q psy2983         143 NIQLMVDPDTGRSKGY-GFITFHSADDAKKAQEQLNGFELAGR--PMKVGTV  191 (370)
Q Consensus       143 ~v~~~~~~~~g~~~g~-afV~f~~~~~a~~A~~~l~g~~i~g~--~l~V~~~  191 (370)
                      +|.-+..     +.|| |+|+|.+.++|..|..+|+|+.|++-  .|+|.++
T Consensus       179 KIiTF~K-----nn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~S  225 (492)
T KOG1190|consen  179 KIITFTK-----NNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFS  225 (492)
T ss_pred             EEEEEec-----ccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehh
Confidence            8755422     2344 99999999999999999999999864  4444443

>KOG0124|consensus

Probab=99.54  E-value=1.2e-14  Score=132.42  Aligned_cols=114  Identities=33%  Similarity=0.597  Sum_probs=103.6

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecC
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~  194 (370)
                      +++|||.+.+.+.++.|+..|.+||+|++|.+--|+-|++++|||||+|+-+|.|+.|++.|||..++||.|+|.+...-
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNm  193 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM  193 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCC
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999864321


Q ss_pred             C------------------CCcCCCCCCCCHHHHHHhcccCCceeeeeeeec
Q psy2983         195 N------------------ESVGGGPSNLDTDEMERAGVDLGATGRLQLMFK  228 (370)
Q Consensus       195 ~------------------~~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~  228 (370)
                      .                  .++......+++++++..|+.||.+..+++.+.
T Consensus       194 pQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~  245 (544)
T KOG0124|consen  194 PQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARA  245 (544)
T ss_pred             cccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeecc
Confidence            1                  114567889999999999999999999999775

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

Probab=99.53  E-value=1.1e-13  Score=127.09  Aligned_cols=158  Identities=29%  Similarity=0.442  Sum_probs=119.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecccc
Q psy2983          16 ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQA   94 (370)
Q Consensus        16 ~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~   94 (370)
                      .++|||+|||..+++++|+++|..||.|..+.+..++.++.++|||||+|.+.++|..|++ ++|..|.|++|.|.+...
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            6999999999999999999999999999999999999899999999999999999999996 999999999999999642


Q ss_pred             -cccccCCC----------CCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEE
Q psy2983          95 -EKNRAGNT----------LPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITF  163 (370)
Q Consensus        95 -~~~~~~~~----------~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f  163 (370)
                       ...+....          ..............+++++++..++..++...|..+|.+....+.............++.+
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  274 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGN  274 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCCCcccccccccch
Confidence             11111100          0111122233456799999999999999999999999997766654433333333344444


Q ss_pred             CCHHHHHHHH
Q psy2983         164 HSADDAKKAQ  173 (370)
Q Consensus       164 ~~~~~a~~A~  173 (370)
                      .....+....
T Consensus       275 ~~~~~~~~~~  284 (306)
T COG0724         275 EASKDALESN  284 (306)
T ss_pred             hHHHhhhhhh
Confidence            3333333333

>KOG0120|consensus

Probab=99.51  E-value=2.2e-13  Score=132.11  Aligned_cols=179  Identities=21%  Similarity=0.343  Sum_probs=140.1

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      ......+||++||...++.++.+++..||++....++.|..+|.++||||.+|.++.....|++ |+|+.+.++.|.|+.
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~  365 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQR  365 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeeh
Confidence            3456789999999999999999999999999999999999999999999999999999999996 999999999999988


Q ss_pred             ccccccccCCCCC-------CCC----CCCCCCCceEEEecCC--CCC-CH-------HHHHhcccCCCceeeEEEeec-
Q psy2983          92 TQAEKNRAGNTLP-------NLQ----PRGTGGPMRLYIGSLH--FNI-TE-------DMLRGIFEPFGKIDNIQLMVD-  149 (370)
Q Consensus        92 ~~~~~~~~~~~~~-------~~~----~~~~~~~~~l~V~nlp--~~~-t~-------e~l~~~f~~~G~i~~v~~~~~-  149 (370)
                      +............       ...    +........|++.|+=  .+. .+       |+++.-+.+||.|..|.+.++ 
T Consensus       366 A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~  445 (500)
T KOG0120|consen  366 AIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPY  445 (500)
T ss_pred             hhccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCC
Confidence            7644322221111       000    1112223345555541  111 11       567777889999999999877 


Q ss_pred             C--CCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         150 P--DTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       150 ~--~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      .  ...-..|..||+|.+.+++++|...|+|..|.||.+...+.
T Consensus       446 ~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYy  489 (500)
T KOG0120|consen  446 PDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYY  489 (500)
T ss_pred             CCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEec
Confidence            2  12346778999999999999999999999999999998884

>KOG0122|consensus

Probab=99.51  E-value=7e-14  Score=121.36  Aligned_cols=84  Identities=33%  Similarity=0.547  Sum_probs=79.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      .....+|.|.||+.++++++|+++|.+||.|..+.+.+|++||.++|||||.|.+.++|.+|+..|||.-++.--|+|.|
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEw  265 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEW  265 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEe
Confidence            34557899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecC
Q psy2983         191 VTDR  194 (370)
Q Consensus       191 ~~~~  194 (370)
                      ++++
T Consensus       266 skP~  269 (270)
T KOG0122|consen  266 SKPS  269 (270)
T ss_pred             cCCC
Confidence            8875

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.50  E-value=1.8e-13  Score=99.77  Aligned_cols=70  Identities=41%  Similarity=0.799  Sum_probs=65.1

Q ss_pred             EEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEE
Q psy2983         117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMK  187 (370)
Q Consensus       117 l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~  187 (370)
                      |||+|||+.+++++|+++|+.||.|..+.+..++. |.++|+|||+|.+.++|.+|+..++|..+.|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999976 99999999999999999999999999999999875

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 ....

>KOG0125|consensus

Probab=99.50  E-value=5.9e-14  Score=126.46  Aligned_cols=83  Identities=33%  Similarity=0.666  Sum_probs=77.4

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEE
Q psy2983         110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG  189 (370)
Q Consensus       110 ~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~  189 (370)
                      ...++++|+|+|||+...+.||+.+|++||.|.+|.|+.+  ...+||||||+|++.++|++|.+.|||..+.||+|.|.
T Consensus        92 s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn  169 (376)
T KOG0125|consen   92 SKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVN  169 (376)
T ss_pred             CCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEe
Confidence            4456789999999999999999999999999999999987  56789999999999999999999999999999999999


Q ss_pred             EeecC
Q psy2983         190 TVTDR  194 (370)
Q Consensus       190 ~~~~~  194 (370)
                      .+..+
T Consensus       170 ~ATar  174 (376)
T KOG0125|consen  170 NATAR  174 (376)
T ss_pred             ccchh
Confidence            98765

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.49  E-value=1.1e-13  Score=123.78  Aligned_cols=78  Identities=29%  Similarity=0.516  Sum_probs=72.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecccc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQA   94 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~~~   94 (370)
                      ..++|||+|||+.+|+++|+++|+.||+|.+|.|++++.   ++|||||+|.++++|..|+.|+|..|.|+.|.|.+...
T Consensus         3 ~~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          3 QVRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEeccC
Confidence            368999999999999999999999999999999998863   46899999999999999999999999999999998765


Q ss_pred             c
Q psy2983          95 E   95 (370)
Q Consensus        95 ~   95 (370)
                      .
T Consensus        80 ~   80 (260)
T PLN03120         80 Y   80 (260)
T ss_pred             C
Confidence            4

>KOG0122|consensus

Probab=99.49  E-value=1.1e-13  Score=120.09  Aligned_cols=82  Identities=28%  Similarity=0.418  Sum_probs=78.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      .+..+|-|.|||.+++|++|+++|.+||+|..+.+.+|+.||.+||||||.|.+.++|.+|++ |+|.-+..--|.|.|+
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws  266 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS  266 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec
Confidence            467889999999999999999999999999999999999999999999999999999999996 9999999999999998


Q ss_pred             ccc
Q psy2983          93 QAE   95 (370)
Q Consensus        93 ~~~   95 (370)
                      ++.
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            753

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.48  E-value=7.2e-14  Score=101.91  Aligned_cols=69  Identities=32%  Similarity=0.566  Sum_probs=62.9

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEE
Q psy2983          19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPII   88 (370)
Q Consensus        19 v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~   88 (370)
                      |||+|||+.+++++|+++|+.+|.|..+.+..++. +.++|+|||+|.+.++|.+|++ ++|..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999877 8999999999999999999997 666999999874

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 ....

>KOG0121|consensus

Probab=99.45  E-value=1.5e-13  Score=107.70  Aligned_cols=83  Identities=19%  Similarity=0.291  Sum_probs=77.0

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEE
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIV   89 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v   89 (370)
                      .+.+.+.||||+||+..++|++|+++|+.+|+|+.|.+=.|+.+...=|||||+|.+.++|..|+. ++|..+..++|.+
T Consensus        31 ~a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~  110 (153)
T KOG0121|consen   31 EALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRI  110 (153)
T ss_pred             HHHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceee
Confidence            346889999999999999999999999999999999888888877788999999999999999998 9999999999999


Q ss_pred             eccc
Q psy2983          90 QPTQ   93 (370)
Q Consensus        90 ~~~~   93 (370)
                      .+..
T Consensus       111 D~D~  114 (153)
T KOG0121|consen  111 DWDA  114 (153)
T ss_pred             eccc
Confidence            8765

>KOG0107|consensus

Probab=99.44  E-value=2.8e-13  Score=112.04  Aligned_cols=77  Identities=29%  Similarity=0.499  Sum_probs=71.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      -.++|||+||+..+++.||...|..||++.+||+.+++     .|||||||+++.+|+.|+. |+|..|.|..|.|+.+.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            36889999999999999999999999999999998865     5999999999999999995 99999999999999887


Q ss_pred             ccc
Q psy2983          94 AEK   96 (370)
Q Consensus        94 ~~~   96 (370)
                      ...
T Consensus        84 G~~   86 (195)
T KOG0107|consen   84 GRP   86 (195)
T ss_pred             CCc
Confidence            543

>KOG0149|consensus

Probab=99.43  E-value=1.7e-13  Score=118.59  Aligned_cols=79  Identities=33%  Similarity=0.591  Sum_probs=73.1

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      -.+||||||++.+..+.|+.+|++||+|.+..++.|+.+|++||||||+|.+.++|.+|++ =.+-.|+||+..|..+.-
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~-dp~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACK-DPNPIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhc-CCCCcccccccccchhhh
Confidence            4689999999999999999999999999999999999999999999999999999999998 456688999999987643

>KOG0125|consensus

Probab=99.43  E-value=4e-13  Score=121.15  Aligned_cols=85  Identities=27%  Similarity=0.430  Sum_probs=76.9

Q ss_pred             CCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeE
Q psy2983           9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPI   87 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l   87 (370)
                      .++.....++|+|.|||....+.||+..|++||+|.+|.|+.+.  +-||||+||.|.+++||++|-+ |||..+.||+|
T Consensus        89 ~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkI  166 (376)
T KOG0125|consen   89 NSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKI  166 (376)
T ss_pred             cCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEE
Confidence            34455667999999999999999999999999999999999976  4579999999999999999995 99999999999


Q ss_pred             EEeccccc
Q psy2983          88 IVQPTQAE   95 (370)
Q Consensus        88 ~v~~~~~~   95 (370)
                      .|..+...
T Consensus       167 EVn~ATar  174 (376)
T KOG0125|consen  167 EVNNATAR  174 (376)
T ss_pred             EEeccchh
Confidence            99887754

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.43  E-value=4.9e-13  Score=117.66  Aligned_cols=78  Identities=23%  Similarity=0.384  Sum_probs=71.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecccc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQA   94 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~~~   94 (370)
                      ..++|||+||++.+|+++|++||+.||+|.+|.|++|.   +.+++|||+|.++++|..|+.|+|..|.+++|.|.+...
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCcc
Confidence            56899999999999999999999999999999999984   456899999999999999999999999999999987654


Q ss_pred             c
Q psy2983          95 E   95 (370)
Q Consensus        95 ~   95 (370)
                      .
T Consensus        81 y   81 (243)
T PLN03121         81 Y   81 (243)
T ss_pred             c
Confidence            3

>KOG1190|consensus

Probab=99.42  E-value=3e-12  Score=118.53  Aligned_cols=168  Identities=18%  Similarity=0.277  Sum_probs=132.7

Q ss_pred             CCeEEEcCCC-CCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          16 ARTIFCMQLS-QRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        16 ~r~v~V~nLp-~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      ...|.|.||- ..+|.+.|..+|.-||.|..|+|+.+++     -.|+|+|.+...|.-|++ |+|..+.|++|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            5788999995 6789999999999999999999998763     469999999999999996 99999999999998887


Q ss_pred             ccccccCCC-----------CCC----CC---C----CCCCCCceEEEecCCCCCCHHHHHhcccCCCce-eeEEEeecC
Q psy2983          94 AEKNRAGNT-----------LPN----LQ---P----RGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKI-DNIQLMVDP  150 (370)
Q Consensus        94 ~~~~~~~~~-----------~~~----~~---~----~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i-~~v~~~~~~  150 (370)
                      ...-.....           ...    ..   .    ....++.+|++.|+|.++++|+++.+|..-|.. ...++.   
T Consensus       372 H~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff---  448 (492)
T KOG1190|consen  372 HTNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF---  448 (492)
T ss_pred             CccccCCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeec---
Confidence            432111110           000    00   0    012344689999999999999999999888754 444443   


Q ss_pred             CCCCcccEEEEEECCHHHHHHHHHHhCCceeCC-eeEEEEEeec
Q psy2983         151 DTGRSKGYGFITFHSADDAKKAQEQLNGFELAG-RPMKVGTVTD  193 (370)
Q Consensus       151 ~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g-~~l~V~~~~~  193 (370)
                        ++.+.+|++.+.+.|+|..|+..+|++.+++ .-++|++++.
T Consensus       449 --~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  449 --QKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             --CCCcceeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence              3346699999999999999999999999885 4899998754

>KOG0126|consensus

Probab=99.42  E-value=6.6e-14  Score=116.24  Aligned_cols=85  Identities=31%  Similarity=0.645  Sum_probs=79.2

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      .+.-|||||||+.+||.+|.-+|++||.|..|.+++|+.||+++||||+.|++..+...|+..|||..|.||.|+|.+..
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            34569999999999999999999999999999999999999999999999999999999999999999999999998876


Q ss_pred             cCCCC
Q psy2983         193 DRNES  197 (370)
Q Consensus       193 ~~~~~  197 (370)
                      ....+
T Consensus       114 ~Yk~p  118 (219)
T KOG0126|consen  114 NYKKP  118 (219)
T ss_pred             cccCC
Confidence            55443

>KOG0126|consensus

Probab=99.41  E-value=6.7e-14  Score=116.18  Aligned_cols=83  Identities=34%  Similarity=0.484  Sum_probs=77.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      +++--|||||||+..||.||.-+|++||.|.+|.+++|..||+|+||||+.|++..+..-|+. ++|..|.||.|+|...
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            567789999999999999999999999999999999999999999999999999999999996 9999999999999876


Q ss_pred             cccc
Q psy2983          93 QAEK   96 (370)
Q Consensus        93 ~~~~   96 (370)
                      ....
T Consensus       113 ~~Yk  116 (219)
T KOG0126|consen  113 SNYK  116 (219)
T ss_pred             cccc
Confidence            5543

>KOG0111|consensus

Probab=99.41  E-value=2.4e-13  Score=116.05  Aligned_cols=98  Identities=32%  Similarity=0.580  Sum_probs=88.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ...++||||+|...+++.-|...|-+||.|..|+++.|-++++++|||||+|.-.|+|..|+..||+.++.||.|+|.++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCcCCCCCCCCHHH
Q psy2983         192 TDRNESVGGGPSNLDTDE  209 (370)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~  209 (370)
                      .|.+...+...+-|.+++
T Consensus        88 kP~kikegsqkPvWADDd  105 (298)
T KOG0111|consen   88 KPEKIKEGSQKPVWADDD  105 (298)
T ss_pred             CCccccCCCCCCcccCcH
Confidence            988877665555555443

>KOG0149|consensus

Probab=99.40  E-value=3.6e-13  Score=116.53  Aligned_cols=79  Identities=22%  Similarity=0.297  Sum_probs=72.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecccc
Q psy2983          16 ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQA   94 (370)
Q Consensus        16 ~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~~~   94 (370)
                      -.+||||||+..+..++|+++|++||+|.+..++.|+.+++||||+||.|++.++|.+|++-..-.|+||+..+..+..
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchhhh
Confidence            3679999999999999999999999999999999999999999999999999999999998777788888777765543

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.40  E-value=1.5e-12  Score=116.37  Aligned_cols=78  Identities=15%  Similarity=0.333  Sum_probs=71.4

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .++|||+|||+.+++++|+++|+.||.|.++.+..+..   ++|||||+|.++++|..|+. |+|..+.|+.|+|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            36899999999999999999999999999999998753   57899999999999999996 999999999999999864


Q ss_pred             CC
Q psy2983         194 RN  195 (370)
Q Consensus       194 ~~  195 (370)
                      ..
T Consensus        80 ~~   81 (260)
T PLN03120         80 YQ   81 (260)
T ss_pred             CC
Confidence            43

>PLN03213 repressor of silencing 3; Provisional

Probab=99.40  E-value=7.5e-13  Score=125.01  Aligned_cols=78  Identities=21%  Similarity=0.346  Sum_probs=69.9

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCC--CChHHHhh-ccCCccCCeeEEE
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDP--ESVPLAMG-LNGQKLLGIPIIV   89 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~--e~A~~Al~-l~g~~i~g~~l~v   89 (370)
                      .....+||||||++.+++++|...|..||.|.+|.|++  .+|  +|||||+|.+.  .++.+|++ |+|..|.|+.|+|
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKV   82 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRL   82 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEE
Confidence            34567899999999999999999999999999999994  456  89999999998  56899996 9999999999999


Q ss_pred             ecccc
Q psy2983          90 QPTQA   94 (370)
Q Consensus        90 ~~~~~   94 (370)
                      ..+++
T Consensus        83 NKAKP   87 (759)
T PLN03213         83 EKAKE   87 (759)
T ss_pred             eeccH
Confidence            88764

>KOG0107|consensus

Probab=99.38  E-value=1.1e-12  Score=108.59  Aligned_cols=78  Identities=26%  Similarity=0.540  Sum_probs=72.6

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .++|||+||+..+++.+|...|..||.|.+|++-..+     .|||||||+++.+|..|+..|+|..|.|..|+|+...-
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            5789999999999999999999999999999998765     89999999999999999999999999999999999865


Q ss_pred             CCC
Q psy2983         194 RNE  196 (370)
Q Consensus       194 ~~~  196 (370)
                      ...
T Consensus        85 ~~r   87 (195)
T KOG0107|consen   85 RPR   87 (195)
T ss_pred             Ccc
Confidence            544

>KOG0113|consensus

Probab=99.37  E-value=2.5e-12  Score=114.76  Aligned_cols=84  Identities=33%  Similarity=0.593  Sum_probs=78.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      .++..+|||+-|+++++|..|+..|+.||+|+.|+++.|+.||+++|||||+|+++-+...|.+..+|..|+|+.|.|.+
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999977


Q ss_pred             eecC
Q psy2983         191 VTDR  194 (370)
Q Consensus       191 ~~~~  194 (370)
                      -..+
T Consensus       178 ERgR  181 (335)
T KOG0113|consen  178 ERGR  181 (335)
T ss_pred             cccc
Confidence            5433

>KOG0121|consensus

Probab=99.37  E-value=1.1e-12  Score=102.92  Aligned_cols=79  Identities=28%  Similarity=0.497  Sum_probs=74.9

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      .+.+|||+||...++||+|.++|+.+|+|+.|.+=.|+.+..+.|||||+|.+.++|..|+..++|..+..++|++.+.
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            3579999999999999999999999999999999888888899999999999999999999999999999999999874

>KOG0109|consensus

Probab=99.36  E-value=1.7e-12  Score=115.35  Aligned_cols=106  Identities=25%  Similarity=0.464  Sum_probs=97.6

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecC
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~  194 (370)
                      .+|||||||..+++.+|+.+|++||.|.+|.|+++        ||||..++...+..|+..|||..+.|..|+|+.++.+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            57999999999999999999999999999999955        9999999999999999999999999999999998877


Q ss_pred             CC-----CcCCCCCCCCHHHHHHhcccCCceeeeeeeec
Q psy2983         195 NE-----SVGGGPSNLDTDEMERAGVDLGATGRLQLMFK  228 (370)
Q Consensus       195 ~~-----~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~  228 (370)
                      ..     .++++....+.++++..|.++|++..+.+.++
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd  113 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD  113 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeeecc
Confidence            33     37788888999999999999999988888765

>smart00362 RRM_2 RNA recognition motif

Probab=99.35  E-value=4.8e-12  Score=91.46  Aligned_cols=72  Identities=43%  Similarity=0.848  Sum_probs=67.4

Q ss_pred             eEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEE
Q psy2983         116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG  189 (370)
Q Consensus       116 ~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~  189 (370)
                      +|+|+|||..+++++|+++|++||.+..+.+..++  +.++|+|||+|.+.++|.+|+..++|..+.|+.++|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            48999999999999999999999999999998775  7889999999999999999999999999999998873

>KOG0113|consensus

Probab=99.34  E-value=3.2e-12  Score=114.05  Aligned_cols=81  Identities=25%  Similarity=0.407  Sum_probs=76.6

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      ..+=+||||+-|+++++|.+|+..|+.||+|..|.|++|..||+++|||||+|....+...|.+ .+|+.|+|+.|.|..
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            4677999999999999999999999999999999999999999999999999999999999995 999999999999976


Q ss_pred             cc
Q psy2983          92 TQ   93 (370)
Q Consensus        92 ~~   93 (370)
                      -.
T Consensus       178 ER  179 (335)
T KOG0113|consen  178 ER  179 (335)
T ss_pred             cc
Confidence            54

>KOG4207|consensus

Probab=99.34  E-value=1.9e-12  Score=109.71  Aligned_cols=86  Identities=26%  Similarity=0.391  Sum_probs=80.6

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPII   88 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~   88 (370)
                      +++.....+|.|-||-+.++.++|+.+|++||.|-+|.|.+|+.|+.++|||||.|....+|+.|++ |+|..++|+.|.
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelr   86 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELR   86 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceee
Confidence            5666778899999999999999999999999999999999999999999999999999999999996 999999999999


Q ss_pred             Eeccccc
Q psy2983          89 VQPTQAE   95 (370)
Q Consensus        89 v~~~~~~   95 (370)
                      |+.+.-.
T Consensus        87 Vq~aryg   93 (256)
T KOG4207|consen   87 VQMARYG   93 (256)
T ss_pred             ehhhhcC
Confidence            9877643

>KOG0114|consensus

Probab=99.34  E-value=5.1e-12  Score=95.52  Aligned_cols=80  Identities=20%  Similarity=0.360  Sum_probs=71.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      ...|-|||+|||.++|.+++.++|.+||.|+.|++-..+   ..+|-|||.|++..+|.+|++ |+|..+.++.+.|-+.
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k---~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyy   92 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK---ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYY   92 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc---CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEec
Confidence            456889999999999999999999999999999985544   458999999999999999996 9999999999999887


Q ss_pred             cccc
Q psy2983          93 QAEK   96 (370)
Q Consensus        93 ~~~~   96 (370)
                      ++..
T Consensus        93 q~~~   96 (124)
T KOG0114|consen   93 QPED   96 (124)
T ss_pred             CHHH
Confidence            7543

>PLN03213 repressor of silencing 3; Provisional

Probab=99.33  E-value=3.7e-12  Score=120.42  Aligned_cols=77  Identities=25%  Similarity=0.535  Sum_probs=71.0

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCH--HHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA--DDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~--~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ...+||||||++.+++++|+.+|..||.|..+.|++  ++|  +|||||+|.+.  .++.+|+..|||..+.|+.|+|..
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            347899999999999999999999999999999994  467  99999999987  789999999999999999999999


Q ss_pred             eec
Q psy2983         191 VTD  193 (370)
Q Consensus       191 ~~~  193 (370)
                      +++
T Consensus        85 AKP   87 (759)
T PLN03213         85 AKE   87 (759)
T ss_pred             ccH
Confidence            864

>smart00362 RRM_2 RNA recognition motif

Probab=99.33  E-value=4.3e-12  Score=91.72  Aligned_cols=71  Identities=35%  Similarity=0.599  Sum_probs=65.5

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        18 ~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      +|||+|||..++.++|+++|++||+|..+.+.++.  +.++|+|||+|.+.++|..|++ +++..+.|+++.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999988876  6778999999999999999996 89999999998763

>smart00360 RRM RNA recognition motif

Probab=99.33  E-value=5.5e-12  Score=90.76  Aligned_cols=71  Identities=52%  Similarity=0.908  Sum_probs=67.0

Q ss_pred             EecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEE
Q psy2983         119 IGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG  189 (370)
Q Consensus       119 V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~  189 (370)
                      |+|||..+++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|..|+..+++..+.|+.++|.
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            57999999999999999999999999999988789999999999999999999999999999999998873

>KOG0130|consensus

Probab=99.32  E-value=3.9e-12  Score=100.72  Aligned_cols=84  Identities=29%  Similarity=0.498  Sum_probs=78.7

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ..-.|||+++....++++|.+.|..||+|+.+++-.|..+|-.+|||+|+|++.++|+.|+..+||..+.|+.|.|.|+.
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~F  150 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCF  150 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEE
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             cCCC
Q psy2983         193 DRNE  196 (370)
Q Consensus       193 ~~~~  196 (370)
                      .+..
T Consensus       151 v~gp  154 (170)
T KOG0130|consen  151 VKGP  154 (170)
T ss_pred             ecCC
Confidence            5443

>KOG0130|consensus

Probab=99.30  E-value=2.5e-12  Score=101.73  Aligned_cols=83  Identities=23%  Similarity=0.398  Sum_probs=76.8

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      .-..--|||.++-..++|++|.+.|..||+|..+.+..|+.||-.||||+|||.+.++|+.|++ +||..+.|++|.|.|
T Consensus        69 SVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw  148 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDW  148 (170)
T ss_pred             ceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEE
Confidence            3344569999999999999999999999999999999999999999999999999999999995 999999999999988


Q ss_pred             cccc
Q psy2983          92 TQAE   95 (370)
Q Consensus        92 ~~~~   95 (370)
                      .-..
T Consensus       149 ~Fv~  152 (170)
T KOG0130|consen  149 CFVK  152 (170)
T ss_pred             EEec
Confidence            7543

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.30  E-value=1.3e-11  Score=108.63  Aligned_cols=76  Identities=17%  Similarity=0.255  Sum_probs=69.9

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      ..+|||+||++.+|+++|+++|+.||.|.+|++++|   +..+|+|||+|.+++.+..|+. |+|..|.+++|.|.....
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D---~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS---GEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC---CCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCcc
Confidence            478999999999999999999999999999999987   3456899999999999999996 999999999999988654

>KOG0108|consensus

Probab=99.29  E-value=6.9e-12  Score=121.07  Aligned_cols=81  Identities=30%  Similarity=0.424  Sum_probs=77.3

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccccc
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQAE   95 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~~   95 (370)
                      +.|||||+|+++++++|.++|+..|+|.+++++.|+.+|+.+||||++|.+.++|..|++ |+|..+.|++|+|.++...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            899999999999999999999999999999999999999999999999999999999996 9999999999999988754


Q ss_pred             cc
Q psy2983          96 KN   97 (370)
Q Consensus        96 ~~   97 (370)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            43

>KOG4207|consensus

Probab=99.28  E-value=4.8e-12  Score=107.29  Aligned_cols=82  Identities=29%  Similarity=0.591  Sum_probs=77.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      .++-..|.|-||-+-++.++|+.+|++||.|-.|.|..|..|+.++|||||.|.+..+|+.|+++|+|..++|+.|.|+.
T Consensus        10 v~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~   89 (256)
T KOG4207|consen   10 VEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQM   89 (256)
T ss_pred             cccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehh
Confidence            44557899999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             ee
Q psy2983         191 VT  192 (370)
Q Consensus       191 ~~  192 (370)
                      +.
T Consensus        90 ar   91 (256)
T KOG4207|consen   90 AR   91 (256)
T ss_pred             hh
Confidence            74

>KOG1456|consensus

Probab=99.28  E-value=1e-10  Score=107.28  Aligned_cols=168  Identities=21%  Similarity=0.259  Sum_probs=132.1

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh---ccCCccCCeeEE
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG---LNGQKLLGIPII   88 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~---l~g~~i~g~~l~   88 (370)
                      ....+-.|+|++|-..++|.+|.+.++.||+|.-+..+..      ++.|.|||++.+.|.+|+.   -+...+.|+.-.
T Consensus        27 k~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~------~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al  100 (494)
T KOG1456|consen   27 KPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPH------KRQALVEFEDIEGAKNCVNFAADNQIYIAGQQAL  100 (494)
T ss_pred             CCCCCceEEEeccccccchhHHHHHHhcCCceEEEEeccc------cceeeeeeccccchhhheehhccCcccccCchhh
Confidence            4567889999999999999999999999999998877543      5679999999999999994   566678888888


Q ss_pred             EecccccccccCCCCCCCCCCCCCCCceE--EEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCH
Q psy2983          89 VQPTQAEKNRAGNTLPNLQPRGTGGPMRL--YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA  166 (370)
Q Consensus        89 v~~~~~~~~~~~~~~~~~~~~~~~~~~~l--~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~  166 (370)
                      +.++..+.-+...      .....++..|  .|-|--+.+|-+-|..++.+.|+|..|-+++.  +|.   .|.|||++.
T Consensus       101 ~NyStsq~i~R~g------~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ngV---QAmVEFdsv  169 (494)
T KOG1456|consen  101 FNYSTSQCIERPG------DESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NGV---QAMVEFDSV  169 (494)
T ss_pred             cccchhhhhccCC------CCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cce---eeEEeechh
Confidence            8877544322221      1111222333  34455578999999999999999999988865  443   699999999


Q ss_pred             HHHHHHHHHhCCceeCC--eeEEEEEeecCCC
Q psy2983         167 DDAKKAQEQLNGFELAG--RPMKVGTVTDRNE  196 (370)
Q Consensus       167 ~~a~~A~~~l~g~~i~g--~~l~V~~~~~~~~  196 (370)
                      +.|++|...|||..|+.  -.|+|.++++..-
T Consensus       170 ~~AqrAk~alNGADIYsGCCTLKIeyAkP~rl  201 (494)
T KOG1456|consen  170 EVAQRAKAALNGADIYSGCCTLKIEYAKPTRL  201 (494)
T ss_pred             HHHHHHHhhcccccccccceeEEEEecCccee
Confidence            99999999999999984  5788888876543

>smart00360 RRM RNA recognition motif

Probab=99.27  E-value=9.8e-12  Score=89.44  Aligned_cols=70  Identities=36%  Similarity=0.612  Sum_probs=65.2

Q ss_pred             EcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          21 CMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        21 V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      |+|||..+++++|+++|+.||.|..+.+..++.++.++|+|||+|.+.++|..|++ +++..+.|+.+.|+
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            68999999999999999999999999999988788999999999999999999996 89999999998763

>KOG0114|consensus

Probab=99.27  E-value=1.9e-11  Score=92.44  Aligned_cols=78  Identities=29%  Similarity=0.489  Sum_probs=70.9

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .+.|||.|||+++|.|+..++|.+||.|..|++=.   +..-+|-|||.|++..+|.+|+..|+|..+.++.+.|.+-++
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~---~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~   94 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGN---TKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQP   94 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecC---ccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCH
Confidence            46899999999999999999999999999999854   445589999999999999999999999999999999998655


Q ss_pred             C
Q psy2983         194 R  194 (370)
Q Consensus       194 ~  194 (370)
                      .
T Consensus        95 ~   95 (124)
T KOG0114|consen   95 E   95 (124)
T ss_pred             H
Confidence            3

>KOG0111|consensus

Probab=99.27  E-value=4.8e-12  Score=108.18  Aligned_cols=85  Identities=22%  Similarity=0.475  Sum_probs=79.8

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      ....|+|||++|...++|.-|...|-+||.|.+|.+..|..+.+++|||||+|.-.|+|..|+. +++..+.|+.|+|.+
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~   86 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNL   86 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEee
Confidence            3467999999999999999999999999999999999999999999999999999999999996 999999999999999


Q ss_pred             cccccc
Q psy2983          92 TQAEKN   97 (370)
Q Consensus        92 ~~~~~~   97 (370)
                      +.+.+.
T Consensus        87 AkP~ki   92 (298)
T KOG0111|consen   87 AKPEKI   92 (298)
T ss_pred             cCCccc
Confidence            876543

>KOG0108|consensus

Probab=99.26  E-value=9e-12  Score=120.28  Aligned_cols=82  Identities=30%  Similarity=0.652  Sum_probs=78.3

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecC
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~  194 (370)
                      +.+||||+|+++++++|..+|+..|.|.++++..|+++|+++||||++|.+.++|..|++.|||.++.||+|+|.++...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999997654


Q ss_pred             CC
Q psy2983         195 NE  196 (370)
Q Consensus       195 ~~  196 (370)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            44

>KOG1365|consensus

Probab=99.25  E-value=7.4e-12  Score=115.01  Aligned_cols=175  Identities=20%  Similarity=0.230  Sum_probs=133.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcC----CCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEe
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSV----GKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQ   90 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~----G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~   90 (370)
                      +.--|..++||+++++.|+.+||.+-    |-...|.+++.+ .|+..|-|||.|..+++|+.||..|...+.-|.|.+.
T Consensus       160 ~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElF  238 (508)
T KOG1365|consen  160 NQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELF  238 (508)
T ss_pred             cceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHH
Confidence            34457788999999999999999742    345667666654 4788899999999999999999988888888888776


Q ss_pred             ccccccc-----ccC--C-----CC------CCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCC-ceee--EEEeec
Q psy2983          91 PTQAEKN-----RAG--N-----TL------PNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFG-KIDN--IQLMVD  149 (370)
Q Consensus        91 ~~~~~~~-----~~~--~-----~~------~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G-~i~~--v~~~~~  149 (370)
                      ++....-     +..  .     ..      +...........+|.+++||+..+.|+|.++|..|- .|..  +++..+
T Consensus       239 RSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N  318 (508)
T KOG1365|consen  239 RSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN  318 (508)
T ss_pred             HHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc
Confidence            6643210     000  0     00      011111222356899999999999999999999886 3444  788877


Q ss_pred             CCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         150 PDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       150 ~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      . .|+..|-|||+|.+.+.|..|....|+.....|-|.|-.+
T Consensus       319 ~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~  359 (508)
T KOG1365|consen  319 G-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPC  359 (508)
T ss_pred             C-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeec
Confidence            4 7999999999999999999999999988888888888553

>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=99.22  E-value=8.9e-11  Score=85.18  Aligned_cols=74  Identities=43%  Similarity=0.837  Sum_probs=68.4

Q ss_pred             eEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       116 ~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      +|+|+|||..+++++|+++|+.+|.|..+.+..++. +.++|+|||+|.+.++|..|+..+++..+.|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~-~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKD-TKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            489999999999999999999999999999998863 47799999999999999999999999999999998863

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).

>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=99.21  E-value=5.6e-11  Score=86.25  Aligned_cols=73  Identities=40%  Similarity=0.652  Sum_probs=66.6

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        18 ~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      +|+|+|||..+++++|+++|+.+|.|..+.+..+..+ ..+|+|||+|.+.++|..|++ +++..+.|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            5899999999999999999999999999999887654 668999999999999999996 999999999998753

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>KOG4212|consensus

Probab=99.20  E-value=3.1e-10  Score=106.08  Aligned_cols=71  Identities=37%  Similarity=0.610  Sum_probs=66.5

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ++|+|.|||.++|.+.|++-|..||.|.+..++   +.|+++|  .|.|.++++|++|+..|+|..+.||.|+|.+
T Consensus       537 ~qIiirNlP~dfTWqmlrDKfre~G~v~yadim---e~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y  607 (608)
T KOG4212|consen  537 CQIIIRNLPFDFTWQMLRDKFREIGHVLYADIM---ENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTY  607 (608)
T ss_pred             cEEEEecCCccccHHHHHHHHHhccceehhhhh---ccCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeee
Confidence            469999999999999999999999999999985   4688887  8999999999999999999999999999986

>KOG4206|consensus

Probab=99.20  E-value=1.8e-10  Score=99.72  Aligned_cols=84  Identities=30%  Similarity=0.566  Sum_probs=75.9

Q ss_pred             CCceEEEecCCCCCCHHHHHh----cccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEE
Q psy2983         113 GPMRLYIGSLHFNITEDMLRG----IFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV  188 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~----~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V  188 (370)
                      +..+|||.||+..+..++|+.    +|++||.|..|...   .+.+.+|-|||.|.+.+.|..|+..|+|..+.|++++|
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~---kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mri   84 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF---KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRI   84 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec---CCCCccCceEEEecChhHHHHHHHHhcCCcccCchhhe
Confidence            345999999999999999988    99999999888776   47789999999999999999999999999999999999


Q ss_pred             EEeecCCCCcC
Q psy2983         189 GTVTDRNESVG  199 (370)
Q Consensus       189 ~~~~~~~~~~~  199 (370)
                      .++..+...+.
T Consensus        85 qyA~s~sdii~   95 (221)
T KOG4206|consen   85 QYAKSDSDIIA   95 (221)
T ss_pred             ecccCccchhh
Confidence            99988766544

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

Probab=99.20  E-value=6.5e-11  Score=108.56  Aligned_cols=80  Identities=40%  Similarity=0.811  Sum_probs=76.8

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      ..+|||+|||..+++++|.++|..||.+..+.+..++.+|.++|||||+|.+.++|..|+..++|..+.|++|.|.+...
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            58999999999999999999999999999999999988999999999999999999999999999999999999999653

>KOG4205|consensus

Probab=99.18  E-value=4.2e-11  Score=110.94  Aligned_cols=122  Identities=29%  Similarity=0.600  Sum_probs=108.2

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ...+|||++|++.++++.|++.|.+||.|..+.+++|+.+++++||+||+|.+++...+++. ...+.|.|+.|.+..+.
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 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            45789999999999999999999999999999999999999999999999999999999987 56788999999999887


Q ss_pred             cCCCC-------------cCCCCCCCCHHHHHHhcccCCceeeeeeeec----cccCCCC
Q psy2983         193 DRNES-------------VGGGPSNLDTDEMERAGVDLGATGRLQLMFK----LAEGTGL  235 (370)
Q Consensus       193 ~~~~~-------------~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~----~~~~~~~  235 (370)
                      ++...             +++++..+++.+++..|..+|.+....+|-+    ..++||+
T Consensus        84 ~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgf  143 (311)
T KOG4205|consen   84 SREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGF  143 (311)
T ss_pred             CcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeeccccccccccee
Confidence            66532             5688999999999999999998888888876    3446664

>PF13893 RRM_5: RNA recognition motif

Probab=99.16  E-value=1.8e-10  Score=80.02  Aligned_cols=56  Identities=41%  Similarity=0.797  Sum_probs=50.5

Q ss_pred             HHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         131 LRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       131 l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      |+++|++||.|.++.+..+.     +|+|||+|.+.++|..|+..|||..+.|++|+|.++
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999997553     689999999999999999999999999999999875

(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 ....

>KOG0105|consensus

Probab=99.16  E-value=1.5e-10  Score=96.66  Aligned_cols=113  Identities=21%  Similarity=0.362  Sum_probs=92.8

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ..++|||+|||.++.+.+|.++|.+||.|..|.+-..   .....||||+|+++.+|..|+..-+|..++|..|+|.++.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            3478999999999999999999999999999988533   2346799999999999999999999999999999999975


Q ss_pred             cCCCC---------------------------------cCCCCCCCCHHHHHHhcccCCceeeeeeeec
Q psy2983         193 DRNES---------------------------------VGGGPSNLDTDEMERAGVDLGATGRLQLMFK  228 (370)
Q Consensus       193 ~~~~~---------------------------------~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~  228 (370)
                      .-...                                 +.++|+.-+=++|+.+.-..|.+--+++.++
T Consensus        82 ggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD  150 (241)
T KOG0105|consen   82 GGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD  150 (241)
T ss_pred             CCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc
Confidence            33111                                 3467777777888888888777766666655

>smart00361 RRM_1 RNA recognition motif

Probab=99.16  E-value=1.3e-10  Score=84.64  Aligned_cols=62  Identities=29%  Similarity=0.523  Sum_probs=55.4

Q ss_pred             HHHHHhccc----CCCceeeEE-EeecCCC--CCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEE
Q psy2983         128 EDMLRGIFE----PFGKIDNIQ-LMVDPDT--GRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG  189 (370)
Q Consensus       128 ~e~l~~~f~----~~G~i~~v~-~~~~~~~--g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~  189 (370)
                      +++|+++|+    .||.|.++. +..++.+  |.++|+|||+|.+.++|.+|+..|||..+.|+.|+++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            567888888    999999995 6666666  8999999999999999999999999999999999863

>KOG0129|consensus

Probab=99.15  E-value=7.4e-10  Score=106.04  Aligned_cols=161  Identities=20%  Similarity=0.243  Sum_probs=116.4

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEee-eCCC--CCeec---EEEEEecCCCChHHHhhccCCccCCe
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLIT-CNKT--RRFKG---IAYIEFKDPESVPLAMGLNGQKLLGI   85 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~-d~~~--~~~kg---~afVeF~~~e~A~~Al~l~g~~i~g~   85 (370)
                      ..+-+|+||||+||.+++|+.|...|..||.+.- .... ....  -..+|   |+|+-|+++..+...+.-.-.  ...
T Consensus       255 ~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~V-dWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~--~~~  331 (520)
T KOG0129|consen  255 SPRYSRKVFVGGLPWDITEAQINASFGQFGSVKV-DWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE--GEG  331 (520)
T ss_pred             ccccccceeecCCCccccHHHHHhhcccccceEe-ecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh--ccc
Confidence            3567899999999999999999999999998763 3332 1111  12456   999999999998888741100  222


Q ss_pred             eEEEeccccccccc---------CC-CCCCCCCCCCCCCceEEEecCCCCCCHHHHHhccc-CCCceeeEEEeecCCCCC
Q psy2983          86 PIIVQPTQAEKNRA---------GN-TLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFE-PFGKIDNIQLMVDPDTGR  154 (370)
Q Consensus        86 ~l~v~~~~~~~~~~---------~~-~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~-~~G~i~~v~~~~~~~~g~  154 (370)
                      .+++..+.......         .+ ..-.......++.+|||||+||.-++.++|..+|+ -||.|..+-|-.|++-+-
T Consensus       332 ~~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KY  411 (520)
T KOG0129|consen  332 NYYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKY  411 (520)
T ss_pred             ceEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCC
Confidence            22222111110000         00 00011334456778999999999999999999998 799999999999988899


Q ss_pred             cccEEEEEECCHHHHHHHHHH
Q psy2983         155 SKGYGFITFHSADDAKKAQEQ  175 (370)
Q Consensus       155 ~~g~afV~f~~~~~a~~A~~~  175 (370)
                      .+|-|-|.|.+..+-.+||.+
T Consensus       412 PkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  412 PKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CCCcceeeecccHHHHHHHhh
Confidence            999999999999999999983

>KOG4454|consensus

Probab=99.10  E-value=3e-11  Score=103.38  Aligned_cols=152  Identities=24%  Similarity=0.368  Sum_probs=124.8

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      +....|||||.|+...++|+-|.++|-+.|+|..|.|..++. ++.| ||||+|.++-.+.-|++ ++|..+.+.++.++
T Consensus         5 aae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~   82 (267)
T KOG4454|consen    5 AAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRT   82 (267)
T ss_pred             CcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccchhhcc
Confidence            445679999999999999999999999999999998876654 5555 99999999999999998 89999999988775


Q ss_pred             cccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHH
Q psy2983          91 PTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAK  170 (370)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~  170 (370)
                      .-.....                      .-|...++++.+...|+..|++..+++..+. +|+++.++|+.+......-
T Consensus        83 ~r~G~sh----------------------apld~r~~~ei~~~v~s~a~p~~~~R~~~~~-d~rnrn~~~~~~qr~~~~P  139 (267)
T KOG4454|consen   83 LRCGNSH----------------------APLDERVTEEILYEVFSQAGPIEGVRIPTDN-DGRNRNFGFVTYQRLCAVP  139 (267)
T ss_pred             cccCCCc----------------------chhhhhcchhhheeeecccCCCCCccccccc-cCCccCccchhhhhhhcCc
Confidence            5331110                      0045667899999999999999999998886 5889999999999888888


Q ss_pred             HHHHHhCCceeCCeeEEE
Q psy2983         171 KAQEQLNGFELAGRPMKV  188 (370)
Q Consensus       171 ~A~~~l~g~~i~g~~l~V  188 (370)
                      .++....+.+..-+++.+
T Consensus       140 ~~~~~y~~l~~~~~~~~~  157 (267)
T KOG4454|consen  140 FALDLYQGLELFQKKVTI  157 (267)
T ss_pred             HHhhhhcccCcCCCCccc
Confidence            888877777665555544

>KOG4210|consensus

Probab=99.08  E-value=1.2e-10  Score=107.68  Aligned_cols=180  Identities=24%  Similarity=0.360  Sum_probs=143.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCC-ccCCeeEEEecc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQ-KLLGIPIIVQPT   92 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~-~i~g~~l~v~~~   92 (370)
                      +...+.|++++...+.+.+...++..+|...............++|++++.|+..+.+..|+++.+. ...++.+.....
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            4678999999999999999999999999888888877777788999999999999999999987775 444444433222


Q ss_pred             cccccccCCCCCCCCCCCCCCCceEE-EecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHH
Q psy2983          93 QAEKNRAGNTLPNLQPRGTGGPMRLY-IGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK  171 (370)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~l~-V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~  171 (370)
                      ........   ............++| +++++..+++++|+..|..+|.|..+++..+..++.++|+|+++|.....+..
T Consensus       166 ~~~~~~~~---n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~  242 (285)
T KOG4210|consen  166 TRRGLRPK---NKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKL  242 (285)
T ss_pred             cccccccc---chhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHH
Confidence            21111010   011112223345566 99999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCceeCCeeEEEEEeecCCCC
Q psy2983         172 AQEQLNGFELAGRPMKVGTVTDRNES  197 (370)
Q Consensus       172 A~~~l~g~~i~g~~l~V~~~~~~~~~  197 (370)
                      ++.. +...+.++++.+.+..++...
T Consensus       243 ~~~~-~~~~~~~~~~~~~~~~~~~~~  267 (285)
T KOG4210|consen  243 ALND-QTRSIGGRPLRLEEDEPRPKS  267 (285)
T ss_pred             Hhhc-ccCcccCcccccccCCCCccc
Confidence            9987 889999999999887766544

>KOG1456|consensus

Probab=99.06  E-value=4.6e-09  Score=96.63  Aligned_cols=166  Identities=21%  Similarity=0.257  Sum_probs=128.9

Q ss_pred             cccCCCCeEEEcCCC-CCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEE
Q psy2983          11 PEERDARTIFCMQLS-QRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPII   88 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp-~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~   88 (370)
                      ...-+...++|.+|. .+++.+.|.++|-.||.|..|++++.+     .|-|.||+.+..+.++|+. |++..+.|.+|.
T Consensus       282 ~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~  356 (494)
T KOG1456|consen  282 GGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLN  356 (494)
T ss_pred             CCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEE
Confidence            445677899999998 567899999999999999999999865     4789999999999999997 999999999999


Q ss_pred             Eeccccccc------------------------ccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCc-eee
Q psy2983          89 VQPTQAEKN------------------------RAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGK-IDN  143 (370)
Q Consensus        89 v~~~~~~~~------------------------~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~-i~~  143 (370)
                      |..++..--                        +..........+-..+++.|+.-|.|..+||+.|..+|...+. -.+
T Consensus       357 v~~SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~s  436 (494)
T KOG1456|consen  357 VCVSKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTS  436 (494)
T ss_pred             EeeccccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcce
Confidence            976652111                        1111111122233345678999999999999999999987653 456


Q ss_pred             EEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCC
Q psy2983         144 IQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG  183 (370)
Q Consensus       144 v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g  183 (370)
                      ++++.-+ +-++ .-+.+||++.++|..|+..+|...+.+
T Consensus       437 vkvFp~k-serS-ssGllEfe~~s~Aveal~~~NH~pi~~  474 (494)
T KOG1456|consen  437 VKVFPLK-SERS-SSGLLEFENKSDAVEALMKLNHYPIEG  474 (494)
T ss_pred             EEeeccc-cccc-ccceeeeehHHHHHHHHHHhccccccC
Confidence            7777554 3332 258999999999999999999998875

>smart00361 RRM_1 RNA recognition motif

Probab=99.04  E-value=4e-10  Score=82.11  Aligned_cols=60  Identities=28%  Similarity=0.408  Sum_probs=54.1

Q ss_pred             HHHHHHHhh----cCCCeeEEE-EeeeCCC--CCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEE
Q psy2983          30 TRDLEEFFS----SVGKVRDVR-LITCNKT--RRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIV   89 (370)
Q Consensus        30 e~~L~~~f~----~~G~v~~v~-i~~d~~~--~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v   89 (370)
                      +++|+++|+    .||.|.++. +..++.+  +.++|||||+|.+.++|.+|+. |+|..+.|+.|.+
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            678999999    999999995 7777666  8899999999999999999996 9999999999875

>PF15519 RBM39linker: linker between RRM2 and RRM3 domains in RBM39 protein; PDB: 3S6E_A 2LQ5_A

Probab=99.02  E-value=9.8e-11  Score=85.01  Aligned_cols=71  Identities=55%  Similarity=0.950  Sum_probs=17.7

Q ss_pred             HHHHHHhcccCCceeeeeeeeccccCCCCCChHHHHHHHhhhcccccCCCCCCCCCCCCCCCCCceEEeecCCCCCCCCC
Q psy2983         207 TDEMERAGVDLGATGRLQLMFKLAEGTGLELPPAAASALNLAQNAILNSSTPQVSSSTAPPIATQCFLLANMFDPATETN  286 (370)
Q Consensus       207 ~~~l~~~~~~~g~~~~~~l~~~~~~~~~~~~~~~a~~a~~~~~~~~~~p~~~~~~~~~~~~~ps~vl~L~Nm~~~~~l~~  286 (370)
                      .++....+..+++.++.+||++++++.+.+.+.+++.+..+.+..            +++..+|+|++|+|||+|.++++
T Consensus         3 ~dd~d~~G~~l~a~sR~~LM~KLA~~~~~~~~~~~~~~~~~~~~~------------~~~~~aS~C~lLkNMFDP~~Ete   70 (73)
T PF15519_consen    3 SDDDDRGGVNLNATSRAALMAKLARGDGPQIPPAAQQALQPNGSI------------PIPPIASRCFLLKNMFDPAEETE   70 (73)
T ss_dssp             ------------------------------------------------------------S---SEEEEESSS-TTCGGS
T ss_pred             cccccccccccccccccccccccccccccccccccccccCcCCCC------------CCCCCCCceeeeecCCCcccccC
Confidence            345667788999999999999999998877766554443322221            22347899999999999999999


Q ss_pred             chh
Q psy2983         287 PTW  289 (370)
Q Consensus       287 d~~  289 (370)
                      ++|
T Consensus        71 ~~W   73 (73)
T PF15519_consen   71 PDW   73 (73)
T ss_dssp             TTH
T ss_pred             CCC
Confidence            887

>KOG0128|consensus

Probab=99.01  E-value=2e-11  Score=122.57  Aligned_cols=151  Identities=24%  Similarity=0.410  Sum_probs=130.9

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecc
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPT   92 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~   92 (370)
                      .|+..++||+||++.+.+.+|...|..+|.+..+++..-...++.+|+||++|..++++.+|+++....+.|+       
T Consensus       664 ~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK-------  736 (881)
T KOG0128|consen  664 IRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGK-------  736 (881)
T ss_pred             HHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhhh-------
Confidence            3666789999999999999999999999988877766444557889999999999999999998776666661       


Q ss_pred             cccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHH
Q psy2983          93 QAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA  172 (370)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A  172 (370)
                                            ..++|.|.|+..|.++++.++..+|.+.+.+++..+ .|+.+|.|+|.|.++.++.++
T Consensus       737 ----------------------~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~  793 (881)
T KOG0128|consen  737 ----------------------ISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRK  793 (881)
T ss_pred             ----------------------hhhheeCCCCCCchHHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhh
Confidence                                  358999999999999999999999999999887775 899999999999999999999


Q ss_pred             HHHhCCceeCCeeEEEEEeec
Q psy2983         173 QEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       173 ~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      +...++..+.-+-+.|...++
T Consensus       794 ~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  794 VASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             cccchhhhhhhcCccccccCC
Confidence            998888888777777766544

>KOG4208|consensus

Probab=99.01  E-value=8.2e-10  Score=94.11  Aligned_cols=81  Identities=26%  Similarity=0.456  Sum_probs=75.0

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCC-CceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPF-GKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~-G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ..-+|+..+|..+.+.++..+|.+| |.+..+++-+++.||.++|||||+|++++.|.-|-+.||++.+.++.|.|++-.
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            3469999999999999999999999 788889998999999999999999999999999999999999999999999865


Q ss_pred             cC
Q psy2983         193 DR  194 (370)
Q Consensus       193 ~~  194 (370)
                      +.
T Consensus       129 pe  130 (214)
T KOG4208|consen  129 PE  130 (214)
T ss_pred             ch
Confidence            43

>PF13893 RRM_5: RNA recognition motif

Probab=98.99  E-value=5e-10  Score=77.77  Aligned_cols=55  Identities=31%  Similarity=0.617  Sum_probs=48.9

Q ss_pred             HHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          33 LEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        33 L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      |+++|++||+|.++.+.++.     +++|||+|.+.++|..|++ |+|..+.|++|+|.++
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68899999999999987643     5899999999999999996 9999999999999874

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>KOG4211|consensus

Probab=98.98  E-value=5.3e-09  Score=99.64  Aligned_cols=173  Identities=21%  Similarity=0.328  Sum_probs=128.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeE-EEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRD-VRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPT   92 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~-v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~   92 (370)
                      -..-.|-+++||..+|++||.+||+..-.|.. |.++.++. +++.|-|||.|++.+.|++||..+...|..+-|.|.++
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~r-gR~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQR-GRPTGEAFVQFESQESAEIALGRHRENIGHRYIEVFRS  179 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCC-CCcccceEEEecCHHHHHHHHHHHHHhhccceEEeehh
Confidence            45678999999999999999999998765555 44555554 66889999999999999999998888888888888554


Q ss_pred             cccccccCC--------------------C---------------------------------CC---------------
Q psy2983          93 QAEKNRAGN--------------------T---------------------------------LP---------------  104 (370)
Q Consensus        93 ~~~~~~~~~--------------------~---------------------------------~~---------------  104 (370)
                      .....+...                    .                                 ..               
T Consensus       180 s~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~gs~~~~~~~~~  259 (510)
T KOG4211|consen  180 SRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFGSYGGGRDPNY  259 (510)
T ss_pred             HHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCcccccccccccccccccccc
Confidence            311100000                    0                                 00               


Q ss_pred             CCC--C----------CCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHH
Q psy2983         105 NLQ--P----------RGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA  172 (370)
Q Consensus       105 ~~~--~----------~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A  172 (370)
                      ...  +          ........++.++||+..++.+|..+|+..-.+ .+++-..+ +|+..|-|+|+|.+.++|..|
T Consensus       260 ~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~-~v~i~ig~-dGr~TGEAdveF~t~edav~A  337 (510)
T KOG4211|consen  260 PVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPY-RVHIEIGP-DGRATGEADVEFATGEDAVGA  337 (510)
T ss_pred             CCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCce-eEEEEeCC-CCccCCcceeecccchhhHhh
Confidence            000  0          001112568999999999999999999987655 67777664 899999999999999999999


Q ss_pred             HHHhCCceeCCeeEEEEE
Q psy2983         173 QEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       173 ~~~l~g~~i~g~~l~V~~  190 (370)
                      +. -++..+..+-+..-.
T Consensus       338 ms-kd~anm~hrYVElFl  354 (510)
T KOG4211|consen  338 MG-KDGANMGHRYVELFL  354 (510)
T ss_pred             hc-cCCcccCcceeeecc
Confidence            98 477777777665533

>KOG0415|consensus

Probab=98.96  E-value=9.3e-10  Score=100.44  Aligned_cols=82  Identities=26%  Similarity=0.387  Sum_probs=77.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ++.+.|||..|.+-+++++|.-+|+.||.|.+|.+++|..+|.+.-||||+|.+.+++.+|.-.|++..|.+++|+|.++
T Consensus       237 PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFS  316 (479)
T KOG0415|consen  237 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFS  316 (479)
T ss_pred             CCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehh
Confidence            34478999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             ec
Q psy2983         192 TD  193 (370)
Q Consensus       192 ~~  193 (370)
                      ..
T Consensus       317 QS  318 (479)
T KOG0415|consen  317 QS  318 (479)
T ss_pred             hh
Confidence            54

>KOG4208|consensus

Probab=98.91  E-value=2.1e-09  Score=91.69  Aligned_cols=84  Identities=20%  Similarity=0.341  Sum_probs=75.1

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcC-CCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEE
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSV-GKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIV   89 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~-G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v   89 (370)
                      .....-.+||..+|..+-+.++..+|.++ |.|..+++.|+++||.|||||||||.+++.|..|-+ ||+..+.|+.|.+
T Consensus        45 ~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c  124 (214)
T KOG4208|consen   45 EQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLEC  124 (214)
T ss_pred             ccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeee
Confidence            34455679999999999999999999998 889999999999999999999999999999999996 9999999999888


Q ss_pred             eccccc
Q psy2983          90 QPTQAE   95 (370)
Q Consensus        90 ~~~~~~   95 (370)
                      ..-.++
T Consensus       125 ~vmppe  130 (214)
T KOG4208|consen  125 HVMPPE  130 (214)
T ss_pred             EEeCch
Confidence            765443

>KOG0415|consensus

Probab=98.88  E-value=2.5e-09  Score=97.68  Aligned_cols=83  Identities=27%  Similarity=0.312  Sum_probs=78.7

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHh-hccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~i~g~~l~v~~   91 (370)
                      ..+.+.|||.-|.+-++.++|.-.|+.||+|.++.+++|.+||.+-.||||||.+.+++++|. +++...|.+++|.|.+
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            457789999999999999999999999999999999999999999999999999999999999 7999999999999998


Q ss_pred             cccc
Q psy2983          92 TQAE   95 (370)
Q Consensus        92 ~~~~   95 (370)
                      ++.-
T Consensus       316 SQSV  319 (479)
T KOG0415|consen  316 SQSV  319 (479)
T ss_pred             hhhh
Confidence            8754

>KOG0153|consensus

Probab=98.86  E-value=8.5e-09  Score=94.23  Aligned_cols=80  Identities=21%  Similarity=0.445  Sum_probs=72.4

Q ss_pred             CCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh--ccCCccCCee
Q psy2983           9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG--LNGQKLLGIP   86 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~--l~g~~i~g~~   86 (370)
                      -+++....++|||++|-..++|.+|+++|.+||+|+++.+...      +++|||+|.+.++|+.|.+  ++...|+|++
T Consensus       221 epPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~R  294 (377)
T KOG0153|consen  221 EPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFR  294 (377)
T ss_pred             CCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceE
Confidence            3556678899999999999999999999999999999998764      5699999999999999995  8888999999


Q ss_pred             EEEecccc
Q psy2983          87 IIVQPTQA   94 (370)
Q Consensus        87 l~v~~~~~   94 (370)
                      |+|.|..+
T Consensus       295 l~i~Wg~~  302 (377)
T KOG0153|consen  295 LKIKWGRP  302 (377)
T ss_pred             EEEEeCCC
Confidence            99999877

>KOG1365|consensus

Probab=98.85  E-value=9.3e-08  Score=88.41  Aligned_cols=175  Identities=21%  Similarity=0.265  Sum_probs=123.6

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEec
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQP   91 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~   91 (370)
                      ...+...|..++||...+..+|..||....-......+.....|+..|.|.|.|.++|.-+.|++-+..-+.++.|.|-.
T Consensus        56 ~~~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryievYk  135 (508)
T KOG1365|consen   56 SADDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYIEVYK  135 (508)
T ss_pred             ccCcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHhhhhhccCCceeeec
Confidence            34556678889999999999999999875322222233333446667899999999999999999888888999998866


Q ss_pred             ccccccccCCC--CCCCCCCCC-CCCceEEEecCCCCCCHHHHHhcccCC----CceeeEEEeecCCCCCcccEEEEEEC
Q psy2983          92 TQAEKNRAGNT--LPNLQPRGT-GGPMRLYIGSLHFNITEDMLRGIFEPF----GKIDNIQLMVDPDTGRSKGYGFITFH  164 (370)
Q Consensus        92 ~~~~~~~~~~~--~~~~~~~~~-~~~~~l~V~nlp~~~t~e~l~~~f~~~----G~i~~v~~~~~~~~g~~~g~afV~f~  164 (370)
                      +..+.--.-..  .....+..+ ...-.|..++||+++++.++.++|.+-    |....+-++..+ +|+..|-|||.|.
T Consensus       136 a~ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa  214 (508)
T KOG1365|consen  136 ATGEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFA  214 (508)
T ss_pred             cCchhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEec
Confidence            65432211110  000001111 122458889999999999999999643    244556666554 7999999999999


Q ss_pred             CHHHHHHHHHHhCCceeCCeeEEE
Q psy2983         165 SADDAKKAQEQLNGFELAGRPMKV  188 (370)
Q Consensus       165 ~~~~a~~A~~~l~g~~i~g~~l~V  188 (370)
                      .+++|+.|+. -|...++.|-|.+
T Consensus       215 ~ee~aq~aL~-khrq~iGqRYIEl  237 (508)
T KOG1365|consen  215 CEEDAQFALR-KHRQNIGQRYIEL  237 (508)
T ss_pred             CHHHHHHHHH-HHHHHHhHHHHHH
Confidence            9999999998 4666666665544

>KOG0112|consensus

Probab=98.79  E-value=4.8e-09  Score=106.15  Aligned_cols=162  Identities=22%  Similarity=0.316  Sum_probs=133.2

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHh-hccCCccCCeeEEEe
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQ   90 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~i~g~~l~v~   90 (370)
                      +.+..+|||++||+..+++.+|+..|..+|.|.+|.|.+-+. +....||||.|.+...+-.|. ++.+..|....+.+.
T Consensus       368 D~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~-~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~g  446 (975)
T KOG0112|consen  368 DFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI-KTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIG  446 (975)
T ss_pred             chhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC-CcccchhhhhhhccccCcccchhhcCCccccCccccc
Confidence            347789999999999999999999999999999999865432 444579999999999999998 588887766555554


Q ss_pred             cccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHH
Q psy2983          91 PTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAK  170 (370)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~  170 (370)
                      ....               .......+++++|+..+....+...|..||.|..|.+-+.      .-||++.|++...++
T Consensus       447 lG~~---------------kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg------q~yayi~yes~~~aq  505 (975)
T KOG0112|consen  447 LGQP---------------KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG------QPYAYIQYESPPAAQ  505 (975)
T ss_pred             cccc---------------ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC------CcceeeecccCccch
Confidence            4432               1223467999999999999999999999999999877533      349999999999999


Q ss_pred             HHHHHhCCceeCC--eeEEEEEeecCC
Q psy2983         171 KAQEQLNGFELAG--RPMKVGTVTDRN  195 (370)
Q Consensus       171 ~A~~~l~g~~i~g--~~l~V~~~~~~~  195 (370)
                      .|+..|-|..|++  ++++|.++.+..
T Consensus       506 ~a~~~~rgap~G~P~~r~rvdla~~~~  532 (975)
T KOG0112|consen  506 AATHDMRGAPLGGPPRRLRVDLASPPG  532 (975)
T ss_pred             hhHHHHhcCcCCCCCcccccccccCCC
Confidence            9999999999985  778888876543

>KOG0226|consensus

Probab=98.76  E-value=6.5e-09  Score=91.17  Aligned_cols=166  Identities=21%  Similarity=0.365  Sum_probs=122.6

Q ss_pred             eEEEcCCCCCCcHHH-H--HHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          18 TIFCMQLSQRIRTRD-L--EEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        18 ~v~V~nLp~~~te~~-L--~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      ..+++++-..+..+- |  ...|+.+-......++++.. +...+++|+.|.....-.++-. -++..+.-.++++...+
T Consensus        98 ~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p-~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gt  176 (290)
T KOG0226|consen   98 RPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRP-QPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGT  176 (290)
T ss_pred             cccccccccccCCCCCCcchhhhccchhhhhhhhhhcCC-CccCcccccCcchhhhhhhhccccccccccCcceeecccc
Confidence            455555554444333 3  56777776666666666654 4567899998877665555553 55556655555554433


Q ss_pred             ccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHH
Q psy2983          94 AEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ  173 (370)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~  173 (370)
                      ....       .....-.....+||.|.|..+++++-|-..|.+|-.-...++++|+.+|+++||+||.|.+.+++..|+
T Consensus       177 swed-------Psl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAm  249 (290)
T KOG0226|consen  177 SWED-------PSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAM  249 (290)
T ss_pred             ccCC-------cccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHH
Confidence            2221       112222344578999999999999999999999988888999999999999999999999999999999


Q ss_pred             HHhCCceeCCeeEEEEEe
Q psy2983         174 EQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       174 ~~l~g~~i~g~~l~V~~~  191 (370)
                      ..|+|.-++.++|+.+..
T Consensus       250 rem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  250 REMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             HhhcccccccchhHhhhh
Confidence            999999999999988654

>KOG0146|consensus

Probab=98.71  E-value=1.5e-08  Score=89.40  Aligned_cols=84  Identities=20%  Similarity=0.359  Sum_probs=77.9

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      +-.+.+.|||..||.+..+.||.+.|-+||.|.+.++..|+.|+.+|.|+||.|.++.+|+.|+. +||..|.=++|+|+
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQ  360 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ  360 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhh
Confidence            34678999999999999999999999999999999999999999999999999999999999995 99999999999998


Q ss_pred             ccccc
Q psy2983          91 PTQAE   95 (370)
Q Consensus        91 ~~~~~   95 (370)
                      ..+++
T Consensus       361 LKRPk  365 (371)
T KOG0146|consen  361 LKRPK  365 (371)
T ss_pred             hcCcc
Confidence            76543

>KOG0132|consensus

Probab=98.70  E-value=2.6e-08  Score=99.48  Aligned_cols=75  Identities=31%  Similarity=0.567  Sum_probs=70.1

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecC
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~  194 (370)
                      +|||||+|+..+++.+|..+|+.||.|.+|.++..      +|+|||......+|.+|+.+|++..+.++.|+|.|+..+
T Consensus       422 rTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  422 RTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             eeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccC
Confidence            68999999999999999999999999999988755      789999999999999999999999999999999998654


Q ss_pred             C
Q psy2983         195 N  195 (370)
Q Consensus       195 ~  195 (370)
                      .
T Consensus       496 G  496 (894)
T KOG0132|consen  496 G  496 (894)
T ss_pred             C
Confidence            3

>KOG0153|consensus

Probab=98.69  E-value=6.1e-08  Score=88.71  Aligned_cols=81  Identities=28%  Similarity=0.462  Sum_probs=70.0

Q ss_pred             CCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhC-CceeCCee
Q psy2983         107 QPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN-GFELAGRP  185 (370)
Q Consensus       107 ~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~-g~~i~g~~  185 (370)
                      .+.......+|||++|...+++.+|+++|.+||.|+++.+...      +|+|||+|.+.++|+.|...+- ...|.|++
T Consensus       221 epPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~R  294 (377)
T KOG0153|consen  221 EPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFR  294 (377)
T ss_pred             CCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceE
Confidence            3334445579999999999999999999999999999998865      5699999999999999888665 46689999


Q ss_pred             EEEEEeec
Q psy2983         186 MKVGTVTD  193 (370)
Q Consensus       186 l~V~~~~~  193 (370)
                      |+|.|..+
T Consensus       295 l~i~Wg~~  302 (377)
T KOG0153|consen  295 LKIKWGRP  302 (377)
T ss_pred             EEEEeCCC
Confidence            99999887

>KOG4660|consensus

Probab=98.66  E-value=3.4e-08  Score=95.62  Aligned_cols=174  Identities=20%  Similarity=0.259  Sum_probs=114.3

Q ss_pred             CCCCCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccC
Q psy2983           5 YSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLL   83 (370)
Q Consensus         5 ~~~~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~   83 (370)
                      .-+.+++..-.+++|+|-|||..+++++|++.|+.||+|+.|+.-+     ...|.+||+|.+..+|+.|++ |++..+.
T Consensus        64 ~~~np~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~-----~~~~~~~v~FyDvR~A~~Alk~l~~~~~~  138 (549)
T KOG4660|consen   64 RPDNPSEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETP-----NKRGIVFVEFYDVRDAERALKALNRREIA  138 (549)
T ss_pred             CcCCCCcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccc-----ccCceEEEEEeehHhHHHHHHHHHHHHhh
Confidence            3356666678899999999999999999999999999999976533     447899999999999999995 9999999


Q ss_pred             CeeEEEecccccccccC-CC--------CCC-CCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCC
Q psy2983          84 GIPIIVQPTQAEKNRAG-NT--------LPN-LQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTG  153 (370)
Q Consensus        84 g~~l~v~~~~~~~~~~~-~~--------~~~-~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g  153 (370)
                      |+.++- .......... ..        .+. ..+.+.-....+ ++.|++..+..-++..+.-+|.+.. +.     ++
T Consensus       139 ~~~~k~-~~~~~~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~-~g~l~P~~s~~~~~~~~~~~~~~~~-~~-----~~  210 (549)
T KOG4660|consen  139 GKRIKR-PGGARRAMGLQSGTSFLNHFGSPLANSPPGGWPRGQL-FGMLSPTRSSILLEHISSVDGSSPG-RE-----TP  210 (549)
T ss_pred             hhhhcC-CCcccccchhcccchhhhhccchhhcCCCCCCcCCcc-eeeeccchhhhhhhcchhccCcccc-cc-----cc
Confidence            998882 1111111000 00        000 001111111223 3338888888767777777776654 32     22


Q ss_pred             CcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         154 RSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       154 ~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      .-.-.-|++|.+..++..+.... |..+.+....+++..
T Consensus       211 ~~~hq~~~~~~~~~s~a~~~~~~-G~~~s~~~~v~t~S~  248 (549)
T KOG4660|consen  211 LLNHQRFVEFADNRSYAFSEPRG-GFLISNSSGVITFSG  248 (549)
T ss_pred             chhhhhhhhhccccchhhcccCC-ceecCCCCceEEecC
Confidence            22225678888888886665533 666666665555543

>KOG4661|consensus

Probab=98.65  E-value=3.8e-08  Score=95.00  Aligned_cols=83  Identities=22%  Similarity=0.357  Sum_probs=76.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      --.|.|||.+|...+...+|+++|++||+|...+++.+..+.-.+.|+||.+.+.++|.+||+ |+...++|+.|.|..+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            346899999999999999999999999999999999999888889999999999999999997 9999999999999887


Q ss_pred             cccc
Q psy2983          93 QAEK   96 (370)
Q Consensus        93 ~~~~   96 (370)
                      +.+.
T Consensus       483 KNEp  486 (940)
T KOG4661|consen  483 KNEP  486 (940)
T ss_pred             ccCc
Confidence            6543

>KOG0132|consensus

Probab=98.63  E-value=4.2e-08  Score=98.03  Aligned_cols=76  Identities=20%  Similarity=0.360  Sum_probs=69.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      --+||||||+||..++|.||.++|+.||.|.+|.++..      +|+|||.+....+|.+|+. |....+.++.|+|.|.
T Consensus       419 V~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa  492 (894)
T KOG0132|consen  419 VCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWA  492 (894)
T ss_pred             EeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeee
Confidence            35799999999999999999999999999999988654      6899999999999999995 9999999999999998


Q ss_pred             ccc
Q psy2983          93 QAE   95 (370)
Q Consensus        93 ~~~   95 (370)
                      ...
T Consensus       493 ~g~  495 (894)
T KOG0132|consen  493 VGK  495 (894)
T ss_pred             ccC
Confidence            654

>KOG0533|consensus

Probab=98.63  E-value=1e-07  Score=85.18  Aligned_cols=85  Identities=27%  Similarity=0.582  Sum_probs=77.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ...+.+|+|.|||+.+++++|+++|..||.+..+-+.+++ .|.+.|.|-|.|...++|.+|++.++|..+.|++|++..
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            3445789999999999999999999999999999999996 999999999999999999999999999999999999988


Q ss_pred             eecCCC
Q psy2983         191 VTDRNE  196 (370)
Q Consensus       191 ~~~~~~  196 (370)
                      ..+...
T Consensus       159 i~~~~~  164 (243)
T KOG0533|consen  159 ISSPSQ  164 (243)
T ss_pred             ecCccc
Confidence            655433

>KOG4307|consensus

Probab=98.59  E-value=1.8e-07  Score=92.43  Aligned_cols=184  Identities=15%  Similarity=0.107  Sum_probs=138.8

Q ss_pred             CCCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCee
Q psy2983           7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIP   86 (370)
Q Consensus         7 ~~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~   86 (370)
                      -..++-..+...+-+++++.+.++.|+++||... .|.++.|..++-.+...|.++|+|....++.+|++-+...+-.|.
T Consensus       302 gstpqvv~d~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~rn~~~~~~R~  380 (944)
T KOG4307|consen  302 GSTPQVVSDKYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTRNPSDDVNRP  380 (944)
T ss_pred             CCCCcccchhheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhcCchhhhhcc
Confidence            3445555667778889999999999999999864 477777777777666689999999999999999998888888888


Q ss_pred             EEEecccccccccCC-----CC--------------C-------CCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCc
Q psy2983          87 IIVQPTQAEKNRAGN-----TL--------------P-------NLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGK  140 (370)
Q Consensus        87 l~v~~~~~~~~~~~~-----~~--------------~-------~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~  140 (370)
                      +.+............     ..              +       ...+.......+|||-.||..+++..+.+.|...-.
T Consensus       381 ~q~~P~g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~  460 (944)
T KOG4307|consen  381 FQTGPPGNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAA  460 (944)
T ss_pred             eeecCCCccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhh
Confidence            888654322111000     00              0       000011112368999999999999999999998887


Q ss_pred             eee-EEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         141 IDN-IQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       141 i~~-v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      |++ |.|.+.+ +++.++.|||+|..++.+..|...-+.+-++.+.|+|.-..
T Consensus       461 Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~  512 (944)
T KOG4307|consen  461 VEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIA  512 (944)
T ss_pred             hhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEeechh
Confidence            777 6665554 78889999999999999999988667777788899997643

>KOG0116|consensus

Probab=98.57  E-value=1.8e-07  Score=90.23  Aligned_cols=82  Identities=18%  Similarity=0.308  Sum_probs=70.2

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecc
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPT   92 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~   92 (370)
                      .+...+|||+|||.+++.++|+++|..||+|....|......++...||||+|.+.+++..|++.+...+.++++.|..-
T Consensus       285 ~~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek  364 (419)
T KOG0116|consen  285 RADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEK  364 (419)
T ss_pred             eecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEec
Confidence            34556699999999999999999999999999988866544455559999999999999999998899999999999755


Q ss_pred             cc
Q psy2983          93 QA   94 (370)
Q Consensus        93 ~~   94 (370)
                      ..
T Consensus       365 ~~  366 (419)
T KOG0116|consen  365 RP  366 (419)
T ss_pred             cc
Confidence            43

>KOG1457|consensus

Probab=98.56  E-value=2.6e-06  Score=73.72  Aligned_cols=81  Identities=20%  Similarity=0.287  Sum_probs=65.6

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEee-cCCCCCcccEEEEEECCHHHHHHHHHHhCCceeC---CeeEEE
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMV-DPDTGRSKGYGFITFHSADDAKKAQEQLNGFELA---GRPMKV  188 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~-~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~---g~~l~V  188 (370)
                      .-++|||.+||.++...+|..+|..|.--+...+-. ++.....+-+||+.|.+..+|..|+.+|||..|+   +..|++
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhi  112 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHI  112 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEe
Confidence            358999999999999999999999986555544432 2222335579999999999999999999999997   788999


Q ss_pred             EEeec
Q psy2983         189 GTVTD  193 (370)
Q Consensus       189 ~~~~~  193 (370)
                      ..++.
T Consensus       113 ElAKS  117 (284)
T KOG1457|consen  113 ELAKS  117 (284)
T ss_pred             eehhc
Confidence            88754

>KOG4209|consensus

Probab=98.51  E-value=1.1e-07  Score=85.27  Aligned_cols=85  Identities=26%  Similarity=0.342  Sum_probs=78.7

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEe
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQ   90 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~   90 (370)
                      +..-+.+.+||+|+...+|-+++...|+.||.|..+.+..|..++.+||||||+|.+.+.+..++.++|..+.|+.+.+.
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVT  175 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceee
Confidence            45668899999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             ccccc
Q psy2983          91 PTQAE   95 (370)
Q Consensus        91 ~~~~~   95 (370)
                      +....
T Consensus       176 ~~r~~  180 (231)
T KOG4209|consen  176 LKRTN  180 (231)
T ss_pred             eeeee
Confidence            76543

>KOG4661|consensus

Probab=98.36  E-value=1.2e-06  Score=85.02  Aligned_cols=80  Identities=24%  Similarity=0.474  Sum_probs=74.5

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .+.|||.+|...+...+|+.+|++||.|.-.+++.+..+...+.|+||++.+.++|.++|..||..++.|+.|.|..++.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            36799999999999999999999999999999998877777788999999999999999999999999999999998754

>KOG0226|consensus

Probab=98.36  E-value=2.8e-07  Score=81.10  Aligned_cols=85  Identities=24%  Similarity=0.421  Sum_probs=76.9

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHh-hccCCccCCeeEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPII   88 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~i~g~~l~   88 (370)
                      .+-..+.-+||++.|..+++.+.|-..|.+|-.-...++++|..+|+++||+||.|.++.++..|+ +++|..++.++|+
T Consensus       184 ~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpik  263 (290)
T KOG0226|consen  184 AEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIK  263 (290)
T ss_pred             ccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhH
Confidence            344566778999999999999999999999988888899999999999999999999999999999 5999999999998


Q ss_pred             Eecccc
Q psy2983          89 VQPTQA   94 (370)
Q Consensus        89 v~~~~~   94 (370)
                      .+.+..
T Consensus       264 lRkS~w  269 (290)
T KOG0226|consen  264 LRKSEW  269 (290)
T ss_pred             hhhhhH
Confidence            876654

>KOG0128|consensus

Probab=98.35  E-value=4.7e-08  Score=98.76  Aligned_cols=201  Identities=16%  Similarity=0.200  Sum_probs=150.7

Q ss_pred             cCCCCeEEEcCCCCCCcHH-HHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTR-DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~-~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~   91 (370)
                      ....+..++.++.+..... ..+..|..+|.|..|++...+.......++++.+....++..|....+..+.++...+..
T Consensus       568 ~~~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~pa~~~~a~~~~av~~  647 (881)
T KOG0128|consen  568 PLERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATVPAGGALANRSAAVGL  647 (881)
T ss_pred             hhhhhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhcccccccccCCccccCCC
Confidence            3455667888887777665 567889999999999886633323333489999999999999999999999999888877


Q ss_pred             ccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHH
Q psy2983          92 TQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK  171 (370)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~  171 (370)
                      +.+.......   ...+...-.-.++|++||+..+.+++|+..|.++|.+..+++......+..+|+|+++|..++++.+
T Consensus       648 ad~~~~~~~~---kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~a  724 (881)
T KOG0128|consen  648 ADAEEKEENF---KVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGA  724 (881)
T ss_pred             CCchhhhhcc---CcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhh
Confidence            6654421111   1111111123579999999999999999999999988887776555689999999999999999999


Q ss_pred             HHHHhCCceeCCeeEEEEEeecCCCCcCCCCCCCCHHHHHHhcccCCceeeeeee
Q psy2983         172 AQEQLNGFELAGRPMKVGTVTDRNESVGGGPSNLDTDEMERAGVDLGATGRLQLM  226 (370)
Q Consensus       172 A~~~l~g~~i~g~~l~V~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~  226 (370)
                      |+...+++.++...+-|          .+.|..-+.+.++..+..+|...+..+.
T Consensus       725 aV~f~d~~~~gK~~v~i----------~g~pf~gt~e~~k~l~~~~gn~~~~~~v  769 (881)
T KOG0128|consen  725 AVAFRDSCFFGKISVAI----------SGPPFQGTKEELKSLASKTGNVTSLRLV  769 (881)
T ss_pred             hhhhhhhhhhhhhhhhe----------eCCCCCCchHHHHhhccccCCccccchh
Confidence            99977776666333333          3456667788899999999988765443

>KOG4676|consensus

Probab=98.35  E-value=1.8e-07  Score=86.84  Aligned_cols=164  Identities=20%  Similarity=0.236  Sum_probs=123.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeC---CCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEeccc
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCN---KTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~---~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~~   93 (370)
                      ..|.|.||.+.+|.++++.+|...|+|.++.++...   ........|||.|.+...+..|-.|....|-++.|.|.+..
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~~   87 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPYG   87 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEecC
Confidence            489999999999999999999999999999987633   23445678999999999999999999999999988885543


Q ss_pred             ccccccC---------CCCCCCCC------------------------CC----------CCCCceEEEecCCCCCCHHH
Q psy2983          94 AEKNRAG---------NTLPNLQP------------------------RG----------TGGPMRLYIGSLHFNITEDM  130 (370)
Q Consensus        94 ~~~~~~~---------~~~~~~~~------------------------~~----------~~~~~~l~V~nlp~~~t~e~  130 (370)
                      .......         ...+...+                        +.          ..-.++++|++|+..+...+
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            2111000         00000000                        00          00014699999999999999


Q ss_pred             HHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCee
Q psy2983         131 LRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRP  185 (370)
Q Consensus       131 l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~  185 (370)
                      +.+.|+.+|.|...++.    .|...-+|.++|....+...|+. ++|.++.-+.
T Consensus       168 ~~e~f~r~Gev~ya~~a----sk~~s~~c~~sf~~qts~~halr-~~gre~k~qh  217 (479)
T KOG4676|consen  168 SGESFERKGEVSYAHTA----SKSRSSSCSHSFRKQTSSKHALR-SHGRERKRQH  217 (479)
T ss_pred             hhhhhhhcchhhhhhhh----ccCCCcchhhhHhhhhhHHHHHH-hcchhhhhhh
Confidence            99999999999877764    44456688899999999999998 7888777433

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

Probab=98.34  E-value=2.1e-06  Score=66.00  Aligned_cols=77  Identities=17%  Similarity=0.190  Sum_probs=65.1

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhc--CCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccC----CeeEEE
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSS--VGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLL----GIPIIV   89 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~--~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~----g~~l~v   89 (370)
                      +||+|+|||...|.++|.+.+..  .|...-+.++.|-.++...|||||-|.+++.|....+ .+|..+.    .+...|
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            58999999999999999999986  3677888888999999999999999999999999995 8988875    334455


Q ss_pred             eccc
Q psy2983          90 QPTQ   93 (370)
Q Consensus        90 ~~~~   93 (370)
                      .++.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            5443

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

>KOG4209|consensus

Probab=98.33  E-value=1.6e-06  Score=77.73  Aligned_cols=82  Identities=23%  Similarity=0.425  Sum_probs=76.3

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      .+...+||+|+.+.++.+++...|+.||.+..+.+..|...|.++|||||+|.+.+.+..|+. |+|..+.|+.+.|.+.
T Consensus        99 ~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~  177 (231)
T KOG4209|consen   99 VDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLK  177 (231)
T ss_pred             cCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeee
Confidence            445689999999999999999999999999999999998888999999999999999999999 9999999999999886


Q ss_pred             ecC
Q psy2983         192 TDR  194 (370)
Q Consensus       192 ~~~  194 (370)
                      .-+
T Consensus       178 r~~  180 (231)
T KOG4209|consen  178 RTN  180 (231)
T ss_pred             eee
Confidence            655

>KOG0116|consensus

Probab=98.33  E-value=1.3e-06  Score=84.31  Aligned_cols=82  Identities=23%  Similarity=0.443  Sum_probs=69.9

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecC
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~  194 (370)
                      ..|||.|||.+++..+|+++|..||.|+...|......++...||||+|.+.+.+..|+.+ +-..++++++.|+--.+.
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~~  367 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRPG  367 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecccc
Confidence            4599999999999999999999999999988876543455558999999999999999994 688899999999876554


Q ss_pred             CCC
Q psy2983         195 NES  197 (370)
Q Consensus       195 ~~~  197 (370)
                      ...
T Consensus       368 ~~g  370 (419)
T KOG0116|consen  368 FRG  370 (419)
T ss_pred             ccc
Confidence            443

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

Probab=98.31  E-value=3.4e-06  Score=64.79  Aligned_cols=78  Identities=23%  Similarity=0.353  Sum_probs=67.2

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCC--CceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeC----CeeEEE
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPF--GKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELA----GRPMKV  188 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~--G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~----g~~l~V  188 (370)
                      ++|.|+|||...|.++|.+++...  |....+.++.|-.++.+.|||||.|.+++.|.+-.+.++|..+.    .+...|
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            579999999999999999988653  67777888999889999999999999999999999999998875    455666


Q ss_pred             EEee
Q psy2983         189 GTVT  192 (370)
Q Consensus       189 ~~~~  192 (370)
                      .+|.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            6654

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

>KOG0533|consensus

Probab=98.31  E-value=1.5e-06  Score=77.78  Aligned_cols=81  Identities=22%  Similarity=0.334  Sum_probs=71.1

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      +..+.+|+|.|||+.++++||+++|+.||.+..+-+-.++ .|++.|.|-|.|...++|..|++ ++|..+.|+++.+..
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            3445779999999999999999999999988888776665 58899999999999999999996 999999999998876


Q ss_pred             ccc
Q psy2983          92 TQA   94 (370)
Q Consensus        92 ~~~   94 (370)
                      ...
T Consensus       159 i~~  161 (243)
T KOG0533|consen  159 ISS  161 (243)
T ss_pred             ecC
Confidence            543

>KOG4454|consensus

Probab=98.31  E-value=2.6e-07  Score=79.54  Aligned_cols=108  Identities=11%  Similarity=0.181  Sum_probs=86.8

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .++|||+|+...++++-|.++|-+.|+|.++.|..++ .++.+ ||||.|.++-+..-|++.+||..+.++.+++++-..
T Consensus         9 drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~G   86 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCG   86 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhcccccC
Confidence            4789999999999999999999999999999998885 67767 999999999999999999999999999999977432


Q ss_pred             CCCCcCCCCCCCCHHHHHHhcccCCceeeeee
Q psy2983         194 RNESVGGGPSNLDTDEMERAGVDLGATGRLQL  225 (370)
Q Consensus       194 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~l  225 (370)
                      ..  ...+...++.+.+...++..+++.....
T Consensus        87 ~s--hapld~r~~~ei~~~v~s~a~p~~~~R~  116 (267)
T KOG4454|consen   87 NS--HAPLDERVTEEILYEVFSQAGPIEGVRI  116 (267)
T ss_pred             CC--cchhhhhcchhhheeeecccCCCCCccc
Confidence            21  1123444555666667777776654444

>KOG4660|consensus

Probab=98.24  E-value=7e-07  Score=86.65  Aligned_cols=70  Identities=31%  Similarity=0.481  Sum_probs=64.2

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEE
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMK  187 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~  187 (370)
                      ...+|+|-|||..+++++|+.+|+.||+|+.++.     +-...|..||+|.|..+|++|+++|++.++.|+.++
T Consensus        74 ~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   74 NQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             ccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            4578999999999999999999999999999765     444589999999999999999999999999999888

>KOG0151|consensus

Probab=98.09  E-value=5.3e-06  Score=82.53  Aligned_cols=85  Identities=14%  Similarity=0.258  Sum_probs=73.2

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeC---CCCCeecEEEEEecCCCChHHHhh-ccCCccCCe
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCN---KTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGI   85 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~---~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~   85 (370)
                      +......+.|||+||++.++++.|...|..||+|.+++|+.-+   ...+.+.++||.|-+..+|++|++ |+|+.+.+.
T Consensus       168 DdgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~  247 (877)
T KOG0151|consen  168 DDGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEY  247 (877)
T ss_pred             CCCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeee
Confidence            3445566889999999999999999999999999999997633   224556799999999999999996 999999999


Q ss_pred             eEEEecccc
Q psy2983          86 PIIVQPTQA   94 (370)
Q Consensus        86 ~l~v~~~~~   94 (370)
                      .+++.|.++
T Consensus       248 e~K~gWgk~  256 (877)
T KOG0151|consen  248 EMKLGWGKA  256 (877)
T ss_pred             eeeeccccc
Confidence            999988854

>KOG2193|consensus

Probab=98.02  E-value=3.8e-07  Score=85.44  Aligned_cols=149  Identities=21%  Similarity=0.399  Sum_probs=118.4

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCC-CeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCC-ccCCeeEEEeccc
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVG-KVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQ-KLLGIPIIVQPTQ   93 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G-~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~-~i~g~~l~v~~~~   93 (370)
                      ..+|++||.+.++..+|..+|...- +...-.++.       .|||||.+.+...|.+|++ ++|. .+.|.++.+..+-
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k-------~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv   74 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK-------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSV   74 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee-------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchh
Confidence            4689999999999999999998751 122222232       4899999999999999997 7665 6889999887776


Q ss_pred             ccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEe-ecCCCCCcccEEEEEECCHHHHHHH
Q psy2983          94 AEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLM-VDPDTGRSKGYGFITFHSADDAKKA  172 (370)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~-~~~~~g~~~g~afV~f~~~~~a~~A  172 (370)
                      ....+.               +++-|.|+|+....+.+..++..||.+..|... .+++    .-..-|+|...+.+..|
T Consensus        75 ~kkqrs---------------rk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~e----tavvnvty~~~~~~~~a  135 (584)
T KOG2193|consen   75 PKKQRS---------------RKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSE----TAVVNVTYSAQQQHRQA  135 (584)
T ss_pred             hHHHHh---------------hhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchH----HHHHHHHHHHHHHHHHH
Confidence            544332               468899999999999999999999999988653 2222    22334788899999999


Q ss_pred             HHHhCCceeCCeeEEEEEe
Q psy2983         173 QEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       173 ~~~l~g~~i~g~~l~V~~~  191 (370)
                      +..|+|..+.+..+++.+-
T Consensus       136 i~kl~g~Q~en~~~k~~Yi  154 (584)
T KOG2193|consen  136 IHKLNGPQLENQHLKVGYI  154 (584)
T ss_pred             HHhhcchHhhhhhhhcccC
Confidence            9999999999999999875

>KOG0106|consensus

Probab=98.01  E-value=4.2e-06  Score=73.39  Aligned_cols=70  Identities=33%  Similarity=0.655  Sum_probs=64.6

Q ss_pred             eEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       116 ~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      ++||++||+.+.+.++..+|..||.+..+.+.        .||+||+|.+..+|..|+..||+.++.|-.+.|.++..
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            58999999999999999999999999988775        56899999999999999999999999998888888764

>KOG0151|consensus

Probab=98.01  E-value=1.4e-05  Score=79.55  Aligned_cols=80  Identities=28%  Similarity=0.522  Sum_probs=71.6

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCC---CCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPD---TGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~---~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ...|||+||++.++++.|...|..||+|..++++....   ....+.+|||-|-+..+|.+|+..|+|..+.+..+++.|
T Consensus       174 TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~gW  253 (877)
T KOG0151|consen  174 TTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLGW  253 (877)
T ss_pred             ccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeecc
Confidence            36799999999999999999999999999999986542   245567999999999999999999999999999999999


Q ss_pred             eec
Q psy2983         191 VTD  193 (370)
Q Consensus       191 ~~~  193 (370)
                      ++.
T Consensus       254 gk~  256 (877)
T KOG0151|consen  254 GKA  256 (877)
T ss_pred             ccc
Confidence            754

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.82  E-value=7.4e-05  Score=54.96  Aligned_cols=69  Identities=23%  Similarity=0.383  Sum_probs=47.2

Q ss_pred             ceEEEecCCCCCCHHH----HHhcccCCC-ceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEE
Q psy2983         115 MRLYIGSLHFNITEDM----LRGIFEPFG-KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG  189 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~----l~~~f~~~G-~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~  189 (370)
                      ..|+|.|||.+.+...    |++++..+| .|..|  .        .|-|++.|.+.+.|.+|.+.|+|..+.|++|.|+
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--~--------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--S--------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--e--------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            3699999999888654    566666776 66554  1        4579999999999999999999999999999999


Q ss_pred             Eeec
Q psy2983         190 TVTD  193 (370)
Q Consensus       190 ~~~~  193 (370)
                      +...
T Consensus        73 ~~~~   76 (90)
T PF11608_consen   73 FSPK   76 (90)
T ss_dssp             SS--
T ss_pred             EcCC
Confidence            8644

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

>KOG1995|consensus

Probab=97.77  E-value=2.3e-05  Score=72.63  Aligned_cols=84  Identities=23%  Similarity=0.360  Sum_probs=76.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceee--------EEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCC
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDN--------IQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG  183 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~--------v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g  183 (370)
                      ....++||.++|..+++++|.++|.++|.|..        |++.+|++|+..||-|.|.|.+...|+.|+.-+++..+.+
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~g  143 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCG  143 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccC
Confidence            34468999999999999999999999998863        7889999999999999999999999999999999999999


Q ss_pred             eeEEEEEeecCC
Q psy2983         184 RPMKVGTVTDRN  195 (370)
Q Consensus       184 ~~l~V~~~~~~~  195 (370)
                      ..|+|..+..+.
T Consensus       144 n~ikvs~a~~r~  155 (351)
T KOG1995|consen  144 NTIKVSLAERRT  155 (351)
T ss_pred             CCchhhhhhhcc
Confidence            999998876655

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.72  E-value=4.7e-05  Score=55.99  Aligned_cols=68  Identities=21%  Similarity=0.331  Sum_probs=45.7

Q ss_pred             CeEEEcCCCCCCcHHHHHHHh----hcC-CCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFF----SSV-GKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f----~~~-G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      ..|+|.|||.+.+...|+.-+    ..| |+|.+|.          .+-|+|.|.+.+.|.+|.+ ++|..+.|+.|.|+
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            359999999998887776544    456 4677762          3679999999999999996 99999999999999


Q ss_pred             cccc
Q psy2983          91 PTQA   94 (370)
Q Consensus        91 ~~~~   94 (370)
                      +...
T Consensus        73 ~~~~   76 (90)
T PF11608_consen   73 FSPK   76 (90)
T ss_dssp             SS--
T ss_pred             EcCC
Confidence            8753

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

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.56  E-value=0.00016  Score=56.84  Aligned_cols=69  Identities=19%  Similarity=0.397  Sum_probs=43.5

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCc-----eeCCeeEEEE
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF-----ELAGRPMKVG  189 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~-----~i~g~~l~V~  189 (370)
                      ..|++.+++..++.++|++.|+.||.|..|.+...      -.-|+|.|.+++.|+.|+..+...     .+.+..+++.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            35889999999999999999999999999988654      237999999999999999977544     4445555443

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG1995|consensus

Probab=97.49  E-value=0.0001  Score=68.37  Aligned_cols=84  Identities=24%  Similarity=0.426  Sum_probs=74.7

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCee--------EEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCc
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVR--------DVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQK   81 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~--------~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~   81 (370)
                      ......-+|||-+||..+++++|.++|.++|.|.        .|++-+|+.|++.|+-|.|.|.+...|..|+. +++..
T Consensus        61 ~~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkd  140 (351)
T KOG1995|consen   61 ADKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKD  140 (351)
T ss_pred             ccccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccc
Confidence            3356678899999999999999999999999774        47788899999999999999999999999997 99999


Q ss_pred             cCCeeEEEecccc
Q psy2983          82 LLGIPIIVQPTQA   94 (370)
Q Consensus        82 i~g~~l~v~~~~~   94 (370)
                      +.|..|+|..+..
T Consensus       141 f~gn~ikvs~a~~  153 (351)
T KOG1995|consen  141 FCGNTIKVSLAER  153 (351)
T ss_pred             ccCCCchhhhhhh
Confidence            9999998876653

>KOG4676|consensus

Probab=97.36  E-value=0.0002  Score=66.92  Aligned_cols=76  Identities=18%  Similarity=0.288  Sum_probs=64.5

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCC---CCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDT---GRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~---g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ..|.|.||.+.++.++++.+|...|.|..+.++.....   ....-.|||.|.+..++..|.. |.+..|-|+.|.|...
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEec
Confidence            47999999999999999999999999999999875432   2344589999999999998876 8888888998888664

>KOG4307|consensus

Probab=97.35  E-value=0.00064  Score=68.00  Aligned_cols=77  Identities=22%  Similarity=0.436  Sum_probs=66.8

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCcee-eEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKID-NIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~-~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      +++.|-+.|+|++++-+||.++|..|-.+- +|.+.++ +.|...|-|.|-|++.++|.+|...|+++.|.++.+++..
T Consensus       866 Gp~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n-d~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  866 GPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CCeEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            345799999999999999999999997554 3454444 6899999999999999999999999999999999998754

>KOG4849|consensus

Probab=97.30  E-value=0.00018  Score=66.30  Aligned_cols=78  Identities=22%  Similarity=0.385  Sum_probs=69.6

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCC--ceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFG--KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G--~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ..++|||||-+.+|+++|.+.+..-|  .+..++++.+..+|.+||||+|...+..+..+.++.|..++|.|+.-.|...
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~  159 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSY  159 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeecc
Confidence            35799999999999999999998877  5778889999889999999999999999999999999999999987666543

>KOG4210|consensus

Probab=97.29  E-value=0.00016  Score=67.13  Aligned_cols=82  Identities=29%  Similarity=0.451  Sum_probs=73.0

Q ss_pred             CCCeEE-EcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEeccc
Q psy2983          15 DARTIF-CMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        15 ~~r~v~-V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~~   93 (370)
                      .+.++| |++|+..+++++|+..|..+|.|..+++..++.++..+|+|||+|.+..++..++......+.++++.+....
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  262 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALNDQTRSIGGRPLRLEEDE  262 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhcccCcccCcccccccCC
Confidence            445566 9999999999999999999999999999999999999999999999999999999557778899999988776


Q ss_pred             ccc
Q psy2983          94 AEK   96 (370)
Q Consensus        94 ~~~   96 (370)
                      ...
T Consensus       263 ~~~  265 (285)
T KOG4210|consen  263 PRP  265 (285)
T ss_pred             CCc
Confidence            543

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.23  E-value=0.0005  Score=63.16  Aligned_cols=113  Identities=14%  Similarity=0.267  Sum_probs=75.0

Q ss_pred             CeEEEcCCCCCCcHHHH------HHHhhcCCCeeEEEEeeeCCCCC-eecE--EEEEecCCCChHHHhh-ccCCccCCee
Q psy2983          17 RTIFCMQLSQRIRTRDL------EEFFSSVGKVRDVRLITCNKTRR-FKGI--AYIEFKDPESVPLAMG-LNGQKLLGIP   86 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L------~~~f~~~G~v~~v~i~~d~~~~~-~kg~--afVeF~~~e~A~~Al~-l~g~~i~g~~   86 (370)
                      .-|||-+||+.+-.+++      .++|.+||.|..|.+.+...+.. ..+.  .||.|.+.|+|.+|++ .+|..++|+-
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~  194 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRV  194 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCce
Confidence            45899999998876663      57999999999988765442222 2233  3999999999999995 9999999999


Q ss_pred             EEEecccccccccCCCCCCCCCCCCCCCceEEEecCC---CCCCHHHHHhc
Q psy2983          87 IIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLH---FNITEDMLRGI  134 (370)
Q Consensus        87 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp---~~~t~e~l~~~  134 (370)
                      |+..+....-=..     ......-..+.+.|+.--.   ...+.++|...
T Consensus       195 lkatYGTTKYCts-----YLRn~~CpNp~CMyLHEpg~e~Ds~tK~el~n~  240 (480)
T COG5175         195 LKATYGTTKYCTS-----YLRNAVCPNPDCMYLHEPGPEKDSLTKDELCNS  240 (480)
T ss_pred             EeeecCchHHHHH-----HHcCCCCCCCCeeeecCCCcccccccHHHHhhh
Confidence            9887754321000     0001112334567765433   33566766544

>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=97.22  E-value=0.001  Score=52.23  Aligned_cols=67  Identities=24%  Similarity=0.350  Sum_probs=41.9

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh---cc---CCccCCeeEEEe
Q psy2983          18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG---LN---GQKLLGIPIIVQ   90 (370)
Q Consensus        18 ~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~---l~---g~~i~g~~l~v~   90 (370)
                      .|++.+++..++-++|++.|+.||.|.-|.+.+.      -.-|||.|.++++|..|++   ..   +..+.+..+.+.
T Consensus         3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            5889999999999999999999999999888653      2369999999999999995   22   445566665554

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG1996|consensus

Probab=97.22  E-value=0.00017  Score=64.92  Aligned_cols=41  Identities=32%  Similarity=0.438  Sum_probs=34.5

Q ss_pred             CCCCCCceEEeecCCCCCCCCCchhhHHhHHHHHHHHhhcCceeeE
Q psy2983         265 APPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHGVGAST  310 (370)
Q Consensus       265 ~~~~ps~vl~L~Nm~~~~~l~~d~~~~ei~eDv~~Ec~kyG~~~~~  310 (370)
                      +...|++||+|.||+.+++     -.+|+.+++++||+|||.|...
T Consensus       276 Il~~ptkvlllrnmVg~ge-----vd~elede~keEceKyg~V~~v  316 (378)
T KOG1996|consen  276 ILKCPTKVLLLRNMVGAGE-----VDEELEDETKEECEKYGKVGNV  316 (378)
T ss_pred             HHhcchHHHHhhhhcCccc-----ccHHHHHHHHHHHHhhcceeeE
Confidence            4567999999999999986     4567889999999999997543

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.21  E-value=0.00056  Score=46.56  Aligned_cols=53  Identities=17%  Similarity=0.317  Sum_probs=43.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHh
Q psy2983          16 ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM   75 (370)
Q Consensus        16 ~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al   75 (370)
                      ++.|-|.|.|++.. +++..+|..||+|.++.+.      ....+.||.|.+..+|++||
T Consensus         1 ~~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~------~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    1 STWISVSGFPPDLA-EEVLEHFASFGEIVDIYVP------ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             CcEEEEEeECchHH-HHHHHHHHhcCCEEEEEcC------CCCcEEEEEECCHHHHHhhC
Confidence            36789999997765 4556699999999998774      23568999999999999986

>KOG2314|consensus

Probab=97.21  E-value=0.00081  Score=65.83  Aligned_cols=79  Identities=30%  Similarity=0.412  Sum_probs=65.5

Q ss_pred             CceEEEecCCCCCC------HHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeC-CeeE
Q psy2983         114 PMRLYIGSLHFNIT------EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELA-GRPM  186 (370)
Q Consensus       114 ~~~l~V~nlp~~~t------~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~-g~~l  186 (370)
                      ...|+|.|+|---.      ..-|..+|+++|++..+.++.+. .|..+||.|++|.+..+|..|++.|||+.+. +++.
T Consensus        58 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   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDE-EGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCc-cCCeeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            35799999985322      35678889999999999988886 5559999999999999999999999999887 7788


Q ss_pred             EEEEeec
Q psy2983         187 KVGTVTD  193 (370)
Q Consensus       187 ~V~~~~~  193 (370)
                      .|...++
T Consensus       137 ~v~~f~d  143 (698)
T KOG2314|consen  137 FVRLFKD  143 (698)
T ss_pred             Eeehhhh
Confidence            8876544

>KOG3152|consensus

Probab=97.15  E-value=0.00018  Score=63.76  Aligned_cols=71  Identities=24%  Similarity=0.413  Sum_probs=61.5

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCC--------CCcccE----EEEEECCHHHHHHHHHHhCCceeC
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDT--------GRSKGY----GFITFHSADDAKKAQEQLNGFELA  182 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~--------g~~~g~----afV~f~~~~~a~~A~~~l~g~~i~  182 (370)
                      -.||+++||+.+...-|+++|+.||.|-.|.+.....+        |.+.++    |.|+|.+...|.+....|||..|+
T Consensus        75 GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~Ig  154 (278)
T KOG3152|consen   75 GVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPIG  154 (278)
T ss_pred             eEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCccC
Confidence            46999999999999999999999999999988776554        333333    789999999999999999999999


Q ss_pred             Cee
Q psy2983         183 GRP  185 (370)
Q Consensus       183 g~~  185 (370)
                      |+.
T Consensus       155 gkk  157 (278)
T KOG3152|consen  155 GKK  157 (278)
T ss_pred             CCC
Confidence            864

>KOG1855|consensus

Probab=96.94  E-value=0.0008  Score=63.81  Aligned_cols=75  Identities=23%  Similarity=0.306  Sum_probs=61.6

Q ss_pred             CCCCCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeee---CCC---CC-------eecEEEEEecCCCCh
Q psy2983           5 YSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITC---NKT---RR-------FKGIAYIEFKDPESV   71 (370)
Q Consensus         5 ~~~~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d---~~~---~~-------~kg~afVeF~~~e~A   71 (370)
                      +-++.+..+.++|+|.+-|||.+-.-+.|.++|..+|.|..|+|..-   +.+   ..       .+-+|+|||...+.|
T Consensus       220 Plp~~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A  299 (484)
T KOG1855|consen  220 PLPEFDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAA  299 (484)
T ss_pred             CCCCccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHH
Confidence            44566677789999999999999999999999999999999998653   111   11       256899999999999


Q ss_pred             HHHhhccC
Q psy2983          72 PLAMGLNG   79 (370)
Q Consensus        72 ~~Al~l~g   79 (370)
                      .+|.++.+
T Consensus       300 ~KA~e~~~  307 (484)
T KOG1855|consen  300 RKARELLN  307 (484)
T ss_pred             HHHHHhhc
Confidence            99998553

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.88  E-value=0.0023  Score=58.95  Aligned_cols=79  Identities=20%  Similarity=0.328  Sum_probs=61.6

Q ss_pred             CceEEEecCCCCCCHHH------HHhcccCCCceeeEEEeecCCCC-CcccE--EEEEECCHHHHHHHHHHhCCceeCCe
Q psy2983         114 PMRLYIGSLHFNITEDM------LRGIFEPFGKIDNIQLMVDPDTG-RSKGY--GFITFHSADDAKKAQEQLNGFELAGR  184 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~------l~~~f~~~G~i~~v~~~~~~~~g-~~~g~--afV~f~~~~~a~~A~~~l~g~~i~g~  184 (370)
                      .+-+||-+||+.+-.|+      =.++|.+||.|.+|.+-+...+. ...+.  .|+.|.+.++|.+|+...+|..++||
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            35699999998887665      35789999999988775442111 11122  39999999999999999999999999


Q ss_pred             eEEEEEee
Q psy2983         185 PMKVGTVT  192 (370)
Q Consensus       185 ~l~V~~~~  192 (370)
                      .|+..+..
T Consensus       194 ~lkatYGT  201 (480)
T COG5175         194 VLKATYGT  201 (480)
T ss_pred             eEeeecCc
Confidence            99998864

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=96.87  E-value=0.0017  Score=50.23  Aligned_cols=78  Identities=17%  Similarity=0.246  Sum_probs=53.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEE-EeeeC------CCCCeecEEEEEecCCCChHHHhhccCCccCCee
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVR-LITCN------KTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIP   86 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~-i~~d~------~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~   86 (370)
                      ...+-|.|-+.|+. ....|.+.|++||.|.+.. +.++.      .......+..|.|.++.+|.+||..||..+.|.-
T Consensus         4 ~~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~   82 (100)
T PF05172_consen    4 DSETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSL   82 (100)
T ss_dssp             GGCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCE
T ss_pred             cCCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcE
Confidence            35577999999988 6778889999999987764 11110      0112356899999999999999999999999865


Q ss_pred             EE-Eecc
Q psy2983          87 II-VQPT   92 (370)
Q Consensus        87 l~-v~~~   92 (370)
                      +- |.+.
T Consensus        83 mvGV~~~   89 (100)
T PF05172_consen   83 MVGVKPC   89 (100)
T ss_dssp             EEEEEE-
T ss_pred             EEEEEEc
Confidence            43 5544

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG0115|consensus

Probab=96.82  E-value=0.0026  Score=56.58  Aligned_cols=99  Identities=27%  Similarity=0.414  Sum_probs=80.4

Q ss_pred             hHHHh-hccCCccCCeeEEEecccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeec
Q psy2983          71 VPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVD  149 (370)
Q Consensus        71 A~~Al-~l~g~~i~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~  149 (370)
                      |..|- +|++....|+.+.|.++..                    ..|||.||...++.+.+.+.|+.||+|....+..|
T Consensus         7 ae~ak~eLd~~~~~~~~lr~rfa~~--------------------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD   66 (275)
T KOG0115|consen    7 AEIAKRELDGRFPKGRSLRVRFAMH--------------------AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD   66 (275)
T ss_pred             HHHHHHhcCCCCCCCCceEEEeecc--------------------ceEEEEecchhhhhHHHHHhhhhcCccchheeeec
Confidence            44455 5999999999999988753                    35999999999999999999999999998777777


Q ss_pred             CCCCCcccEEEEEECCHHHHHHHHHHhCCce----eCCeeEEEEE
Q psy2983         150 PDTGRSKGYGFITFHSADDAKKAQEQLNGFE----LAGRPMKVGT  190 (370)
Q Consensus       150 ~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~----i~g~~l~V~~  190 (370)
                       +.++..+-++|+|...-.|.+|...+..--    ..+++.-|..
T Consensus        67 -~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP  110 (275)
T KOG0115|consen   67 -DRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEP  110 (275)
T ss_pred             -ccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCCh
Confidence             589999999999999999999999774322    3345554443

>KOG0129|consensus

Probab=96.74  E-value=0.0044  Score=60.37  Aligned_cols=70  Identities=21%  Similarity=0.236  Sum_probs=63.0

Q ss_pred             CCCcccCCCCeEEEcCCCCCCcHHHHHHHhh-cCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhc
Q psy2983           8 DLSPEERDARTIFCMQLSQRIRTRDLEEFFS-SVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGL   77 (370)
Q Consensus         8 ~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~-~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l   77 (370)
                      +..+...+.||||||+||..++.++|..+|+ -||-|.-+-|=.|++-+-.||-|-|.|.+..+-.+||+.
T Consensus       362 d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  362 DHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             ccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            4456667889999999999999999999999 599999999988988788899999999999999999963

>KOG3152|consensus

Probab=96.64  E-value=0.0012  Score=58.69  Aligned_cols=74  Identities=18%  Similarity=0.226  Sum_probs=60.5

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCC--------CCeec----EEEEEecCCCChHHHhh-ccC
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKT--------RRFKG----IAYIEFKDPESVPLAMG-LNG   79 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~--------~~~kg----~afVeF~~~e~A~~Al~-l~g   79 (370)
                      .+..-.||+++||+.+....|+++|+.||.|-.|.+-....+        |..++    -|.|||.+...|..+-+ ||+
T Consensus        71 krk~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn  150 (278)
T KOG3152|consen   71 KRKTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNN  150 (278)
T ss_pred             hccceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCC
Confidence            345578999999999999999999999999999988665443        22222    26799999999998885 999


Q ss_pred             CccCCee
Q psy2983          80 QKLLGIP   86 (370)
Q Consensus        80 ~~i~g~~   86 (370)
                      ..|.|+.
T Consensus       151 ~~Iggkk  157 (278)
T KOG3152|consen  151 TPIGGKK  157 (278)
T ss_pred             CccCCCC
Confidence            9999873

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.63  E-value=0.0035  Score=42.60  Aligned_cols=52  Identities=23%  Similarity=0.417  Sum_probs=41.2

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHH
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ  173 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~  173 (370)
                      +.|-|.|.+.+..+. +...|..||.|..+.+..      .....++.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPE------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCC------CCcEEEEEECCHHHHHhhC
Confidence            467889998777655 455888999999987752      2448999999999999985

>KOG1996|consensus

Probab=96.59  E-value=0.0051  Score=55.73  Aligned_cols=65  Identities=26%  Similarity=0.373  Sum_probs=54.0

Q ss_pred             HHHHHhcccCCCceeeEEEeecCCCCCccc-EEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         128 EDMLRGIFEPFGKIDNIQLMVDPDTGRSKG-YGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       128 ~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g-~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ++++++-+++||.|..|-++.++....... --||+|...++|.+|+-.|||..|+||.++.++.+
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            468899999999999998887753322222 37999999999999999999999999999988854

>KOG2314|consensus

Probab=96.55  E-value=0.0055  Score=60.22  Aligned_cols=76  Identities=20%  Similarity=0.264  Sum_probs=60.3

Q ss_pred             CCCCeEEEcCCCC--CCcHHHH----HHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccC-Ce
Q psy2983          14 RDARTIFCMQLSQ--RIRTRDL----EEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLL-GI   85 (370)
Q Consensus        14 ~~~r~v~V~nLp~--~~te~~L----~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~-g~   85 (370)
                      --...|.|.|+|.  ....+.|    ..+|+++|++..+.+..+..+| ++||.|+||.+..+|..|++ +||..+. ++
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknH  134 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNH  134 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccc
Confidence            4557799999983  3333443    4578899999999998888766 89999999999999999995 9999885 44


Q ss_pred             eEEEe
Q psy2983          86 PIIVQ   90 (370)
Q Consensus        86 ~l~v~   90 (370)
                      ...|.
T Consensus       135 tf~v~  139 (698)
T KOG2314|consen  135 TFFVR  139 (698)
T ss_pred             eEEee
Confidence            56554

>KOG4849|consensus

Probab=96.44  E-value=0.0016  Score=60.17  Aligned_cols=74  Identities=19%  Similarity=0.227  Sum_probs=64.6

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCC--CeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVG--KVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G--~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      --+||+||-..+|.+||.+.+...|  .+.++++..++.+|.+||||+|-..+.....+.++ |....|+|+.-.|.
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            4489999999999999999999877  47788888899999999999999999998888888 88888999865553

>KOG1855|consensus

Probab=96.44  E-value=0.0039  Score=59.31  Aligned_cols=68  Identities=24%  Similarity=0.365  Sum_probs=57.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeec---CCC--CCc--------ccEEEEEECCHHHHHHHHHHhCC
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVD---PDT--GRS--------KGYGFITFHSADDAKKAQEQLNG  178 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~---~~~--g~~--------~g~afV~f~~~~~a~~A~~~l~g  178 (370)
                      -+.++|.+.|||.+-.-+.|.++|..+|.|..|+|.+.   +.+  |..        +-+|+|+|...+.|.+|.+.|+.
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            35689999999999999999999999999999999876   332  222        44699999999999999997754


Q ss_pred             c
Q psy2983         179 F  179 (370)
Q Consensus       179 ~  179 (370)
                      .
T Consensus       309 e  309 (484)
T KOG1855|consen  309 E  309 (484)
T ss_pred             h
Confidence            3

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.34  E-value=0.009  Score=49.16  Aligned_cols=57  Identities=23%  Similarity=0.427  Sum_probs=45.5

Q ss_pred             HHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEeccccc
Q psy2983          31 RDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAE   95 (370)
Q Consensus        31 ~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~~~~   95 (370)
                      .+|.+.|..||.+.=++++.        +.-+|.|.+-+.|-+|++++|..+.|+.|.|+...+.
T Consensus        51 ~~ll~~~~~~GevvLvRfv~--------~~mwVTF~dg~sALaals~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   51 DELLQKFAQYGEVVLVRFVG--------DTMWVTFRDGQSALAALSLDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHHCCS-ECEEEEET--------TCEEEEESSCHHHHHHHHGCCSEETTEEEEEEE----
T ss_pred             HHHHHHHHhCCceEEEEEeC--------CeEEEEECccHHHHHHHccCCcEECCEEEEEEeCCcc
Confidence            46778888999988777764        3489999999999999999999999999999876543

; PDB: 1UFW_A 2DNR_A.

>KOG0112|consensus

Probab=96.07  E-value=0.0029  Score=65.23  Aligned_cols=110  Identities=17%  Similarity=0.303  Sum_probs=89.2

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecC
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~  194 (370)
                      ++||+|||+..+++.+|+..|..+|.|..|.+-... -+.-..||||.|.+...+..|...+.+..|....+++.+....
T Consensus       373 rTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~~k  451 (975)
T KOG0112|consen  373 RTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQPK  451 (975)
T ss_pred             hhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCcccccccccc
Confidence            579999999999999999999999999999886553 3344459999999999999999999999888666666665332


Q ss_pred             -----CCCcCCCCCCCCHHHHHHhcccCCceeeeee
Q psy2983         195 -----NESVGGGPSNLDTDEMERAGVDLGATGRLQL  225 (370)
Q Consensus       195 -----~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~l  225 (370)
                           ...++++........+.+.|..||.+..+.+
T Consensus       452 st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy  487 (975)
T KOG0112|consen  452 STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDY  487 (975)
T ss_pred             cccceeeccCCCCCCChHHHHHHHhhccCcceeeec
Confidence                 1225566677778889999999999977555

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.05  E-value=0.013  Score=43.23  Aligned_cols=54  Identities=15%  Similarity=0.321  Sum_probs=40.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG   76 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~   76 (370)
                      ...+..||+ +|..+...||.++|++||.|.- ..+.|       .-|||.....+.|..++.
T Consensus         7 ~RdHVFhlt-FPkeWK~~DI~qlFspfG~I~V-sWi~d-------TSAfV~l~~r~~~~~v~~   60 (87)
T PF08675_consen    7 SRDHVFHLT-FPKEWKTSDIYQLFSPFGQIYV-SWIND-------TSAFVALHNRDQAKVVMN   60 (87)
T ss_dssp             SGCCEEEEE---TT--HHHHHHHCCCCCCEEE-EEECT-------TEEEEEECCCHHHHHHHH
T ss_pred             CcceEEEEe-CchHhhhhhHHHHhccCCcEEE-EEEcC-------CcEEEEeecHHHHHHHHH
Confidence            344566666 9999999999999999999874 44443       359999999999999885

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.04  E-value=0.024  Score=46.70  Aligned_cols=57  Identities=26%  Similarity=0.455  Sum_probs=46.1

Q ss_pred             HHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecC
Q psy2983         129 DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       129 e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~  194 (370)
                      .+|.+.|..||.+.=+++..+        .-+|+|.+.++|.+|+. ++|..+.|+.|+|+...+.
T Consensus        51 ~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   51 DELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE----
T ss_pred             HHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCcc
Confidence            378888899999888887633        47999999999999999 9999999999999886543

; PDB: 1UFW_A 2DNR_A.

>KOG2416|consensus

Probab=96.00  E-value=0.0047  Score=61.03  Aligned_cols=77  Identities=13%  Similarity=0.229  Sum_probs=62.9

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhh-cCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCcc---CCe
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFS-SVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL---LGI   85 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~-~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i---~g~   85 (370)
                      ...+.++.|||.||-..+|.-+|++++. .+|.|.+.||=      +-|..|||.|.+.++|.+... |+|..|   +++
T Consensus       439 sR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmD------kIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK  512 (718)
T KOG2416|consen  439 SRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMD------KIKSHCYVSYSSVEEAAATREALHNVQWPPSNPK  512 (718)
T ss_pred             CCCCccceEeeecccccchHHHHHHHHhhccCchHHHHHH------HhhcceeEecccHHHHHHHHHHHhccccCCCCCc
Confidence            3677899999999999999999999999 57788887652      236689999999999999995 999887   456


Q ss_pred             eEEEeccc
Q psy2983          86 PIIVQPTQ   93 (370)
Q Consensus        86 ~l~v~~~~   93 (370)
                      .|.+.+..
T Consensus       513 ~L~adf~~  520 (718)
T KOG2416|consen  513 HLIADFVR  520 (718)
T ss_pred             eeEeeecc
Confidence            66665544

>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=95.93  E-value=0.023  Score=43.99  Aligned_cols=75  Identities=17%  Similarity=0.199  Sum_probs=49.9

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEE-EeecC------CCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeE-
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQ-LMVDP------DTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM-  186 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~-~~~~~------~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l-  186 (370)
                      .-|.|-+.|+. ....+.+.|++||.|.+.. +.++.      ........-.++|.++.+|.+|+. -||..+.|..| 
T Consensus         7 ~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~mv   84 (100)
T PF05172_consen    7 TWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLMV   84 (100)
T ss_dssp             CEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEEE
T ss_pred             eEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEEE
Confidence            45888899888 5577888899999987764 11100      011224578999999999999999 79999998654 


Q ss_pred             EEEEe
Q psy2983         187 KVGTV  191 (370)
Q Consensus       187 ~V~~~  191 (370)
                      -|.++
T Consensus        85 GV~~~   89 (100)
T PF05172_consen   85 GVKPC   89 (100)
T ss_dssp             EEEE-
T ss_pred             EEEEc
Confidence            35554

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.

>KOG2193|consensus

Probab=95.77  E-value=0.006  Score=57.91  Aligned_cols=105  Identities=25%  Similarity=0.365  Sum_probs=79.4

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCc-eeCCeeEEEEEeec
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF-ELAGRPMKVGTVTD  193 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~-~i~g~~l~V~~~~~  193 (370)
                      +++|++||.+.++..++..+|...-.-.+-.++.      ..||+||.+.+...|.+|++.++|+ ++.|.++.+....+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            3689999999999999999997542111112221      2579999999999999999999985 68899999988755


Q ss_pred             CCC-----CcCCCCCCCCHHHHHHhcccCCceeeeee
Q psy2983         194 RNE-----SVGGGPSNLDTDEMERAGVDLGATGRLQL  225 (370)
Q Consensus       194 ~~~-----~~~~~~~~~~~~~l~~~~~~~g~~~~~~l  225 (370)
                      +..     ...+++....-+-+..+...+|...++..
T Consensus        76 kkqrsrk~Qirnippql~wevld~Ll~qyg~ve~~eq  112 (584)
T KOG2193|consen   76 KKQRSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQ  112 (584)
T ss_pred             HHHHhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhh
Confidence            433     35567777777778888888888776544

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=95.55  E-value=0.083  Score=41.71  Aligned_cols=77  Identities=19%  Similarity=0.200  Sum_probs=54.3

Q ss_pred             CCCCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCC-CeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccC
Q psy2983           6 SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVG-KVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLL   83 (370)
Q Consensus         6 ~~~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G-~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~   83 (370)
                      +....+..+....+.+...|.-++.++|..+.+.+- .|..+++++|..  ..+=.+++.|++.++|..... .||..++
T Consensus         3 ~~~~~~~~~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen    3 SESDLPDERRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             CccCCCCCCCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            444455556666566655555566677776666653 488889988754  234468999999999999995 9999875


Q ss_pred             C
Q psy2983          84 G   84 (370)
Q Consensus        84 g   84 (370)
                      -
T Consensus        81 s   81 (110)
T PF07576_consen   81 S   81 (110)
T ss_pred             C
Confidence            4

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=95.39  E-value=0.093  Score=38.83  Aligned_cols=55  Identities=22%  Similarity=0.402  Sum_probs=42.2

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCC
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNG  178 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g  178 (370)
                      +..+|+ +|..+...||.++|++||.| .|..+-|.       -|||...+.+.|..++..+.-
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEECCCHHHHHHHHHHTT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEeecHHHHHHHHHHhcc
Confidence            455666 99999999999999999998 56666553       699999999999999998753

; 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.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=95.05  E-value=0.087  Score=36.88  Aligned_cols=55  Identities=18%  Similarity=0.299  Sum_probs=45.0

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCC---CceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHh
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPF---GKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL  176 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~---G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l  176 (370)
                      +.+|+|.|+. +++.++|+.+|..|   .....|..+-|.       -|-|.|.+.+.|.+|+.+|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            4679999984 58889999999988   134578888764       4889999999999999864

>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=94.81  E-value=0.092  Score=45.25  Aligned_cols=79  Identities=16%  Similarity=0.227  Sum_probs=50.8

Q ss_pred             CceEEEecCCCCCCHHHHHhcccC-CCce---eeEEEeecCCCCC--cccEEEEEECCHHHHHHHHHHhCCceeCC----
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEP-FGKI---DNIQLMVDPDTGR--SKGYGFITFHSADDAKKAQEQLNGFELAG----  183 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~-~G~i---~~v~~~~~~~~g~--~~g~afV~f~~~~~a~~A~~~l~g~~i~g----  183 (370)
                      ..+|.|++||+.+|++++.+.+.+ ++.-   ..+.-......-.  ...-|||.|.+.+++..-...++|+.|.+    
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg~   86 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKGN   86 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS-
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCCC
Confidence            468999999999999999998888 6655   3333222221111  22349999999999999999999988753    


Q ss_pred             -eeEEEEEee
Q psy2983         184 -RPMKVGTVT  192 (370)
Q Consensus       184 -~~l~V~~~~  192 (370)
                       ....|.++.
T Consensus        87 ~~~~~VE~Ap   96 (176)
T PF03467_consen   87 EYPAVVEFAP   96 (176)
T ss_dssp             EEEEEEEE-S
T ss_pred             CcceeEEEcc
Confidence             244455543

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.

>KOG2202|consensus

Probab=94.80  E-value=0.011  Score=52.66  Aligned_cols=62  Identities=24%  Similarity=0.391  Sum_probs=50.5

Q ss_pred             HHHHhccc-CCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         129 DMLRGIFE-PFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       129 e~l~~~f~-~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      +++...|+ +||.|+++.+-.+. .-.-.|-++|.|...++|++|++.|||.-+.|++|...++
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            34444444 89999998766543 3445788999999999999999999999999999999875

>KOG0804|consensus

Probab=94.47  E-value=0.3  Score=47.20  Aligned_cols=68  Identities=16%  Similarity=0.344  Sum_probs=58.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCC-CeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCC
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVG-KVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLG   84 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G-~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g   84 (370)
                      .++.|+|-.+|..++..||..|...+- .|.+++++||..-+  +=.++|.|++.++|..+.+ +||..|+.
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pn--rymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPN--RYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCc--eEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            389999999999999999999999764 48999999965422  3358999999999999995 99998864

>KOG2416|consensus

Probab=94.22  E-value=0.046  Score=54.26  Aligned_cols=75  Identities=16%  Similarity=0.213  Sum_probs=60.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHhccc-CCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeC---CeeEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFE-PFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELA---GRPMK  187 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~-~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~---g~~l~  187 (370)
                      ...+.|||.||-..+|.-+|+.++. ..|.|...+|-+-      +..|||.|.+.++|.....+|||..+-   .+.|.
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkI------KShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~  515 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKI------KSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLI  515 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHHHHHHh------hcceeEecccHHHHHHHHHHHhccccCCCCCceeE
Confidence            3457899999999999999999998 5667777643222      557999999999999999999998763   56777


Q ss_pred             EEEee
Q psy2983         188 VGTVT  192 (370)
Q Consensus       188 V~~~~  192 (370)
                      +.|..
T Consensus       516 adf~~  520 (718)
T KOG2416|consen  516 ADFVR  520 (718)
T ss_pred             eeecc
Confidence            77753

>KOG2202|consensus

Probab=93.89  E-value=0.015  Score=51.89  Aligned_cols=62  Identities=19%  Similarity=0.339  Sum_probs=47.9

Q ss_pred             HHHHHHhh-cCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          31 RDLEEFFS-SVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        31 ~~L~~~f~-~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      ++|...|+ +||.|..+.+..+ ..-.-.|-+||.|...|+|++|++ |++.-+.|++|....+.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~N-l~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDN-LGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcc-cchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            34444444 7899999865443 334557889999999999999996 99999999999876654

>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=93.41  E-value=0.056  Score=46.61  Aligned_cols=71  Identities=17%  Similarity=0.232  Sum_probs=43.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhc-CCCe---eEEEEeeeCCC--CCeecEEEEEecCCCChHHHhh-ccCCccCC
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSS-VGKV---RDVRLITCNKT--RRFKGIAYIEFKDPESVPLAMG-LNGQKLLG   84 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~-~G~v---~~v~i~~d~~~--~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g   84 (370)
                      ....+|-|++||+++|++++.+.+.. ++.-   ..+.-......  ...-.-|||.|.+.+++..... ++|..|.+
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D   82 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVD   82 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEEC
Confidence            45568999999999999999997776 5544   23321111111  1123469999999999888885 88887743

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=93.29  E-value=0.059  Score=40.58  Aligned_cols=72  Identities=14%  Similarity=0.105  Sum_probs=48.2

Q ss_pred             EEEEecCCCChHHHhh--ccCCccCCeeEEEecccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhccc
Q psy2983          61 AYIEFKDPESVPLAMG--LNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFE  136 (370)
Q Consensus        61 afVeF~~~e~A~~Al~--l~g~~i~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~  136 (370)
                      |+|.|.+++-|++.+.  -+...+++..+.|+.+........    .........+++|.|+|||..+.+++|++.++
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~----k~qv~~~vs~rtVlvsgip~~l~ee~l~D~Le   74 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQ----KFQVFSGVSKRTVLVSGIPDVLDEEELRDKLE   74 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCce----EEEEEEcccCCEEEEeCCCCCCChhhheeeEE
Confidence            6899999999999996  444566777776654432221111    11111223457899999999999999998754

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=92.83  E-value=0.32  Score=34.03  Aligned_cols=52  Identities=21%  Similarity=0.347  Sum_probs=42.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcC----CCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh
Q psy2983          16 ARTIFCMQLSQRIRTRDLEEFFSSV----GKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG   76 (370)
Q Consensus        16 ~r~v~V~nLp~~~te~~L~~~f~~~----G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~   76 (370)
                      ...|+|+|+ .+++.++|+.+|..|    + ...|..+-|.       -|=|.|.+.+.|.+||.
T Consensus         5 peavhirGv-d~lsT~dI~~y~~~y~~~~~-~~~IEWIdDt-------ScNvvf~d~~~A~~AL~   60 (62)
T PF10309_consen    5 PEAVHIRGV-DELSTDDIKAYFSEYFDEEG-PFRIEWIDDT-------SCNVVFKDEETAARALV   60 (62)
T ss_pred             eceEEEEcC-CCCCHHHHHHHHHHhcccCC-CceEEEecCC-------cEEEEECCHHHHHHHHH
Confidence            357999999 458999999999998    4 4467777764       38899999999999984

>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=92.73  E-value=1.3  Score=35.00  Aligned_cols=67  Identities=19%  Similarity=0.284  Sum_probs=51.3

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCC-ceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCC
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFG-KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG  183 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G-~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g  183 (370)
                      ..+.+...|.-++.++|..+.+++- .|..+++++|.  ..++=.+++.|.+.++|..-....||+.+..
T Consensus        14 ~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   14 TLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             eEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            4455555666667777877766664 67788998874  3456679999999999999999999998864

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG0115|consensus

Probab=91.97  E-value=0.13  Score=46.07  Aligned_cols=59  Identities=15%  Similarity=0.193  Sum_probs=51.4

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG   76 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~   76 (370)
                      ..|||.||+..++.+.+.+.|+.||+|..-.++-|.. ++..+-++|+|...-.|.+|+.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r-~k~t~eg~v~~~~k~~a~~a~r   90 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDR-GKPTREGIVEFAKKPNARKAAR   90 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeeccc-ccccccchhhhhcchhHHHHHH
Confidence            5689999999999999999999999998766655543 6777889999999999999996

>KOG2135|consensus

Probab=91.46  E-value=0.19  Score=48.78  Aligned_cols=77  Identities=16%  Similarity=0.123  Sum_probs=63.6

Q ss_pred             cCCCCeEEEcCCCCCC-cHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRI-RTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~-te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~   91 (370)
                      ..+.+.+-+.-.|... +-.+|...|.+||.|..|.+-..      .-.|.|.|.+..+|-.|...++..|+|+.|+|.|
T Consensus       369 ~~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~s~~avlnnr~iKl~w  442 (526)
T KOG2135|consen  369 VVDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYASHGAVLNNRFIKLFW  442 (526)
T ss_pred             hcccchhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhccccceecCceeEEEE
Confidence            3455666777777766 56889999999999999987443      2459999999999999999999999999999999


Q ss_pred             cccc
Q psy2983          92 TQAE   95 (370)
Q Consensus        92 ~~~~   95 (370)
                      ..+.
T Consensus       443 hnps  446 (526)
T KOG2135|consen  443 HNPS  446 (526)
T ss_pred             ecCC
Confidence            8753

>KOG4285|consensus

Probab=91.39  E-value=0.76  Score=42.23  Aligned_cols=65  Identities=14%  Similarity=0.110  Sum_probs=52.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeE
Q psy2983          16 ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPI   87 (370)
Q Consensus        16 ~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l   87 (370)
                      ..=|-|-++|+. ...-|...|++||.|.+....      ....+-+|.|.+.-+|++||..+|..|.|..+
T Consensus       197 D~WVTVfGFppg-~~s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALskng~ii~g~vm  261 (350)
T KOG4285|consen  197 DTWVTVFGFPPG-QVSIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALSKNGTIIDGDVM  261 (350)
T ss_pred             cceEEEeccCcc-chhHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhhhcCeeeccceE
Confidence            445888899876 456778899999999887553      22468999999999999999999999988643

>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=91.36  E-value=0.52  Score=40.88  Aligned_cols=61  Identities=16%  Similarity=0.226  Sum_probs=45.8

Q ss_pred             CHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhC--CceeCCeeEEEEEeec
Q psy2983         127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN--GFELAGRPMKVGTVTD  193 (370)
Q Consensus       127 t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~--g~~i~g~~l~V~~~~~  193 (370)
                      ..+.|+++|..++.+..+..++.      -+-..|.|.+.+.|.+|...|+  +..+.|..+++.++..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            45789999999999888777643      3458999999999999999999  9999999999988743

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.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=90.50  E-value=0.52  Score=38.56  Aligned_cols=74  Identities=22%  Similarity=0.187  Sum_probs=52.5

Q ss_pred             cCCCCeEEEcCCCCCC----cHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEE
Q psy2983          13 ERDARTIFCMQLSQRI----RTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPII   88 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~----te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~   88 (370)
                      +.+-.||.|+=|..++    +...+...++.||+|.+|.+.-       +.-|.|.|++..+|.+|+..-+....|..+.
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-------rqsavVvF~d~~SAC~Av~Af~s~~pgtm~q  155 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-------RQSAVVVFKDITSACKAVSAFQSRAPGTMFQ  155 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-------CceEEEEehhhHHHHHHHHhhcCCCCCceEE
Confidence            3456778887665554    3445556677899999997643       3469999999999999996444456677666


Q ss_pred             Eeccc
Q psy2983          89 VQPTQ   93 (370)
Q Consensus        89 v~~~~   93 (370)
                      ..|-.
T Consensus       156 CsWqq  160 (166)
T PF15023_consen  156 CSWQQ  160 (166)
T ss_pred             eeccc
Confidence            65543

>KOG2253|consensus

Probab=89.02  E-value=0.29  Score=49.48  Aligned_cols=70  Identities=11%  Similarity=0.283  Sum_probs=61.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      .+..++||+|+...+..+-++.++..+|.|.++....         |||++|....-+.+|+..++...++|+.+.+..
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            4457899999999999999999999999987765432         899999999999999999999999988877654

>KOG2068|consensus

Probab=88.64  E-value=0.14  Score=47.62  Aligned_cols=76  Identities=13%  Similarity=0.225  Sum_probs=57.4

Q ss_pred             CeEEEcCCCCCCcHHHHH---HHhhcCCCeeEEEEeeeCC--CCC-eecEEEEEecCCCChHHHhh-ccCCccCCeeEEE
Q psy2983          17 RTIFCMQLSQRIRTRDLE---EFFSSVGKVRDVRLITCNK--TRR-FKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIV   89 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~---~~f~~~G~v~~v~i~~d~~--~~~-~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v   89 (370)
                      +-+||-+|+.....+.+.   ++|.+||.|..|.+.++..  ++. ..--+||.|...|+|..|+. .+|....|+.++.
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            558889998777555553   4899999999998887662  111 11238999999999999996 9999999998665


Q ss_pred             ecc
Q psy2983          90 QPT   92 (370)
Q Consensus        90 ~~~   92 (370)
                      ...
T Consensus       158 ~~g  160 (327)
T KOG2068|consen  158 SLG  160 (327)
T ss_pred             hhC
Confidence            443

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=88.59  E-value=0.93  Score=37.15  Aligned_cols=70  Identities=17%  Similarity=0.256  Sum_probs=52.4

Q ss_pred             CceEEEecCCCCCC-HH---HHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEE
Q psy2983         114 PMRLYIGSLHFNIT-ED---MLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG  189 (370)
Q Consensus       114 ~~~l~V~nlp~~~t-~e---~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~  189 (370)
                      -.+|.|+=|..++. .+   .+..-++.||+|.++.+.     |  +--|.|.|.+..+|-+|+.+++. ..-|..+.+.
T Consensus        86 MsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----G--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCs  157 (166)
T PF15023_consen   86 MSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----G--RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCS  157 (166)
T ss_pred             ceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----C--CceEEEEehhhHHHHHHHHhhcC-CCCCceEEee
Confidence            35788887776653 23   445556889999998774     2  33699999999999999998876 5567778877


Q ss_pred             Ee
Q psy2983         190 TV  191 (370)
Q Consensus       190 ~~  191 (370)
                      |-
T Consensus       158 Wq  159 (166)
T PF15023_consen  158 WQ  159 (166)
T ss_pred             cc
Confidence            64

>KOG4574|consensus

Probab=88.48  E-value=0.22  Score=51.67  Aligned_cols=71  Identities=21%  Similarity=0.350  Sum_probs=60.3

Q ss_pred             EEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeC--CeeEEEEEeec
Q psy2983         117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELA--GRPMKVGTVTD  193 (370)
Q Consensus       117 l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~--g~~l~V~~~~~  193 (370)
                      .++.|.+-..+...|..+|+.||.|.+.+.+++      -..|.|+|...++|..|+.+|+|.++.  |-+.+|.+++.
T Consensus       301 ~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~------~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  301 QSLENNAVNLTSSSLATLCSDYGSVASAWTLRD------LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhcchhhheeccc------ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            455555667788899999999999999998877      348999999999999999999998865  77888888764

>KOG2591|consensus

Probab=87.83  E-value=1  Score=44.78  Aligned_cols=69  Identities=17%  Similarity=0.292  Sum_probs=55.2

Q ss_pred             ceEEEecCCCCCCHHHHHhcccC--CCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCC--ceeCCeeEEEEE
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEP--FGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNG--FELAGRPMKVGT  190 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~--~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g--~~i~g~~l~V~~  190 (370)
                      +.+.++-||..+-.|+++.+|..  +-.+.+|.+-.+.       -=||+|++..+|+.|...|..  ++|.|++|..++
T Consensus       176 cIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpImARI  248 (684)
T KOG2591|consen  176 CIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMARI  248 (684)
T ss_pred             eEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhhhh
Confidence            45778999999999999999975  5677788876553       259999999999999998865  567787766544

>KOG2068|consensus

Probab=87.73  E-value=0.26  Score=45.92  Aligned_cols=79  Identities=25%  Similarity=0.487  Sum_probs=60.4

Q ss_pred             CceEEEecCCCCCCHHHHH---hcccCCCceeeEEEeecCC----CCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeE
Q psy2983         114 PMRLYIGSLHFNITEDMLR---GIFEPFGKIDNIQLMVDPD----TGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM  186 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~---~~f~~~G~i~~v~~~~~~~----~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l  186 (370)
                      .+.+||-+|+..+..+.+.   +.|.+||.|.++...++.-    .+.+. -++|+|...++|..|+...+|....|+.+
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~-s~yITy~~~eda~rci~~v~g~~~dg~~l  155 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTC-SVYITYEEEEDADRCIDDVDGFVDDGRAL  155 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCC-cccccccchHhhhhHHHHhhhHHhhhhhh
Confidence            3568899999887665543   5677888999988877651    12222 28999999999999999999999999998


Q ss_pred             EEEEeec
Q psy2983         187 KVGTVTD  193 (370)
Q Consensus       187 ~V~~~~~  193 (370)
                      +..+...
T Consensus       156 ka~~gtt  162 (327)
T KOG2068|consen  156 KASLGTT  162 (327)
T ss_pred             HHhhCCC
Confidence            8776543

>KOG2135|consensus

Probab=85.74  E-value=0.44  Score=46.33  Aligned_cols=72  Identities=26%  Similarity=0.283  Sum_probs=57.3

Q ss_pred             EEEecCCCCC-CHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecCC
Q psy2983         117 LYIGSLHFNI-TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRN  195 (370)
Q Consensus       117 l~V~nlp~~~-t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~~  195 (370)
                      |-+.-.|+.. +.++|...|.+||.|..|.+-..      .--|.|+|.+..+|-.|.. .++..|.+|.|+|.|-++..
T Consensus       375 l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps~  447 (526)
T KOG2135|consen  375 LALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPSP  447 (526)
T ss_pred             hhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhc-cccceecCceeEEEEecCCc
Confidence            3444445554 56899999999999999987544      2268999999999988877 79999999999999977643

>KOG0804|consensus

Probab=83.52  E-value=3.7  Score=39.97  Aligned_cols=68  Identities=22%  Similarity=0.258  Sum_probs=58.6

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCC-ceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCC
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFG-KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG  183 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G-~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g  183 (370)
                      +..|+|-.+|..++-.||..++..|- .|..+++++|.  -.++=..++.|.+.++|....+.+||..|..
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~--~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDG--MPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecC--CCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            57899999999999999999998775 68899999874  2334469999999999999999999998874

>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=82.19  E-value=5.3  Score=28.36  Aligned_cols=56  Identities=16%  Similarity=0.250  Sum_probs=44.4

Q ss_pred             CCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEE
Q psy2983         124 FNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV  188 (370)
Q Consensus       124 ~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V  188 (370)
                      ..++-++++..+..|+-.   ++..|+ +    | =||.|.+..+|.++....+|..+.+..|.+
T Consensus        10 ~~~~v~d~K~~Lr~y~~~---~I~~d~-t----G-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   10 HGVTVEDFKKRLRKYRWD---RIRDDR-T----G-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CCccHHHHHHHHhcCCcc---eEEecC-C----E-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            456789999999999743   344553 2    3 389999999999999999999998877654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=81.73  E-value=3.2  Score=34.36  Aligned_cols=121  Identities=14%  Similarity=0.095  Sum_probs=79.4

Q ss_pred             CCCeEEEcCCC--CCCcHHHHHHHhhc-CCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEec
Q psy2983          15 DARTIFCMQLS--QRIRTRDLEEFFSS-VGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQP   91 (370)
Q Consensus        15 ~~r~v~V~nLp--~~~te~~L~~~f~~-~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~   91 (370)
                      ..+...|+.+.  ...+-..|.+.+.. .+....+.+..-     ..++..+.|.+.+++..++......+.|..+.++.
T Consensus        14 ~~~~~lVg~~l~~~~~~~~~l~~~l~~~W~~~~~~~i~~l-----~~~~fl~~F~~~~d~~~vl~~~p~~~~~~~~~l~~   88 (153)
T PF14111_consen   14 RWQLCLVGRVLSPKPISLSALEQELAKIWKLKGGVKIRDL-----GDNLFLFQFESEEDRQRVLKGGPWNFNGHFLILQR   88 (153)
T ss_pred             hcCeEEEEEECCCCCCCHHHHHHHHHHHhCCCCcEEEEEe-----CCCeEEEEEEeccceeEEEecccccccccchhhhh
Confidence            33445555553  34667777777765 344334444331     24789999999999999998888888888888876


Q ss_pred             ccccccccCCCCCCCCCCCCCCCceEEEecCCCC-CCHHHHHhcccCCCceeeEEEe
Q psy2983          92 TQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFN-ITEDMLRGIFEPFGKIDNIQLM  147 (370)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~-~t~e~l~~~f~~~G~i~~v~~~  147 (370)
                      -.+......       ......+-=|.|.|||.. .+++-++.+.+.+|.+..+...
T Consensus        89 W~~~~~~~~-------~~~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~~  138 (153)
T PF14111_consen   89 WSPDFNPSE-------VKFEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDEN  138 (153)
T ss_pred             hcccccccc-------cceeccchhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEcC
Confidence            553221111       000111234778899977 6788899999999999877654

>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=81.58  E-value=4.1  Score=35.34  Aligned_cols=60  Identities=25%  Similarity=0.264  Sum_probs=43.1

Q ss_pred             cHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-cc--CCccCCeeEEEecccc
Q psy2983          29 RTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LN--GQKLLGIPIIVQPTQA   94 (370)
Q Consensus        29 te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~--g~~i~g~~l~v~~~~~   94 (370)
                      ..+.|+++|..++.+..+..++.      -+-..|.|.+.++|..|.. ++  +..+.|..+++.+.+.
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            45789999999999888766542      2458999999999999996 88  8999999999987743

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.

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=80.16  E-value=5.6  Score=28.76  Aligned_cols=59  Identities=22%  Similarity=0.351  Sum_probs=34.5

Q ss_pred             CCCCHHHHHhcccCCC-----ceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         124 FNITEDMLRGIFEPFG-----KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       124 ~~~t~e~l~~~f~~~G-----~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ..++..+|..++...+     .|-.|++..+        |+||+-... .|..++..|++..+.|++++|+.+
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            4567777777776653     3556777633        899998654 788999999999999999999864

; PDB: 2G0C_A 3MOJ_B.

>KOG2318|consensus

Probab=80.08  E-value=5.7  Score=39.91  Aligned_cols=129  Identities=16%  Similarity=0.306  Sum_probs=75.5

Q ss_pred             ccCCCCeEEEcCCCC-CCcHHHHHHHhhcC----CCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCee
Q psy2983          12 EERDARTIFCMQLSQ-RIRTRDLEEFFSSV----GKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIP   86 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~-~~te~~L~~~f~~~----G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~   86 (370)
                      ....+++|-|-||.. .+...+|.-+|+.|    |.|.+|.|..... |+.                  .|..-.++|-+
T Consensus       170 ~~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeF-Gke------------------RM~eEeV~GP~  230 (650)
T KOG2318|consen  170 LGEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEF-GKE------------------RMKEEEVHGPP  230 (650)
T ss_pred             cccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhh-hHH------------------HhhhhcccCCh
Confidence            356789999999994 57899999999876    5899998865432 111                  02222333433


Q ss_pred             EEEecccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCH
Q psy2983          87 IIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA  166 (370)
Q Consensus        87 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~  166 (370)
                      +.+..........                .     ......++-.++.+..|+ +..++.+          ||.|+|.+.
T Consensus       231 ~el~~~~e~~~~s----------------~-----sD~ee~~~~~~~kLR~Yq-~~rLkYY----------yAVvecDsi  278 (650)
T KOG2318|consen  231 KELFKPVEEYKES----------------E-----SDDEEEEDVDREKLRQYQ-LNRLKYY----------YAVVECDSI  278 (650)
T ss_pred             hhhccccccCccc----------------c-----cchhhhhhHHHHHHHHHH-hhhheeE----------EEEEEecCc
Confidence            3221111100000                0     011111112233333333 2333333          899999999


Q ss_pred             HHHHHHHHHhCCceeC--CeeEEEEEe
Q psy2983         167 DDAKKAQEQLNGFELA--GRPMKVGTV  191 (370)
Q Consensus       167 ~~a~~A~~~l~g~~i~--g~~l~V~~~  191 (370)
                      ++|......++|.++.  +..+-+++.
T Consensus       279 ~tA~~vYe~CDG~EfEsS~~~~DLRFI  305 (650)
T KOG2318|consen  279 ETAKAVYEECDGIEFESSANKLDLRFI  305 (650)
T ss_pred             hHHHHHHHhcCcceeccccceeeeeec
Confidence            9999999999999998  456666664

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	370
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		1e-36
2cq4_A	114	Solution Structure Of Rna Binding Domain In Rna Bin		1e-34
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		3e-33
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		1e-17
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		5e-11
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		1e-17
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		7e-11
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		1e-16
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		2e-10
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		8e-15
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		3e-08
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		2e-12
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		2e-08
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		3e-12
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		1e-08
2lq5_A	113	Nmr Structure Of The Rna Binding Motif 39 (Rbm39) F		9e-12
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		9e-12
3s6e_A	114	Crystal Structure Of A Rna Binding Motif Protein 39		1e-11
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		2e-11
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		3e-11
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		4e-11
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		7e-11
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		7e-11
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		8e-08
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		7e-11
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		9e-08
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		7e-11
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		8e-08
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		7e-11
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		1e-07
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		8e-11
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-07
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		9e-11
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		1e-10
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		1e-10
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		1e-10
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		9e-08
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		2e-10
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		3e-09
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		2e-10
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		5e-10
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		5e-10
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		6e-10
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		1e-09
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		1e-09
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		1e-09
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		1e-09
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		2e-09
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		2e-09
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		2e-09
1fje_B	175	Solution Structure Of Nucleolin Rbd12 In Complex Wi		2e-09
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		2e-09
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		3e-09
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		3e-09
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		3e-09
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		4e-09
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		4e-09
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		5e-09
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		5e-09
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		6e-09
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		8e-09
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		1e-08
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		1e-08
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		2e-08
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		2e-08
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		2e-08
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		3e-08
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		4e-08
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		5e-08
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		7e-08
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		7e-08
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		7e-08
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		8e-08
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		8e-08
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		8e-08
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		9e-08
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		9e-08
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		1e-07
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		2e-07
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		2e-07
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		3e-07
2cpf_A	98	Solution Structure Of The Penultimate Rna Recogniti		4e-07
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		5e-07
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		5e-07
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		6e-05
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		6e-07
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		6e-07
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		9e-07
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		9e-07
4a8x_A	88	Structure Of The Core Asap Complex Length = 88		1e-06
2dgv_A	92	Solution Structure Of The Rna Binding Domain In Het		2e-06
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		2e-06
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		3e-06
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		3e-06
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		3e-06
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		3e-06
2khc_A	118	Bruno Rrm3+ Length = 118		3e-06
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		3e-06
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		3e-06
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		5e-06
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		5e-06
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		5e-06
1x4h_A	111	Solution Structure Of Rrm Domain In Rna-Binding Pro		5e-06
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		5e-06
2dh9_A	89	Solution Structure Of The C-Terminal Rna Binding Do		6e-06
1fjc_A	96	Solution Structure Of Nucleolin Rbd2 Length = 96		7e-06
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		7e-06
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		8e-06
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		8e-06
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		9e-06
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		1e-05
1no8_A	106	Solution Structure Of The Nuclear Factor Aly Rbd Do		1e-05
2dgp_A	106	Solution Structure Of The N-Terminal Rna Binding Do		1e-05
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		2e-05
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		2e-05
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		2e-05
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		2e-05
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		3e-05
2dno_A	102	Solution Structure Of Rna Binding Domain In Trinucl		3e-05
2dgq_A	108	Solution Structure Of The N-Terminal Rna Binding Do		4e-05
2cpj_A	99	Solution Structure Of The N-Terminal Rna Recognitio		4e-05
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		6e-05
2fc9_A	101	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		7e-05
1wtb_A	79	Complex Structure Of The C-Terminal Rna-Binding Dom		7e-05
2osq_A	74	Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length		7e-05
3b4d_A	96	Crystal Structure Of Human Pabpn1 Rrm Length = 96		8e-05
3ulh_A	107	Crystal Structure Of A Rna Binding Domain Of Tho Co		8e-05
3ucg_A	89	Crystal Structure Of A Rna Binding Domain Of Hypoth		8e-05
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		9e-05
2jvo_A	108	Segmental Isotope Labeling Of Npl3 Length = 108		9e-05
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		1e-04
1iqt_A	75	Solution Structure Of The C-Terminal Rna-Binding Do		1e-04
2dnh_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		1e-04
2dgu_A	103	Solution Structure Of The Rna Binding Domain In Het		2e-04
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		2e-04
2dnq_A	90	Solution Structure Of Rna Binding Domain 1 In Rna-B		2e-04
1sxl_A	97	Resonance Assignments And Solution Structure Of The		2e-04
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		2e-04
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		7e-04
2u2f_A	85	Solution Structure Of The Second Rna-Binding Domain		3e-04
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		3e-04
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		4e-04
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		5e-04
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		5e-04
3lqv_A	115	Branch Recognition By Sf3b14 Length = 115		5e-04
2f9d_A	125	2.5 Angstrom Resolution Structure Of The Spliceosom		6e-04
2f3j_A	177	The Solution Structure Of The Ref2-I Mrna Export Fa		6e-04
2fho_B	87	Nmr Solution Structure Of The Human Spliceosomal Pr		6e-04
2dng_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		8e-04

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score =  150 bits (379), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 71/92 (77%), Positives = 83/92 (90%), Gaps = 1/92 (1%)
Query: 105 NLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFH 164
           NLQ +G+ GPMRLY+GSLHFNITEDMLRGIFEPFG+I++IQLM+D +TGRSKGYGFITF 
Sbjct: 18  NLQ-KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFS 76
Query: 165 SADDAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
            ++ AKKA EQLNGFELAGRPMKVG VT+R +
Sbjct: 77  DSECAKKALEQLNGFELAGRPMKVGHVTERTD 108

>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 23 Length = 114

Iteration: 1
 Score =  144 bits (362), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 67/92 (72%), Positives = 82/92 (89%)
Query: 7   DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
           D+LSPEERDART+FCMQL+ RIR RDLE+FFS+VGKVRDVR+I+   +RR KGIAY+EF 
Sbjct: 16  DNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFC 75
Query: 67  DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNR 98
           + +SVPLA+GL GQ+LLG+PIIVQ +QAEKNR
Sbjct: 76  EIQSVPLAIGLTGQRLLGVPIIVQASQAEKNR 107

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score =  139 bits (350), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 69/95 (72%), Positives = 79/95 (83%), Gaps = 1/95 (1%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           G+ G   LY+GSLHFNITEDMLRGIFEPFGKIDNI LM D DTGRSKGYGFITF  ++ A
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           ++A EQLNGFELAGRPM+VG VT+R +  G GPS+
Sbjct: 61  RRALEQLNGFELAGRPMRVGHVTERLDG-GSGPSS 94

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 87.4 bits (215), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 52/172 (30%), Positives = 89/172 (51%), Gaps = 31/172 (18%)
Query: 33  LEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLG-------- 84
           + + F+  G ++ + +   + T + KG A++E++ PE+  LA+      +LG        
Sbjct: 30  IRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGR 89
Query: 85  -------IPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEP 137
                   PII Q   AE+ RA N              R+Y+ S+H ++++D ++ +FE 
Sbjct: 90  PSNIGQAQPIIDQ--LAEEARAFN--------------RIYVASVHQDLSDDDIKSVFEA 133
Query: 138 FGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
           FGKI +  L  DP TG+ KGYGFI +  A  ++ A   +N F+L G+ ++VG
Sbjct: 134 FGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVG 185

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 65.5 bits (158), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 46/74 (62%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           R+Y+GS+++ + ED +R  F PFG I +I +  D  T + KG+ F+ +   + A+ A EQ
Sbjct: 15  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 176 LNGFELAGRPMKVG 189
           +N   L GR +KVG
Sbjct: 75  MNSVMLGGRNIKVG 88

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 87.0 bits (214), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 52/172 (30%), Positives = 89/172 (51%), Gaps = 31/172 (18%)
Query: 33  LEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLG-------- 84
           + + F+  G ++ + +   + T + KG A++E++ PE+  LA+      +LG        
Sbjct: 45  IRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGR 104
Query: 85  -------IPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEP 137
                   PII Q   AE+ RA N              R+Y+ S+H ++++D ++ +FE 
Sbjct: 105 PSNIGQAQPIIDQ--LAEEARAFN--------------RIYVASVHQDLSDDDIKSVFEA 148
Query: 138 FGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
           FGKI +  L  DP TG+ KGYGFI +  A  ++ A   +N F+L G+ ++VG
Sbjct: 149 FGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVG 200

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 64.7 bits (156), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 46/74 (62%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           R+Y+GS+++ + ED +R  F PFG I +I +  D  T + KG+ F+ +   + A+ A EQ
Sbjct: 30  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 176 LNGFELAGRPMKVG 189
           +N   L GR +KVG
Sbjct: 90  MNSVMLGGRNIKVG 103

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 84.0 bits (206), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 51/170 (30%), Positives = 89/170 (52%), Gaps = 27/170 (15%)
Query: 33  LEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM------GLNGQKL-LGI 85
           + + F+  G ++ +     + T + KG A++E++ PE+  LA+       L G+ + +G 
Sbjct: 29  IRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKVGR 88
Query: 86  PIIVQPTQ------AEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFG 139
           P  +   Q      AE+ RA N              R+Y+ S+H ++++D ++ +FE FG
Sbjct: 89  PSNIGQAQPIIDQLAEEARAFN--------------RIYVASVHQDLSDDDIKSVFEAFG 134
Query: 140 KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
           KI +  L  DP TG+ KGYGFI +  A  ++ A    N F+L G+ ++VG
Sbjct: 135 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVG 184

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 63.9 bits (154), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 44/74 (59%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           R+Y+GS+++ + ED +R  F PFG I +I    D  T + KG+ F+ +   + A+ A EQ
Sbjct: 14  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 176 LNGFELAGRPMKVG 189
            N   L GR +KVG
Sbjct: 74  XNSVXLGGRNIKVG 87

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 78.2 bits (191), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 46/174 (26%), Positives = 91/174 (52%), Gaps = 15/174 (8%)
Query: 17  RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
           R ++   L + I    L+++F   G + +++ I  +K  +    A++E+       +A+ 
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIK-IMIDKNNKNVNYAFVEYHQSHDANIALQ 59
Query: 76  GLNGQKLLG-IPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGI 134
            LNG+++   I  I    Q++++ + +T              L++G L+ N+ ++ LR  
Sbjct: 60  TLNGKQIENNIVKINWAFQSQQSSSDDTF------------NLFVGDLNVNVDDETLRNA 107
Query: 135 FEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
           F+ F    +  +M D  TG S+GYGF++F S DDA+ A + + G +L GRP+++
Sbjct: 108 FKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 161

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 56.2 bits (134), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 35/126 (27%), Positives = 63/126 (50%), Gaps = 10/126 (7%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+G+L   ITED+L+  F+  G I NI++M+D +  ++  Y F+ +H + DA  A + L
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNN-KNVNYAFVEYHQSHDANIALQTL 61
Query: 177 NGFELAGRPMKVGTVTDRNES---------VGGGPSNLDTDEMERAGVDLGATGRLQLMF 227
           NG ++    +K+       +S         VG    N+D + +  A  D  +     +M+
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW 121
Query: 228 KLAEGT 233
            +  G+
Sbjct: 122 DMQTGS 127

>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 = 70.1 bits (170), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 50/165 (30%), Positives = 81/165 (49%), Gaps = 14/165 (8%)
Query: 33  LEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP 91
           L E FS  G +  +R+     TRR  G AY+ F+ P     A+  +N   + G P+ +  
Sbjct: 27  LYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW 86
Query: 92  TQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPD 151
           +Q +        P+L+  G G    ++I +L  +I    L   F  FG I + +++ D +
Sbjct: 87  SQRD--------PSLRKSGVGN---IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN 135
Query: 152 TGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
              SKGYGF+ F + + A++A E++NG  L  R + VG    R E
Sbjct: 136 G--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE 178

>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 = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/84 (35%), Positives = 48/84 (57%), Gaps = 1/84 (1%)
Query: 106 LQPRGTGGPM-RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFH 164
           + P     PM  LY+G LH ++TE ML   F P G I +I++  D  T RS GY ++ F 
Sbjct: 1   MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQ 60
Query: 165 SADDAKKAQEQLNGFELAGRPMKV 188
              DA++A + +N   + G+P+++
Sbjct: 61  QPADAERALDTMNFDVIKGKPVRI 84

>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 = 69.3 bits (168), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 50/165 (30%), Positives = 81/165 (49%), Gaps = 14/165 (8%)
Query: 33  LEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP 91
           L E FS  G +  +R+     TRR  G AY+ F+ P     A+  +N   + G P+ +  
Sbjct: 32  LYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW 91
Query: 92  TQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPD 151
           +Q +        P+L+  G G    ++I +L  +I    L   F  FG I + +++ D +
Sbjct: 92  SQRD--------PSLRKSGVGN---IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN 140
Query: 152 TGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
              SKGYGF+ F + + A++A E++NG  L  R + VG    R E
Sbjct: 141 G--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE 183

>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 = 57.8 bits (138), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 31/87 (35%), Positives = 50/87 (57%), Gaps = 1/87 (1%)
Query: 103 LPNLQPRGTGGPM-RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFI 161
           L ++ P     PM  LY+G LH ++TE ML   F P G I +I++  D  T RS GY ++
Sbjct: 3   LGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 62
Query: 162 TFHSADDAKKAQEQLNGFELAGRPMKV 188
            F    DA++A + +N   + G+P+++
Sbjct: 63  NFQQPADAERALDTMNFDVIKGKPVRI 89

>pdb|2LQ5|A Chain A, Nmr Structure Of The Rna Binding Motif 39 (Rbm39) From Mus Musculus Length = 113

Iteration: 1
 Score = 67.8 bits (164), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 28/39 (71%), Positives = 32/39 (82%)
Query: 267 PIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
           P+ATQCF L+NMF+P TE    WD EI+DDVIEECNKHG
Sbjct: 3   PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHG 41

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 67.8 bits (164), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 40/96 (41%), Positives = 54/96 (56%), Gaps = 2/96 (2%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKI-DNIQLMVDPDTGRSKGYGFITFHSADD 168
           G+ G   ++IG+L   I E +L   F  FG I    ++M DPDTG SKGY FI F S D 
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 169 AKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           +  A E +NG  L  RP+ V +   + +S G GPS+
Sbjct: 61  SDAAIEAMNGQYLCNRPITV-SYAFKKDSKGSGPSS 95

>pdb|3S6E|A Chain A, Crystal Structure Of A Rna Binding Motif Protein 39 (Rbm39) From Mus Musculus At 0.95 A Resolution Length = 114

Iteration: 1
 Score = 67.4 bits (163), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 27/39 (69%), Positives = 31/39 (79%)
Query: 267 PIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
           P+ATQCF L+N F+P TE    WD EI+DDVIEECNKHG
Sbjct: 4   PLATQCFQLSNXFNPQTEEEVGWDTEIKDDVIEECNKHG 42

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 32/86 (37%), Positives = 52/86 (60%), Gaps = 1/86 (1%)
Query: 113 GPMRL-YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
           GP R+ Y+GS+ ++ TE+ +  +    G + N+++M DP TGRSKGY FI F   + +  
Sbjct: 1   GPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 60
Query: 172 AQEQLNGFELAGRPMKVGTVTDRNES 197
           A   LNG++L  R +K G  ++ + S
Sbjct: 61  AVRNLNGYQLGSRFLKCGYSSNSDIS 86

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 66.2 bits (160), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 28/73 (38%), Positives = 47/73 (64%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L++G L F+  E  L  +F  +G+I  + ++ D +T RS+G+GF+TF + DDAK A   
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 176 LNGFELAGRPMKV 188
           +NG  + GR ++V
Sbjct: 74  MNGKSVDGRQIRV 86

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 65.5 bits (158), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 28/72 (38%), Positives = 47/72 (65%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++G L+ N+ ++ LR  F+ F    +  +M D  TG S+GYGF++F S DDA+ A + +
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 177 NGFELAGRPMKV 188
            G +L GRP+++
Sbjct: 64  QGQDLNGRPLRI 75

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 65.1 bits (157), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 47/77 (61%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +Y+GS+ ++ TE+ +  +    G + N+++M DP TGRSKGY FI F   + +  A   L
Sbjct: 7   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 177 NGFELAGRPMKVGTVTD 193
           NG++L  R +K G  ++
Sbjct: 67  NGYQLGSRFLKCGYSSN 83

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 64.7 bits (156), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 44/163 (26%), Positives = 75/163 (46%), Gaps = 8/163 (4%)
Query: 10  SPEE-RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDP 68
           SP+E    R +F   LS       L   F   G + D  ++    T+R +G  ++ +   
Sbjct: 5   SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 64
Query: 69  ESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITE 128
           E V  AM     K+ G   +V+P      RA +   + +P       ++++G +  +  E
Sbjct: 65  EEVDAAMNARPHKVDGR--VVEP-----KRAVSREDSQRPGAHLTVKKIFVGGIKEDTEE 117
Query: 129 DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
             LR  FE +GKI+ I++M D  +G+ +G+ F+TF   D   K
Sbjct: 118 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 160

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 54.7 bits (130), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 8/73 (10%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L+IG L F  T++ LR  FE +G + +  +M DP+T RS+G+GF+T+ + ++   A   
Sbjct: 14  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 70
Query: 176 LNGFELAGRPMKV 188
                +  RP KV
Sbjct: 71  -----MNARPHKV 78

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 64.7 bits (156), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 45/167 (26%), Positives = 76/167 (45%), Gaps = 8/167 (4%)
Query: 6   SDDLSPEE-RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIE 64
           S   SP+E    R +F   LS       L   F   G + D  ++    T+R +G  ++ 
Sbjct: 3   SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 62
Query: 65  FKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHF 124
           +   E V  AM     K+ G   +V+P      RA +   + +P       ++++G +  
Sbjct: 63  YATVEEVDAAMNARPHKVDGR--VVEP-----KRAVSREDSQRPGAHLTVKKIFVGGIKE 115
Query: 125 NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
           +  E  LR  FE +GKI+ I++M D  +G+ +G+ F+TF   D   K
Sbjct: 116 DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 162

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 54.7 bits (130), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 8/73 (10%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L+IG L F  T++ LR  FE +G + +  +M DP+T RS+G+GF+T+ + ++   A   
Sbjct: 16  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 72
Query: 176 LNGFELAGRPMKV 188
                +  RP KV
Sbjct: 73  -----MNARPHKV 80

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 64.7 bits (156), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 44/163 (26%), Positives = 75/163 (46%), Gaps = 8/163 (4%)
Query: 10  SPEE-RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDP 68
           SP+E    R +F   LS       L   F   G + D  ++    T+R +G  ++ +   
Sbjct: 6   SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 65
Query: 69  ESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITE 128
           E V  AM     K+ G   +V+P      RA +   + +P       ++++G +  +  E
Sbjct: 66  EEVDAAMNARPHKVDGR--VVEP-----KRAVSREDSQRPGAHLTVKKIFVGGIKEDTEE 118
Query: 129 DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
             LR  FE +GKI+ I++M D  +G+ +G+ F+TF   D   K
Sbjct: 119 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 161

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 54.7 bits (130), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 8/73 (10%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L+IG L F  T++ LR  FE +G + +  +M DP+T RS+G+GF+T+ + ++   A   
Sbjct: 15  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 71
Query: 176 LNGFELAGRPMKV 188
                +  RP KV
Sbjct: 72  -----MNARPHKV 79

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 64.7 bits (156), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 44/163 (26%), Positives = 75/163 (46%), Gaps = 8/163 (4%)
Query: 10  SPEE-RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDP 68
           SP+E    R +F   LS       L   F   G + D  ++    T+R +G  ++ +   
Sbjct: 6   SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 65
Query: 69  ESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITE 128
           E V  AM     K+ G   +V+P      RA +   + +P       ++++G +  +  E
Sbjct: 66  EEVDAAMNARPHKVDGR--VVEP-----KRAVSREDSQRPGAHLTVKKIFVGGIKEDTEE 118
Query: 129 DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
             LR  FE +GKI+ I++M D  +G+ +G+ F+TF   D   K
Sbjct: 119 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 161

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 8/73 (10%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L+IG L F  T++ LR  FE +G + +  +M DP+T RS+G+GF+T+ + ++   A   
Sbjct: 15  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 71
Query: 176 LNGFELAGRPMKV 188
                +  RP KV
Sbjct: 72  -----MNARPHKV 79

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 64.7 bits (156), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 44/163 (26%), Positives = 75/163 (46%), Gaps = 8/163 (4%)
Query: 10  SPEE-RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDP 68
           SP+E    R +F   LS       L   F   G + D  ++    T+R +G  ++ +   
Sbjct: 4   SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 63
Query: 69  ESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITE 128
           E V  AM     K+ G   +V+P      RA +   + +P       ++++G +  +  E
Sbjct: 64  EEVDAAMNARPHKVDGR--VVEP-----KRAVSREDSQRPGAHLTVKKIFVGGIKEDTEE 116
Query: 129 DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
             LR  FE +GKI+ I++M D  +G+ +G+ F+TF   D   K
Sbjct: 117 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 159

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 8/73 (10%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L+IG L F  T++ LR  FE +G + +  +M DP+T RS+G+GF+T+ + ++   A   
Sbjct: 13  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 69
Query: 176 LNGFELAGRPMKV 188
                +  RP KV
Sbjct: 70  -----MNARPHKV 77

>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 = 64.7 bits (156), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 31/95 (32%), Positives = 56/95 (58%)
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
           G++  + Q + T     +++G L   IT + ++  F PFG+I + +++ D  TG+SKGYG
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR 194
           F++F +  DA+ A +Q+ G  L GR ++    T +
Sbjct: 61  FVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 95

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 64.3 bits (155), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 31/85 (36%), Positives = 51/85 (60%), Gaps = 1/85 (1%)
Query: 114 PMRL-YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
           P R+ Y+GS+ ++ TE+ +  +    G + N+++M DP TGRSKGY FI F   + +  A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 173 QEQLNGFELAGRPMKVGTVTDRNES 197
              LNG++L  R +K G  ++ + S
Sbjct: 61  VRNLNGYQLGSRFLKCGYSSNSDIS 85

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 64.3 bits (155), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 35/105 (33%), Positives = 59/105 (56%), Gaps = 1/105 (0%)
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
           G++  + Q + T     +++G L   IT + ++  F PFGKI + +++ D  TG+SKGYG
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYG 60
Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           F++F++  DA+ A   + G  L GR ++    T R      GPS+
Sbjct: 61  FVSFYNKLDAENAIVHMGGQWLGGRQIRTNWAT-RKPPAPSGPSS 104

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 64.3 bits (155), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 41/155 (26%), Positives = 71/155 (45%), Gaps = 7/155 (4%)
Query: 17  RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
           R +F   LS       L   F   G + D  ++    T+R +G  ++ +   E V  AM 
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 77  LNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFE 136
               K+ G   +V+P      RA +   + +P       ++++G +  +  E  LR  FE
Sbjct: 67  ARPHKVDGR--VVEP-----KRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 119
Query: 137 PFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
            +GKI+ I++M D  +G+ +G+ F+TF   D   K
Sbjct: 120 QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 154

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 8/73 (10%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L+IG L F  T++ LR  FE +G + +  +M DP+T RS+G+GF+T+ + ++   A   
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 64
Query: 176 LNGFELAGRPMKV 188
                +  RP KV
Sbjct: 65  -----MNARPHKV 72

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 40/136 (29%), Positives = 71/136 (52%), Gaps = 14/136 (10%)
Query: 32  DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQP 91
           +L E+F   G V D++++    T R +G  ++ F+ P SV     +  Q +L   +I  P
Sbjct: 19  NLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV--VKTQHILDGKVI-DP 75
Query: 92  TQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPD 151
            +A        +P  +   TG   ++++G +  ++        F  +G I + QLM+D D
Sbjct: 76  KRA--------IPRDEQDKTG---KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKD 124
Query: 152 TGRSKGYGFITFHSAD 167
           TG+S+G+GF+T+ SAD
Sbjct: 125 TGQSRGFGFVTYDSAD 140

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 27/66 (40%), Positives = 45/66 (68%), Gaps = 3/66 (4%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFH---SADDAKKA 172
           +++IG L+++ TED LR  F  +G + ++++M DP TGRS+G+GF++F    S D+  K 
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 173 QEQLNG 178
           Q  L+G
Sbjct: 65  QHILDG 70

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 35/103 (33%), Positives = 55/103 (53%), Gaps = 7/103 (6%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L +  L  N+T+D  + +F   G I++ +L+ D  TG+S GYGF+ +   +DA KA   L
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 177 NGFELAGRPMKV-------GTVTDRNESVGGGPSNLDTDEMER 212
           NG +L  + +KV        ++ D N  V G P  +   EME+
Sbjct: 67  NGLKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQ 109

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 62.0 bits (149), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 34/90 (37%), Positives = 55/90 (61%), Gaps = 3/90 (3%)
Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           + LY+ +L   I ++ LR  F PFG I + ++M++   GRSKG+GF+ F S ++A KA  
Sbjct: 16  VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVT 73
Query: 175 QLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           ++NG  +A +P+ V  +  R E    GPS+
Sbjct: 74  EMNGRIVATKPLYV-ALAQRKEERQSGPSS 102

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 62.0 bits (149), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 33/106 (31%), Positives = 55/106 (51%), Gaps = 7/106 (6%)
Query: 113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
           G   L +  L  N+T+D LR +F   G++++ +L+ D   G S GYGF+ + +A DA++A
Sbjct: 1   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 173 QEQLNGFELAGRPMKVG-------TVTDRNESVGGGPSNLDTDEME 211
              LNG  L  + +KV         + D N  + G P  +   ++E
Sbjct: 61  INTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVE 106

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 62.0 bits (149), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 33/106 (31%), Positives = 55/106 (51%), Gaps = 7/106 (6%)
Query: 113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
           G   L +  L  N+T+D LR +F   G++++ +L+ D   G S GYGF+ + +A DA++A
Sbjct: 1   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 173 QEQLNGFELAGRPMKVG-------TVTDRNESVGGGPSNLDTDEME 211
              LNG  L  + +KV         + D N  + G P  +   ++E
Sbjct: 61  INTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVE 106

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/72 (38%), Positives = 45/72 (62%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L +  L    TE  LR +F  +G I ++ ++ D  + RS+G+ F+ F + DDAK+A+E+ 
Sbjct: 18  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 177 NGFELAGRPMKV 188
           NG EL GR ++V
Sbjct: 78  NGMELDGRRIRV 89

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 34/103 (33%), Positives = 55/103 (53%), Gaps = 7/103 (6%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L +  L  N+T++  R +F   G+I++ +L+ D  TG+S GYGF+ +    DA+KA   L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 177 NGFELAGRPMKV-------GTVTDRNESVGGGPSNLDTDEMER 212
           NG  L  + +KV        ++ D N  V G P  +   E+E+
Sbjct: 65  NGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQ 107

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/72 (38%), Positives = 45/72 (62%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L +  L    TE  LR +F  +G I ++ ++ D  + RS+G+ F+ F + DDAK+A+E+ 
Sbjct: 18  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 177 NGFELAGRPMKV 188
           NG EL GR ++V
Sbjct: 78  NGMELDGRRIRV 89

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/72 (38%), Positives = 45/72 (62%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L +  L    TE  LR +F  +G I ++ ++ D  + RS+G+ F+ F + DDAK+A+E+ 
Sbjct: 15  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 177 NGFELAGRPMKV 188
           NG EL GR ++V
Sbjct: 75  NGMELDGRRIRV 86

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 60.1 bits (144), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/72 (38%), Positives = 45/72 (62%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L +  L    TE  LR +F  +G I ++ ++ D  + RS+G+ F+ F + DDAK+A+E+ 
Sbjct: 49  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 177 NGFELAGRPMKV 188
           NG EL GR ++V
Sbjct: 109 NGMELDGRRIRV 120

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 60.1 bits (144), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 53/183 (28%), Positives = 88/183 (48%), Gaps = 22/183 (12%)
Query: 15  DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTR--RFKGIAYIEFKDPESVP 72
           DA  +F  Q+ +    +DL E F   G V ++ ++        + KG  ++ F   ++  
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 73  LAM-GLNGQKLL-GI--PIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITE 128
            A   L+  K+L G+  PI ++P  +EKN A      ++ R      +L+IG +    TE
Sbjct: 62  EAQNALHNMKVLPGMHHPIQMKPADSEKNNA------VEDR------KLFIGMISKKCTE 109
Query: 129 DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS---ADDAKKAQEQLNGFELAGRP 185
           + +R +F  FG+I+  +++  PD G S+G  F+TF +   A  A KA  Q    E    P
Sbjct: 110 NDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSP 168
Query: 186 MKV 188
           M V
Sbjct: 169 MVV 171

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 60.1 bits (144), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 53/183 (28%), Positives = 88/183 (48%), Gaps = 22/183 (12%)
Query: 15  DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLIT--CNKTRRFKGIAYIEFKDPESVP 72
           DA  +F  Q+ +    +DL E F   G V ++ ++        + KG  ++ F   ++  
Sbjct: 14  DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 73
Query: 73  LAM-GLNGQKLL-GI--PIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITE 128
            A   L+  K+L G+  PI ++P  +EKN A      ++ R      +L+IG +    TE
Sbjct: 74  EAQNALHNMKVLPGMHHPIQMKPADSEKNNA------VEDR------KLFIGMISKKCTE 121
Query: 129 DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS---ADDAKKAQEQLNGFELAGRP 185
           + +R +F  FG+I+  +++  PD G S+G  F+TF +   A  A KA  Q    E    P
Sbjct: 122 NDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSP 180
Query: 186 MKV 188
           M V
Sbjct: 181 MVV 183

>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre Rna Length = 175

Iteration: 1
 Score = 60.1 bits (144), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 47/147 (31%), Positives = 72/147 (48%), Gaps = 28/147 (19%)
Query: 43  VRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQ---AEKNRA 99
           V DVR  T    R+F    Y++F+  E +  A+ L G K+ G  I ++  +   ++K RA
Sbjct: 45  VVDVRTGT---NRKF---GYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRA 98
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
             TL                 +L FNITED L+ +FE     D +++ +    G+SKG  
Sbjct: 99  ARTL--------------LAKNLSFNITEDELKEVFE-----DALEIRLVSQDGKSKGIA 139
Query: 160 FITFHSADDAKKAQEQLNGFELAGRPM 186
           +I F S  DA+K  E+  G E+ GR +
Sbjct: 140 YIEFKSEADAEKNLEEKQGAEIDGRSV 166

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 60.1 bits (144), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 47/78 (60%), Gaps = 2/78 (2%)
Query: 113 GPMR--LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAK 170
           GP R  L +  L  N+T+D LR +F   G++++ +L+ D   G S GYGF+ + +A DA+
Sbjct: 1   GPGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAE 60
Query: 171 KAQEQLNGFELAGRPMKV 188
           +A   LNG  L  + +KV
Sbjct: 61  RAINTLNGLRLQSKTIKV 78

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 44/73 (60%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+G L   + + +L   F PFG I +IQ+ +D +T + +G+ F+ F  A+DA  A + +
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 177 NGFELAGRPMKVG 189
           N  EL GR ++V 
Sbjct: 126 NESELFGRTIRVN 138

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 45/75 (60%), Gaps = 1/75 (1%)
Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
           P +L+IG L+    E ML+ +F   G I  + L+ D  T +S+G+ FITF +  DAK A 
Sbjct: 7   PGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAA 65
Query: 174 EQLNGFELAGRPMKV 188
           + +NG  L G+ +KV
Sbjct: 66  KDMNGKSLHGKAIKV 80

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 34/95 (35%), Positives = 52/95 (54%), Gaps = 14/95 (14%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L+IG L F  TE+ LR  +E +GK+ +  +M DP + RS+G+GF+TF S  +   A   
Sbjct: 29  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA--- 85
Query: 176 LNGFELAGRPMKV-GTVTDRNESV-----GGGPSN 204
                +A RP  + G V +   +V     G GPS+
Sbjct: 86  -----MAARPHSIDGRVVEPKRAVAREESGSGPSS 115

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 59.3 bits (142), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 44/72 (61%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+G L   + + +L   F PFG I +IQ+ +D +T + +G+ F+ F  A+DA  A + +
Sbjct: 5   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 177 NGFELAGRPMKV 188
           N  EL GR ++V
Sbjct: 65  NESELFGRTIRV 76

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 58.9 bits (141), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 44/72 (61%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+G L   + + +L   F PFG I +IQ+ +D +T + +G+ F+ F  A+DA  A + +
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 177 NGFELAGRPMKV 188
           N  EL GR ++V
Sbjct: 70  NESELFGRTIRV 81

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 58.9 bits (141), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 44/72 (61%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+G L   + + +L   F PFG I +IQ+ +D +T + +G+ F+ F  A+DA  A + +
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 177 NGFELAGRPMKV 188
           N  EL GR ++V
Sbjct: 68  NESELFGRTIRV 79

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 58.5 bits (140), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 33/96 (34%), Positives = 57/96 (59%), Gaps = 9/96 (9%)
Query: 106 LQPRGT-------GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGY 158
           L PRG+         P RL++ ++ F   +  LR +F  FGKI +++++ +     SKG+
Sbjct: 14  LVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGF 71
Query: 159 GFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR 194
           GF+TF ++ DA +A+E+L+G  + GR ++V   T R
Sbjct: 72  GFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 58.5 bits (140), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 52/81 (64%), Gaps = 2/81 (2%)
Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
           P RL++ ++ F   +  LR +F  FGKI +++++ +     SKG+GF+TF ++ DA +A+
Sbjct: 15  PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAR 72
Query: 174 EQLNGFELAGRPMKVGTVTDR 194
           E+L+G  + GR ++V   T R
Sbjct: 73  EKLHGTVVEGRKIEVNNATAR 93

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 58.2 bits (139), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 25/72 (34%), Positives = 44/72 (61%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++G++ +  TE+ L+ IF   G + + +L+ D +TG+ KGYGF  +   + A  A   L
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 177 NGFELAGRPMKV 188
           NG E +GR ++V
Sbjct: 71  NGREFSGRALRV 82

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 44/72 (61%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+G L   + + +L   F PFG I +IQ+ +D +T + +G+ F+ F  A+DA  A + +
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 177 NGFELAGRPMKV 188
           N  EL GR ++V
Sbjct: 75  NESELFGRTIRV 86

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 31/84 (36%), Positives = 48/84 (57%), Gaps = 4/84 (4%)
Query: 105 NLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFH 164
           NL  +GT     L +  L  N T+D LR +F   G++++ +L+ D   G S GYGF+ + 
Sbjct: 14  NLYFQGTN----LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYV 69
Query: 165 SADDAKKAQEQLNGFELAGRPMKV 188
           +A DA++A   LNG  L  + +KV
Sbjct: 70  TAKDAERAINTLNGLRLQSKTIKV 93

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 26/83 (31%), Positives = 48/83 (57%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L +  +   + E  LR +FE +G I++++++ D +T +S+GYGF+ F S   A++A   L
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 177 NGFELAGRPMKVGTVTDRNESVG 199
           NGF +  + +KV      ++  G
Sbjct: 105 NGFNILNKRLKVALAASGHQRPG 127

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 26/84 (30%), Positives = 49/84 (58%), Gaps = 5/84 (5%)
Query: 110 GTGGP-----MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFH 164
           G+ GP     + L + +L +  + D LR +FE +G++ ++ +  +P T   +G+ F+ FH
Sbjct: 4   GSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFH 63
Query: 165 SADDAKKAQEQLNGFELAGRPMKV 188
              DA+ A+  ++G EL GR ++V
Sbjct: 64  DRRDAQDAEAAMDGAELDGRELRV 87

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/82 (36%), Positives = 46/82 (56%), Gaps = 6/82 (7%)
Query: 113 GPMR------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA 166
           GP R      L++ S+H    ED ++  F  +G+I NI L +D  TG SKGY  + + + 
Sbjct: 65  GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 124
Query: 167 DDAKKAQEQLNGFELAGRPMKV 188
             A  A+E LNG E+ G+ ++V
Sbjct: 125 KQALAAKEALNGAEIMGQTIQV 146

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 56.2 bits (134), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 30/82 (36%), Positives = 46/82 (56%), Gaps = 6/82 (7%)
Query: 113 GPMR------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA 166
           GP R      L++ S+H    ED ++  F  +G+I NI L +D  TG SKGY  + + + 
Sbjct: 19  GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 78
Query: 167 DDAKKAQEQLNGFELAGRPMKV 188
             A  A+E LNG E+ G+ ++V
Sbjct: 79  KQALAAKEALNGAEIMGQTIQV 100

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 55.8 bits (133), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 24/58 (41%), Positives = 36/58 (62%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           +++G L  N T + ++  FE FGK+D+  LM D  T R +G+GF+TF S D  +K  E
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 55.1 bits (131), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 28/82 (34%), Positives = 46/82 (56%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L +  L  N+T+D  + +F   G I++ +L+ D  TG+S GYGF+ +   +DA KA   L
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 177 NGFELAGRPMKVGTVTDRNESV 198
           NG +L  + +KV      + S+
Sbjct: 67  NGLKLQTKTIKVSYARPSSASI 88

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 55.1 bits (131), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 26/72 (36%), Positives = 42/72 (58%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++  +H   TE+ +   F  +G+I NI L +D  TG  KGY  + + +  +A+ A E L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 177 NGFELAGRPMKV 188
           NG +L G+P+ V
Sbjct: 70  NGQDLMGQPISV 81

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 55.1 bits (131), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 29/82 (35%), Positives = 45/82 (54%), Gaps = 6/82 (7%)
Query: 113 GPMR------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA 166
           GP R      L++  +H   TE+ +   F  +G+I NI L +D  TG  KGY  + + + 
Sbjct: 15  GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 74
Query: 167 DDAKKAQEQLNGFELAGRPMKV 188
            +A+ A E LNG +L G+P+ V
Sbjct: 75  KEAQAAMEGLNGQDLMGQPISV 96

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 54.7 bits (130), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 51/183 (27%), Positives = 82/183 (44%), Gaps = 22/183 (12%)
Query: 15  DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLIT--CNKTRRFKGIAYIEFKDPESVP 72
           DA   F  Q+ +    +DL E F   G V ++ ++        + KG  ++ F   ++  
Sbjct: 2   DAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 73  LAM-GLNGQKLL---GIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITE 128
            A   L+  K+L     PI  +P  +EKN A      ++ R      +L+IG +    TE
Sbjct: 62  EAQNALHNXKVLPGXHHPIQXKPADSEKNNA------VEDR------KLFIGXISKKCTE 109
Query: 129 DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS---ADDAKKAQEQLNGFELAGRP 185
           + +R  F  FG+I+  +++  PD G S+G  F+TF +   A  A KA  Q    E    P
Sbjct: 110 NDIRVXFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAXAQTAIKAXHQAQTXEGCSSP 168
Query: 186 MKV 188
             V
Sbjct: 169 XVV 171

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 54.7 bits (130), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 29/82 (35%), Positives = 45/82 (54%), Gaps = 6/82 (7%)
Query: 113 GPMR------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA 166
           GP R      L++  +H   TE+ +   F  +G+I NI L +D  TG  KGY  + + + 
Sbjct: 2   GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 61
Query: 167 DDAKKAQEQLNGFELAGRPMKV 188
            +A+ A E LNG +L G+P+ V
Sbjct: 62  KEAQAAMEGLNGQDLMGQPISV 83

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 54.7 bits (130), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 29/82 (35%), Positives = 45/82 (54%), Gaps = 6/82 (7%)
Query: 113 GPMR------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA 166
           GP R      L++  +H   TE+ +   F  +G+I NI L +D  TG  KGY  + + + 
Sbjct: 16  GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 75
Query: 167 DDAKKAQEQLNGFELAGRPMKV 188
            +A+ A E LNG +L G+P+ V
Sbjct: 76  KEAQAAMEGLNGQDLMGQPISV 97

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 54.7 bits (130), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 26/71 (36%), Positives = 41/71 (57%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +Y+ +L F++T + L  IF  +GK+  + +M D DT +SKG  FI F   D A+     +
Sbjct: 19  VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 177 NGFELAGRPMK 187
           N  +L GR +K
Sbjct: 79  NNKQLFGRVIK 89

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 54.7 bits (130), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 42/72 (58%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++  +H   TE+ +   F  +G+I NI L +D  TG  KGY  + + +  +A+ A E L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 177 NGFELAGRPMKV 188
           NG +L G+P+ V
Sbjct: 70  NGQDLMGQPISV 81

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 42/72 (58%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++  +H   TE+ +   F  +G+I NI L +D  TG  KGY  + + +  +A+ A E L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 177 NGFELAGRPMKV 188
           NG +L G+P+ V
Sbjct: 70  NGQDLMGQPISV 81

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 53.9 bits (128), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 44/76 (57%)
Query: 113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
           G   L + +L +  + D LR +FE +G++ ++ +  D  T  S+G+ F+ FH   DA+ A
Sbjct: 69  GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 128
Query: 173 QEQLNGFELAGRPMKV 188
            + ++G  L GR ++V
Sbjct: 129 MDAMDGAVLDGRELRV 144

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/84 (30%), Positives = 49/84 (58%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +Y+G L   ++E +L  +F   G + N  +  D  TG+ +GYGF+ F S +DA  A + +
Sbjct: 18  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 177 NGFELAGRPMKVGTVTDRNESVGG 200
           +  +L G+P++V   +  N+++ G
Sbjct: 78  DMIKLYGKPIRVNKASAHNKNLSG 101

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 43/77 (55%), Gaps = 7/77 (9%)
Query: 110 GTGGPMR-------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFIT 162
           G+ GP R       + + +L  +  E  L+ +F PFG I  I L  D  TG+SKG+ FI+
Sbjct: 4   GSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFIS 63
Query: 163 FHSADDAKKAQEQLNGF 179
           FH  +DA +A   ++GF
Sbjct: 64  FHRREDAARAIAGVSGF 80

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 43/72 (59%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L + +L +  + D LR +FE +G++ ++ +  D  T  S+G+ F+ FH   DA+ A + +
Sbjct: 50  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 177 NGFELAGRPMKV 188
           +G  L GR ++V
Sbjct: 110 DGAVLDGRELRV 121

>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 98

Iteration: 1
 Score = 52.4 bits (124), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 29/98 (29%), Positives = 53/98 (54%), Gaps = 4/98 (4%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTG---RSKGYGFITFHSA 166
           G+ G   L+I +L+F+ TE+ L+G+F   G I +  +    +      S G+GF+ +   
Sbjct: 1   GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 167 DDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           + A+KA +QL G  + G  ++V  +++R      GPS+
Sbjct: 61  EQAQKALKQLQGHTVDGHKLEV-RISERATKPASGPSS 97

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 52.0 bits (123), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 24/66 (36%), Positives = 40/66 (60%), Gaps = 4/66 (6%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ- 175
           ++IG L ++ T+  L+  F  FG++ +  L +DP TGRS+G+GF+ F  ++   K  +Q 
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 176 ---LNG 178
              LNG
Sbjct: 62  EHKLNG 67

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 52.0 bits (123), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 48/186 (25%), Positives = 81/186 (43%), Gaps = 15/186 (8%)
Query: 6   SDDLSPEERDART-IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIE 64
           SDDL  + R + T +    L Q    R+L   F ++G +   R+    KT    G A+++
Sbjct: 3   SDDLMNDPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVD 62
Query: 65  FKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHF 124
           F        A+ +    L GI +  +  +    R G          +     LY+ +L  
Sbjct: 63  FTSEXDSQRAIKV----LNGITVRNKRLKVSYARPGGE--------SIKDTNLYVTNLPR 110
Query: 125 NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF--ELA 182
            IT+D L  IF  +G I    ++ D  TGR +G  F+ ++  ++A++A   LN    E  
Sbjct: 111 TITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGG 170
Query: 183 GRPMKV 188
            +P+ V
Sbjct: 171 SQPLSV 176

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 28/102 (27%), Positives = 49/102 (48%), Gaps = 7/102 (6%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L +  L  + T+  L  +F   G I+  ++  D  TG S GY F+ F S  D+++A + L
Sbjct: 17  LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 177 NGFELAGRPMKVG-------TVTDRNESVGGGPSNLDTDEME 211
           NG  +  + +KV        ++ D N  V   P  +  D+++
Sbjct: 77  NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLD 118

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 52.0 bits (123), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 48/83 (57%)
Query: 112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
           G    +++G L   IT   +   F PFG+I + +++ D  TG+SKGYGF++F +  DA+ 
Sbjct: 4   GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 63
Query: 172 AQEQLNGFELAGRPMKVGTVTDR 194
           A +Q+ G  L GR ++    T +
Sbjct: 64  AIQQMGGQWLGGRQIRTNWATRK 86

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 51.6 bits (122), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 26/89 (29%), Positives = 48/89 (53%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL++ +L +  +E+ L  +F  +G +  +   +D  T + KG+ F+TF   + A KA  +
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 176 LNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           ++G    GR + V   T + E+   GPS+
Sbjct: 70  VDGQVFQGRMLHVLPSTIKKEASQSGPSS 98

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 51.2 bits (121), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 31/93 (33%), Positives = 50/93 (53%), Gaps = 5/93 (5%)
Query: 104 PNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITF 163
           P+L+  G G    ++I +L  +I    L   F  FG I + +++ D +   SKGYGF+ F
Sbjct: 4   PSLRKSGVGN---IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHF 58
Query: 164 HSADDAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
            + + A++A E++NG  L  R + VG    R E
Sbjct: 59  ETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE 91

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 51.2 bits (121), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 41/144 (28%), Positives = 69/144 (47%), Gaps = 22/144 (15%)
Query: 43  VRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNT 102
           V DVR+     TR+F    Y++F+  E +  A+ L G K+ G  I     + EK +  ++
Sbjct: 39  VVDVRI---GMTRKF---GYVDFESAEDLEKALELTGLKVFGNEI-----KLEKPKGKDS 87
Query: 103 LPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFIT 162
                 R       L   +L + +T+D L+ +FE     D  ++ +    G+SKG  +I 
Sbjct: 88  KKERDAR------TLLAKNLPYKVTQDELKEVFE-----DAAEIRLVSKDGKSKGIAYIE 136
Query: 163 FHSADDAKKAQEQLNGFELAGRPM 186
           F +  DA+K  E+  G E+ GR +
Sbjct: 137 FKTEADAEKTFEEKQGTEIDGRSI 160

>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex Length = 88

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 26/79 (32%), Positives = 47/79 (59%), Gaps = 1/79 (1%)
Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDP-DTGRSKGYGFITFHSADDAKKA 172
           P +++IG L  N+T+D +  IF  +GKI  I + V+      SKGY ++ F + D+A+KA
Sbjct: 4   PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKA 63
Query: 173 QEQLNGFELAGRPMKVGTV 191
            + ++G ++ G+ +    V
Sbjct: 64  LKHMDGGQIDGQEITATAV 82

>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 92

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/95 (32%), Positives = 53/95 (55%), Gaps = 7/95 (7%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           G+ G  ++++ +L F+ T  ML+  F   G +  +   +  + G+SKG G + F S + A
Sbjct: 4   GSSGACQIFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVA 61
Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           ++A   +NG +L+GR + V    DRN S   GPS+
Sbjct: 62  ERACRMMNGMKLSGREIDVR--IDRNAS---GPSS 91

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 21/72 (29%), Positives = 45/72 (62%), Gaps = 1/72 (1%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +Y+G+L ++ T + ++ +F  FGK+ N++L+ D +T + KG+GF+     +   +A  +L
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 177 NGFELAGRPMKV 188
           +  +  GR ++V
Sbjct: 63  DNTDFMGRTIRV 74

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 25/82 (30%), Positives = 45/82 (54%), Gaps = 3/82 (3%)
Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
           P G   P  +++G +   + E  +R  F  +G +  ++++ D  TG SKGYGF++F++  
Sbjct: 3   PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDV 61
Query: 168 DAKKAQEQLNGFELAGRPMKVG 189
           D +K  E    F   G+ +K+G
Sbjct: 62  DVQKIVESQINFH--GKKLKLG 81

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 42/167 (25%), Positives = 74/167 (44%), Gaps = 14/167 (8%)
Query: 24  LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLL 83
           L Q +  R+L   F ++G +   R++   KT    G A+++F        A+ +    L 
Sbjct: 11  LPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV----LN 66
Query: 84  GIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDN 143
           GI +  +  +    R G          +     LY+ +L   IT+D L  IF  +G I  
Sbjct: 67  GITVRNKRLKVSYARPGGE--------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQ 118
Query: 144 IQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF--ELAGRPMKV 188
             ++ D  TGR +G  F+ ++  ++A++A   LN    E   +P+ V
Sbjct: 119 KNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 165

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 29/102 (28%), Positives = 51/102 (50%), Gaps = 7/102 (6%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L +  L  ++T+  L  +F   G I+  ++M D  TG S GY F+ F S  D+++A + L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 177 NGFELAGRPMKVG-------TVTDRNESVGGGPSNLDTDEME 211
           NG  +  + +KV        ++ D N  V   P  +  D+++
Sbjct: 66  NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLD 107

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 25/82 (30%), Positives = 45/82 (54%), Gaps = 3/82 (3%)
Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
           P G   P  +++G +   + E  +R  F  +G +  ++++ D  TG SKGYGF++F++  
Sbjct: 3   PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDV 61
Query: 168 DAKKAQEQLNGFELAGRPMKVG 189
           D +K  E    F   G+ +K+G
Sbjct: 62  DVQKIVESQINFH--GKKLKLG 81

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 24/72 (33%), Positives = 42/72 (58%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L+I  L    T+  L   F PFG + + ++ +D  T  SK +GF++F + D A+ A + +
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 177 NGFELAGRPMKV 188
           NGF++  + +KV
Sbjct: 103 NGFQVGTKRLKV 114

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/62 (35%), Positives = 38/62 (61%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++G L ++ T+  LR  FE FG I+   ++ D  TG+S+GYGF+T      A++A + 
Sbjct: 19  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 176 LN 177
            N
Sbjct: 79  PN 80

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 30/89 (33%), Positives = 48/89 (53%), Gaps = 5/89 (5%)
Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
           P G+G    ++I +L  +I    L   F  FG I + +++ D +   SKGYGF+ F + +
Sbjct: 2   PLGSGN---IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQE 56
Query: 168 DAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
            A++A E++NG  L  R + VG    R E
Sbjct: 57  AAERAIEKMNGMLLNDRKVFVGRFKSRKE 85

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 48.9 bits (115), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 20/60 (33%), Positives = 37/60 (61%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           + ++G L ++ ++  L+  F  FG++ +  +  DP+TGRS+G+GFI F  A   +K  +Q
Sbjct: 13  KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 48.9 bits (115), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 26/84 (30%), Positives = 47/84 (55%), Gaps = 5/84 (5%)
Query: 108 PRGTGG--PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS 165
           P G+G   P  +++G +   + E  +R  F  +G +  ++++ D  TG SKGYGF++F++
Sbjct: 2   PLGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYN 60
Query: 166 ADDAKKAQEQLNGFELAGRPMKVG 189
             D +K  E    F   G+ +K+G
Sbjct: 61  DVDVQKIVESQINFH--GKKLKLG 82

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 48.5 bits (114), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 105 NLQPRGT---GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFI 161
            L PRG+       +++IG L +  T++ LR  F  FG++    +M DP T RS+G+GF+
Sbjct: 13  GLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV 72
Query: 162 TFHSADDAKKAQEQ 175
           TF       K   Q
Sbjct: 73  TFMDQAGVDKVLAQ 86

>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28 Length = 111

Iteration: 1
 Score = 48.5 bits (114), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 27/93 (29%), Positives = 49/93 (52%), Gaps = 6/93 (6%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA---- 172
           ++I +L F+  E+ L  + + FG +  +++++ PDT  SKG  F  F + + A+K     
Sbjct: 18  VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 77
Query: 173 --QEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
             + +  G +L GR +KV     R+E+  G  S
Sbjct: 78  SLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSS 110

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 48.5 bits (114), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 52/90 (57%), Gaps = 10/90 (11%)
Query: 99  AGNTLPNL--QPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSK 156
           +G++ PN   QP  T     L++  L  + TE+ L+  F+  G +   +++ D +TG SK
Sbjct: 3   SGSSGPNARSQPSKT-----LFVKGLSEDTTEETLKESFD--GSV-RARIVTDRETGSSK 54
Query: 157 GYGFITFHSADDAKKAQEQLNGFELAGRPM 186
           G+GF+ F+S +DAK A+E +   E+ G  +
Sbjct: 55  GFGFVDFNSEEDAKAAKEAMEDGEIDGNKV 84

>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 89

Iteration: 1
 Score = 48.5 bits (114), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 31/95 (32%), Positives = 52/95 (54%), Gaps = 7/95 (7%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           G+ G   +++ +L F+ T  ML+  F   G +  +   +  + G+SKG G + F S + A
Sbjct: 1   GSSGSSGIFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVA 58
Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           ++A   +NG +L+GR + V    DRN S   GPS+
Sbjct: 59  ERACRMMNGMKLSGREIDVR--IDRNAS---GPSS 88

>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2 Length = 96

Iteration: 1
 Score = 48.5 bits (114), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 26/68 (38%), Positives = 40/68 (58%), Gaps = 5/68 (7%)
Query: 121 SLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFE 180
           +L FNITED L+ +FE     D +++ +    G+SKG  +I F S  DA+K  E+  G E
Sbjct: 23  NLSFNITEDELKEVFE-----DALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAE 77
Query: 181 LAGRPMKV 188
           + GR + +
Sbjct: 78  IDGRSVSL 85

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 48.1 bits (113), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 35/131 (26%), Positives = 57/131 (43%), Gaps = 13/131 (9%)
Query: 58  KGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRL 117
           K  A++EF+  +    AM  +G       II Q    +  R  +  P        G  +L
Sbjct: 51  KNFAFLEFRSVDETTQAMAFDG-------IIFQGQSLKIRRPHDYQP------LPGAHKL 97
Query: 118 YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN 177
           +IG L   + +D ++ +   FG +    L+ D  TG SKGY F  +   +   +A   LN
Sbjct: 98  FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 157
Query: 178 GFELAGRPMKV 188
           G +L  + + V
Sbjct: 158 GMQLGDKKLLV 168

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 48.1 bits (113), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 24/77 (31%), Positives = 48/77 (62%), Gaps = 2/77 (2%)
Query: 128 EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMK 187
           +D+L+ +F PFG + + ++ +D  T  SK +GF+++ +   A+ A + +NGF++  + +K
Sbjct: 40  QDLLQ-MFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLK 98
Query: 188 VGTVTDRNESVGGGPSN 204
           V     +N+S   GPS+
Sbjct: 99  VQLKRSKNDS-KSGPSS 114

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 48.1 bits (113), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 35/131 (26%), Positives = 57/131 (43%), Gaps = 13/131 (9%)
Query: 58  KGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRL 117
           K  A++EF+  +    AM  +G       II Q    +  R  +  P        G  +L
Sbjct: 53  KNFAFLEFRSVDETTQAMAFDG-------IIFQGQSLKIRRPHDYQP------LPGAHKL 99
Query: 118 YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN 177
           +IG L   + +D ++ +   FG +    L+ D  TG SKGY F  +   +   +A   LN
Sbjct: 100 FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 159
Query: 178 GFELAGRPMKV 188
           G +L  + + V
Sbjct: 160 GMQLGDKKLLV 170

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 47.8 bits (112), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 20/48 (41%), Positives = 32/48 (66%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITF 163
           +++IG L +  T++ LR  F  FG++    +M DP T RS+G+GF+TF
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/82 (31%), Positives = 43/82 (52%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L +  L  ++T+  L  +F   G I+  ++M D  TG S GY F+ F S  D+++A + L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 177 NGFELAGRPMKVGTVTDRNESV 198
           NG  +  + +KV       ES+
Sbjct: 66  NGITVRNKRLKVSYARPGGESI 87

>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain Length = 106

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L + +L F +++  ++ +F  FG +    +  D  +GRS G   + F    DA KA +Q
Sbjct: 30  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQ 88
Query: 176 LNGFELAGRPMKVGTVT 192
            NG  L GRPM +  VT
Sbjct: 89  YNGVPLDGRPMNIQLVT 105

>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 4 Rna-Binding Protein Length = 106

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/63 (38%), Positives = 38/63 (60%)
Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           ++L+IG +  N+ E  L+ +FE FGKI  + ++ D  TG  KG  F+T+   + A KAQ 
Sbjct: 14  IKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQS 73
Query: 175 QLN 177
            L+
Sbjct: 74  ALH 76

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 42/178 (23%), Positives = 71/178 (39%), Gaps = 31/178 (17%)
Query: 14  RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
           R+ R I    L   +  +++ +  S      D  L  C    ++KG A++   + E    
Sbjct: 20  RNRRKILIRGLPGDVTNQEVHDLLS------DYELKYCF-VDKYKGTAFVTLLNGEQAEA 72
Query: 74  AMGLNGQKLL---GIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDM 130
           A+    Q  L    + + +QPT A                      L + +L  ++T+  
Sbjct: 73  AINAFHQSRLRERELSVQLQPTDA---------------------LLCVANLPPSLTQQQ 111
Query: 131 LRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
              +  PFG ++   L+    TG+SKGYGF  +   D A +A+  L G  L  R + V
Sbjct: 112 FEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 42/178 (23%), Positives = 71/178 (39%), Gaps = 31/178 (17%)
Query: 14  RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
           R+ R I    L   +  +++ +  S      D  L  C    ++KG A++   + E    
Sbjct: 20  RNRRKILIRGLPGDVTNQEVHDLLS------DYELKYCF-VDKYKGTAFVTLLNGEQAEA 72
Query: 74  AMGLNGQKLL---GIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDM 130
           A+    Q  L    + + +QPT A                      L + +L  ++T+  
Sbjct: 73  AINAFHQSRLRERELSVQLQPTDA---------------------LLCVANLPPSLTQQQ 111
Query: 131 LRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
              +  PFG ++   L+    TG+SKGYGF  +   D A +A+  L G  L  R + V
Sbjct: 112 FEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/63 (38%), Positives = 36/63 (57%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           G+ G   LYI  L    T+  L  + +P+GKI + + ++D  T + KGYGF+ F S   A
Sbjct: 1   GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 170 KKA 172
           +KA
Sbjct: 61  QKA 63

>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 = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 42/178 (23%), Positives = 71/178 (39%), Gaps = 31/178 (17%)
Query: 14  RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
           R+ R I    L   +  +++ +  S      D  L  C    ++KG A++   + E    
Sbjct: 18  RNRRKILIRGLPGDVTNQEVHDLLS------DYELKYCF-VDKYKGTAFVTLLNGEQAEA 70
Query: 74  AMGLNGQKLL---GIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDM 130
           A+    Q  L    + + +QPT A                      L + +L  ++T+  
Sbjct: 71  AINAFHQSRLRERELSVQLQPTDA---------------------LLCVANLPPSLTQQQ 109
Query: 131 LRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
              +  PFG ++   L+    TG+SKGYGF  +   D A +A+  L G  L  R + V
Sbjct: 110 FEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 167

>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4 Rna Binding Protein Length = 105

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/63 (36%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L++G L+   +ED +R +FE FG I+   ++  PD G SKG  F+ + S  +A+ A   
Sbjct: 17  KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPD-GNSKGCAFVKYSSHAEAQAAINA 75
Query: 176 LNG 178
           L+G
Sbjct: 76  LHG 78

>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide Repeat Containing 4 Variant Length = 102

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/62 (37%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L++G L    T++ +R +FEPFG ID   ++  PD G SKG  F+ F +  +A+ A   
Sbjct: 14  KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPD-GTSKGCAFVKFQTHAEAQAAINT 72
Query: 176 LN 177
           L+
Sbjct: 73  LH 74

>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 6 Rna-Binding Protein Length = 108

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/63 (34%), Positives = 38/63 (60%)
Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           ++L++G +   + E  L+ +FE FG+I  + ++ D  TG  KG  F+T+ + D A KAQ 
Sbjct: 16  IKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQS 75
Query: 175 QLN 177
            L+
Sbjct: 76  ALH 78

>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif Of Nono Length = 99

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 50/89 (56%), Gaps = 7/89 (7%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL++G+L  +ITE+ +R +FE +GK   + +  D      KG+GFI   +   A+ A+ +
Sbjct: 17  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 176 LNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           L+   L G+ ++V      + S+  GPS+
Sbjct: 71  LDNMPLRGKQLRV-RFACHSASLTSGPSS 98

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 44/77 (57%), Gaps = 6/77 (7%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL++G+L  +ITE+  + +FE +G+   + +       R +G+GFI   S   A+ A+ +
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 77
Query: 176 LNGFELAGRPMKVGTVT 192
           L+G  L  RP+++   T
Sbjct: 78  LDGTILKSRPLRIRFAT 94

>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 101

Iteration: 1
 Score = 45.1 bits (105), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 32/90 (35%), Positives = 48/90 (53%), Gaps = 9/90 (10%)
Query: 117 LYIGSLHFNITEDMLRGIFEP--FGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           L + +L ++ TE+ L+ +FE   F K+   Q       G+SKGY FI F S +DAK+A  
Sbjct: 18  LVLSNLSYSATEETLQEVFEKATFIKVPQNQ------NGKSKGYAFIEFASFEDAKEALN 71
Query: 175 QLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
             N  E+ GR +++     R  S   GPS+
Sbjct: 72  SCNKREIEGRAIRLELQGPRG-SPNSGPSS 100

>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of Hnrnp D (Auf1) With Telomere Dna Length = 79

Iteration: 1
 Score = 45.1 bits (105), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 19/60 (31%), Positives = 37/60 (61%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++G L  +  E+ +R  F  FG++++I+L +D  T + +G+ FITF   +  KK  E+
Sbjct: 3   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62

>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length = 74

Iteration: 1
 Score = 45.1 bits (105), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 8/73 (10%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL++     ++ E  L  IF PFG +  ++++         G+ F+ F  A+ A KA E+
Sbjct: 6   RLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEE 57
Query: 176 LNGFELAGRPMKV 188
           ++G   A +P++V
Sbjct: 58  VHGKSFANQPLEV 70

>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm Length = 96

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 30/88 (34%), Positives = 41/88 (46%), Gaps = 2/88 (2%)
Query: 13  ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVP 72
           E DAR+I+   +       +LE  F   G V  V ++    +   KG AYIEF D ESV 
Sbjct: 2   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 61
Query: 73  LAMGLNGQKLLGIPIIVQPTQAEKNRAG 100
            ++ L+     G  I V P +   NR G
Sbjct: 62  TSLALDESLFRGRQIKVIPKRT--NRPG 87

>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A Resolution Length = 107

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L + +L F +++  ++ +F  FG +    +  D  +GRS G   + F    DA KA +Q
Sbjct: 31  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAXKQ 89
Query: 176 LNGFELAGRPMKVGTVT 192
            NG  L GRP  +  VT
Sbjct: 90  YNGVPLDGRPXNIQLVT 106

>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens At 1.95 A Resolution Length = 89

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 30/88 (34%), Positives = 41/88 (46%), Gaps = 2/88 (2%)
Query: 13  ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVP 72
           E DAR+I+   +       +LE  F   G V  V ++    +   KG AYIEF D ESV 
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62
Query: 73  LAMGLNGQKLLGIPIIVQPTQAEKNRAG 100
            ++ L+     G  I V P +   NR G
Sbjct: 63  TSLALDESLFRGRQIKVIPKRT--NRPG 88

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 44.7 bits (104), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 6/73 (8%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL++G+L  +ITE+ +R +FE +GK   + +  D      KG+GFI   +   A+ A+ +
Sbjct: 24  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 77
Query: 176 LNGFELAGRPMKV 188
           L+   L G+ ++V
Sbjct: 78  LDNMPLRGKQLRV 90

>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3 Length = 108

Iteration: 1
 Score = 44.7 bits (104), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 8/73 (10%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL++     ++ E  L  IF PFG +  ++++         G+ F+ F  A+ A KA E+
Sbjct: 33  RLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEE 84
Query: 176 LNGFELAGRPMKV 188
           ++G   A +P++V
Sbjct: 85  VHGKSFANQPLEV 97

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/89 (26%), Positives = 47/89 (52%), Gaps = 2/89 (2%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++G +  N  E  LR  F+ FG +  + ++ D +  R +G+GFITF       +A   
Sbjct: 12  KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-N 70
Query: 176 LNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           ++  ++ G+ ++V     R +S   GPS+
Sbjct: 71  MHFHDIMGKKVEVKRAEPR-DSKSSGPSS 98

>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1) Length = 75

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/59 (32%), Positives = 36/59 (61%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +++G L  +  E+ +R  F  FG++++I+L +D  T + +G+ FITF   +  KK  E+
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5 Rna Binding Protein Length = 105

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 23/63 (36%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L++G L+   +E+ +  +F+PFG ID   ++  PD G SKG  F+ F S  +A+ A   
Sbjct: 17  KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKFSSHTEAQAAIHA 75
Query: 176 LNG 178
           L+G
Sbjct: 76  LHG 78

>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein Q Length = 103

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 8/72 (11%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++ +L   +TE++L   F  FGK++ ++ + D        Y FI F   D A KA E++
Sbjct: 14  LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 177 NGFELAGRPMKV 188
           NG +L G  +++
Sbjct: 66  NGKDLEGENIEI 77

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 16/48 (33%), Positives = 32/48 (66%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITF 163
           +L++G L ++ T++ LR  F  +G++ +  +M D  T +S+G+GF+ F
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65

>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding Protein 30 Length = 90

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/95 (27%), Positives = 49/95 (51%), Gaps = 9/95 (9%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           G+ G ++L+IG+L    TE  +R +FE +GK+    ++        K YGF+       A
Sbjct: 4   GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAA 55
Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           + A   L+ ++L G  + V    +++++   GPS+
Sbjct: 56  EDAIRNLHHYKLHGVNINVEASKNKSKA-SSGPSS 89

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+ +L   IT+D L  IF  +G I    ++ D  TGR +G  F+ ++  ++A++A   L
Sbjct: 16  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 177 NGF--ELAGRPMKV 188
           N    E   +P+ V
Sbjct: 76  NNVIPEGGSQPLSV 89

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 29/79 (36%), Positives = 40/79 (50%), Gaps = 2/79 (2%)
Query: 12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
          +E   RT+F   L  R+R   L E F   G +  V  I  ++  + K   ++ FK PESV
Sbjct: 12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVT-ICKDREGKPKSFGFVCFKHPESV 70
Query: 72 PLAMG-LNGQKLLGIPIIV 89
            A+  LNG +L G PI V
Sbjct: 71 SYAIALLNGIRLYGRPINV 89

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 41.6 bits (96), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++G+L   + E++L  +F   G +  + +  D + G+ K +GF+ F   +    A   L
Sbjct: 19  VFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALL 77
Query: 177 NGFELAGRPMKV 188
           NG  L GRP+ V
Sbjct: 78  NGIRLYGRPINV 89

>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of Hu2af65 Length = 85

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/73 (30%), Positives = 37/73 (50%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L+IG L   + +D ++ +   FG +    L+ D  TG SKGY F  +   +   +A   
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 176 LNGFELAGRPMKV 188
           LNG +L  + + V
Sbjct: 63  LNGMQLGDKKLLV 75

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 41/188 (21%), Positives = 80/188 (42%), Gaps = 18/188 (9%)
Query: 16  ARTIFCMQLSQRIRTRDLEEFFSSVGKV--------RDVRLITCNKTRRFKGIAYIEFKD 67
           AR ++   +   I    + +FF++  ++          V  +  N+ + F   A++EF+ 
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNF---AFLEFRS 60
Query: 68  PESVPLAMGLNGQKLLGIPI-IVQPTQAEKNRAGNTLPNLQPRGTGGPM------RLYIG 120
            +    AM  +G    G  + I +P   +     +  P++   G    +      +L+IG
Sbjct: 61  VDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIG 120
Query: 121 SLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFE 180
            L   + +D ++ +   FG +    L+ D  TG SKGY F  +   +   +A   LNG +
Sbjct: 121 GLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQ 180
Query: 181 LAGRPMKV 188
           L  + + V
Sbjct: 181 LGDKKLLV 188

>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of Xenopus Laevis Epabp2 Length = 124

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 27/86 (31%), Positives = 42/86 (48%), Gaps = 3/86 (3%)
Query: 9   LSPEER---DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
           LS EE+   D R+++   +      +DLE  FSS G +  + ++    +   KG AYIEF
Sbjct: 26  LSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEF 85
Query: 66  KDPESVPLAMGLNGQKLLGIPIIVQP 91
            +  SV  A+ ++     G  I V P
Sbjct: 86  AERNSVDAAVAMDETVFRGRTIKVLP 111

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/62 (32%), Positives = 37/62 (59%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+  L   +++  +  +F  +G+I   ++++D  TG S+G GFI F    +A++A + L
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 177 NG 178
           NG
Sbjct: 64  NG 65

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 38/72 (52%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+G+L F  TE+ +  +F   G I  I + +D     + G+ F+ ++S  DA+ A   +
Sbjct: 42  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 177 NGFELAGRPMKV 188
           NG  L  R ++ 
Sbjct: 102 NGTRLDDRIIRT 113

>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14 Length = 115

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LYI +L + IT + +  IF  +G I  I++   P+T   +G  ++ +    DAK A + L
Sbjct: 11  LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNAVDHL 67
Query: 177 NGFELAGRPMKV 188
           +GF ++ R + V
Sbjct: 68  SGFNVSNRYLVV 79

>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal Protein P14 Bound To Region Of Sf3b155 Length = 125

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LYI +L + IT + +  IF  +G I  I++   P+T   +G  ++ +    DAK A + L
Sbjct: 21  LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNACDHL 77
Query: 177 NGFELAGRPMKV 188
           +GF +  R + V
Sbjct: 78  SGFNVCNRYLVV 89

>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor (Residues 1-155) Length = 177

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L + +L F +++  ++ +F  FG +    +  D  +GRS G   + F    DA KA +Q
Sbjct: 90  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQ 148
Query: 176 LNGFELAGRPMKVGTVT 192
             G  L GRPM +  V 
Sbjct: 149 YKGVPLDGRPMDIQLVA 165

>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein Complex P14-Sf3b155 Length = 87

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LYI +L + IT + +  IF  +G I  I++   P+T   +G  ++ +    DAK A + L
Sbjct: 15  LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNACDHL 71
Query: 177 NGFELAGRPMKV 188
           +GF +  R + V
Sbjct: 72  SGFNVCNRYLVV 83

>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 4h Length = 103

Iteration: 1
 Score = 41.6 bits (96), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 31/106 (29%), Positives = 51/106 (48%), Gaps = 9/106 (8%)
Query: 99  AGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGY 158
           +G  LP      T  P   Y+G+L FN  +  +  IF+    I +++L+ D DT + KG+
Sbjct: 6   SGKELP------TEPPYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGF 58
Query: 159 GFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
            ++ F   D  K+A    +G  L  R ++V     R +    GPS+
Sbjct: 59  CYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQD-KSGPSS 102

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	370
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-67
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-28
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-66
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-25
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-65
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-22
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-12
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-58
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-24
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-11
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-51
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-22
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-05
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-46
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-10
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-43
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-12
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-41
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-41
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	5e-11
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	4e-41
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	3e-23
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-40
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-39
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-39
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	8e-39
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	5e-28
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	6e-08
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-38
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-27
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-07
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-38
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-21
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-37
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-10
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-36
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-12
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	3e-36
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-12
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	5e-36
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	8e-13
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-35
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-34
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-22
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-08
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-35
1x4e_A	85	RNA binding motif, single-stranded interacting pro	7e-08
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-35
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-09
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	6e-35
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-12
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	6e-35
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	7e-12
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-34
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-12
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-34
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-11
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	6e-34
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	7e-09
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	6e-34
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-11
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-33
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	4e-13
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-33
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	8e-09
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-33
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	6e-12
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-33
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	7e-12
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	4e-33
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	6e-10
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	4e-33
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-11
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	6e-33
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	5e-09
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-32
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-07
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	5e-32
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	4e-07
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-32
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-12
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	6e-32
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-11
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-32
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-09
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	8e-32
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-09
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-31
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	8e-10
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-31
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-12
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	4e-31
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-13
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-31
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-08
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	8e-31
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	9e-12
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-30
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	9e-15
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-30
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	5e-15
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-30
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	4e-11
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	3e-30
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	5e-11
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-30
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-12
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-30
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-11
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	4e-30
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	9e-22
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	5e-30
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-08
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-29
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	3e-13
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-29
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	7e-12
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	4e-29
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	9e-08
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	4e-29
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	7e-09
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	5e-29
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-07
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	6e-29
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	5e-13
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	9e-29
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-11
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-28
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	3e-08
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-28
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-07
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	4e-28
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	5e-09
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	4e-28
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-08
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	6e-28
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	5e-07
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-27
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-07
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-27
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	6e-08
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	6e-27
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	6e-11
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	7e-27
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-14
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-26
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-07
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-26
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-13
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-26
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-12
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-06
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-26
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	4e-06
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	5e-26
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	6e-11
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	5e-26
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	5e-08
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	9e-26
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-14
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-25
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-12
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-25
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-13
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-25
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-11
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	4e-25
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	4e-10
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	9e-25
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-10
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-24
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-07
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-24
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	5e-10
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-24
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-18
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	3e-24
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	3e-12
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-24
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-08
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	5e-24
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	4e-17
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	5e-24
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	9e-15
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	6e-24
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-12
2div_A	99	TRNA selenocysteine associated protein; structural	6e-24
2div_A	99	TRNA selenocysteine associated protein; structural	3e-08
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	8e-24
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	9e-08
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-23
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-13
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-23
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-12
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-23
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	5e-13
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-23
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	8e-09
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-23
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	5e-06
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	6e-23
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-13
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	6e-23
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	3e-14
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-22
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-11
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-22
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-08
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-22
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-09
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-22
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	4e-09
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	5e-22
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-10
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	8e-22
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-08
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-21
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-12
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-21
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	9e-07
1x5p_A	97	Negative elongation factor E; structure genomics,	2e-21
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-05
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-21
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	7e-13
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-21
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-11
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	8e-21
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	4e-11
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-20
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-14
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-20
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	6e-08
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	3e-20
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	7e-08
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	4e-20
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	3e-07
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	5e-20
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	5e-12
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	5e-20
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	4e-07
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	7e-20
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-19
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-07
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-19
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	3e-09
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	4e-19
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-06
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-18
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-09
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-18
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	6e-07
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-18
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	9e-07
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-18
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	9e-09
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-18
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	3e-06
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-18
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-07
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-18
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-16
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	5e-18
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	8e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	6e-18
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-08
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	7e-18
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	5e-06
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-17
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-07
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-17
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	5e-05
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-17
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	8e-16
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-17
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-12
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-09
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	8e-04
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-17
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	6e-10
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	4e-17
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	6e-10
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	3e-16
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	4e-06
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	5e-16
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-15
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	5e-06
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	4e-15
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	7e-15
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-06
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	8e-15
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	8e-09
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	9e-15
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	6e-14
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-14
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	3e-13
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-14
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	8e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-14
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-14
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-07
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	3e-14
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	7e-11
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	3e-14
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	7e-05
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-14
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-12
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	5e-14
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-10
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	6e-14
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	1e-13
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-13
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-11
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-13
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-05
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	4e-13
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	4e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	4e-13
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	6e-09
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	4e-13
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	3e-06
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	4e-13
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	7e-06
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	1e-12
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	1e-10
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-12
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	4e-07
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	6e-12
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	8e-12
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-11
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-10
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	1e-11
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-11
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	6e-10
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	3e-11
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	3e-10
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	9e-11
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	9e-11
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	4e-10
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	4e-05
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	5e-10
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	6e-10
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	3e-05
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	4e-09
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	6e-08
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	9e-08
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	1e-07
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	8e-07
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-06
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	4e-06
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	5e-05
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	8e-04
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	1e-04
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	2e-04

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  211 bits (539), Expect = 1e-67
 Identities = 47/195 (24%), Positives = 90/195 (46%), Gaps = 3/195 (1%)

Query: 1   MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
           M    +            ++   +   +    + + F+  G ++ + +   + T + KG 
Sbjct: 13  MGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGF 72

Query: 61  AYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYI 119
           A++E++ PE+  LA+  +N   L G  I V             + +          R+Y+
Sbjct: 73  AFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQA--QPIIDQLAEEARAFNRIYV 130

Query: 120 GSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF 179
            S+H ++++D ++ +FE FGKI +  L  DP TG+ KGYGFI +  A  ++ A   +N F
Sbjct: 131 ASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLF 190

Query: 180 ELAGRPMKVGTVTDR 194
           +L G+ ++VG     
Sbjct: 191 DLGGQYLRVGKAVTP 205

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  110 bits (276), Expect = 1e-28
 Identities = 31/94 (32%), Positives = 52/94 (55%), Gaps = 1/94 (1%)

Query: 104 PNLQPRGTGGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFIT 162
              Q +G    M  +Y+GS+++ + ED +R  F PFG I +I +  D  T + KG+ F+ 
Sbjct: 17  SAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE 76

Query: 163 FHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
           +   + A+ A EQ+N   L GR +KVG  ++  +
Sbjct: 77  YEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQ 110

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score =  206 bits (527), Expect = 3e-66
 Identities = 43/185 (23%), Positives = 78/185 (42%), Gaps = 17/185 (9%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
             E      +F   L+      +L+   S +    D+ ++   +T   +   Y++F+  E
Sbjct: 7   GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVD-VRTGTNRKFGYVDFESAE 65

Query: 70  SVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITED 129
            +  A+ L G K+ G  I ++  +   ++                  L   +L FNITED
Sbjct: 66  DLEKALELTGLKVFGNEIKLEKPKGRDSKKVR-----------AARTLLAKNLSFNITED 114

Query: 130 MLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
            L+ +FE   +I      +    G+SKG  +I F S  DA+K  E+  G E+ GR + + 
Sbjct: 115 ELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY 169

Query: 190 TVTDR 194
              ++
Sbjct: 170 YTGEK 174

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 99.2 bits (248), Expect = 5e-25
 Identities = 24/93 (25%), Positives = 46/93 (49%), Gaps = 2/93 (2%)

Query: 113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
            P  L+IG+L+ N +   L+         +++ ++ D  TG ++ +G++ F SA+D +KA
Sbjct: 12  TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKA 70

Query: 173 QEQLNGFELAGRPMKVGTVTDRNESVGGGPSNL 205
            E L G ++ G  +K+     R+         L
Sbjct: 71  LE-LTGLKVFGNEIKLEKPKGRDSKKVRAARTL 102

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score =  205 bits (523), Expect = 2e-65
 Identities = 37/194 (19%), Positives = 77/194 (39%), Gaps = 12/194 (6%)

Query: 16  ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCN-----KTRRFKGIAYIEFKDPES 70
           AR ++   +   I    + +FF++  ++  +     N     +  + K  A++EF+  + 
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63

Query: 71  VPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTG-------GPMRLYIGSLH 123
              AM  +G    G  + ++     +   G +                    +L+IG L 
Sbjct: 64  TTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLP 123

Query: 124 FNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG 183
             + +D ++ +   FG +    L+ D  TG SKGY F  +   +   +A   LNG +L  
Sbjct: 124 NYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD 183

Query: 184 RPMKVGTVTDRNES 197
           + + V   +   ++
Sbjct: 184 KKLLVQRASVGAKN 197

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 93.6 bits (233), Expect = 1e-22
 Identities = 21/99 (21%), Positives = 41/99 (41%), Gaps = 7/99 (7%)

Query: 112 GGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQL-----MVDPDTGRSKGYGFITFHS 165
           G   R LY+G++ F ITE+ +   F    ++  +       ++     + K + F+ F S
Sbjct: 1   GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60

Query: 166 ADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
            D+  +A    +G    G+ +K+    D     G   + 
Sbjct: 61  VDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENP 98

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 63.9 bits (156), Expect = 3e-12
 Identities = 23/98 (23%), Positives = 40/98 (40%), Gaps = 2/98 (2%)

Query: 2   RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIA 61
                   +     A  +F   L   +    ++E  +S G ++   L+  + T   KG A
Sbjct: 100 VYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYA 159

Query: 62  YIEFKDPESVPLAM-GLNGQKLLGIPIIVQ-PTQAEKN 97
           + E+ D      A+ GLNG +L    ++VQ  +   KN
Sbjct: 160 FCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKN 197

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score =  186 bits (475), Expect = 2e-58
 Identities = 38/179 (21%), Positives = 74/179 (41%), Gaps = 18/179 (10%)

Query: 16  ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCN-----KTRRFKGIAYIEFKDPES 70
           AR ++   +   I    + +FF++  ++  +     N     +  + K  A++EF+  + 
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63

Query: 71  VPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDM 130
              AM  +G    G  + +        R  +       +   G  +L+IG L   + +D 
Sbjct: 64  TTQAMAFDGIIFQGQSLKI-------RRPHD------YQPLPGAHKLFIGGLPNYLNDDQ 110

Query: 131 LRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
           ++ +   FG +    L+ D  TG SKGY F  +   +   +A   LNG +L  + + V 
Sbjct: 111 VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQ 169

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 96.1 bits (240), Expect = 5e-24
 Identities = 24/107 (22%), Positives = 48/107 (44%), Gaps = 13/107 (12%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQL-----MVDPDTGRSKGYGFITFHSADDAK 170
           RLY+G++ F ITE+ +   F    ++  +       ++     + K + F+ F S D+  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 171 KAQEQLNGFELAGRPMKVGTVTDRNES-------VGGGPSNLDTDEM 210
           +A    +G    G+ +K+    D           +GG P+ L+ D++
Sbjct: 66  QAMA-FDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQV 111

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 61.5 bits (150), Expect = 1e-11
 Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 1/81 (1%)

Query: 11  PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
                A  +F   L   +    ++E  +S G ++   L+  + T   KG A+ E+ D   
Sbjct: 89  QPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINV 148

Query: 71  VPLAM-GLNGQKLLGIPIIVQ 90
              A+ GLNG +L    ++VQ
Sbjct: 149 TDQAIAGLNGMQLGDKKLLVQ 169

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score =  168 bits (428), Expect = 1e-51
 Identities = 48/183 (26%), Positives = 84/183 (45%), Gaps = 22/183 (12%)

Query: 15  DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKT--RRFKGIAYIEFKDPESVP 72
           DA  +F  Q+ +    +DL E F   G V ++ ++        + KG  ++ F   ++  
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 73  LAM-GLNGQKLLG---IPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITE 128
            A   L+  K+L     PI ++P  +EKN A                +L+IG +    TE
Sbjct: 62  EAQNALHNMKVLPGMHHPIQMKPADSEKNNAVED------------RKLFIGMISKKCTE 109

Query: 129 DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNG---FELAGRP 185
           + +R +F  FG+I+  +++  PD G S+G  F+TF +   A+ A + ++     E    P
Sbjct: 110 NDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSP 168

Query: 186 MKV 188
           M V
Sbjct: 169 MVV 171

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 91.9 bits (229), Expect = 2e-22
 Identities = 20/113 (17%), Positives = 46/113 (40%), Gaps = 13/113 (11%)

Query: 113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTG--RSKGYGFITFHSADDAK 170
             +++++G +    +E  LR +FE +G +  I ++ D      +SKG  F+TF++   A 
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 171 KAQEQLNGFELAGRPMKVGTVTDRNES-----------VGGGPSNLDTDEMER 212
           +AQ  L+  ++         +   +             +G        +++  
Sbjct: 62  EAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRV 114

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 43.8 bits (104), Expect = 2e-05
 Identities = 16/94 (17%), Positives = 41/94 (43%), Gaps = 5/94 (5%)

Query: 1   MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
           ++   +D       + R +F   +S++    D+   FSS G++ + R++        +G 
Sbjct: 80  IQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILR-GPDGLSRGC 138

Query: 61  AYIEFKDPESVPLAM-GLNGQKLLGI---PIIVQ 90
           A++ F        A+  ++  + +     P++V+
Sbjct: 139 AFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK 172

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score =  153 bits (389), Expect = 2e-46
 Identities = 69/105 (65%), Positives = 83/105 (79%)

Query: 92  TQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPD 151
                +     + N   +G+ GPMRLY+GSLHFNITEDMLRGIFEPFG+I++IQLM+D +
Sbjct: 4   HHHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSE 63

Query: 152 TGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
           TGRSKGYGFITF  ++ AKKA EQLNGFELAGRPMKVG VT+R +
Sbjct: 64  TGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 56.2 bits (136), Expect = 3e-10
 Identities = 25/90 (27%), Positives = 41/90 (45%), Gaps = 1/90 (1%)

Query: 1   MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
           M  A +++L         ++   L   I    L   F   G++  ++L+  ++T R KG 
Sbjct: 11  MAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGY 70

Query: 61  AYIEFKDPESVPLAM-GLNGQKLLGIPIIV 89
            +I F D E    A+  LNG +L G P+ V
Sbjct: 71  GFITFSDSECAKKALEQLNGFELAGRPMKV 100

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score =  146 bits (370), Expect = 2e-43
 Identities = 32/113 (28%), Positives = 52/113 (46%), Gaps = 4/113 (3%)

Query: 80  QKLLGIPIIVQPTQAEKNR----AGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIF 135
           + L  +P  V  T           G+               LY+G L   + + +L   F
Sbjct: 25  EILSNLPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAF 84

Query: 136 EPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
            PFG I +IQ+ +D +T + +G+ F+ F  A+DA  A + +N  EL GR ++V
Sbjct: 85  IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 137

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 62.1 bits (151), Expect = 4e-12
 Identities = 18/81 (22%), Positives = 37/81 (45%), Gaps = 1/81 (1%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
                  R ++   L++ +  + L   F   G + D+++    +T + +G A++EF+  E
Sbjct: 57  GGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 116

Query: 70  SVPLAM-GLNGQKLLGIPIIV 89
               A+  +N  +L G  I V
Sbjct: 117 DAAAAIDNMNESELFGRTIRV 137

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score =  142 bits (360), Expect = 2e-41
 Identities = 44/174 (25%), Positives = 89/174 (51%), Gaps = 13/174 (7%)

Query: 17  RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
           R ++   L + I    L+++F   G + +++++  +K  +    A++E+       +A+ 
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMI-DKNNKNVNYAFVEYHQSHDANIALQ 59

Query: 76  GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIF 135
            LNG+++    + +       N A  +    Q   +     L++G L+ N+ ++ LR  F
Sbjct: 60  TLNGKQIENNIVKI-------NWAFQS----QQSSSDDTFNLFVGDLNVNVDDETLRNAF 108

Query: 136 EPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
           + F    +  +M D  TG S+GYGF++F S DDA+ A + + G +L GRP+++ 
Sbjct: 109 KDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN 162

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score =  139 bits (352), Expect = 3e-41
 Identities = 69/95 (72%), Positives = 79/95 (83%), Gaps = 1/95 (1%)

Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           G+ G   LY+GSLHFNITEDMLRGIFEPFGKIDNI LM D DTGRSKGYGFITF  ++ A
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60

Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           ++A EQLNGFELAGRPM+VG VT+R +  G GPS+
Sbjct: 61  RRALEQLNGFELAGRPMRVGHVTERLDG-GSGPSS 94

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 57.9 bits (141), Expect = 5e-11
 Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 1/76 (1%)

Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
           +  ++   L   I    L   F   GK+ ++ L+  + T R KG  +I F D E    A
Sbjct: 4  GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63

Query: 75 M-GLNGQKLLGIPIIV 89
          +  LNG +L G P+ V
Sbjct: 64 LEQLNGFELAGRPMRV 79

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score =  139 bits (352), Expect = 4e-41
 Identities = 67/96 (69%), Positives = 82/96 (85%)

Query: 7   DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
           D+LSPEERDART+FCMQL+ RIR RDLE+FFS+VGKVRDVR+I+   +RR KGIAY+EF 
Sbjct: 16  DNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFC 75

Query: 67  DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNT 102
           + +SVPLA+GL GQ+LLG+PIIVQ +QAEKNR    
Sbjct: 76  EIQSVPLAIGLTGQRLLGVPIIVQASQAEKNRLSGP 111

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 92.0 bits (229), Expect = 3e-23
 Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           ++   L   I    L   F   GK+ +++++ D ++ RSKG  ++ F        A   L
Sbjct: 28  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA-IGL 86

Query: 177 NGFELAGRPMKV 188
            G  L G P+ V
Sbjct: 87  TGQRLLGVPIIV 98

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score =  143 bits (362), Expect = 2e-40
 Identities = 40/189 (21%), Positives = 71/189 (37%), Gaps = 27/189 (14%)

Query: 2   RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIA 61
                +    + R+ R I    L   +  +++ +  S         L  C    ++KG A
Sbjct: 8   IRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE------LKYC-FVDKYKGTA 60

Query: 62  YIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIG 120
           ++   + E    A+   +  +L    + V                LQP        L + 
Sbjct: 61  FVTLLNGEQAEAAINAFHQSRLRERELSV---------------QLQPTDA----LLCVA 101

Query: 121 SLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFE 180
           +L  ++T+     +  PFG ++   L+    TG+SKGYGF  +   D A +A+  L G  
Sbjct: 102 NLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKP 161

Query: 181 LAGRPMKVG 189
           L  R + V 
Sbjct: 162 LGPRTLYVH 170

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score =  139 bits (352), Expect = 5e-39
 Identities = 35/174 (20%), Positives = 62/174 (35%), Gaps = 13/174 (7%)

Query: 18  TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
            +    L   +  +  EE     G +    L+   +T + KG  + E+   +S   A   
Sbjct: 97  LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156

Query: 77  LNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITE-DMLRGIF 135
           L G+ L    + V  T A +                    L +  L     + D L    
Sbjct: 157 LLGKPLGPRTLYVHWTDAGQLTPALLHSR----------CLCVDRLPPGFNDVDALCRAL 206

Query: 136 EPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
                    QL      G+ KG+  + + +A+ A++AQ+Q +G  L G  ++V 
Sbjct: 207 SAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVS 259

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score =  138 bits (349), Expect = 2e-39
 Identities = 55/229 (24%), Positives = 95/229 (41%), Gaps = 28/229 (12%)

Query: 3   PAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAY 62
           P  S + S       +++   L   +    L E FS  G +  +R+     TRR  G AY
Sbjct: 2   PLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAY 61

Query: 63  IEFKDPESVPLAM-GLNGQKLLGIPIIV----QPTQAEKNRAGNTLPNLQPRGTGGPMRL 117
           + F+ P     A+  +N   + G P+ +    +     K+  GN               +
Sbjct: 62  VNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN---------------I 106

Query: 118 YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN 177
           +I +L  +I    L   F  FG I + +++ D     SKGYGF+ F + + A++A E++N
Sbjct: 107 FIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMN 164

Query: 178 GFELAGRPMKVGTVT---DRNESVGGGPSNLDTDEMERAGVDLGATGRL 223
           G  L  R + VG      +R   +G         ++       G++GR+
Sbjct: 165 GMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPDYA---GSSGRI 210

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score =  135 bits (342), Expect = 8e-39
 Identities = 42/175 (24%), Positives = 74/175 (42%), Gaps = 16/175 (9%)

Query: 17  RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
             +    L Q +  R+L   F ++G +   R++   KT    G A+++F        A+ 
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63

Query: 76  GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIF 135
            LNG  +    + V   +       +T              LY+ +L   IT+D L  IF
Sbjct: 64  VLNGITVRNKRLKVSYARPGGESIKDT-------------NLYVTNLPRTITDDQLDTIF 110

Query: 136 EPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG--RPMKV 188
             +G I    ++ D  TGR +G  F+ ++  ++A++A   LN     G  +P+ V
Sbjct: 111 GKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 165

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score =  106 bits (268), Expect = 5e-28
 Identities = 29/104 (27%), Positives = 49/104 (47%), Gaps = 7/104 (6%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L +  L  ++T+  L  +F   G I+  ++M D  TG S GY F+ F S  D+++A + L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65

Query: 177 NGFELAGRPMKVGTVTDRNES-------VGGGPSNLDTDEMERA 213
           NG  +  + +KV       ES       V   P  +  D+++  
Sbjct: 66  NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTI 109

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 50.6 bits (122), Expect = 6e-08
 Identities = 18/92 (19%), Positives = 36/92 (39%), Gaps = 4/92 (4%)

Query: 1   MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
           ++ +Y+     E      ++   L + I    L+  F   G +    ++    T R +G+
Sbjct: 75  LKVSYAR-PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGV 133

Query: 61  AYIEFKDPESVPLAM-GLNGQKLLG--IPIIV 89
           A++ +   E    A+  LN     G   P+ V
Sbjct: 134 AFVRYNKREEAQEAISALNNVIPEGGSQPLSV 165

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score =  134 bits (340), Expect = 1e-38
 Identities = 43/174 (24%), Positives = 77/174 (44%), Gaps = 16/174 (9%)

Query: 18  TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
            +    L Q +   +    F S+G++   +L+    T +  G  ++ + DP+    A+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 77  LNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFE 136
           LNG +L    I V   +       +               LY+  L   +T+  L  +F 
Sbjct: 64  LNGLRLQTKTIKVSYARPSSASIRDA-------------NLYVSGLPKTMTQKELEQLFS 110

Query: 137 PFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG--RPMKV 188
            +G+I   +++VD  TG S+G GFI F    +A++A + LNG + +G   P+ V
Sbjct: 111 QYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV 164

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score =  104 bits (261), Expect = 4e-27
 Identities = 30/95 (31%), Positives = 48/95 (50%), Gaps = 3/95 (3%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L +  L  N+T++  R +F   G+I++ +L+ D  TG+S GYGF+ +    DA+KA   L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 177 NGFELAGRPMKVGTVTDRNESVGGGP---SNLDTD 208
           NG  L  + +KV      + S+       S L   
Sbjct: 65  NGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKT 99

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 50.3 bits (121), Expect = 1e-07
 Identities = 24/92 (26%), Positives = 43/92 (46%), Gaps = 4/92 (4%)

Query: 1   MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
           ++ +Y+   S        ++   L + +  ++LE+ FS  G++   R++    T   +G+
Sbjct: 74  IKVSYAR-PSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGV 132

Query: 61  AYIEFKDPESVPLAM-GLNGQKLLGI--PIIV 89
            +I F        A+ GLNGQK  G   PI V
Sbjct: 133 GFIRFDKRIEAEEAIKGLNGQKPSGATEPITV 164

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score =  135 bits (342), Expect = 2e-38
 Identities = 46/195 (23%), Positives = 78/195 (40%), Gaps = 8/195 (4%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
             E    R +F   LS       L   F   G + D  ++    T+R +G  ++ +   E
Sbjct: 7   PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66

Query: 70  SVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITED 129
            V  AM     K+ G  +       E  RA +   + +P       ++++G +  +  E 
Sbjct: 67  EVDAAMNARPHKVDGRVV-------EPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEH 119

Query: 130 MLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
            LR  FE +GKI+ I++M D  +G+ +G+ F+TF   D   K   Q     + G   +V 
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVR 178

Query: 190 TVTDRNESVGGGPSN 204
               + E      S 
Sbjct: 179 KALSKQEMASASSSQ 193

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 89.7 bits (223), Expect = 2e-21
 Identities = 30/118 (25%), Positives = 55/118 (46%), Gaps = 14/118 (11%)

Query: 107 QPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA 166
            P+      +L+IG L F  T++ LR  FE +G + +  +M DP+T RS+G+GF+T+ + 
Sbjct: 6   SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 65

Query: 167 DDAKKAQEQLNGFELAGRPMKVGTVTDRNES-------------VGGGPSNLDTDEME 211
           ++   A       ++ GR ++      R +S             VGG   + +   + 
Sbjct: 66  EEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLR 122

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score =  130 bits (328), Expect = 2e-37
 Identities = 31/105 (29%), Positives = 58/105 (55%)

Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
           G++  + Q + T     +++G L   IT + ++  F PFG+I + +++ D  TG+SKGYG
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60

Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           F++F +  DA+ A +Q+ G  L GR ++    T +  +      +
Sbjct: 61  FVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYES 105

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 57.0 bits (138), Expect = 2e-10
 Identities = 23/98 (23%), Positives = 40/98 (40%), Gaps = 2/98 (2%)

Query: 18  TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
            +F   LS  I T D++  F+  G++ D R++    T + KG  ++ F +      A+  
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76

Query: 77  LNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGP 114
           + GQ L G  I        K  A  +      + +G  
Sbjct: 77  MGGQWLGGRQIRTNWAT-RKPPAPKSTYESNTKQSGPS 113

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score =  126 bits (318), Expect = 3e-36
 Identities = 31/92 (33%), Positives = 52/92 (56%), Gaps = 1/92 (1%)

Query: 114 PMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
           P R +Y+GS+ ++ TE+ +  +    G + N+++M DP TGRSKGY FI F   + +  A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

Query: 173 QEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
              LNG++L  R +K G  ++ + S      +
Sbjct: 61  VRNLNGYQLGSRFLKCGYSSNSDISGVSLEHH 92

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 61.9 bits (151), Expect = 2e-12
 Identities = 21/87 (24%), Positives = 41/87 (47%), Gaps = 1/87 (1%)

Query: 16  ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM 75
           +R ++   +        + +  S+VG V +++++   +T R KG A+IEF+D ES   A+
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61

Query: 76  -GLNGQKLLGIPIIVQPTQAEKNRAGN 101
             LNG +L    +    +        +
Sbjct: 62  RNLNGYQLGSRFLKCGYSSNSDISGVS 88

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score =  125 bits (317), Expect = 3e-36
 Identities = 26/87 (29%), Positives = 48/87 (55%), Gaps = 1/87 (1%)

Query: 111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVD-PDTGRSKGYGFITFHSADDA 169
           +  P +++IG L  N+T+D +  IF  +GKI  I + V+      SKGY ++ F + D+A
Sbjct: 1   SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60

Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNE 196
           +KA + ++G ++ G+ +    V     
Sbjct: 61  EKALKHMDGGQIDGQEITATAVLAPWP 87

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 61.8 bits (151), Expect = 1e-12
 Identities = 19/83 (22%), Positives = 39/83 (46%), Gaps = 2/83 (2%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLIT-CNKTRRFKGIAYIEFKDPESVPLAM- 75
           +   +L++ +    + E FS+ GK++ + +          KG AY+EF++P+    A+ 
Sbjct: 6  KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 76 GLNGQKLLGIPIIVQPTQAEKNR 98
           ++G ++ G  I      A   R
Sbjct: 66 HMDGGQIDGQEITATAVLAPWPR 88

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score =  127 bits (320), Expect = 5e-36
 Identities = 30/120 (25%), Positives = 57/120 (47%), Gaps = 4/120 (3%)

Query: 90  QPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVD 149
           Q  Q ++ +  +  P            L +  +   + E  LR +FE +G I++++++ D
Sbjct: 18  QLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCD 77

Query: 150 PDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNE----SVGGGPSNL 205
            +T +S+GYGF+ F S   A++A   LNGF +  + +KV      ++    +   G  N 
Sbjct: 78  RETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGNG 137

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 64.4 bits (157), Expect = 8e-13
 Identities = 24/120 (20%), Positives = 47/120 (39%), Gaps = 8/120 (6%)

Query: 1   MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
            +      ++PE    R +    +   +    L + F   G +  V+++   +TR+ +G 
Sbjct: 27  QQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGY 86

Query: 61  AYIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYI 119
            +++F+   S   A+ GLNG  +L   + V    +   R G         G  G    Y+
Sbjct: 87  GFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIA-------GAVGDGNGYL 139

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score =  130 bits (328), Expect = 2e-35
 Identities = 27/182 (14%), Positives = 63/182 (34%), Gaps = 22/182 (12%)

Query: 7   DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
           ++     R+  T+    L +      + ++F   G +  V +      ++    A IEF 
Sbjct: 32  NEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVAD--SLKKNFRFARIEFA 89

Query: 67  DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
             +    A+    + +    IIV       +                   L++ +   + 
Sbjct: 90  RYDGALAAITKTHKVVGQNEIIV-------SHLTEC-------------TLWMTNFPPSY 129

Query: 127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
           T+  +R + +    +     +       S+ + +I   S +DA+   E+LNG ++ G  +
Sbjct: 130 TQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTL 189

Query: 187 KV 188
             
Sbjct: 190 VT 191

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score =  126 bits (319), Expect = 4e-34
 Identities = 34/175 (19%), Positives = 68/175 (38%), Gaps = 10/175 (5%)

Query: 17  RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
            T++          R++ +    +  V     +   +    +  AYI+    E     + 
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177

Query: 76  GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNIT-EDMLRGI 134
            LNG K+ G  ++ + +   +         L+ R       + I +L   +  E++LR  
Sbjct: 178 KLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGR------EIMIRNLSTELLDENLLRES 231

Query: 135 FEPFGKIDNIQLMVD-PDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
           FE FG I+ I +     +   +    F+ F + D A++A + +N   L  R + V
Sbjct: 232 FEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISV 285

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 93.5 bits (233), Expect = 5e-22
 Identities = 12/95 (12%), Positives = 35/95 (36%), Gaps = 3/95 (3%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           + + +L  +  ++ +   F+  G I ++ +       ++  +  I F   D A  A  + 
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGALAAITKT 101

Query: 177 NGFELAGRPMKVGTVTDRNESVGGGPSNLDTDEME 211
           +   +    + V  +T+    +   P +     + 
Sbjct: 102 HK-VVGQNEIIVSHLTECTLWMTNFPPSYTQRNIR 135

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 54.6 bits (132), Expect = 1e-08
 Identities = 17/76 (22%), Positives = 28/76 (36%), Gaps = 2/76 (2%)

Query: 17  RTIFCMQLSQRIRT-RDLEEFFSSVGKVRDVRLITCNK-TRRFKGIAYIEFKDPESVPLA 74
           R I    LS  +     L E F   G +  + +    K        A++ F++ +S   A
Sbjct: 211 REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 270

Query: 75  MGLNGQKLLGIPIIVQ 90
           + +N   L    I V 
Sbjct: 271 LQMNRSLLGNREISVS 286

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score =  123 bits (311), Expect = 2e-35
 Identities = 26/79 (32%), Positives = 40/79 (50%)

Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           G+ G   LYI  L    T+  L  + +P+GKI + + ++D  T + KGYGF+ F S   A
Sbjct: 1   GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60

Query: 170 KKAQEQLNGFELAGRPMKV 188
           +KA   L    +  +  K 
Sbjct: 61  QKAVTALKASGVQAQMAKQ 79

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 48.7 bits (117), Expect = 7e-08
 Identities = 13/71 (18%), Positives = 27/71 (38%), Gaps = 1/71 (1%)

Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
           +  ++   L      +DL +     GK+   + I    T + KG  +++F  P +   A
Sbjct: 4  GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63

Query: 75 M-GLNGQKLLG 84
          +  L    +  
Sbjct: 64 VTALKASGVQA 74

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score =  123 bits (311), Expect = 3e-35
 Identities = 29/84 (34%), Positives = 48/84 (57%)

Query: 111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAK 170
            G    +++G L   IT   +   F PFG+I + +++ D  TG+SKGYGF++F +  DA+
Sbjct: 3   LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62

Query: 171 KAQEQLNGFELAGRPMKVGTVTDR 194
            A +Q+ G  L GR ++    T +
Sbjct: 63  NAIQQMGGQWLGGRQIRTNWATRK 86

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 53.7 bits (130), Expect = 1e-09
 Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
          +F   LS  I T  +   F+  G++ D R++    T + KG  ++ F +      A+  +
Sbjct: 9  VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68

Query: 78 NGQKLLGIPIIV 89
           GQ L G  I  
Sbjct: 69 GGQWLGGRQIRT 80

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score =  123 bits (311), Expect = 6e-35
 Identities = 25/98 (25%), Positives = 43/98 (43%), Gaps = 1/98 (1%)

Query: 92  TQAEKNRAGNTLPNLQPRGTGGP-MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDP 150
           +          +P       G P   LY+ +L   +TE  L  +F  F +     +    
Sbjct: 2   SSGSSGEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRM 61

Query: 151 DTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
            TGR +G  FITF + + A +A   +NG++L G+ + +
Sbjct: 62  MTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVI 99

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 62.3 bits (152), Expect = 2e-12
 Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 1/83 (1%)

Query: 17  RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
           + ++   LS R+  RDL   F+   + +   +     T R +G A+I F + E    A+ 
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85

Query: 76  GLNGQKLLGIPIIVQPTQAEKNR 98
            +NG KL G  ++++  + +K R
Sbjct: 86  LVNGYKLYGKILVIEFGKNKKQR 108

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score =  124 bits (315), Expect = 6e-35
 Identities = 43/183 (23%), Positives = 81/183 (44%), Gaps = 17/183 (9%)

Query: 14  RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
           +++  +F   L+      +L E+F   G V D++++    T R +G  ++ F+ P SV  
Sbjct: 1   KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60

Query: 74  AMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMR-LYIGSLHFNITEDMLR 132
            +      L G  I       +  RA        PR        +++G +  ++      
Sbjct: 61  VVK-TQHILDGKVI-------DPKRA-------IPRDEQDKTGKIFVGGIGPDVRPKEFE 105

Query: 133 GIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT 192
             F  +G I + QLM+D DTG+S+G+GF+T+ SAD   +  +     +   R +++    
Sbjct: 106 EFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN-KFIDFKDRKIEIKRAE 164

Query: 193 DRN 195
            R+
Sbjct: 165 PRH 167

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 62.2 bits (152), Expect = 7e-12
 Identities = 16/79 (20%), Positives = 32/79 (40%)

Query: 11  PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
            E+     IF   +   +R ++ EEFFS  G + D +L+    T + +G  ++ +   ++
Sbjct: 82  DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141

Query: 71  VPLAMGLNGQKLLGIPIIV 89
           V               I +
Sbjct: 142 VDRVCQNKFIDFKDRKIEI 160

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score =  122 bits (308), Expect = 1e-34
 Identities = 28/97 (28%), Positives = 51/97 (52%)

Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
             G+ G  RL++ +L +  +E+ L  +F  +G +  +   +D  T + KG+ F+TF   +
Sbjct: 2   SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61

Query: 168 DAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
            A KA  +++G    GR + V   T + E+   GPS+
Sbjct: 62  HAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSS 98

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 61.8 bits (151), Expect = 2e-12
 Identities = 24/91 (26%), Positives = 42/91 (46%), Gaps = 1/91 (1%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
          S     +  +F   LS      DLE+ FS+ G + ++     + T++ KG A++ F  PE
Sbjct: 2  SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61

Query: 70 SVPLAM-GLNGQKLLGIPIIVQPTQAEKNRA 99
              A   ++GQ   G  + V P+  +K  +
Sbjct: 62 HAVKAYAEVDGQVFQGRMLHVLPSTIKKEAS 92

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score =  121 bits (306), Expect = 1e-34
 Identities = 30/82 (36%), Positives = 47/82 (57%), Gaps = 1/82 (1%)

Query: 108 PRGTGGPM-RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA 166
            R    P   L +  L    TE  LR +F  +G I ++ ++ D  + RS+G+ F+ F + 
Sbjct: 8   NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 67

Query: 167 DDAKKAQEQLNGFELAGRPMKV 188
           DDAK+A+E+ NG EL GR ++V
Sbjct: 68  DDAKEAKERANGMELDGRRIRV 89

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 59.1 bits (144), Expect = 2e-11
 Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 1/85 (1%)

Query: 11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
                  +    LS     RDL E FS  G + DV ++   ++RR +G A++ F++ + 
Sbjct: 10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 69

Query: 71 VPLAM-GLNGQKLLGIPIIVQPTQA 94
             A    NG +L G  I V    +
Sbjct: 70 AKEAKERANGMELDGRRIRVSGPSS 94

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score =  120 bits (302), Expect = 6e-34
 Identities = 27/97 (27%), Positives = 48/97 (49%), Gaps = 3/97 (3%)

Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTG---RSKGYGFITFHSA 166
           G+ G   L+I +L+F+ TE+ L+G+F   G I +  +    +      S G+GF+ +   
Sbjct: 1   GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60

Query: 167 DDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
           + A+KA +QL G  + G  ++V       +   G  S
Sbjct: 61  EQAQKALKQLQGHTVDGHKLEVRISERATKPASGPSS 97

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 51.9 bits (125), Expect = 7e-09
 Identities = 18/90 (20%), Positives = 34/90 (37%), Gaps = 4/90 (4%)

Query: 15  DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLIT---CNKTRRFKGIAYIEFKDPESV 71
            +  +F   L+       L+  FS VG ++   +             G  ++E+K PE  
Sbjct: 4   GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63

Query: 72  PLAM-GLNGQKLLGIPIIVQPTQAEKNRAG 100
             A+  L G  + G  + V+ ++     A 
Sbjct: 64  QKALKQLQGHTVDGHKLEVRISERATKPAS 93

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score =  120 bits (303), Expect = 6e-34
 Identities = 31/106 (29%), Positives = 52/106 (49%), Gaps = 1/106 (0%)

Query: 89  VQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMV 148
           +   +  +N   + L     R   G   L++ S+H    ED ++  F  +G+I NI L +
Sbjct: 2   IHSYERVRNEDDDELEPGPQRSVEG-WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL 60

Query: 149 DPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR 194
           D  TG SKGY  + + +   A  A+E LNG E+ G+ ++V     +
Sbjct: 61  DRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK 106

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 59.6 bits (145), Expect = 2e-11
 Identities = 17/76 (22%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 15  DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
           +   +F   + +  +  +++E F   G+++++ L    +T   KG A +E++  +    A
Sbjct: 25  EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84

Query: 75  M-GLNGQKLLGIPIIV 89
              LNG +++G  I V
Sbjct: 85  KEALNGAEIMGQTIQV 100

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score =  119 bits (300), Expect = 1e-33
 Identities = 28/88 (31%), Positives = 43/88 (48%), Gaps = 5/88 (5%)

Query: 112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
                L   +L FNITED L+ +FE   +I      +    G+SKG  +I F S  DA+K
Sbjct: 14  RAARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEK 68

Query: 172 AQEQLNGFELAGRPMKVGTVTDRNESVG 199
             E+  G E+ GR + +    ++  + G
Sbjct: 69  NLEEKQGAEIDGRSVSLYYTGEKGGTRG 96

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 63.8 bits (156), Expect = 4e-13
 Identities = 26/92 (28%), Positives = 40/92 (43%), Gaps = 6/92 (6%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
           S + R ART+    LS  I   +L+E F    ++R V      +  + KGIAYIEFK   
Sbjct: 10  SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEA 64

Query: 70  SVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAG 100
                +    G ++ G  + +  T  +    G
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYYTGEKGGTRG 96

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score =  120 bits (302), Expect = 1e-33
 Identities = 27/113 (23%), Positives = 49/113 (43%), Gaps = 3/113 (2%)

Query: 84  GIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDN 143
           G  +   P + + +   +        G     +L + +L F +++  ++ +F  FG +  
Sbjct: 7   GQQMGRDPDKWQHDLFDSGCGG--GEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKK 64

Query: 144 IQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
             +  D  +GRS G   + F    DA KA +Q  G  L GRPM +  V  + +
Sbjct: 65  AAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQID 116

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 52.4 bits (126), Expect = 8e-09
 Identities = 16/76 (21%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 24  LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKL 82
           L   +   D++E F+  G ++   +   +++ R  G A + F+       AM    G  L
Sbjct: 43  LDFGVSDADIQELFAEFGTLKKAAVDY-DRSGRSLGTADVHFERRADALKAMKQYKGVPL 101

Query: 83  LGIPIIVQPTQAEKNR 98
            G P+ +Q   ++ + 
Sbjct: 102 DGRPMDIQLVASQIDL 117

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score =  118 bits (297), Expect = 2e-33
 Identities = 29/81 (35%), Positives = 46/81 (56%), Gaps = 5/81 (6%)

Query: 113 GPM-----RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
           G M      LY+G L   + + +L   F PFG I +IQ+ +D +T + +G+ F+ F  A+
Sbjct: 1   GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60

Query: 168 DAKKAQEQLNGFELAGRPMKV 188
           DA  A + +N  EL GR ++V
Sbjct: 61  DAAAAIDNMNESELFGRTIRV 81

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 60.2 bits (147), Expect = 6e-12
 Identities = 18/80 (22%), Positives = 37/80 (46%), Gaps = 1/80 (1%)

Query: 11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
                R ++   L++ +  + L   F   G + D+++    +T + +G A++EF+  E 
Sbjct: 2  SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61

Query: 71 VPLAM-GLNGQKLLGIPIIV 89
             A+  +N  +L G  I V
Sbjct: 62 AAAAIDNMNESELFGRTIRV 81

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score =  118 bits (298), Expect = 4e-33
 Identities = 29/90 (32%), Positives = 46/90 (51%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
              LY+G L   + + +L   F PFG I +IQ+ +D +T + +G+ F+ F  A+DA  A 
Sbjct: 12  KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 71

Query: 174 EQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
           + +N  EL GR ++V           G  S
Sbjct: 72  DNMNESELFGRTIRVNLAKPMRIKESGPSS 101

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 60.3 bits (147), Expect = 7e-12
 Identities = 20/96 (20%), Positives = 42/96 (43%), Gaps = 1/96 (1%)

Query: 6   SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
           S   S      R ++   L++ +  + L   F   G + D+++    +T + +G A++EF
Sbjct: 2   SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61

Query: 66  KDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAG 100
           +  E    A+  +N  +L G  I V   +  + +  
Sbjct: 62  ELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKES 97

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score =  118 bits (298), Expect = 4e-33
 Identities = 32/104 (30%), Positives = 59/104 (56%), Gaps = 2/104 (1%)

Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
           G++  +        P RL++ ++ F   +  LR +F  FGKI +++++ +     SKG+G
Sbjct: 1   GSSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFG 58

Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
           F+TF ++ DA +A+E+L+G  + GR ++V   T R  +  G  S
Sbjct: 59  FVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSGPSS 102

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 55.0 bits (133), Expect = 6e-10
 Identities = 23/94 (24%), Positives = 36/94 (38%), Gaps = 3/94 (3%)

Query: 6  SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
          S   S  +   + +    +  R R  DL + F   GK+ DV +I     R  KG  ++ F
Sbjct: 5  SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF--NERGSKGFGFVTF 62

Query: 66 KDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
          ++      A   L+G  + G  I V    A    
Sbjct: 63 ENSADADRAREKLHGTVVEGRKIEVNNATARVMT 96

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score =  118 bits (298), Expect = 4e-33
 Identities = 31/94 (32%), Positives = 47/94 (50%), Gaps = 6/94 (6%)

Query: 107 QPRGTGGPMR------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGF 160
           Q     GP R      L++  +H   TE+ +   F  +G+I NI L +D  TG  KGY  
Sbjct: 10  QDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTL 69

Query: 161 ITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR 194
           + + +  +A+ A E LNG +L G+P+ V     R
Sbjct: 70  VEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVR 103

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 60.0 bits (146), Expect = 1e-11
 Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
          +   +F   + +     D+ + F+  G+++++ L    +T   KG   +E++  +    A
Sbjct: 22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81

Query: 75 M-GLNGQKLLGIPIIV 89
          M GLNGQ L+G PI V
Sbjct: 82 MEGLNGQDLMGQPISV 97

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score =  118 bits (297), Expect = 6e-33
 Identities = 30/109 (27%), Positives = 60/109 (55%), Gaps = 5/109 (4%)

Query: 89  VQPTQAEKNRAGNTLP---NLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQ 145
           +  +    + +   +P   ++       P RL++ ++ F   +  LR +F  FGKI +++
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVE 60

Query: 146 LMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR 194
           ++ +     SKG+GF+TF ++ DA +A+E+L+G  + GR ++V   T R
Sbjct: 61  IIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 52.7 bits (127), Expect = 5e-09
 Identities = 22/90 (24%), Positives = 37/90 (41%), Gaps = 3/90 (3%)

Query: 1   MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
           + P  S   +  +   + +    +  R R  DL + F   GK+ DV +I     R  KG 
Sbjct: 14  LVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF--NERGSKGF 71

Query: 61  AYIEFKDPESVPLAM-GLNGQKLLGIPIIV 89
            ++ F++      A   L+G  + G  I V
Sbjct: 72  GFVTFENSADADRAREKLHGTVVEGRKIEV 101

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score =  116 bits (294), Expect = 1e-32
 Identities = 27/85 (31%), Positives = 42/85 (49%), Gaps = 1/85 (1%)

Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
             G     +L + +L F +++  ++ +F  FG +    +  D  +GRS G   + F    
Sbjct: 23  GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKA 81

Query: 168 DAKKAQEQLNGFELAGRPMKVGTVT 192
           DA KA +Q NG  L GRPM +  VT
Sbjct: 82  DALKAMKQYNGVPLDGRPMNIQLVT 106

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 2/68 (2%)

Query: 24  LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKL 82
           L   +   D++E F+  G ++   +   +++ R  G A + F+       AM   NG  L
Sbjct: 37  LDFGVSDADIQELFAEFGTLKKAAVHY-DRSGRSLGTADVHFERKADALKAMKQYNGVPL 95

Query: 83  LGIPIIVQ 90
            G P+ +Q
Sbjct: 96  DGRPMNIQ 103

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score =  114 bits (289), Expect = 5e-32
 Identities = 39/96 (40%), Positives = 52/96 (54%), Gaps = 2/96 (2%)

Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKI-DNIQLMVDPDTGRSKGYGFITFHSADD 168
           G+ G   ++IG+L   I E +L   F  FG I    ++M DPDTG SKGY FI F S D 
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60

Query: 169 AKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           +  A E +NG  L  RP+ V     ++   G GPS+
Sbjct: 61  SDAAIEAMNGQYLCNRPITVSYAFKKDSK-GSGPSS 95

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 46.8 bits (112), Expect = 4e-07
 Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKV-RDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
           IF   L   I  + L + FS+ G + +  +++    T   KG A+I F   ++   A+ 
Sbjct: 7  GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 76 GLNGQKLLGIPIIVQPTQAEKNR 98
           +NGQ L   PI V     + ++
Sbjct: 67 AMNGQYLCNRPITVSYAFKKDSK 89

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score =  115 bits (289), Expect = 5e-32
 Identities = 26/74 (35%), Positives = 41/74 (55%)

Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
             +Y+ +L F++T + L  IF  +GK+  + +M D DT +SKG  FI F   D A+    
Sbjct: 17  STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76

Query: 175 QLNGFELAGRPMKV 188
            +N  +L GR +K 
Sbjct: 77  AINNKQLFGRVIKA 90

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 61.9 bits (151), Expect = 2e-12
 Identities = 24/87 (27%), Positives = 36/87 (41%), Gaps = 1/87 (1%)

Query: 4  AYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYI 63
            S           T++   L   +   DL   FS  GKV  V ++    TR+ KG+A+I
Sbjct: 4  GSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFI 63

Query: 64 EFKDPESVPLAM-GLNGQKLLGIPIIV 89
           F D +S       +N ++L G  I  
Sbjct: 64 LFLDKDSAQNCTRAINNKQLFGRVIKA 90

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score =  115 bits (289), Expect = 6e-32
 Identities = 31/94 (32%), Positives = 49/94 (52%), Gaps = 4/94 (4%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
            ++L+IG +  N+ E  L+ +FE FGKI  + ++ D  TG  KG  F+T+   + A KAQ
Sbjct: 13  AIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQ 72

Query: 174 EQLNG---FELAGRPMKVGTVTDRNESVGGGPSN 204
             L+         RP++V      +   G GPS+
Sbjct: 73  SALHEQKTLPGMNRPIQVKPADSESR-GGSGPSS 105

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 59.3 bits (144), Expect = 2e-11
 Identities = 25/95 (26%), Positives = 45/95 (47%), Gaps = 4/95 (4%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
             ++ DA  +F  Q+ + +  +DL+  F   GK+ ++ ++    T   KG A++ + + E
Sbjct: 7   GMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERE 66

Query: 70  SVPLAM-GLNGQKLL---GIPIIVQPTQAEKNRAG 100
           S   A   L+ QK L     PI V+P  +E     
Sbjct: 67  SALKAQSALHEQKTLPGMNRPIQVKPADSESRGGS 101

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score =  114 bits (287), Expect = 8e-32
 Identities = 28/79 (35%), Positives = 47/79 (59%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            L++G L+ N+ ++ LR  F+ F    +  +M D  TG S+GYGF++F S DDA+ A + 
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62

Query: 176 LNGFELAGRPMKVGTVTDR 194
           + G +L GRP+++      
Sbjct: 63  MQGQDLNGRPLRINWAAKL 81

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 52.9 bits (128), Expect = 2e-09
 Identities = 14/72 (19%), Positives = 27/72 (37%), Gaps = 1/72 (1%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
          +F   L+  +    L   F          ++   +T   +G  ++ F   +    AM  +
Sbjct: 4  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63

Query: 78 NGQKLLGIPIIV 89
           GQ L G P+ +
Sbjct: 64 QGQDLNGRPLRI 75

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score =  116 bits (292), Expect = 8e-32
 Identities = 28/130 (21%), Positives = 46/130 (35%), Gaps = 2/130 (1%)

Query: 77  LNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFE 136
           L  Q +   P + Q    + N     +             +Y+GS  +  T+  L  +  
Sbjct: 18  LYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIR 77

Query: 137 PFGKID--NIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR 194
             G  D   ++   +   G+SKGY  +   S +   K  E L G  L G  + V   T +
Sbjct: 78  SIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ 137

Query: 195 NESVGGGPSN 204
           N S     + 
Sbjct: 138 NLSQFEAQAR 147

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 55.3 bits (133), Expect = 1e-09
 Identities = 19/111 (17%), Positives = 35/111 (31%), Gaps = 3/111 (2%)

Query: 1   MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVG--KVRDVRLITCNKTRRFK 58
             PA     S        ++    S     + L +   S+G   V +++        + K
Sbjct: 40  KTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSK 99

Query: 59  GIAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQP 108
           G A +      SV   +  L G+ L G  + V+P   +           + 
Sbjct: 100 GYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKRE 150

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score =  113 bits (286), Expect = 2e-31
 Identities = 29/98 (29%), Positives = 45/98 (45%), Gaps = 5/98 (5%)

Query: 107 QPRGTGGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS 165
                 G  + L + +L ++ TE+ L+ +FE    I     +     G+SKGY FI F S
Sbjct: 7   GNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEFAS 62

Query: 166 ADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
            +DAK+A    N  E+ GR +++     R     G  S
Sbjct: 63  FEDAKEALNSCNKREIEGRAIRLELQGPRGSPNSGPSS 100

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 54.6 bits (132), Expect = 8e-10
 Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 5/81 (6%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
          S    +++T+    LS       L+E F     ++    +  N+  + KG A+IEF   E
Sbjct: 9  STWSGESKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFE 64

Query: 70 SVPLAM-GLNGQKLLGIPIIV 89
              A+   N +++ G  I +
Sbjct: 65 DAKEALNSCNKREIEGRAIRL 85

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score =  113 bits (286), Expect = 2e-31
 Identities = 32/105 (30%), Positives = 50/105 (47%), Gaps = 3/105 (2%)

Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
           G++  +   R       + + +L  +  E  L+ +F PFG I  I L  D  TG+SKG+ 
Sbjct: 1   GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60

Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           FI+FH  +DA +A   ++GF      + V        S   GPS+
Sbjct: 61  FISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNS---GPSS 102

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 61.9 bits (151), Expect = 2e-12
 Identities = 24/92 (26%), Positives = 38/92 (41%), Gaps = 1/92 (1%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
           +    D  TI    LS+  R  DL+E F   G +  + L     T + KG A+I F   E
Sbjct: 9   NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 68

Query: 70  SVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAG 100
               A+ G++G     + + V+  +   N   
Sbjct: 69  DAARAIAGVSGFGYDHLILNVEWAKPSTNSGP 100

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score =  113 bits (284), Expect = 4e-31
 Identities = 27/96 (28%), Positives = 49/96 (51%), Gaps = 1/96 (1%)

Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
                G + L + +L +  + D LR +FE +G++ ++ +  +P T   +G+ F+ FH   
Sbjct: 7   GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRR 66

Query: 168 DAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
           DA+ A+  ++G EL GR ++V            GPS
Sbjct: 67  DAQDAEAAMDGAELDGRELRVQVARYGRRD-LSGPS 101

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 64.2 bits (157), Expect = 3e-13
 Identities = 24/97 (24%), Positives = 39/97 (40%), Gaps = 3/97 (3%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
            P+     T+    L+ R     L   F   G+V DV +     T+  +G A++ F D  
Sbjct: 7   GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRR 66

Query: 70  SVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPN 105
               A   ++G +L G  + VQ   A   R   + P+
Sbjct: 67  DAQDAEAAMDGAELDGRELRVQ--VARYGRRDLSGPS 101

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score =  111 bits (281), Expect = 6e-31
 Identities = 25/91 (27%), Positives = 48/91 (52%), Gaps = 2/91 (2%)

Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           G+ G  ++++ +L F+ T  ML+  F   G +    + ++   G+SKG G + F S + A
Sbjct: 4   GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVA 61

Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNESVGG 200
           ++A   +NG +L+GR + V    + +    G
Sbjct: 62  ERACRMMNGMKLSGREIDVRIDRNASGPSSG 92

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 49.5 bits (119), Expect = 3e-08
 Identities = 24/93 (25%), Positives = 38/93 (40%), Gaps = 4/93 (4%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
           S     A  IF   L      + L++ F+  G V    +    +  + KG   ++F+ PE
Sbjct: 2   SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVKFESPE 59

Query: 70  SVPLAM-GLNGQKLLGIPIIVQPTQ-AEKNRAG 100
               A   +NG KL G  I V+  + A    +G
Sbjct: 60  VAERACRMMNGMKLSGREIDVRIDRNASGPSSG 92

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score =  112 bits (283), Expect = 8e-31
 Identities = 31/93 (33%), Positives = 51/93 (54%), Gaps = 1/93 (1%)

Query: 97  NRAGNTLPNLQPRGTGGPM-RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRS 155
            + G    ++  R    P   L +  L    TE  LR +F  +G I ++ ++ D  + RS
Sbjct: 28  QQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRS 87

Query: 156 KGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
           +G+ F+ F + DDAK+A+E+ NG EL GR ++V
Sbjct: 88  RGFAFVYFENVDDAKEAKERANGMELDGRRIRV 120

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 60.9 bits (148), Expect = 9e-12
 Identities = 25/99 (25%), Positives = 40/99 (40%), Gaps = 3/99 (3%)

Query: 2   RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIA 61
           R +              +    LS     RDL E FS  G + DV ++   ++RR +G A
Sbjct: 32  RGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 91

Query: 62  YIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRA 99
           ++ F++ +    A    NG +L G  I V    +   R 
Sbjct: 92  FVYFENVDDAKEAKERANGMELDGRRIRVD--FSITKRP 128

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score =  111 bits (280), Expect = 1e-30
 Identities = 24/93 (25%), Positives = 49/93 (52%), Gaps = 2/93 (2%)

Query: 107 QPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA 166
           +   +  P  L+IG+L+ N +   L+         +++ ++ D  TG ++ +G++ F SA
Sbjct: 10  EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESA 68

Query: 167 DDAKKAQEQLNGFELAGRPMKVGTVTDRNESVG 199
           +D +KA E L G ++ G  +K+     R+ + G
Sbjct: 69  EDLEKALE-LTGLKVFGNEIKLEKPKGRDGTRG 100

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 68.4 bits (168), Expect = 9e-15
 Identities = 17/92 (18%), Positives = 36/92 (39%), Gaps = 1/92 (1%)

Query: 9   LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDP 68
              E      +F   L+      +L+   S +    D+ ++   +T   +   Y++F+  
Sbjct: 10  EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVD-VRTGTNRKFGYVDFESA 68

Query: 69  ESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAG 100
           E +  A+ L G K+ G  I ++  +      G
Sbjct: 69  EDLEKALELTGLKVFGNEIKLEKPKGRDGTRG 100

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score =  111 bits (280), Expect = 1e-30
 Identities = 15/79 (18%), Positives = 36/79 (45%)

Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           G      +    L+ N+ E  L+ +   +G+++ +++++ P T +  G   + F S   A
Sbjct: 2   GQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGA 61

Query: 170 KKAQEQLNGFELAGRPMKV 188
           K+  + L+   + G  +  
Sbjct: 62  KETVKNLHLTSVMGNIIHA 80

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 69.3 bits (170), Expect = 5e-15
 Identities = 20/103 (19%), Positives = 40/103 (38%), Gaps = 9/103 (8%)

Query: 17  RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
           + +   +L+  +R   L++     G+V +V ++   +TR+  G+A + F         + 
Sbjct: 7   KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 76  GLNGQKLLGIPIIVQ--------PTQAEKNRAGNTLPNLQPRG 110
            L+   ++G  I  Q            E    G+  P   P G
Sbjct: 67  NLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGSYTPQTVPTG 109

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score =  110 bits (278), Expect = 2e-30
 Identities = 30/90 (33%), Positives = 52/90 (57%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
             +L++G L F+  E  L  +F  +G+I  + ++ D +T RS+G+GF+TF + DDAK A 
Sbjct: 12  EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 71

Query: 174 EQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
             +NG  + GR ++V      +++  G  S
Sbjct: 72  MAMNGKSVDGRQIRVDQAGKSSDNRSGPSS 101

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 58.4 bits (142), Expect = 4e-11
 Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 1/85 (1%)

Query: 6  SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
          S   S    D   +F   LS     + LE+ FS  G++ +V ++   +T+R +G  ++ F
Sbjct: 2  SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61

Query: 66 KDPESVPLAM-GLNGQKLLGIPIIV 89
          ++ +    AM  +NG+ + G  I V
Sbjct: 62 ENIDDAKDAMMAMNGKSVDGRQIRV 86

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score =  111 bits (279), Expect = 3e-30
 Identities = 30/110 (27%), Positives = 54/110 (49%), Gaps = 7/110 (6%)

Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
           G++  +  P        ++I +L F+  E+ L  + + FG +  +++++ PDT  SKG  
Sbjct: 1   GSSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCA 60

Query: 160 FITFHSADDAKKAQEQLN------GFELAGRPMKVGTVTDRNESVGGGPS 203
           F  F + + A+K     +      G +L GR +KV     R+E+   GPS
Sbjct: 61  FAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEA-ASGPS 109

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 58.5 bits (142), Expect = 5e-11
 Identities = 23/101 (22%), Positives = 36/101 (35%), Gaps = 7/101 (6%)

Query: 6   SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
           S  L  +  + +T+F   LS       L E     G ++ VR++    T   KG A+ +F
Sbjct: 5   SSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQF 64

Query: 66  KDPESVPLAM-------GLNGQKLLGIPIIVQPTQAEKNRA 99
              E+    +          G KL G  + V         A
Sbjct: 65  MTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA 105

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score =  112 bits (282), Expect = 3e-30
 Identities = 28/137 (20%), Positives = 52/137 (37%), Gaps = 1/137 (0%)

Query: 53  KTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTG 112
             +  KG    E  D  +                        +         +       
Sbjct: 8   NGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDV 67

Query: 113 GPM-RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
             M  L + +L +  + D LR +FE +G++ ++ +  D  T  S+G+ F+ FH   DA+ 
Sbjct: 68  EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127

Query: 172 AQEQLNGFELAGRPMKV 188
           A + ++G  L GR ++V
Sbjct: 128 AMDAMDGAVLDGRELRV 144

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 62.6 bits (152), Expect = 4e-12
 Identities = 20/92 (21%), Positives = 36/92 (39%), Gaps = 1/92 (1%)

Query: 11  PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
            +     ++    L+ R     L   F   G+V DV +     T+  +G A++ F D   
Sbjct: 65  MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 124

Query: 71  VPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGN 101
              AM  ++G  L G  + VQ  +  +    +
Sbjct: 125 AEDAMDAMDGAVLDGRELRVQMARYGRPPDSH 156

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score =  112 bits (282), Expect = 3e-30
 Identities = 28/106 (26%), Positives = 49/106 (46%)

Query: 89  VQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMV 148
              +        +      P+ +     L++ S+H    ED ++  F  +G+I NI L +
Sbjct: 47  AIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL 106

Query: 149 DPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR 194
           D  TG SKGY  + + +   A  A+E LNG E+ G+ ++V     +
Sbjct: 107 DRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK 152

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 61.0 bits (148), Expect = 2e-11
 Identities = 17/88 (19%), Positives = 40/88 (45%), Gaps = 1/88 (1%)

Query: 15  DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
           +   +F   + +  +  +++E F   G+++++ L    +T   KG A +E++  +    A
Sbjct: 71  EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130

Query: 75  M-GLNGQKLLGIPIIVQPTQAEKNRAGN 101
              LNG +++G  I V     +  +   
Sbjct: 131 KEALNGAEIMGQTIQVDWCFVKGPKRVK 158

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score =  115 bits (289), Expect = 4e-30
 Identities = 41/208 (19%), Positives = 74/208 (35%), Gaps = 30/208 (14%)

Query: 2   RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIA 61
             ++             +F   L   I   D +  F   G+  +V +       R +G  
Sbjct: 8   IKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN------RDRGFG 61

Query: 62  YIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIG 120
           +I  +      +A   L+G  L   P+ +                    G      L + 
Sbjct: 62  FIRLESRTLAEIAKAELDGTILKSRPLRI---------------RFATHGA----ALTVK 102

Query: 121 SLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN-GF 179
           +L   ++ ++L   F  FG ++   ++VD D GR+ G GF+ F +   A+KA E+   G 
Sbjct: 103 NLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGA 161

Query: 180 ELAGRPMKVGTVT--DRNESVGGGPSNL 205
            L     +   V   ++ +   G P  L
Sbjct: 162 FLLTTTPRPVIVEPMEQFDDEDGLPEKL 189

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 92.4 bits (230), Expect = 9e-22
 Identities = 27/99 (27%), Positives = 52/99 (52%), Gaps = 7/99 (7%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL++G+L  +ITE+  + +FE +G+   + +       R +G+GFI   S   A+ A+ +
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFIN------RDRGFGFIRLESRTLAEIAKAE 77

Query: 176 LNGFELAGRPMKVGTVT-DRNESVGGGPSNLDTDEMERA 213
           L+G  L  RP+++   T     +V      +  + +E+A
Sbjct: 78  LDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQA 116

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score =  112 bits (281), Expect = 5e-30
 Identities = 25/89 (28%), Positives = 42/89 (47%), Gaps = 1/89 (1%)

Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
             G     +L + +L F +++  ++ +F  FG +    +  D  +GRS G   + F    
Sbjct: 82  GEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRA 140

Query: 168 DAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
           DA KA +Q  G  L GRPM +  V  + +
Sbjct: 141 DALKAMKQYKGVPLDGRPMDIQLVASQID 169

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 53.3 bits (128), Expect = 1e-08
 Identities = 16/76 (21%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 24  LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKL 82
           L   +   D++E F+  G ++   +   +++ R  G A + F+       AM    G  L
Sbjct: 96  LDFGVSDADIQELFAEFGTLKKAAVDY-DRSGRSLGTADVHFERRADALKAMKQYKGVPL 154

Query: 83  LGIPIIVQPTQAEKNR 98
            G P+ +Q   ++ + 
Sbjct: 155 DGRPMDIQLVASQIDL 170

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score =  108 bits (273), Expect = 2e-29
 Identities = 29/98 (29%), Positives = 54/98 (55%), Gaps = 7/98 (7%)

Query: 110 GTGGPMR-------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFIT 162
           G+ GP+        +Y+G L   ++E +L  +F   G + N  +  D  TG+ +GYGF+ 
Sbjct: 4   GSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVE 63

Query: 163 FHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGG 200
           F S +DA  A + ++  +L G+P++V   +  N+++ G
Sbjct: 64  FLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSG 101

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 64.6 bits (158), Expect = 3e-13
 Identities = 21/90 (23%), Positives = 35/90 (38%), Gaps = 1/90 (1%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
            E     T++   L +++    L E F   G V +  +     T + +G  ++EF   E
Sbjct: 9  ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 68

Query: 70 SVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
              A+  ++  KL G PI V    A    
Sbjct: 69 DADYAIKIMDMIKLYGKPIRVNKASAHNKN 98

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score =  109 bits (275), Expect = 2e-29
 Identities = 27/98 (27%), Positives = 50/98 (51%)

Query: 91  PTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDP 150
            T  ++   G+      P    G   L + +L +  + D LR +FE +G++ ++ +  D 
Sbjct: 24  MTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDR 83

Query: 151 DTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
            T  S+G+ F+ FH   DA+ A + ++G  L GR ++V
Sbjct: 84  YTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 121

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 61.3 bits (149), Expect = 7e-12
 Identities = 21/92 (22%), Positives = 37/92 (40%), Gaps = 1/92 (1%)

Query: 11  PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
           P+     ++    L+ R     L   F   G+V DV +     T+  +G A++ F D   
Sbjct: 42  PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 101

Query: 71  VPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGN 101
              AM  ++G  L G  + VQ  +  +    +
Sbjct: 102 AEDAMDAMDGAVLDGRELRVQMARYGRPPDSH 133

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score =  108 bits (271), Expect = 4e-29
 Identities = 26/100 (26%), Positives = 46/100 (46%)

Query: 89  VQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMV 148
             P  +    A       +         L+I  L    T+  L   F PFG + + ++ +
Sbjct: 15  TSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFI 74

Query: 149 DPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
           D  T  SK +GF++F + D A+ A + +NGF++  + +KV
Sbjct: 75  DKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV 114

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 49.3 bits (118), Expect = 9e-08
 Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 19  IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
           +F   L Q     DL   F   G V   ++    +T   K   ++ F +P+S  +A+  +
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102

Query: 78  NGQKLLGIPIIVQ 90
           NG ++    + VQ
Sbjct: 103 NGFQVGTKRLKVQ 115

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score =  111 bits (279), Expect = 4e-29
 Identities = 36/160 (22%), Positives = 58/160 (36%), Gaps = 9/160 (5%)

Query: 64  EFKDPESVPL------AMGLNGQKLLGIPIIVQPTQAEKNRAGNTL-PNLQPRGTGGPMR 116
           E+   + + L          NG        +        +  G    PN+    TG  + 
Sbjct: 11  EYGGHDQIDLYDDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIA 70

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKID--NIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           LYIG+L +  T++ L       G  D   I+   +   G+SKG+  +   S   +KK  +
Sbjct: 71  LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 130

Query: 175 QLNGFELAGRPMKVGTVTDRNESVGGGPSNLDTDEMERAG 214
            L   EL G+   V  V  +  S     S   T   + +G
Sbjct: 131 LLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSG 170

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 54.7 bits (131), Expect = 7e-09
 Identities = 21/160 (13%), Positives = 41/160 (25%), Gaps = 7/160 (4%)

Query: 2   RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVG--KVRDVRLITCNKTRRFKG 59
           + A  + +         ++   L+      DL E   S+G   + +++        + KG
Sbjct: 54  KGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKG 113

Query: 60  IAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMR-- 116
            A +      S    M  L  ++L G   +V P   +             +         
Sbjct: 114 FALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGK 173

Query: 117 --LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGR 154
                GS      +        P       +       G 
Sbjct: 174 AGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGG 213

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score =  107 bits (269), Expect = 5e-29
 Identities = 24/89 (26%), Positives = 46/89 (51%), Gaps = 3/89 (3%)

Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
           P G   P  +++G +   + E  +R  F  +G +  ++++ D  TG SKGYGF++F++  
Sbjct: 3   PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDV 61

Query: 168 DAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
           D +K  E  +     G+ +K+G    +  
Sbjct: 62  DVQKIVE--SQINFHGKKLKLGPAIRKQN 88

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 23/100 (23%), Positives = 48/100 (48%), Gaps = 6/100 (6%)

Query: 11  PEERD-ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
           PE +    T+F   +  R+   ++  FF+  G V++V++IT ++T   KG  ++ F +  
Sbjct: 3   PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIIT-DRTGVSKGYGFVSFYNDV 61

Query: 70  SVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPR 109
            V   +  +     G  + + P   ++N +     ++QPR
Sbjct: 62  DVQKIV-ESQINFHGKKLKLGPAIRKQNLSTY---HVQPR 97

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score =  106 bits (268), Expect = 6e-29
 Identities = 22/91 (24%), Positives = 41/91 (45%), Gaps = 1/91 (1%)

Query: 99  AGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGY 158
             +    + P        +++G+L   + E++L  +F   G +  + +  D + G+ K +
Sbjct: 1   GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSF 59

Query: 159 GFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
           GF+ F   +    A   LNG  L GRP+ V 
Sbjct: 60  GFVCFKHPESVSYAIALLNGIRLYGRPINVS 90

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 63.4 bits (155), Expect = 5e-13
 Identities = 29/88 (32%), Positives = 41/88 (46%), Gaps = 2/88 (2%)

Query: 3  PAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAY 62
             S     +E   RT+F   L  R+R   L E F   G +  V +   ++  + K   +
Sbjct: 3  SGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICK-DREGKPKSFGF 61

Query: 63 IEFKDPESVPLAM-GLNGQKLLGIPIIV 89
          + FK PESV  A+  LNG +L G PI V
Sbjct: 62 VCFKHPESVSYAIALLNGIRLYGRPINV 89

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score =  107 bits (269), Expect = 9e-29
 Identities = 31/101 (30%), Positives = 47/101 (46%), Gaps = 6/101 (5%)

Query: 110 GTGGPMR------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITF 163
              GP R      L++  +H   TE+ +   F  +G+I NI L +D  TG  KGY  + +
Sbjct: 12  DEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 71

Query: 164 HSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
            +  +A+ A E LNG +L G+P+ V     R    G     
Sbjct: 72  ETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGG 112

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 59.7 bits (145), Expect = 3e-11
 Identities = 25/103 (24%), Positives = 44/103 (42%), Gaps = 3/103 (2%)

Query: 15  DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
           +   +F   + +     D+ + F+  G+++++ L    +T   KG   +E++  +    A
Sbjct: 21  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 80

Query: 75  M-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMR 116
           M GLNGQ L+G PI V          G        R +  P R
Sbjct: 81  MEGLNGQDLMGQPISVDWCFVRGPPKGKRRGG--RRRSRSPDR 121

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score =  106 bits (266), Expect = 1e-28
 Identities = 28/96 (29%), Positives = 43/96 (44%), Gaps = 8/96 (8%)

Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           G+ G  +LYIG+L   +T D LR +F            +        GY F+ +   + A
Sbjct: 4   GSSGMNKLYIGNLSPAVTADDLRQLFGDRKLP------LAGQVLLKSGYAFVDYPDQNWA 57

Query: 170 KKAQEQLNG-FELAGRPMKVGTVTDRNESVGGGPSN 204
            +A E L+G  EL G+ M+V     +      GPS+
Sbjct: 58  IRAIETLSGKVELHGKIMEVDYSVSKKLR-SSGPSS 92

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 49.9 bits (120), Expect = 3e-08
 Identities = 16/86 (18%), Positives = 34/86 (39%), Gaps = 8/86 (9%)

Query: 17  RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
             ++   LS  +   DL + F         +           G A++++ D      A+ 
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQ------VLLKSGYAFVDYPDQNWAIRAIE 62

Query: 76  GLNGQ-KLLGIPIIVQPTQAEKNRAG 100
            L+G+ +L G  + V  + ++K R+ 
Sbjct: 63  TLSGKVELHGKIMEVDYSVSKKLRSS 88

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score =  106 bits (266), Expect = 1e-28
 Identities = 24/110 (21%), Positives = 47/110 (42%), Gaps = 6/110 (5%)

Query: 94  AEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTG 153
           +  N       ++  + +     +Y G +   +T+ ++R  F PFG+I  I++  +    
Sbjct: 5   SSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE---- 60

Query: 154 RSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
             KGY F+ F + + A  A   +NG  + G  +K     +  +   G  S
Sbjct: 61  --KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGPSS 108

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 48.1 bits (115), Expect = 2e-07
 Identities = 20/112 (17%), Positives = 46/112 (41%), Gaps = 15/112 (13%)

Query: 3   PAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAY 62
             + D ++       T++C  ++  +  + + + FS  G++ ++R+         KG ++
Sbjct: 12  LRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSF 65

Query: 63  IEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGG 113
           + F   ES   A+  +NG  + G  +        K   G   P++    + G
Sbjct: 66  VRFSTHESAAHAIVSVNGTTIEGHVV--------KCYWGKESPDMTSGPSSG 109

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score =  106 bits (266), Expect = 4e-28
 Identities = 31/111 (27%), Positives = 48/111 (43%), Gaps = 10/111 (9%)

Query: 88  IVQPTQAEKNRAG----NTLPNLQPRGTGGP-MRLYIGSLHFNITEDMLRGIFEPFGKID 142
            +   + EK R       TL   +    G P  R+Y+ +L  ++ E  L+ IF  +    
Sbjct: 14  CISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFS 73

Query: 143 NIQLMVDPD-----TGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
           +    +  D      GR KG  FI   +   A KA ++ NG+ L G+PM V
Sbjct: 74  SETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVV 124

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 53.7 bits (129), Expect = 5e-09
 Identities = 21/88 (23%), Positives = 40/88 (45%), Gaps = 6/88 (6%)

Query: 17  RTIFCMQLSQRIRTRDLEEFFSSVGKV-----RDVRLITCNKTRRFKGIAYIEFKDPESV 71
             I+   L++ ++ +DL+  F           R +  I   K  R KG A+I   + ++ 
Sbjct: 46  CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105

Query: 72  PLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
             A+   NG  L G P++VQ  ++ + +
Sbjct: 106 AKALKEANGYVLFGKPMVVQFARSARPK 133

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score =  104 bits (262), Expect = 4e-28
 Identities = 22/84 (26%), Positives = 35/84 (41%), Gaps = 2/84 (2%)

Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKID--NIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
           + LYIG+L +  T++ L       G  D   I+   +   G+SKG+  +   S   +KK 
Sbjct: 2   IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61

Query: 173 QEQLNGFELAGRPMKVGTVTDRNE 196
            + L   EL G+   V        
Sbjct: 62  MDLLPKRELHGQNPVVTPSNKLEH 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 Length = 90

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 3/70 (4%)

Query: 32 DLEEFFSSVG--KVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPII 88
          DL E   S+G   + +++        + KG A +      S    M  L  ++L G   +
Sbjct: 17 DLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPV 76

Query: 89 VQPTQAEKNR 98
          V P+   ++ 
Sbjct: 77 VTPSNKLEHH 86

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score =  104 bits (261), Expect = 6e-28
 Identities = 26/104 (25%), Positives = 50/104 (48%), Gaps = 6/104 (5%)

Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
           G++  +   +      RL++G+L  +ITE+ +R +FE +GK   + +       + KG+G
Sbjct: 1   GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFG 54

Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
           FI   +   A+ A+ +L+   L G+ ++V           G  S
Sbjct: 55  FIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSGPSS 98

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 46.5 bits (111), Expect = 5e-07
 Identities = 16/85 (18%), Positives = 28/85 (32%), Gaps = 7/85 (8%)

Query: 6  SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
          S            +F   L   I   ++ + F   GK  +V +       + KG  +I  
Sbjct: 5  SSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRL 58

Query: 66 KDPESVPLAM-GLNGQKLLGIPIIV 89
          +      +A   L+   L G  + V
Sbjct: 59 ETRTLAEIAKVELDNMPLRGKQLRV 83

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score =  103 bits (258), Expect = 2e-27
 Identities = 28/111 (25%), Positives = 47/111 (42%), Gaps = 15/111 (13%)

Query: 79  GQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPF 138
           G + +G+P  V P   +     + + +  PR T      YIG++    TE  L  +F+ F
Sbjct: 1   GSQTIGLPPQVNPQAVD-----HIIRSAPPRVT----TAYIGNIPHFATEADLIPLFQNF 51

Query: 139 GKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
           G I + +   +      KG  FI + + + A      L  F   GR ++ G
Sbjct: 52  GFILDFKHYPE------KGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTG 96

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 46.5 bits (111), Expect = 6e-07
 Identities = 13/86 (15%), Positives = 25/86 (29%), Gaps = 7/86 (8%)

Query: 3  PAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAY 62
           A    +        T +   +       DL   F + G + D +          KG  +
Sbjct: 14 QAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCF 67

Query: 63 IEFKDPESVPLAM-GLNGQKLLGIPI 87
          I++   E   + +  L      G  +
Sbjct: 68 IKYDTHEQAAVCIVALANFPFQGRNL 93

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score =  103 bits (259), Expect = 2e-27
 Identities = 28/115 (24%), Positives = 53/115 (46%), Gaps = 10/115 (8%)

Query: 99  AGNTLPNLQPRGTGGPMR---------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVD 149
             +    L  +  G             L+I  L     +  L  +F PFG + + ++ +D
Sbjct: 1   GSSGSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFID 60

Query: 150 PDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
             T  SK +GF+++ +   A+ A + +NGF++  + +KV     +N+S   GPS+
Sbjct: 61  KQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS-KSGPSS 114

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 49.6 bits (119), Expect = 6e-08
 Identities = 17/81 (20%), Positives = 36/81 (44%), Gaps = 1/81 (1%)

Query: 19  IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
           +F   L Q    +DL + F   G V   ++    +T   K   ++ + +P S   A+  +
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87

Query: 78  NGQKLLGIPIIVQPTQAEKNR 98
           NG ++    + VQ  +++ + 
Sbjct: 88  NGFQIGMKRLKVQLKRSKNDS 108

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score =  102 bits (256), Expect = 6e-27
 Identities = 32/89 (35%), Positives = 48/89 (53%), Gaps = 1/89 (1%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
           P +L+IG L+    E ML+ +F   G I  + L+ D  T +S+G+ FITF +  DAK A 
Sbjct: 7   PGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAA 65

Query: 174 EQLNGFELAGRPMKVGTVTDRNESVGGGP 202
           + +NG  L G+ +KV      +   GG  
Sbjct: 66  KDMNGKSLHGKAIKVEQAKKPSFQSGGRR 94

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 58.1 bits (141), Expect = 6e-11
 Identities = 24/111 (21%), Positives = 46/111 (41%), Gaps = 5/111 (4%)

Query: 12  EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
           E      +F   L++    + L+  F   G + +V LI  ++T + +G A+I F++P   
Sbjct: 3   EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIK-DRTSKSRGFAFITFENPADA 61

Query: 72  PLAM-GLNGQKLLGIPIIV---QPTQAEKNRAGNTLPNLQPRGTGGPMRLY 118
             A   +NG+ L G  I V   +    +         + + R   G +  +
Sbjct: 62  KNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLEHH 112

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score =  101 bits (254), Expect = 7e-27
 Identities = 28/93 (30%), Positives = 49/93 (52%), Gaps = 5/93 (5%)

Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
             +++G++ +  TE+ L+ IF   G + + +L+ D +TG+ KGYGF  +   + A  A  
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68

Query: 175 QLNGFELAGRPMKVGTVTDR-----NESVGGGP 202
            LNG E +GR ++V            +S+G G 
Sbjct: 69  NLNGREFSGRALRVDNAASEKNKEELKSLGTGA 101

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 67.7 bits (166), Expect = 2e-14
 Identities = 32/103 (31%), Positives = 51/103 (49%), Gaps = 6/103 (5%)

Query: 13  ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVP 72
           +R  R++F   +        L++ FS VG V   RL+   +T + KG  + E++D E+  
Sbjct: 5   DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64

Query: 73  LAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGP 114
            AM  LNG++  G  + V    +EKN+       L+  GTG P
Sbjct: 65  SAMRNLNGREFSGRALRVDNAASEKNK-----EELKSLGTGAP 102

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score =  101 bits (254), Expect = 1e-26
 Identities = 22/90 (24%), Positives = 38/90 (42%), Gaps = 1/90 (1%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
           P  LYI +L  ++ E  L  + +PFG++ + +++ D  +G S+G GF    S +  +   
Sbjct: 25  PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVI 83

Query: 174 EQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
              NG  +   P              G  S
Sbjct: 84  GHFNGKFIKTPPGVSAPTEPLLCKFSGPSS 113

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 15/84 (17%), Positives = 36/84 (42%), Gaps = 2/84 (2%)

Query: 11  PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
            +E+D   ++   L   +  ++LE      G+V   R++  + +   +G+ +   +  E 
Sbjct: 20  QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILR-DSSGTSRGVGFARMESTEK 78

Query: 71  VPLAM-GLNGQKLLGIPIIVQPTQ 93
               +   NG+ +   P +  PT+
Sbjct: 79  CEAVIGHFNGKFIKTPPGVSAPTE 102

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score =  100 bits (252), Expect = 1e-26
 Identities = 17/90 (18%), Positives = 44/90 (48%), Gaps = 1/90 (1%)

Query: 99  AGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGY 158
           +  +    +   +    +L+I  L F+ T++ L  I +  G + +++L+ +   G+ KG 
Sbjct: 2   SSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGL 60

Query: 159 GFITFHSADDAKKAQEQLNGFELAGRPMKV 188
            ++ + +   A +A  +++G  +    +KV
Sbjct: 61  AYVEYENESQASQAVMKMDGMTIKENIIKV 90

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 63.8 bits (156), Expect = 4e-13
 Identities = 21/89 (23%), Positives = 42/89 (47%), Gaps = 2/89 (2%)

Query: 11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
              +   +F   L       +LEE   + G V+D+RL+T N+  + KG+AY+E+++   
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVT-NRAGKPKGLAYVEYENESQ 70

Query: 71 VPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
             A+  ++G  +    I V  + +  + 
Sbjct: 71 ASQAVMKMDGMTIKENIIKVAISNSGPSS 99

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score =  103 bits (257), Expect = 3e-26
 Identities = 30/200 (15%), Positives = 59/200 (29%), Gaps = 31/200 (15%)

Query: 15  DARTIFCMQLS-QRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
           D+  +    L   ++    +   F   G V  V+    +K     G A +E  D  +V  
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVK-FMKSK----PGAAMVEMADGYAVDR 57

Query: 74  AM-GLNGQKLLGIPIIV---------------QPTQAEKNRAGNTLPNLQPRGTGGPMR- 116
           A+  LN   + G  + V                   +   +  +   N +        + 
Sbjct: 58  AITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKN 117

Query: 117 --------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADD 168
                   L+  +    +TE+    I +  G      + V          G + + S  D
Sbjct: 118 RIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSD 177

Query: 169 AKKAQEQLNGFELAGRPMKV 188
           A +    LN +++       
Sbjct: 178 ALETLGFLNHYQMKNPNGPY 197

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 64.3 bits (156), Expect = 2e-12
 Identities = 13/74 (17%), Positives = 26/74 (35%), Gaps = 6/74 (8%)

Query: 117 LYIGSLH-FNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           L +  L    +  D +  +F  +G ++ ++ M         G   +         +A   
Sbjct: 7   LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITH 61

Query: 176 LNGFELAGRPMKVG 189
           LN   + G+ M V 
Sbjct: 62  LNNNFMFGQKMNVC 75

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 46.2 bits (109), Expect = 4e-06
 Identities = 6/73 (8%), Positives = 19/73 (26%), Gaps = 1/73 (1%)

Query: 13  ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVP 72
           +  +  +        +   +  E    +G  R   +   +          +E+       
Sbjct: 120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDAL 179

Query: 73  LAM-GLNGQKLLG 84
             +  LN  ++  
Sbjct: 180 ETLGFLNHYQMKN 192

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score =   99 bits (250), Expect = 3e-26
 Identities = 33/90 (36%), Positives = 54/90 (60%), Gaps = 3/90 (3%)

Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           + LY+ +L   I ++ LR  F PFG I + ++M++   GRSKG+GF+ F S ++A KA  
Sbjct: 16  VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVT 73

Query: 175 QLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           ++NG  +A +P+ V     + E    GPS+
Sbjct: 74  EMNGRIVATKPLYVALAQRKEER-QSGPSS 102

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 44.1 bits (105), Expect = 4e-06
 Identities = 20/86 (23%), Positives = 39/86 (45%), Gaps = 4/86 (4%)

Query: 19  IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
           ++   L   I    L + FS  G +   +++   +  R KG  ++ F  PE    A+  +
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATKAVTEM 75

Query: 78  NGQKLLGIPIIVQPTQA-EKNRAGNT 102
           NG+ +   P+ V   Q  E+ ++G +
Sbjct: 76  NGRIVATKPLYVALAQRKEERQSGPS 101

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 99.7 bits (249), Expect = 5e-26
 Identities = 25/106 (23%), Positives = 47/106 (44%), Gaps = 2/106 (1%)

Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPD-TGRSKGY 158
           G++  + Q        ++ + ++ F   +  +R +F  FG++  ++L      TG  +G+
Sbjct: 1   GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60

Query: 159 GFITFHSADDAKKAQEQL-NGFELAGRPMKVGTVTDRNESVGGGPS 203
           GF+ F +  DAKKA   L +   L GR + +           G  S
Sbjct: 61  GFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSS 106

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 58.1 bits (141), Expect = 6e-11
 Identities = 17/92 (18%), Positives = 39/92 (42%), Gaps = 3/92 (3%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLIT-CNKTRRFKGIAYIEFKDP 68
            P+++    I    +  +   R++ E FS+ G+++ VRL      T   +G  +++F   
Sbjct: 9   VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 68

Query: 69  ESVPLAMG--LNGQKLLGIPIIVQPTQAEKNR 98
           +    A     +   L G  ++++   +E   
Sbjct: 69  QDAKKAFNALCHSTHLYGRRLVLEWADSEVTV 100

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 99.3 bits (248), Expect = 5e-26
 Identities = 29/101 (28%), Positives = 50/101 (49%), Gaps = 4/101 (3%)

Query: 104 PNLQPRGTGGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFIT 162
            +  P     P + L++  L  + TE+ L+   E F      +++ D +TG SKG+GF+ 
Sbjct: 4   GSSGPNARSQPSKTLFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGSSKGFGFVD 60

Query: 163 FHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
           F+S +DAK A+E +   E+ G  + +     + E   G  S
Sbjct: 61  FNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSGPSS 101

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 49.6 bits (119), Expect = 5e-08
 Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 4/85 (4%)

Query: 6  SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
          S   +   + ++T+F   LS+      L+E F         R++T  +T   KG  +++F
Sbjct: 5  SSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDF 61

Query: 66 KDPESVPLAM-GLNGQKLLGIPIIV 89
             E    A   +   ++ G  + +
Sbjct: 62 NSEEDAKAAKEAMEDGEIDGNKVTL 86

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 99.0 bits (247), Expect = 9e-26
 Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 3/73 (4%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LYI +L + IT + +  IF  +G I  I++    +T  ++G  ++ +    DAK A + L
Sbjct: 11  LYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKNAVDHL 67

Query: 177 NGFELAGRPMKVG 189
           +GF ++ R + V 
Sbjct: 68  SGFNVSNRYLVVL 80

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 68.6 bits (168), Expect = 1e-14
 Identities = 20/93 (21%), Positives = 39/93 (41%), Gaps = 6/93 (6%)

Query: 8  DLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKD 67
           L PE    R ++   L  +I   ++ + F   G +R +R+     T   +G AY+ ++D
Sbjct: 2  RLPPEVN--RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYED 56

Query: 68 PESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRA 99
                A+  L+G  +    ++V    A +   
Sbjct: 57 IFDAKNAVDHLSGFNVSNRYLVVLYYNANRAFQ 89

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 98.1 bits (245), Expect = 2e-25
 Identities = 24/97 (24%), Positives = 46/97 (47%), Gaps = 9/97 (9%)

Query: 93  QAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDT 152
            +     G+ + + Q  G     RL++     ++ E  L  IF PFG +  ++++     
Sbjct: 11  SSGLVPRGSHMHHRQ-EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL----- 64

Query: 153 GRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
               G+ F+ F  A+ A KA E+++G   A +P++V 
Sbjct: 65  ---NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV 98

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 61.5 bits (150), Expect = 3e-12
 Identities = 20/100 (20%), Positives = 43/100 (43%), Gaps = 11/100 (11%)

Query: 2   RPAYSDDLSPEERDA--RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKG 59
            P  S     +E +     +F       ++  +L E F   G +++V+++         G
Sbjct: 15  VPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NG 66

Query: 60  IAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
            A++EF++ ES   A+  ++G+     P+ V  ++    R
Sbjct: 67  FAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKR 106

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 97.9 bits (244), Expect = 2e-25
 Identities = 27/99 (27%), Positives = 44/99 (44%), Gaps = 8/99 (8%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDN--------IQLMVDPDTGRSKGYGFITFHS 165
              +++  L  N+T + +   F+  G I          I L  D +TG+ KG   ++F  
Sbjct: 7   NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 66

Query: 166 ADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
              AK A +  +G E +G P+KV   T R +   GG + 
Sbjct: 67  PPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNG 105

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 65.5 bits (160), Expect = 2e-13
 Identities = 27/101 (26%), Positives = 45/101 (44%), Gaps = 11/101 (10%)

Query: 12  EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVR--------DVRLITCNKTRRFKGIAYI 63
           +  D  TIF   L + +    + ++F  +G ++         + L T  +T + KG A +
Sbjct: 3   DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 62

Query: 64  EFKDPESVPLAM-GLNGQKLLGIPIIVQPTQ--AEKNRAGN 101
            F DP S   A+   +G++  G PI V      A+ NR G 
Sbjct: 63  SFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGG 103

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 97.3 bits (243), Expect = 3e-25
 Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 7/77 (9%)

Query: 116 RLYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
            +YI +L+  I +D L+     IF  FG+I +I +     + + +G  F+ F     A  
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS---RSLKMRGQAFVIFKEVSSATN 66

Query: 172 AQEQLNGFELAGRPMKV 188
           A   + GF    +PM++
Sbjct: 67  ALRSMQGFPFYDKPMRI 83

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 59.2 bits (144), Expect = 2e-11
 Identities = 21/93 (22%), Positives = 47/93 (50%), Gaps = 8/93 (8%)

Query: 11 PEERDARTIFCMQLSQRIRTRDLEE----FFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
          PE R   TI+   L+++I+  +L++     FS  G++ D+ +    ++ + +G A++ FK
Sbjct: 3  PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS---RSLKMRGQAFVIFK 59

Query: 67 DPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
          +  S   A+  + G      P+ +Q  + + + 
Sbjct: 60 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDI 92

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 96.9 bits (242), Expect = 4e-25
 Identities = 26/105 (24%), Positives = 51/105 (48%), Gaps = 3/105 (2%)

Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
           G++  +      G P  LY+G+L  ++TE ++  +F   G   + +++ +  +     Y 
Sbjct: 1   GSSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YC 58

Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           F+ F+   DA  A   +NG ++ G+ +KV   T  +     GPS+
Sbjct: 59  FVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQ-KSGPSS 102

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 55.7 bits (135), Expect = 4e-10
 Identities = 18/90 (20%), Positives = 42/90 (46%), Gaps = 3/90 (3%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
            ++   RT++   LS+ +    + + FS +G  +  ++IT + +       ++EF +  
Sbjct: 9  MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSND--PYCFVEFYEHR 66

Query: 70 SVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
              A+  +NG+K+LG  + V       ++
Sbjct: 67 DAAAALAAMNGRKILGKEVKVNWATTPSSQ 96

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 97.6 bits (243), Expect = 9e-25
 Identities = 22/73 (30%), Positives = 38/73 (52%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            LY+G+L F  TE+ +  +F   G I  I + +D     + G+ F+ ++S  DA+ A   
Sbjct: 41  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100

Query: 176 LNGFELAGRPMKV 188
           +NG  L  R ++ 
Sbjct: 101 INGTRLDDRIIRT 113

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 58.3 bits (141), Expect = 1e-10
 Identities = 17/89 (19%), Positives = 34/89 (38%), Gaps = 3/89 (3%)

Query: 2   RPAYSDDLSPEER--DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKG 59
           +    D+   E+    + T++   LS       + E FS  G ++ + +      +   G
Sbjct: 23  QHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG 82

Query: 60  IAYIEFKDPESVPLAM-GLNGQKLLGIPI 87
             ++E+        AM  +NG +L    I
Sbjct: 83  FCFVEYYSRADAENAMRYINGTRLDDRII 111

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 96.0 bits (239), Expect = 1e-24
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 118 YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN 177
            I S    + +  L  +F   GK+ N++  +D  TG++KG+ F+   S +DAKK  +  +
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 178 GFELAGRP-MKVGTVTD 193
           G  L  +  + + T+ D
Sbjct: 76  GKRLDLKHRLFLYTMKD 92

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 1/54 (1%)

Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLG 84
           L   FS  GKV ++       T + KG  ++E          +   +G++L  
Sbjct: 28 ALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDL 81

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 95.3 bits (238), Expect = 1e-24
 Identities = 21/74 (28%), Positives = 45/74 (60%), Gaps = 1/74 (1%)

Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
             +Y+G+L ++ T + ++ +F  FGK+ N++L+ D +T + KG+GF+     +   +A  
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIA 60

Query: 175 QLNGFELAGRPMKV 188
           +L+  +  GR ++V
Sbjct: 61  KLDNTDFMGRTIRV 74

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 54.9 bits (133), Expect = 5e-10
 Identities = 21/85 (24%), Positives = 39/85 (45%)

Query: 17  RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
           R I+   L     +  ++E FS  GKV +V+LI   +T++ KG  ++E ++         
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61

Query: 77  LNGQKLLGIPIIVQPTQAEKNRAGN 101
           L+    +G  I V     +K+   +
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSLEHH 86

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 94.5 bits (236), Expect = 2e-24
 Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            +Y+G++ +  T + L   F   G ++ + ++ D  +G  KG+ +I F   +  + +   
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA- 66

Query: 176 LNGFELAGRPMKV 188
           L+     GR +KV
Sbjct: 67  LDESLFRGRQIKV 79

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 77.6 bits (192), Expect = 4e-18
 Identities = 29/88 (32%), Positives = 39/88 (44%), Gaps = 2/88 (2%)

Query: 13  ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVP 72
           E DAR+I+   +       +LE  F   G V  V ++    +   KG AYIEF D ESV 
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 73  LAMGLNGQKLLGIPIIVQPTQAEKNRAG 100
            ++ L+     G  I V       NR G
Sbjct: 63  TSLALDESLFRGRQIKV--IPKRTNRPG 88

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 94.6 bits (236), Expect = 3e-24
 Identities = 27/93 (29%), Positives = 45/93 (48%), Gaps = 2/93 (2%)

Query: 111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAK 170
           T  P   Y+G+L FN  +  +  IF+    I +++L+ D DT + KG+ ++ F   D  K
Sbjct: 12  TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLK 70

Query: 171 KAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
           +A    +G  L  R ++V     R +   G  S
Sbjct: 71  EALT-YDGALLGDRSLRVDIAEGRKQDKSGPSS 102

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 61.5 bits (150), Expect = 3e-12
 Identities = 21/85 (24%), Positives = 36/85 (42%), Gaps = 1/85 (1%)

Query: 17  RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
            T +   L       D++  F  +  +R VRL+    T +FKG  Y+EF + +S+  A+ 
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 74

Query: 77  LNGQKLLGIPIIVQPTQAEKNRAGN 101
            +G  L    + V   +  K     
Sbjct: 75  YDGALLGDRSLRVDIAEGRKQDKSG 99

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 94.3 bits (235), Expect = 5e-24
 Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 1/88 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            +++ +L + +    L+ +F   G +    ++ D D G+S+G G +TF  + +A +A   
Sbjct: 17  TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAISM 75

Query: 176 LNGFELAGRPMKVGTVTDRNESVGGGPS 203
            NG  L  RPM V             P 
Sbjct: 76  FNGQLLFDRPMHVKMDERALPKGDFFPP 103

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 26/110 (23%), Positives = 46/110 (41%), Gaps = 3/110 (2%)

Query: 6   SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
           S       R   T+F   L  ++  + L+E FS  G V    ++  +K  + +GI  + F
Sbjct: 5   SSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILE-DKDGKSRGIGTVTF 63

Query: 66  KDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGP 114
           +       A+   NGQ L   P+ V+  +      G+  P  +P+ +G  
Sbjct: 64  EQSIEAVQAISMFNGQLLFDRPMHVKMDE-RALPKGDFFPPERPQQSGPS 112

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 94.8 bits (236), Expect = 5e-24
 Identities = 21/99 (21%), Positives = 39/99 (39%), Gaps = 1/99 (1%)

Query: 90  QPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVD 149
           + T            + + +       +Y+G++ +  T   L   F   G I+ I ++ D
Sbjct: 12  KMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCD 71

Query: 150 PDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
             +G  KGY +I F   +    A   ++     GR +KV
Sbjct: 72  KFSGHPKGYAYIEFAERNSVDAAVA-MDETVFRGRTIKV 109

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 75.9 bits (187), Expect = 4e-17
 Identities = 27/99 (27%), Positives = 42/99 (42%), Gaps = 2/99 (2%)

Query: 2   RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIA 61
            P        +E D R+++   +      +DLE  FSS G +  + ++    +   KG A
Sbjct: 22  PPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYA 81

Query: 62  YIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAG 100
           YIEF +  SV  A+ ++     G  I V P     N  G
Sbjct: 82  YIEFAERNSVDAAVAMDETVFRGRTIKVLP--KRTNMPG 118

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 96.9 bits (241), Expect = 5e-24
 Identities = 34/197 (17%), Positives = 68/197 (34%), Gaps = 34/197 (17%)

Query: 17  RTIFCMQLS-QRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM 75
             +    L+ +R+  + L   F   G V+ V+++        K  A ++  D     LAM
Sbjct: 4   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKIL-----FNKKENALVQMADGNQAQLAM 58

Query: 76  -GLNGQKLLGIPIIVQP----------------------TQAEKNRAGNTLPNLQPRGTG 112
             LNG KL G PI +                          +  +R              
Sbjct: 59  SHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFP 118

Query: 113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
               L++ ++  +++E+ L+ +F   G +            + +    I   S ++A +A
Sbjct: 119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQA 174

Query: 173 QEQLNGFELA-GRPMKV 188
              L+  +L     ++V
Sbjct: 175 LIDLHNHDLGENHHLRV 191

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 71.1 bits (174), Expect = 9e-15
 Identities = 15/74 (20%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 117 LYIGSLH-FNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           L + +L+   +T   L  +F  +G +  ++++ +      K    +     + A+ A   
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSH 60

Query: 176 LNGFELAGRPMKVG 189
           LNG +L G+P+++ 
Sbjct: 61  LNGHKLHGKPIRIT 74

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 94.2 bits (235), Expect = 6e-24
 Identities = 29/88 (32%), Positives = 45/88 (51%), Gaps = 2/88 (2%)

Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           G  G   ++I +L  +I    L   F  FG I + +++ D     SKGYGF+ F + + A
Sbjct: 1   GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAA 58

Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNES 197
           ++A E++NG  L  R + VG    R E 
Sbjct: 59  ERAIEKMNGMLLNDRKVFVGRFKSRKER 86

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 61.9 bits (151), Expect = 3e-12
 Identities = 24/112 (21%), Positives = 43/112 (38%), Gaps = 8/112 (7%)

Query: 19  IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
           IF   L + I  + L + FS+ G +   +++        KG  ++ F+  E+   A+  +
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIEKM 65

Query: 78  NGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITED 129
           NG  L    + V   ++ K R    L       T     +YI +     T  
Sbjct: 66  NGMLLNDRKVFVGRFKSRKEREAE-LGARAKEFT----NVYIKNFGPGSTRA 112

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 93.5 bits (233), Expect = 6e-24
 Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 11/93 (11%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFG-KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           L++G L   + E+ +   F   G  + +++++ +  TG   GY F+ F     A+K   +
Sbjct: 12  LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71

Query: 176 LNGFELAG----RPMKVGTVTDRNESVGGGPSN 204
           +NG  L G    +  K+      N +   GPS+
Sbjct: 72  INGKPLPGATPAKRFKL------NYATYSGPSS 98

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 50.0 bits (120), Expect = 3e-08
 Identities = 17/83 (20%), Positives = 34/83 (40%), Gaps = 2/83 (2%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVG-KVRDVRLITCNKTRRFKGIAYIEFKDP 68
          S     A +++   L   +    +   F+++G  V  V++I    T    G  ++EF D 
Sbjct: 3  SGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADL 62

Query: 69 ESVPLAM-GLNGQKLLGIPIIVQ 90
           +    +  +NG+ L G     +
Sbjct: 63 ATAEKCLHKINGKPLPGATPAKR 85

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 93.5 bits (233), Expect = 8e-24
 Identities = 27/92 (29%), Positives = 46/92 (50%), Gaps = 4/92 (4%)

Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
           G++  +      G   +L++G L+   +E+ +  +F+PFG ID   ++  PD G SKG  
Sbjct: 1   GSSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCA 59

Query: 160 FITFHSADDAKKAQEQLNG---FELAGRPMKV 188
           F+ F S  +A+ A   L+G      A   + V
Sbjct: 60  FVKFSSHTEAQAAIHALHGSQTMPGASSSLVV 91

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 48.8 bits (117), Expect = 9e-08
 Identities = 16/98 (16%), Positives = 36/98 (36%), Gaps = 5/98 (5%)

Query: 6   SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
           S          R +F   L+++    D+   F   G + +  ++        KG A+++F
Sbjct: 5   SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLR-GPDGSSKGCAFVKF 63

Query: 66  KDPESVPLAM-GLNGQKLL---GIPIIVQPTQAEKNRA 99
                   A+  L+G + +      ++V+    +K   
Sbjct: 64  SSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKESG 101

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 97.0 bits (241), Expect = 1e-23
 Identities = 35/212 (16%), Positives = 71/212 (33%), Gaps = 34/212 (16%)

Query: 2   RPAYSDDLSPEERDARTIFCMQLSQ-RIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
                            +    L+  R+  + L   F   G V+ V+++   K       
Sbjct: 20  HMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK-----EN 74

Query: 61  AYIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRG---TGGPMR 116
           A ++  D     LAM  LNG KL G PI +  ++ +  +        Q         P+ 
Sbjct: 75  ALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLH 134

Query: 117 -------------------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKG 157
                              L++ ++  +++E+ L+ +F   G +            + + 
Sbjct: 135 RFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRK 190

Query: 158 YGFITFHSADDAKKAQEQLNGFELA-GRPMKV 188
              I   S ++A +A   L+  +L     ++V
Sbjct: 191 MALIQMGSVEEAVQALIDLHNHDLGENHHLRV 222

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 68.1 bits (166), Expect = 2e-13
 Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 7/85 (8%)

Query: 107 QPRGTGGPMR-LYIGSLH-FNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFH 164
            P   G     L + +L+   +T   L  +F  +G +  ++++ +      K    +   
Sbjct: 26  IPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMA 80

Query: 165 SADDAKKAQEQLNGFELAGRPMKVG 189
             + A+ A   LNG +L G+P+++ 
Sbjct: 81  DGNQAQLAMSHLNGHKLHGKPIRIT 105

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 92.6 bits (231), Expect = 1e-23
 Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 8/95 (8%)

Query: 109 RGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADD 168
            G+ G ++L+IG+L    TE  +R +FE +GK+    ++        K YGF+       
Sbjct: 3   SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTA 54

Query: 169 AKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
           A+ A   L+ ++L G  + V    +++++  G  S
Sbjct: 55  AEDAIRNLHHYKLHGVNINVEASKNKSKASSGPSS 89

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 60.3 bits (147), Expect = 5e-12
 Identities = 17/92 (18%), Positives = 36/92 (39%), Gaps = 9/92 (9%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
           S        +F   L +    +++   F   GKV +  +I        K   ++  +D  
Sbjct: 2   SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKT 53

Query: 70  SVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAG 100
           +   A+  L+  KL G+ I V+ ++ +   + 
Sbjct: 54  AAEDAIRNLHHYKLHGVNINVEASKNKSKASS 85

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 92.3 bits (230), Expect = 2e-23
 Identities = 21/91 (23%), Positives = 39/91 (42%), Gaps = 3/91 (3%)

Query: 107 QPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDP-DTGRSKGYGFITFHS 165
                  P   ++G+L +++TE+ ++  F     I  ++L  +P +  R KG+G+  F  
Sbjct: 12  SRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFED 70

Query: 166 ADDAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
            D    A   LN   L  R ++V       +
Sbjct: 71  LDSLLSALS-LNEESLGNRRIRVDVADQAQD 100

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 63.8 bits (156), Expect = 5e-13
 Identities = 23/97 (23%), Positives = 37/97 (38%), Gaps = 2/97 (2%)

Query: 2   RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTR-RFKGI 60
              +       +    T F   L   +    ++EFF  +  +  VRL        R KG 
Sbjct: 5   HHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGF 63

Query: 61  AYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKN 97
            Y EF+D +S+  A+ LN + L    I V      ++
Sbjct: 64  GYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQAQD 100

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 91.6 bits (228), Expect = 3e-23
 Identities = 26/98 (26%), Positives = 44/98 (44%), Gaps = 17/98 (17%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            L++ +L   +TE++L   F  FGK++ ++ +        K Y FI F   D A KA E+
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEE 64

Query: 176 LNGFELAGRPMKVG---------TVTDRNESVGGGPSN 204
           +NG +L G  +++                     GPS+
Sbjct: 65  MNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGPSS 102

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 51.9 bits (125), Expect = 8e-09
 Identities = 25/106 (23%), Positives = 41/106 (38%), Gaps = 11/106 (10%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
           S      + +F   L+  +    LE+ FS  GK+  V+ +        K  A+I F + +
Sbjct: 5   SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERD 56

Query: 70  SVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGP 114
               AM  +NG+ L G  I +    A+           Q +   GP
Sbjct: 57  GAVKAMEEMNGKDLEGENIEI--VFAKPPDQKRKERKAQRQAASGP 100

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 91.2 bits (227), Expect = 4e-23
 Identities = 16/78 (20%), Positives = 38/78 (48%), Gaps = 6/78 (7%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGK--IDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           + + ++  +   D +     P+    ++NI+L+ D  T +++G+ F+   SA DA +  +
Sbjct: 12  IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71

Query: 175 QLNG----FELAGRPMKV 188
            L       ++ G+ + V
Sbjct: 72  ILQSLHPPLKIDGKTIGV 89

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 43.5 bits (103), Expect = 5e-06
 Identities = 11/72 (15%), Positives = 24/72 (33%), Gaps = 3/72 (4%)

Query: 12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGK--VRDVRLITCNKTRRFKGIAYIEFKDPE 69
                TI    ++       +    S      V ++RLI   +T++ +G A+++     
Sbjct: 5  HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64

Query: 70 SVPLAM-GLNGQ 80
               +  L   
Sbjct: 65 DASQLLQILQSL 76

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 91.2 bits (227), Expect = 6e-23
 Identities = 22/98 (22%), Positives = 41/98 (41%), Gaps = 3/98 (3%)

Query: 107 QPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDP-DTGRSKGYGFITFHS 165
                  P   ++G+L +++TE+ ++  F     I  ++L  +P +  R KG+G+  F  
Sbjct: 8   SRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFED 66

Query: 166 ADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
            D    A   LN   L  + ++V       +   G  S
Sbjct: 67  LDSLLSALS-LNEESLGNKRIRVDVADQAQDKDSGPSS 103

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 65.4 bits (160), Expect = 1e-13
 Identities = 24/100 (24%), Positives = 40/100 (40%), Gaps = 2/100 (2%)

Query: 3   PAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLIT-CNKTRRFKGIA 61
            + S      +    T F   L   +    ++EFF  +  +  VRL    +   R KG  
Sbjct: 2   SSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFG 60

Query: 62  YIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGN 101
           Y EF+D +S+  A+ LN + L    I V      +++   
Sbjct: 61  YAEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDKDSG 100

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 90.8 bits (226), Expect = 6e-23
 Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 8/81 (9%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKID--------NIQLMVDPDTGRSKGYGFITFHSAD 167
            +++  L  N+T + +   F+  G I          I L  D +TG+ KG   ++F    
Sbjct: 15  TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74

Query: 168 DAKKAQEQLNGFELAGRPMKV 188
            AK A +  +G E +G P+KV
Sbjct: 75  SAKAAIDWFDGKEFSGNPIKV 95

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 66.9 bits (164), Expect = 3e-14
 Identities = 23/95 (24%), Positives = 39/95 (41%), Gaps = 9/95 (9%)

Query: 6  SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRD--------VRLITCNKTRRF 57
                   D  TIF   L + +    + ++F  +G ++         + L T  +T + 
Sbjct: 3  HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62

Query: 58 KGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQP 91
          KG A + F DP S   A+   +G++  G PI V  
Sbjct: 63 KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 91.1 bits (226), Expect = 1e-22
 Identities = 16/103 (15%), Positives = 39/103 (37%), Gaps = 7/103 (6%)

Query: 90  QPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLR----GIFEPFGKIDNIQ 145
              + E+    +      P  T     + I +++  + ++ L+     +    G I +I 
Sbjct: 5   AAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIV 64

Query: 146 LMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
           +     +  + G  +I F + + A+   E   G+   G P+ +
Sbjct: 65  VD---LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVI 104

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 60.7 bits (147), Expect = 1e-11
 Identities = 17/95 (17%), Positives = 32/95 (33%), Gaps = 8/95 (8%)

Query: 1   MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEE----FFSSVGKVRDVRLITCNKTRR 56
           M         P    ++ +    ++  +    L+       SS G + D+ +     +  
Sbjct: 14  MDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD---LSDD 70

Query: 57  FKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQ 90
             G AYI F   ES    +    G    G P+++ 
Sbjct: 71  NSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVIT 105

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 89.6 bits (223), Expect = 2e-22
 Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 6/87 (6%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+ +L  + +E+M+   F         ++       + + Y F+ F + +DA +A + L
Sbjct: 18  LYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKAL 71

Query: 177 NGFELAGRPMKVGTVTDRNESVGGGPS 203
           NG  L G P++V      ++   G  S
Sbjct: 72  NGKVLDGSPIEVTLAKPVDKDSSGPSS 98

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 50.4 bits (121), Expect = 2e-08
 Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 7/74 (9%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
          + ++   L        +E+ F+++      R       ++ +  A++ F + E    AM 
Sbjct: 16 KILYVRNLMLSTSEEMIEKEFNNIKPGAVER------VKKIRDYAFVHFSNREDAVEAMK 69

Query: 76 GLNGQKLLGIPIIV 89
           LNG+ L G PI V
Sbjct: 70 ALNGKVLDGSPIEV 83

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 89.3 bits (222), Expect = 2e-22
 Identities = 19/89 (21%), Positives = 37/89 (41%)

Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
           G++  +    G  GP  + + ++ F ++ D +   F  +  I     +   + G   G  
Sbjct: 1   GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKV 188
            + F S D+A  A   LN   +  R +K+
Sbjct: 61  MVAFESRDEATAAVIDLNDRPIGSRKVKL 89

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 12/85 (14%), Positives = 29/85 (34%), Gaps = 1/85 (1%)

Query: 4  AYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYI 63
          + S   S  +     I    +   +   ++ +FF     +     +  N+     G A +
Sbjct: 3  SGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62

Query: 64 EFKDPESVPLAM-GLNGQKLLGIPI 87
           F+  +    A+  LN + +    +
Sbjct: 63 AFESRDEATAAVIDLNDRPIGSRKV 87

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 89.3 bits (222), Expect = 3e-22
 Identities = 19/89 (21%), Positives = 37/89 (41%)

Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
           G++  +    G  GP  + + ++ F ++ D +   F  +  I     +   + G   G  
Sbjct: 1   GSSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKV 188
            + F S D+A  A   LN   +  R +K+
Sbjct: 61  MVAFESRDEATAAVIDLNDRPIGSRKVKL 89

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 52.7 bits (127), Expect = 4e-09
 Identities = 10/75 (13%), Positives = 26/75 (34%), Gaps = 1/75 (1%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
           I    +   +   ++ +FF     +     +  N+     G A + F+  +    A+  
Sbjct: 17 IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76

Query: 77 LNGQKLLGIPIIVQP 91
          LN + +    + +  
Sbjct: 77 LNDRPIGSRKVKLVL 91

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 88.3 bits (219), Expect = 5e-22
 Identities = 18/82 (21%), Positives = 43/82 (52%), Gaps = 3/82 (3%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L I ++  ++  ++L  +   +G +++ + +   +T        +T+ S D A++A ++
Sbjct: 17  KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQV---NTDSETAVVNVTYSSKDQARQALDK 73

Query: 176 LNGFELAGRPMKVGTVTDRNES 197
           LNGF+L    +KV  + D   +
Sbjct: 74  LNGFQLENFTLKVAYIPDEMAA 95

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 56.3 bits (136), Expect = 2e-10
 Identities = 12/81 (14%), Positives = 27/81 (33%), Gaps = 4/81 (4%)

Query: 11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
          P+ +  R +    +   ++   L+      G V     +    T     +  + +   + 
Sbjct: 10 PKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQV---NTDSETAVVNVTYSSKDQ 66

Query: 71 VPLAM-GLNGQKLLGIPIIVQ 90
             A+  LNG +L    + V 
Sbjct: 67 ARQALDKLNGFQLENFTLKVA 87

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 88.0 bits (219), Expect = 8e-22
 Identities = 22/88 (25%), Positives = 43/88 (48%), Gaps = 1/88 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++G +  N  E  LR  F+ FG +  + ++ D +  R +G+GFITF       +A   
Sbjct: 12  KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71

Query: 176 LNGFELAGRPMKVGTVTDRNESVGGGPS 203
            +  ++ G+ ++V     R+    G  S
Sbjct: 72  -HFHDIMGKKVEVKRAEPRDSKSSGPSS 98

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 51.0 bits (123), Expect = 1e-08
 Identities = 18/75 (24%), Positives = 35/75 (46%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
                +  IF   +       +L E+F   G V +V +I   + +R +G  +I F+D +
Sbjct: 4  GSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQ 63

Query: 70 SVPLAMGLNGQKLLG 84
          SV  A+ ++   ++G
Sbjct: 64 SVDQAVNMHFHDIMG 78

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 88.2 bits (219), Expect = 1e-21
 Identities = 25/112 (22%), Positives = 46/112 (41%), Gaps = 8/112 (7%)

Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKI--------DNIQLMVDPD 151
           G++  +  P        +Y+  L+ ++T D L   F+  G +          I + +D +
Sbjct: 1   GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60

Query: 152 TGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
           TG+ KG   +++     AK A E  +G +  G  +KV     +     G  S
Sbjct: 61  TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSS 112

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 63.2 bits (154), Expect = 1e-12
 Identities = 20/98 (20%), Positives = 40/98 (40%), Gaps = 9/98 (9%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVR--------DVRLITCNKTRRFKGIA 61
             E+ D   I+   L+  +   DL +FF   G V+         + +    +T + KG A
Sbjct: 9   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 68

Query: 62  YIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
            + ++DP +   A+   +G+   G  + V   + +   
Sbjct: 69  TVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 106

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 87.0 bits (216), Expect = 2e-21
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 8/72 (11%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+     ++T  +LRG F PFG I ++ +         +   F+T+   + A +A  +L
Sbjct: 18  LYVY--GEDMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAEL 69

Query: 177 NGFELAGRPMKV 188
           NG ++    +KV
Sbjct: 70  NGTQVESVQLKV 81

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 9/82 (10%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
              R   T++       +    L   FS  G + D+           +  A++ ++  E
Sbjct: 9  RRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDL------SMDPPRNCAFVTYEKME 60

Query: 70 SVPLAM-GLNGQKLLGIPIIVQ 90
          S   A+  LNG ++  + + V 
Sbjct: 61 SADQAVAELNGTQVESVQLKVN 82

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 88.4 bits (219), Expect = 2e-21
 Identities = 28/140 (20%), Positives = 52/140 (37%), Gaps = 9/140 (6%)

Query: 53  KTRRFKGIAYIEFKDPESVPLAMG--LNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRG 110
             +  KG    E  D  +         N   + G       T+      G+   +     
Sbjct: 8   NGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHR 67

Query: 111 TGGPM--RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADD 168
              P+  ++Y+G+L  N  +  L   F  +G + ++ +  +P      G+ F+ F    D
Sbjct: 68  DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRD 122

Query: 169 AKKAQEQLNGFELAGRPMKV 188
           A  A  +L+G  L G  ++V
Sbjct: 123 AADAVRELDGRTLCGCRVRV 142

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 64.9 bits (158), Expect = 7e-13
 Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 6/84 (7%)

Query: 14  RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
                ++   L       +LE  F   G +R V +      R   G A++EF+DP     
Sbjct: 71  PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVA-----RNPPGFAFVEFEDPRDAAD 125

Query: 74  AM-GLNGQKLLGIPIIVQPTQAEK 96
           A+  L+G+ L G  + V+ +  EK
Sbjct: 126 AVRELDGRTLCGCRVRVELSNGEK 149

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 86.1 bits (214), Expect = 3e-21
 Identities = 24/92 (26%), Positives = 41/92 (44%), Gaps = 8/92 (8%)

Query: 111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAK 170
           +G   ++++G++    T   LR +FE  G++    ++        K Y F+      DAK
Sbjct: 6   SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAK 57

Query: 171 KAQEQLNGFELAGRPMKVGTVTDRNESVGGGP 202
            A  QLNG E+ G+ + V   T   +  G   
Sbjct: 58  AAIAQLNGKEVKGKRINVELSTKGQKKSGPSS 89

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 58.8 bits (143), Expect = 2e-11
 Identities = 18/92 (19%), Positives = 39/92 (42%), Gaps = 9/92 (9%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
           S    +   IF   +S    +++L   F   G+V +  ++        K  A++  +   
Sbjct: 3   SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEA 54

Query: 70  SVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAG 100
               A+  LNG+++ G  I V+ +   + ++G
Sbjct: 55  DAKAAIAQLNGKEVKGKRINVELSTKGQKKSG 86

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 85.0 bits (211), Expect = 8e-21
 Identities = 24/91 (26%), Positives = 39/91 (42%), Gaps = 8/91 (8%)

Query: 113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
              +L++G++    T   LR  FE +G +    ++        K Y F+    A+DA +A
Sbjct: 9   ASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEA 60

Query: 173 QEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
              L+  E  G+ M V   T R  +  G  S
Sbjct: 61  IRGLDNTEFQGKRMHVQLSTSRLRTASGPSS 91

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 58.0 bits (141), Expect = 4e-11
 Identities = 17/106 (16%), Positives = 36/106 (33%), Gaps = 21/106 (19%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
               + +  +    +S     ++L   F   G V +  ++        K  A++  +  E
Sbjct: 4   GSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAE 55

Query: 70  SVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGP 114
               A+ GL+  +  G  + VQ + +            + R   GP
Sbjct: 56  DAVEAIRGLDNTEFQGKRMHVQLSTS------------RLRTASGP 89

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 84.7 bits (210), Expect = 2e-20
 Identities = 18/91 (19%), Positives = 37/91 (40%), Gaps = 3/91 (3%)

Query: 98  RAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKG 157
              +    ++        R+Y+G+L  +I    +  +F  +G I +I L           
Sbjct: 6   SGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPP 62

Query: 158 YGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
           + F+ F    DA+ A    +G++  G  ++V
Sbjct: 63  FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV 93

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 67.3 bits (165), Expect = 3e-14
 Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 4/90 (4%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
            P   +   I+   L   IRT+D+E+ F   G +RD+ L      R     A++EF+DP 
Sbjct: 16  GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPR 72

Query: 70  SVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
               A+ G +G    G  + V+  ++ +  
Sbjct: 73  DAEDAVYGRDGYDYDGYRLRVEFPRSGRGT 102

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 82.9 bits (206), Expect = 2e-20
 Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++G L  +  E+ +R  F  FG++++I+L +D  T + +G+ FITF   +  KK  E+
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 176 LNGFELAGRPMKV 188
                +     ++
Sbjct: 61  -KYHNVGLSKCEI 72

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 48.3 bits (116), Expect = 6e-08
 Identities = 19/66 (28%), Positives = 28/66 (42%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLN 78
          IF   LS       + E+F   G+V  + L   NKT + +G  +I FK+ E V   M   
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 79 GQKLLG 84
             +  
Sbjct: 62 YHNVGL 67

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 82.9 bits (206), Expect = 3e-20
 Identities = 25/73 (34%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++G L  N T + ++  FE FGK+D+  LM D  T R +G+GF+TF S D  +K  E 
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 176 LNGFELAGRPMKV 188
            +  E+  + ++ 
Sbjct: 61  -HFHEINNKMVEC 72

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 48.2 bits (116), Expect = 7e-08
 Identities = 14/61 (22%), Positives = 27/61 (44%)

Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLL 83
          LS      D++ +F   GKV D  L+    T R +G  ++ F+  + V     ++  ++ 
Sbjct: 7  LSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEIN 66

Query: 84 G 84
           
Sbjct: 67 N 67

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 83.9 bits (208), Expect = 4e-20
 Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++G L ++ T+  LR  FE FG I+   ++ D  TG+S+GYGF+T      A++A + 
Sbjct: 19  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78

Query: 176 LNGFELAGRPMKV 188
            N   + GR   V
Sbjct: 79  PNP-IIDGRKANV 90

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 47.7 bits (114), Expect = 3e-07
 Identities = 19/111 (17%), Positives = 36/111 (32%), Gaps = 10/111 (9%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
           S ++     IF   L        L ++F   G + +  +IT  +T + +G  ++   D  
Sbjct: 11  SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRA 70

Query: 70  SVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIG 120
           +   A       + G    V       N A       +PR       + + 
Sbjct: 71  AAERACKDPNPIIDGRKANV-------NLA---YLGAKPRSLQTGFAIGVS 111

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 83.1 bits (206), Expect = 5e-20
 Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 5/74 (6%)

Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           M++Y+G+L     +  L   F  +G +  + +  +P      G+ F+ F    DA+ A  
Sbjct: 1   MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVR 55

Query: 175 QLNGFELAGRPMKV 188
            L+G  + G  ++V
Sbjct: 56  GLDGKVICGSRVRV 69

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 60.8 bits (148), Expect = 5e-12
 Identities = 25/99 (25%), Positives = 40/99 (40%), Gaps = 15/99 (15%)

Query: 19  IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
           ++   L       +LE  FS  G +R V +      R   G A++EF+DP     A+ GL
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIA-----RNPPGFAFVEFEDPRDAEDAVRGL 57

Query: 78  NGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMR 116
           +G+ + G  + V+ +     R          R    P R
Sbjct: 58  DGKVICGSRVRVELSTGMPRR---------SRFDRPPAR 87

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 83.0 bits (206), Expect = 5e-20
 Identities = 26/104 (25%), Positives = 42/104 (40%), Gaps = 2/104 (1%)

Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
           G++  +   R       L +  L +  TE  L+  F  FG++  +Q+  D  TG SKG+G
Sbjct: 1   GSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60

Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
           F+ F   +   K   Q +   + GR         +     G  S
Sbjct: 61  FVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQDSGPSS 102

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 46.8 bits (112), Expect = 4e-07
 Identities = 17/70 (24%), Positives = 33/70 (47%)

Query: 6  SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
          S  +    +    +  + L  +   +DL+E+FS+ G+V  V++    KT   KG  ++ F
Sbjct: 5  SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64

Query: 66 KDPESVPLAM 75
           + E+    M
Sbjct: 65 TEYETQVKVM 74

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 82.7 bits (205), Expect = 7e-20
 Identities = 26/94 (27%), Positives = 47/94 (50%), Gaps = 6/94 (6%)

Query: 116 RLYIGSLHFNITEDMLRGIF-EPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
            L++G L  ++ + ML   F + +      ++++D  TG SKGYGF+ F    + K+A  
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALT 69

Query: 175 QLNG-FELAGRPMKVGTVT---DRNESVGGGPSN 204
           +  G   L  +P+++        R + V  GPS+
Sbjct: 70  ECQGAVGLGSKPVRLSVAIPKASRVKPVESGPSS 103

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 81.9 bits (203), Expect = 2e-19
 Identities = 31/88 (35%), Positives = 47/88 (53%), Gaps = 1/88 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L+IG L F  TE+ LR  +E +GK+ +  +M DP + RS+G+GF+TF S  +   A   
Sbjct: 29  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88

Query: 176 LNGFELAGRPMKVGTVTDRNESVGGGPS 203
                + GR ++      R ES  G  S
Sbjct: 89  -RPHSIDGRVVEPKRAVAREESGSGPSS 115

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 16/75 (21%), Positives = 29/75 (38%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
            E+   R +F   LS       L  ++   GK+ D  ++    ++R +G  ++ F    
Sbjct: 21 KREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMA 80

Query: 70 SVPLAMGLNGQKLLG 84
           V  AM      + G
Sbjct: 81 EVDAAMAARPHSIDG 95

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 80.9 bits (200), Expect = 2e-19
 Identities = 20/86 (23%), Positives = 39/86 (45%), Gaps = 10/86 (11%)

Query: 113 GPM----RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLM-----VDPDTGRSKGYGFITF 163
           GP+    RLY+G++ F ITE+ +   F    ++  +        +     + K + F+ F
Sbjct: 1   GPLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF 60

Query: 164 HSADDAKKAQEQLNGFELAGRPMKVG 189
            S D+  +A    +G    G+ +K+ 
Sbjct: 61  RSVDETTQAM-AFDGIIFQGQSLKIR 85

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 52.8 bits (127), Expect = 3e-09
 Identities = 14/81 (17%), Positives = 33/81 (40%), Gaps = 5/81 (6%)

Query: 14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCN-----KTRRFKGIAYIEFKDP 68
            AR ++   +   I    + +FF++  ++  +     N     +  + K  A++EF+  
Sbjct: 4  GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 63

Query: 69 ESVPLAMGLNGQKLLGIPIIV 89
          +    AM  +G    G  + +
Sbjct: 64 DETTQAMAFDGIIFQGQSLKI 84

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 80.0 bits (198), Expect = 4e-19
 Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 7/74 (9%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA-QEQ 175
           LY+G L   ITE  LR  F  FG+I  I ++        +   FI F +   A+ A ++ 
Sbjct: 15  LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKS 68

Query: 176 LNGFELAGRPMKVG 189
            N   + GR + V 
Sbjct: 69  FNKLIVNGRRLNVK 82

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 17/83 (20%), Positives = 36/83 (43%), Gaps = 8/83 (9%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
          S E++   T++   L   I   DL   F   G++R + ++      + +  A+I+F   +
Sbjct: 6  SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV------QRQQCAFIQFATRQ 59

Query: 70 SVPLAM--GLNGQKLLGIPIIVQ 90
          +  +A     N   + G  + V+
Sbjct: 60 AAEVAAEKSFNKLIVNGRRLNVK 82

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 79.3 bits (196), Expect = 1e-18
 Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 9/86 (10%)

Query: 104 PNLQPRGTGGPMRLYIGSL-HFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFIT 162
             L PRG+    RL+IG+L   N++++ L  IF P+G I  I +           +GFI 
Sbjct: 12  SGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQ 63

Query: 163 FHSADDAKKAQEQLNGFELAGRPMKV 188
           F +    + A E  +     G+ + +
Sbjct: 64  FDNPQSVRDAIEXESQEMNFGKKLIL 89

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 53.9 bits (130), Expect = 1e-09
 Identities = 18/89 (20%), Positives = 36/89 (40%), Gaps = 11/89 (12%)

Query: 6  SDDLSPEERDART-IFCMQLS-QRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYI 63
          S  L P     ++ +F   L  + +   DL   FS  G +  + +             +I
Sbjct: 11 SSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFI 62

Query: 64 EFKDPESVPLAM-GLNGQKLLGIPIIVQP 91
          +F +P+SV  A+   + +   G  +I++ 
Sbjct: 63 QFDNPQSVRDAIEXESQEMNFGKKLILEV 91

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 78.3 bits (194), Expect = 1e-18
 Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +++IG L +  T++ LR  F  FG++    +M DP T RS+G+GF+TF       K   Q
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 176 LNGFELAGR 184
            +  EL  +
Sbjct: 62  -SRHELDSK 69

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 45.6 bits (109), Expect = 6e-07
 Identities = 14/61 (22%), Positives = 28/61 (45%)

Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLL 83
          LS +     L E+F   G+V++  ++    T+R +G  ++ F D   V   +  +  +L 
Sbjct: 8  LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELD 67

Query: 84 G 84
           
Sbjct: 68 S 68

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 79.2 bits (196), Expect = 1e-18
 Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 6/73 (8%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL++G L  N +   L   F+ FG I  I      D  +   + +I + S D A+ A  +
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTI------DHVKGDSFAYIQYESLDAAQAACAK 72

Query: 176 LNGFELAGRPMKV 188
           + GF L G   ++
Sbjct: 73  MRGFPLGGPDRRL 85

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 45.7 bits (109), Expect = 9e-07
 Identities = 13/86 (15%), Positives = 29/86 (33%), Gaps = 9/86 (10%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
            ++   L        L   F   G +R +  +      +    AYI+++  ++   A  
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQAACA 71

Query: 76 GLNGQKLLG--IPIIVQPTQAEKNRA 99
           + G  L G    + V   ++  +  
Sbjct: 72 KMRGFPLGGPDRRLRVDFAKSGPSSG 97

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 78.4 bits (194), Expect = 2e-18
 Identities = 23/73 (31%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++G L ++ ++  L+  F  FG++ +  + +DP+TGRS+G+GFI F  A   +K  +Q
Sbjct: 13  KMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ 72

Query: 176 LNGFELAGRPMKV 188
                L GR +  
Sbjct: 73  KEH-RLDGRVIDP 84

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 51.0 bits (123), Expect = 9e-09
 Identities = 24/75 (32%), Positives = 36/75 (48%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
          S  E DA  +F   LS     +DL+++F+  G+V D  +     T R +G  +I FKD  
Sbjct: 5  SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAA 64

Query: 70 SVPLAMGLNGQKLLG 84
          SV   +     +L G
Sbjct: 65 SVEKVLDQKEHRLDG 79

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 79.0 bits (195), Expect = 2e-18
 Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 3/77 (3%)

Query: 118 YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN 177
            +G       ++++  IF  FGKI N       + G++KGY F+ + S   A  A +  +
Sbjct: 25  QVGPDRLEKLKNVIHKIFSKFGKITND--FYPEEDGKTKGYIFLEYASPAHAVDAVKNAD 82

Query: 178 GFELAGR-PMKVGTVTD 193
           G++L  +   +V   TD
Sbjct: 83  GYKLDKQHTFRVNLFTD 99

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 44.7 bits (106), Expect = 3e-06
 Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 3/55 (5%)

Query: 31 RDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLG 84
            + + FS  GK+ +       +  + KG  ++E+  P     A+   +G KL  
Sbjct: 36 NVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK 88

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 78.8 bits (195), Expect = 2e-18
 Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 1/88 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L++G L ++ T++ LR  F  +G++ +  +M D  T +S+G+GF+ F   +        
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77

Query: 176 LNGFELAGRPMKVGTVTDRNESVGGGPS 203
                L GR +     T R     G  S
Sbjct: 78  -RPHTLDGRNIDPKPCTPRGMQPSGPSS 104

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 17/75 (22%), Positives = 30/75 (40%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
          +    +   +F   L        L  +FS  G+V D  ++    T + +G  +++FKDP 
Sbjct: 10 NSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPN 69

Query: 70 SVPLAMGLNGQKLLG 84
           V   +      L G
Sbjct: 70 CVGTVLASRPHTLDG 84

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 78.2 bits (193), Expect = 4e-18
 Identities = 20/80 (25%), Positives = 32/80 (40%), Gaps = 2/80 (2%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +YI     + T D ++   E  G++ NIQ+         KG  F+ F S + AKK  E  
Sbjct: 14  VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVET- 71

Query: 177 NGFELAGRPMKVGTVTDRNE 196
            G +     + +    D   
Sbjct: 72  PGQKYKETDLLILFKDDYFA 91

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 72.8 bits (179), Expect = 3e-16
 Identities = 17/90 (18%), Positives = 37/90 (41%), Gaps = 4/90 (4%)

Query: 12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
           +   R+++           D++E+    G+V ++++      + FKG  ++ F   ES 
Sbjct: 7  NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRR-TLHKAFKGSIFVVFDSIESA 65

Query: 72 PLAMGLNGQKLLGIPIIVQPTQ---AEKNR 98
             +   GQK     +++       A+KN 
Sbjct: 66 KKFVETPGQKYKETDLLILFKDDYFAKKNE 95

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 77.7 bits (192), Expect = 5e-18
 Identities = 27/80 (33%), Positives = 41/80 (51%), Gaps = 4/80 (5%)

Query: 108 PRGTGGPMR---LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFH 164
           PRG+        ++IG L +  T++ LR  F  FG++    +M DP T RS+G+GF+TF 
Sbjct: 16  PRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFM 75

Query: 165 SADDAKKAQEQLNGFELAGR 184
                 K   Q +  EL  +
Sbjct: 76  DQAGVDKVLAQ-SRHELDSK 94

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 49.2 bits (118), Expect = 8e-08
 Identities = 16/75 (21%), Positives = 31/75 (41%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
          S        +F   LS +     L E+F   G+V++  ++    T+R +G  ++ F D  
Sbjct: 19 SHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQA 78

Query: 70 SVPLAMGLNGQKLLG 84
           V   +  +  +L  
Sbjct: 79 GVDKVLAQSRHELDS 93

>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* Length = 437

 Score = 83.7 bits (206), Expect = 6e-18
 Identities = 25/100 (25%), Positives = 47/100 (47%), Gaps = 1/100 (1%)

Query: 90  QPTQAEKNRAGNTLPNLQPRGTGGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMV 148
           +  Q  +       P+  P   G   + L++  ++++ TE  LR  FE +G I  I ++ 
Sbjct: 77  RRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVY 136

Query: 149 DPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
              +G+ +GY FI +    D   A +  +G ++ GR + V
Sbjct: 137 SKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV 176

>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* Length = 437

 Score = 55.2 bits (132), Expect = 1e-08
 Identities = 25/141 (17%), Positives = 50/141 (35%), Gaps = 3/141 (2%)

Query: 17  RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
           +T+F  +++       L   F   G ++ + ++   ++ + +G A+IE++    +  A  
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162

Query: 77  -LNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIF 135
             +G+K+ G  ++V              P     G GG  R        +   D      
Sbjct: 163 HADGKKIDGRRVLVD--VERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYD 220

Query: 136 EPFGKIDNIQLMVDPDTGRSK 156
           E  G         D D  R +
Sbjct: 221 ERPGPSPLPHRDRDRDRERER 241

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 77.6 bits (191), Expect = 7e-18
 Identities = 23/108 (21%), Positives = 47/108 (43%), Gaps = 13/108 (12%)

Query: 109 RGTGGPMR------LYIGSLHFNIT-EDMLRG--IFEPFGKIDNIQLMVDPDTGRSK--- 156
             +G  +R      +++  L   +   ++L+    F  FGKI  + +        S+   
Sbjct: 4   GSSGASVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPS 63

Query: 157 GYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
              ++T+  ++DA +A + +N   + GR +K    T +  S   GPS+
Sbjct: 64  ASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKYCS-YSGPSS 110

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 44.1 bits (104), Expect = 5e-06
 Identities = 16/77 (20%), Positives = 33/77 (42%), Gaps = 7/77 (9%)

Query: 18 TIFCMQLSQRIRTRDL---EEFFSSVGKVRDVRLI---TCNKTRRFKGIAYIEFKDPESV 71
           +F + LSQR+   ++    E+F   GK+  V +    +   ++     AY+ +   E  
Sbjct: 17 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76

Query: 72 PLAM-GLNGQKLLGIPI 87
            A+  +N   + G  +
Sbjct: 77 LRAIQCVNNVVVDGRTL 93

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 77.1 bits (190), Expect = 1e-17
 Identities = 14/77 (18%), Positives = 33/77 (42%), Gaps = 4/77 (5%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGK-IDNIQLMVDP-DTGRSKGYGFITFHSADDAKKAQ 173
           RL+IG +      + +        + + ++ +     D  +++G+ F+ + S   A  A+
Sbjct: 10  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69

Query: 174 EQLN--GFELAGRPMKV 188
            +L     +L G  + V
Sbjct: 70  RKLMPGRIQLWGHQIAV 86

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 47.5 bits (113), Expect = 3e-07
 Identities = 14/81 (17%), Positives = 33/81 (40%), Gaps = 5/81 (6%)

Query: 14 RDARTIFCMQLSQRIRTRDLEEFFSSVGK-VRDVRLIT-CNKTRRFKGIAYIEFKDPESV 71
               +F   + +  +  ++ E  + V + V DV +        + +G A++E++   + 
Sbjct: 6  SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 65

Query: 72 PLA---MGLNGQKLLGIPIIV 89
           +A   +     +L G  I V
Sbjct: 66 AMARRKLMPGRIQLWGHQIAV 86

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 75.9 bits (187), Expect = 2e-17
 Identities = 14/95 (14%), Positives = 38/95 (40%), Gaps = 8/95 (8%)

Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           G+ G   + + +L  +     +  + + +        +      R+K   F+T  + + A
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQA 53

Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           + A +  + +   G+ + V  +   +  +  GPS+
Sbjct: 54  QNAIQMFHQYSFRGKDLIV-QLQPTDALLCSGPSS 87

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 40.5 bits (95), Expect = 5e-05
 Identities = 12/78 (15%), Positives = 26/78 (33%), Gaps = 8/78 (10%)

Query: 14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
            +  I    L Q    +++ +          ++    +   R K  A++   + E    
Sbjct: 3  SGSSGILVKNLPQDSNCQEVHDLLKDYD----LKYCYVD---RNKRTAFVTLLNGEQAQN 55

Query: 74 AM-GLNGQKLLGIPIIVQ 90
          A+   +     G  +IVQ
Sbjct: 56 AIQMFHQYSFRGKDLIVQ 73

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 76.3 bits (188), Expect = 2e-17
 Identities = 21/90 (23%), Positives = 43/90 (47%), Gaps = 3/90 (3%)

Query: 107 QPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKI-DNIQLMVDPDTGRSKGYGFITFHS 165
           +       +  +I ++ F+IT+  +    E      + + ++VD + G+  G   + F +
Sbjct: 8   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNN-GQGLGQALVQFKN 66

Query: 166 ADDAKKAQEQLNGFELAGRPMKVGTVTDRN 195
            DDA+K++  L+  +L GR   V  VT  +
Sbjct: 67  EDDARKSER-LHRKKLNGREAFVHVVTLED 95

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 71.7 bits (176), Expect = 8e-16
 Identities = 19/115 (16%), Positives = 36/115 (31%), Gaps = 3/115 (2%)

Query: 2   RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIA 61
               S +               +   I   D+ +F   +    +   +  +   +  G A
Sbjct: 2   SSGSSGEGDVNS-AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQA 60

Query: 62  YIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMR 116
            ++FK+ +    +  L+ +KL G    V     E  R      N   +G  GP  
Sbjct: 61  LVQFKNEDDARKSERLHRKKLNGREAFVHVVTLEDMRE--IEKNPPAQGKSGPSS 113

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 80.3 bits (197), Expect = 2e-17
 Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 12/89 (13%)

Query: 104 PNLQPRGTGGPMRLYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGYG 159
           P  +P  T     +YI +L+  I +D L+     IF  FG+I +I +     + + +G  
Sbjct: 4   PETRPNHT-----IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS---RSLKMRGQA 55

Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKV 188
           F+ F     A  A   + GF    +PM++
Sbjct: 56  FVIFKEVSSATNALRSMQGFPFYDKPMRI 84

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 64.5 bits (156), Expect = 6e-12
 Identities = 23/123 (18%), Positives = 41/123 (33%), Gaps = 6/123 (4%)

Query: 68  PESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNIT 127
           P  +P    +    L    I       ++   G   P            L++ +L     
Sbjct: 161 PPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETN 220

Query: 128 EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFEL-AGRPM 186
           E ML  +F  F     ++L+            F+ F +   A  A++ L GF++     M
Sbjct: 221 ELMLSMLFNQFPGFKEVRLVPG-----RHDIAFVEFDNEVQAGAARDALQGFKITQNNAM 275

Query: 187 KVG 189
           K+ 
Sbjct: 276 KIS 278

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 56.4 bits (135), Expect = 3e-09
 Identities = 27/175 (15%), Positives = 59/175 (33%), Gaps = 13/175 (7%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEE----FFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
            PE R   TI+   L+++I+  +L++     FS  G++ D+     +++ + +G A++ F
Sbjct: 3   VPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDIL---VSRSLKMRGQAFVIF 59

Query: 66  KDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHF 124
           K+  S   A+  + G      P+ +Q  + + +           R      R        
Sbjct: 60  KEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKR-----KPK 114

Query: 125 NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF 179
           +      +   +  G    +  +  P  G                +       G 
Sbjct: 115 SQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGM 169

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 39.9 bits (92), Expect = 8e-04
 Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 7/75 (9%)

Query: 18  TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
            +F   L +      L   F+     ++VRL+          IA++EF +      A   
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLV-----PGRHDIAFVEFDNEVQAGAARDA 263

Query: 77  LNGQKLL-GIPIIVQ 90
           L G K+     + + 
Sbjct: 264 LQGFKITQNNAMKIS 278

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 75.3 bits (186), Expect = 3e-17
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 9/74 (12%)

Query: 116 RLYIGSLHF-NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           RL+IG+L   N++++ L  IF P+G I  I +           +GFI F +    + A E
Sbjct: 12  RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIE 63

Query: 175 QLNGFELAGRPMKV 188
             +     G+ + +
Sbjct: 64  CESQEMNFGKKLIL 77

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 54.9 bits (133), Expect = 6e-10
 Identities = 13/78 (16%), Positives = 31/78 (39%), Gaps = 9/78 (11%)

Query: 25  SQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLL 83
            + +   DL   FS  G +  + +             +I+F +P+SV  A+   + +   
Sbjct: 20  LKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNF 71

Query: 84  GIPIIVQPTQAEKNRAGN 101
           G  +I++ + +      +
Sbjct: 72  GKKLILEVSSSNARPQFD 89

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 75.1 bits (185), Expect = 4e-17
 Identities = 24/114 (21%), Positives = 46/114 (40%), Gaps = 11/114 (9%)

Query: 91  PTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFN-ITEDMLRGIFEPFGKIDNIQLMVD 149
              + K +A N      P+      R++IG+L+   + +  +  IF  +G++    +   
Sbjct: 6   SGMSLKLQASNVTNKNDPKSINS--RVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH-- 61

Query: 150 PDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
                 KGY F+ + +   A+ A    NG  LAG+ + +    +      G  S
Sbjct: 62  ------KGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSGPSS 109

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 55.1 bits (133), Expect = 6e-10
 Identities = 18/100 (18%), Positives = 40/100 (40%), Gaps = 10/100 (10%)

Query: 1   MRPAYSDDLSPEERDARTIFCMQLS-QRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKG 59
           ++ +   + +  +     +F   L+   ++  D+E  FS  G+V    +         KG
Sbjct: 12  LQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KG 63

Query: 60  IAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
            A++++ +      A+ G NG+ L G  + +      K  
Sbjct: 64  YAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPD 103

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 72.0 bits (177), Expect = 3e-16
 Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 2/66 (3%)

Query: 119 IGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNG 178
           +G       ++++  IF  FGKI N       + G++KGY F+ + S   A  A +  +G
Sbjct: 12  VGPDRLEKLKNVIHKIFSKFGKITND--FYPEEDGKTKGYIFLEYASPAHAVDAVKNADG 69

Query: 179 FELAGR 184
           ++L  +
Sbjct: 70  YKLDKQ 75

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 43.5 bits (103), Expect = 4e-06
 Identities = 12/51 (23%), Positives = 23/51 (45%), Gaps = 3/51 (5%)

Query: 33 LEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKL 82
          + + FS  GK+ +       +  + KG  ++E+  P     A+   +G KL
Sbjct: 24 IHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKL 72

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 72.7 bits (178), Expect = 5e-16
 Identities = 16/64 (25%), Positives = 32/64 (50%), Gaps = 6/64 (9%)

Query: 120 GSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF 179
           G L   ++ + L  + E  G +D +  ++ P+    K Y F  + + +++K+A   LNG 
Sbjct: 33  GGLGNGVSRNQLLPVLEKCGLVDAL--LMPPN----KPYSFARYRTTEESKRAYVTLNGK 86

Query: 180 ELAG 183
           E+  
Sbjct: 87  EVVD 90

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 70.3 bits (173), Expect = 1e-15
 Identities = 18/94 (19%), Positives = 39/94 (41%), Gaps = 7/94 (7%)

Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           G+ G   +++G    ++TED LR  F  +G + ++ +         + + F+TF     A
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIA 55

Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
           +    +     + G  + +     ++ S  G  S
Sbjct: 56  QSLCGE--DLIIKGISVHISNAEPKHNSNSGPSS 87

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 43.4 bits (103), Expect = 5e-06
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 6/76 (7%)

Query: 14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
            +  +F  + +  +   +L EFFS  G V DV +      + F+  A++ F D +    
Sbjct: 3  SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIAQS 57

Query: 74 AMGLNGQKLLGIPIIV 89
            G     + GI + +
Sbjct: 58 LCG-EDLIIKGISVHI 72

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Length = 114

 Score = 69.7 bits (171), Expect = 4e-15
 Identities = 28/40 (70%), Positives = 32/40 (80%)

Query: 266 PPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
            P+ATQCF L+NMF+P TE    WD EI+DDVIEECNKHG
Sbjct: 3   QPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHG 42

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 69.1 bits (169), Expect = 7e-15
 Identities = 15/88 (17%), Positives = 28/88 (31%), Gaps = 9/88 (10%)

Query: 104 PNLQPRGTGGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFIT 162
            +            +++  L  ++ E  L    E FG I  + +M        K    + 
Sbjct: 4   GSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM------PFKRQALVE 57

Query: 163 FHSADDAKKAQE--QLNGFELAGRPMKV 188
           F + D AK+           +AG+    
Sbjct: 58  FENIDSAKECVTFAADVPVYIAGQQAFF 85

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 45.6 bits (108), Expect = 1e-06
 Identities = 18/93 (19%), Positives = 31/93 (33%), Gaps = 10/93 (10%)

Query: 17  RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
             +    L + +   DL E     G +  V +        FK  A +EF++ +S    + 
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMM------MPFKRQALVEFENIDSAKECVT 69

Query: 76  --GLNGQKLLGIPIIVQP-TQAEKNRAGNTLPN 105
                   + G        T     R GN+ P+
Sbjct: 70  FAADVPVYIAGQQAFFNYSTSKRITRPGNSGPS 102

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 69.1 bits (169), Expect = 8e-15
 Identities = 11/72 (15%), Positives = 23/72 (31%), Gaps = 6/72 (8%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +   +L        ++  F  FG +  + L              + F    +A+KA   L
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKAFRHL 66

Query: 177 NGFELAGRPMKV 188
              +    P+ +
Sbjct: 67  AYSKFHHVPLYL 78

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 52.1 bits (125), Expect = 8e-09
 Identities = 17/82 (20%), Positives = 27/82 (32%), Gaps = 7/82 (8%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
              R    I    L       +++E FS  G +  V L            A +EF +P 
Sbjct: 4  GSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPL 57

Query: 70 SVPLAM-GLNGQKLLGIPIIVQ 90
              A   L   K   +P+ ++
Sbjct: 58 EARKAFRHLAYSKFHHVPLYLE 79

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 68.6 bits (168), Expect = 9e-15
 Identities = 17/94 (18%), Positives = 40/94 (42%), Gaps = 1/94 (1%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
           SP+  +   +    L       ++ +FFS +  V +   +  +   R  G A+++F   E
Sbjct: 9   SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQE 68

Query: 70  SVPLAMGLNGQKLLGIPIIVQP-TQAEKNRAGNT 102
               A+  + +++    I +   ++AE   +G +
Sbjct: 69  IAEKALKKHKERIGHRYIEIFKSSRAEVRTSGPS 102

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 66.3 bits (162), Expect = 6e-14
 Identities = 19/104 (18%), Positives = 40/104 (38%), Gaps = 1/104 (0%)

Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
           G++  +     T     + +  L F  +++ +   F     + N   +     GRS G  
Sbjct: 1   GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60

Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
           F+ F S + A+KA  + +   +  R +++   +       G  S
Sbjct: 61  FVQFASQEIAEKA-LKKHKERIGHRYIEIFKSSRAEVRTSGPSS 103

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 68.2 bits (167), Expect = 1e-14
 Identities = 22/94 (23%), Positives = 41/94 (43%), Gaps = 3/94 (3%)

Query: 111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAK 170
               + + +  + F+  E+ +R  F    ++D + L+ D   GR+ G G + F S  D  
Sbjct: 13  NPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTF 70

Query: 171 KAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           +A +  N   +  R ++V   T+R     GG   
Sbjct: 71  EALK-RNRMLMIQRYVEVSPATERQWVAAGGHIT 103

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 64.8 bits (158), Expect = 3e-13
 Identities = 19/97 (19%), Positives = 38/97 (39%), Gaps = 3/97 (3%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
            P   D   +    +       D+ +FF  + +V  V L+  +   R  G   ++F  P+
Sbjct: 10  LPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLK-DHVGRNNGNGLVKFLSPQ 67

Query: 70  SVPLAMGLNGQKLLGIPIIVQP-TQAEKNRAGNTLPN 105
               A+  N   ++   + V P T+ +   AG  + +
Sbjct: 68  DTFEALKRNRMLMIQRYVEVSPATERQWVAAGGHITS 104

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 67.9 bits (166), Expect = 1e-14
 Identities = 17/74 (22%), Positives = 25/74 (33%), Gaps = 8/74 (10%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           ++I  L   + E  L    + FG I  + +M        K    + F     A  A    
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNAVNYA 77

Query: 177 --NGFELAGRPMKV 188
             N   +AG P  V
Sbjct: 78  ADNQIYIAGHPAFV 91

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 45.9 bits (109), Expect = 8e-07
 Identities = 16/77 (20%), Positives = 25/77 (32%), Gaps = 9/77 (11%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
            +    L   +   DL E     G +  V ++        K  A +EF+D      A+ 
Sbjct: 22 PVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNAVN 75

Query: 76 --GLNGQKLLGIPIIVQ 90
              N   + G P  V 
Sbjct: 76 YAADNQIYIAGHPAFVN 92

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 68.0 bits (166), Expect = 2e-14
 Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 9/85 (10%)

Query: 107 QPRGTGGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS 165
              G+G P R ++I  L  ++TE  +  +  PFGK+ N+ ++      + K   FI  ++
Sbjct: 8   HHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNT 61

Query: 166 ADDAKKAQE--QLNGFELAGRPMKV 188
            + A             L G+P+ +
Sbjct: 62  EEAANTMVNYYTSVTPVLRGQPIYI 86

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 47.9 bits (114), Expect = 2e-07
 Identities = 18/93 (19%), Positives = 34/93 (36%), Gaps = 9/93 (9%)

Query: 1  MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
          MR ++          +R I   +L   +   ++       GKV ++ ++      + K  
Sbjct: 1  MRGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQ 54

Query: 61 AYIEFKDPESVPLAM---GLNGQKLLGIPIIVQ 90
          A+IE    E+    +         L G PI +Q
Sbjct: 55 AFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ 87

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 68.0 bits (166), Expect = 2e-14
 Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 9/85 (10%)

Query: 107 QPRGTGGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS 165
             R  G P R ++I  L  ++TE  +  +  PFGK+ N+ ++      + K   FI  ++
Sbjct: 23  DSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNT 76

Query: 166 ADDAKKAQE--QLNGFELAGRPMKV 188
            + A             L G+P+ +
Sbjct: 77  EEAANTMVNYYTSVTPVLRGQPIYI 101

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 48.4 bits (115), Expect = 2e-07
 Identities = 18/92 (19%), Positives = 34/92 (36%), Gaps = 9/92 (9%)

Query: 2   RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIA 61
           R ++  D       +R I   +L   +   ++       GKV ++ ++      + K  A
Sbjct: 17  RGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQA 70

Query: 62  YIEFKDPESVPLAM---GLNGQKLLGIPIIVQ 90
           +IE    E+    +         L G PI +Q
Sbjct: 71  FIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ 102

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 68.3 bits (167), Expect = 3e-14
 Identities = 14/95 (14%), Positives = 36/95 (37%), Gaps = 3/95 (3%)

Query: 94  AEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTG 153
             +     +  +     +     +++  L +  TE+ +   F P      + + + PD G
Sbjct: 26  GGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-G 83

Query: 154 RSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
           R  G   + F + ++A  A    +   +  R +++
Sbjct: 84  RVTGEADVEFATHEEAVAAMS-KDRANMQHRYIEL 117

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 58.7 bits (142), Expect = 7e-11
 Identities = 21/110 (19%), Positives = 37/110 (33%), Gaps = 3/110 (2%)

Query: 2   RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIA 61
           R +   + + +      +    L  +    D+  FFS +  VR V  I      R  G A
Sbjct: 32  RGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR-VH-IEIGPDGRVTGEA 89

Query: 62  YIEFKDPESVPLAMGLNGQKLLGIPIIVQP-TQAEKNRAGNTLPNLQPRG 110
            +EF   E    AM  +   +    I +   +    +    +   +Q  G
Sbjct: 90  DVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTGASNGAYSSQVMQGMG 139

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 67.5 bits (165), Expect = 3e-14
 Identities = 15/93 (16%), Positives = 30/93 (32%), Gaps = 3/93 (3%)

Query: 96  KNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRS 155
            +       +   +      R+ + +L    +   L+ +                +T   
Sbjct: 10  HSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLE---TTFSSVNTRDF 66

Query: 156 KGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
            G G + F S +   +A E+LN  E  G  + V
Sbjct: 67  DGTGALEFPSEEILVEALERLNNIEFRGSVITV 99

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 41.0 bits (96), Expect = 7e-05
 Identities = 18/81 (22%), Positives = 27/81 (33%), Gaps = 4/81 (4%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
          S        I    L +    +DL++             +    TR F G   +EF   E
Sbjct: 22 SKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVN---TRDFDGTGALEFPSEE 78

Query: 70 SVPLAMG-LNGQKLLGIPIIV 89
           +  A+  LN  +  G  I V
Sbjct: 79 ILVEALERLNNIEFRGSVITV 99

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 67.2 bits (164), Expect = 5e-14
 Identities = 18/116 (15%), Positives = 39/116 (33%), Gaps = 3/116 (2%)

Query: 75  MGLNGQKL-LGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMR-LYIGSLHFNITEDMLR 132
           MG +         ++ + +       G  +              + +  L F  T++ + 
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIV 60

Query: 133 GIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
             F     + N   +     G+  G  F+ F S + A+KA    +   +  R ++V
Sbjct: 61  QFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEV 115

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 61.8 bits (150), Expect = 4e-12
 Identities = 16/90 (17%), Positives = 36/90 (40%), Gaps = 1/90 (1%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
           S +  +   +    L       ++ +FFS +  V +   +  +   +  G A+++F   E
Sbjct: 36  SADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQE 95

Query: 70  SVPLAMGLNGQKLLGIPIIVQP-TQAEKNR 98
               A+G + +++    I V   +Q E   
Sbjct: 96  LAEKALGKHKERIGHRYIEVFKSSQEEVRS 125

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 66.3 bits (162), Expect = 5e-14
 Identities = 19/98 (19%), Positives = 40/98 (40%), Gaps = 4/98 (4%)

Query: 107 QPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA 166
               +     +++  L +  TE+ +   F P      + + + PD GR  G   + F + 
Sbjct: 8   SSFQSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGPD-GRVTGEADVEFATH 65

Query: 167 DDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           +DA  A    +   +  R +++  +     + G GPS+
Sbjct: 66  EDAVAAMA-KDKANMQHRYVEL-FLNSTAGTSGSGPSS 101

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 55.9 bits (135), Expect = 3e-10
 Identities = 19/96 (19%), Positives = 32/96 (33%), Gaps = 3/96 (3%)

Query: 6   SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
           S   S +      +    L  R    D+  FFS +     V +       R  G A +EF
Sbjct: 5   SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEI-GPDGRVTGEADVEF 62

Query: 66  KDPESVPLAMGLNGQKLLGIPIIVQP-TQAEKNRAG 100
              E    AM  +   +    + +   + A  + +G
Sbjct: 63  ATHEDAVAAMAKDKANMQHRYVELFLNSTAGTSGSG 98

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 67.2 bits (164), Expect = 6e-14
 Identities = 15/82 (18%), Positives = 33/82 (40%), Gaps = 1/82 (1%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
              +Y+  L F      +   F+    +++   +     G++ G GF+ F +  D K A 
Sbjct: 25  GFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL 84

Query: 174 EQLNGFELAGRPMKVGTVTDRN 195
              +   +  R ++V  +T + 
Sbjct: 85  C-RHKQYMGNRFIQVHPITKKG 105

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 66.0 bits (161), Expect = 1e-13
 Identities = 14/92 (15%), Positives = 29/92 (31%)

Query: 7   DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
                       ++   L      + + +FF  +  V D   I      +  G  ++EF+
Sbjct: 16  SRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFR 75

Query: 67  DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNR 98
           +      A+  + Q +    I V P   +   
Sbjct: 76  NEADYKAALCRHKQYMGNRFIQVHPITKKGML 107

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 65.4 bits (160), Expect = 1e-13
 Identities = 13/81 (16%), Positives = 29/81 (35%), Gaps = 6/81 (7%)

Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
             G+ G   +++      +    L   F  FG + ++  ++D D G    +  +      
Sbjct: 2   SSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVG 56

Query: 168 DAKKAQEQLNGFELAGRPMKV 188
             +    Q +   L G  ++V
Sbjct: 57  AREAVLSQ-SQHSLGGHRLRV 76

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 57.7 bits (140), Expect = 4e-11
 Identities = 19/101 (18%), Positives = 40/101 (39%), Gaps = 8/101 (7%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
           S      R++F     + + +  L E+F + G V  V +        F   A +E  D  
Sbjct: 2   SSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDK--DKGVF---AIVEMGDVG 56

Query: 70  SVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRG 110
           +    +  +   L G  + V+P + ++ ++     +  P+G
Sbjct: 57  AREAVLSQSQHSLGGHRLRVRPREQKEFQSP---ASKSPKG 94

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 64.8 bits (158), Expect = 2e-13
 Identities = 15/99 (15%), Positives = 29/99 (29%), Gaps = 10/99 (10%)

Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
           P       R+ +  L  + +   L+      G +    +          G G + F   +
Sbjct: 9   PPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGVVEFVRKE 61

Query: 168 DAKKAQEQLNGFELAGRPMKVGTVT---DRNESVGGGPS 203
           D   A  +L+  +      +   +    D   S   G S
Sbjct: 62  DMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRS 100

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 14/80 (17%), Positives = 23/80 (28%), Gaps = 8/80 (10%)

Query: 11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
          P  R    +    L      +DL++     G V    +          G   +EF   E 
Sbjct: 10 PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKED 62

Query: 71 VPLAM-GLNGQKLLGIPIIV 89
          +  A+  L+  K        
Sbjct: 63 MTYAVRKLDNTKFRSHEGET 82

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 63.9 bits (156), Expect = 4e-13
 Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           + +    FN+TE  +     P  K   I+++ +   G   GY F+ F + ++ K+A +  
Sbjct: 13  VKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAH-GNKTGYIFVDFSNEEEVKQALK-C 69

Query: 177 NGFELAGRPMKV 188
           N   + GR ++V
Sbjct: 70  NREYMGGRYIEV 81

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 55.0 bits (133), Expect = 4e-10
 Identities = 15/84 (17%), Positives = 33/84 (39%), Gaps = 3/84 (3%)

Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
             T+        +  +++ EF + + K   +R++  N      G  +++F + E V  A
Sbjct: 9  TCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVR-NAHGNKTGYIFVDFSNEEEVKQA 66

Query: 75 MGLNGQKLLGIPIIVQP-TQAEKN 97
          +  N + + G  I V        +
Sbjct: 67 LKCNREYMGGRYIEVFREKSGPSS 90

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 63.7 bits (155), Expect = 4e-13
 Identities = 16/83 (19%), Positives = 32/83 (38%), Gaps = 7/83 (8%)

Query: 108 PRGTGGPM--RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS 165
           P G G P+   +Y+G+L  +     L+      G +      +       +   F+ +  
Sbjct: 11  PPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-----LRLTWQGPRRRAFLHYPD 65

Query: 166 ADDAKKAQEQLNGFELAGRPMKV 188
           +  A++A   L G  L    ++V
Sbjct: 66  SAAAQQAVSCLQGLRLGTDTLRV 88

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 52.1 bits (125), Expect = 6e-09
 Identities = 16/88 (18%), Positives = 36/88 (40%), Gaps = 6/88 (6%)

Query: 12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
              A  ++   L +  R  DL+     +G V  +RL      +  +  A++ + D  + 
Sbjct: 15 GAPLAADVYVGNLPRDARVSDLKRALRELGSV-PLRL----TWQGPRRRAFLHYPDSAAA 69

Query: 72 PLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
            A+  L G +L    + V   + ++++
Sbjct: 70 QQAVSCLQGLRLGTDTLRVALARQQRDK 97

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 63.7 bits (155), Expect = 4e-13
 Identities = 19/85 (22%), Positives = 34/85 (40%), Gaps = 9/85 (10%)

Query: 107 QPRGTGGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS 165
             +  G P R L+I  L   +TE  +  +  PFGK+ NI ++      + K   F+   +
Sbjct: 7   GDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML------KGKNQAFLELAT 60

Query: 166 ADDAKKAQE--QLNGFELAGRPMKV 188
            + A             L  +P+ +
Sbjct: 61  EEAAITMVNYYSAVTPHLRNQPIYI 85

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 44.4 bits (105), Expect = 3e-06
 Identities = 13/77 (16%), Positives = 28/77 (36%), Gaps = 9/77 (11%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
          R +   +L   +   ++       GKV ++ ++      + K  A++E    E+    + 
Sbjct: 16 RVLHIRKLPGEVTETEVIALGLPFGKVTNILML------KGKNQAFLELATEEAAITMVN 69

Query: 76 --GLNGQKLLGIPIIVQ 90
                  L   PI +Q
Sbjct: 70 YYSAVTPHLRNQPIYIQ 86

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 64.1 bits (156), Expect = 4e-13
 Identities = 11/96 (11%), Positives = 27/96 (28%), Gaps = 7/96 (7%)

Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
           P       R+ +  L  + +   L+      G +    +          G G + F   +
Sbjct: 10  PPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGVVEFVRKE 62

Query: 168 DAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
           D   A  +L+  +      +   +  + +       
Sbjct: 63  DMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSY 98

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 43.7 bits (103), Expect = 7e-06
 Identities = 14/89 (15%), Positives = 23/89 (25%), Gaps = 8/89 (8%)

Query: 2  RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIA 61
                   P  R    +    L      +DL++     G V    +          G  
Sbjct: 2  GAPRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTG 54

Query: 62 YIEFKDPESVPLAM-GLNGQKLLGIPIIV 89
           +EF   E +  A+  L+  K        
Sbjct: 55 VVEFVRKEDMTYAVRKLDNTKFRSHEGET 83

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 63.0 bits (153), Expect = 1e-12
 Identities = 21/109 (19%), Positives = 36/109 (33%), Gaps = 5/109 (4%)

Query: 9   LSPEERDARTIFCMQLSQRIRTRDLEEFFSS---VGKVRDVRLITCNKTRRFKGIAYIEF 65
           L PE  +   +    L       D++ F S       V  V  I   +  R  G A++E 
Sbjct: 10  LGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIY-TREGRQSGEAFVEL 68

Query: 66  KDPESVPLAMGLNGQKLLGIPIIVQP-TQAEKNRAGNTLPNLQPRGTGG 113
           +  + V LA+  + + +    I V    + E +            G   
Sbjct: 69  ESEDDVKLALKKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGPSS 117

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 57.2 bits (138), Expect = 1e-10
 Identities = 17/92 (18%), Positives = 38/92 (41%), Gaps = 6/92 (6%)

Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPF---GKIDNIQLMVDPDTGRSK 156
           G++   L P G  G + + +  L ++ + + ++           +  +  +   + GR  
Sbjct: 4   GSSGMMLGPEGGEGYV-VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQS 61

Query: 157 GYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
           G  F+   S DD K A +  +   +  R ++V
Sbjct: 62  GEAFVELESEDDVKLALK-KDRESMGHRYIEV 92

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 61.5 bits (150), Expect = 2e-12
 Identities = 10/81 (12%), Positives = 34/81 (41%), Gaps = 7/81 (8%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++G    ++T + L+  F  +G++ ++ +         + + F+TF     A+    +
Sbjct: 13  KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCGE 67

Query: 176 LNGFELAGRPMKVGTVTDRNE 196
                + G  + +     ++ 
Sbjct: 68  --DLIIKGISVHISNAEPKHN 86

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 46.8 bits (112), Expect = 4e-07
 Identities = 17/91 (18%), Positives = 37/91 (40%), Gaps = 9/91 (9%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
                   +F  + ++ +   +L++FF   G+V DV +      + F+  A++ F D +
Sbjct: 5  HHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFI-----PKPFRAFAFVTFADDK 59

Query: 70 SVPLAMGLNGQKLLGIPIIV---QPTQAEKN 97
                G     + GI + +   +P   + N
Sbjct: 60 VAQSLCG-EDLIIKGISVHISNAEPKHNKLN 89

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 62.4 bits (151), Expect = 6e-12
 Identities = 15/85 (17%), Positives = 33/85 (38%), Gaps = 4/85 (4%)

Query: 104 PNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITF 163
             +   G    +R+ + +L + +T D+L  IF  FG +  I          ++    + +
Sbjct: 36  AGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQY 91

Query: 164 HSADDAKKAQEQLNGFELAGRPMKV 188
                A+ A+  L+G  +      +
Sbjct: 92  ADPVSAQHAKLSLDGQNIYNACCTL 116

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 61.2 bits (148), Expect = 8e-12
 Identities = 15/85 (17%), Positives = 33/85 (38%), Gaps = 4/85 (4%)

Query: 104 PNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITF 163
             +   G    +R+ + +L + +T D+L  IF  FG +  I          ++    + +
Sbjct: 18  AGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQY 73

Query: 164 HSADDAKKAQEQLNGFELAGRPMKV 188
                A+ A+  L+G  +      +
Sbjct: 74  ADPVSAQHAKLSLDGQNIYNACCTL 98

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 60.8 bits (147), Expect = 1e-11
 Identities = 19/102 (18%), Positives = 34/102 (33%), Gaps = 5/102 (4%)

Query: 2   RPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSS---VGKVRDVRLITCNKTRRFK 58
               S  L PE  +   +    L       D++ F S          V  I   +  R  
Sbjct: 30  MGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIY-TREGRQS 88

Query: 59  GIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQP-TQAEKNRA 99
           G A++E    + V +A+  + + +    I V    + E +  
Sbjct: 89  GEAFVELGSEDDVKMALKKDRESMGHRYIEVFKSHRTEMDWV 130

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 57.7 bits (139), Expect = 2e-10
 Identities = 13/88 (14%), Positives = 31/88 (35%), Gaps = 5/88 (5%)

Query: 104 PNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPF---GKIDNIQLMVDPDTGRSKGYGF 160
             +     G    + +  L ++ + + ++              +  +   + GR  G  F
Sbjct: 34  SMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAF 92

Query: 161 ITFHSADDAKKAQEQLNGFELAGRPMKV 188
           +   S DD K A +  +   +  R ++V
Sbjct: 93  VELGSEDDVKMALK-KDRESMGHRYIEV 119

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 112

 Score = 60.1 bits (146), Expect = 1e-11
 Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 1/42 (2%)

Query: 265 APPIATQCFLLANMFDPA-TETNPTWDVEIRDDVIEECNKHG 305
           +     +  ++ NMF P   E +P    EIR+D+  EC+K G
Sbjct: 10  SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFG 51

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 59.5 bits (144), Expect = 2e-11
 Identities = 17/97 (17%), Positives = 31/97 (31%), Gaps = 5/97 (5%)

Query: 7  DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSS---VGKVRDVRLITCNKTRRFKGIAYI 63
            L  E  D   I    L       D+  FFS          +  +  N+  + +G A I
Sbjct: 2  SKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLL-NRDGKRRGDALI 60

Query: 64 EFKDPESVPLAMGLNGQKLLGIPIIVQP-TQAEKNRA 99
          E +  + V  A+  +   +    + V      + +  
Sbjct: 61 EMESEQDVQKALEKHRMYMGQRYVEVYEINNEDVDAL 97

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 55.2 bits (133), Expect = 6e-10
 Identities = 15/75 (20%), Positives = 31/75 (41%), Gaps = 5/75 (6%)

Query: 117 LYIGSLHFNITEDMLRGIFEPF---GKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
           +    L ++ T + +   F         + I  +++ D G+ +G   I   S  D +KA 
Sbjct: 14  IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKAL 72

Query: 174 EQLNGFELAGRPMKV 188
           E  +   +  R ++V
Sbjct: 73  E-KHRMYMGQRYVEV 86

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 59.1 bits (143), Expect = 3e-11
 Identities = 24/117 (20%), Positives = 41/117 (35%), Gaps = 14/117 (11%)

Query: 99  AGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKI----DNIQLMVDPDTGR 154
            G +    Q       + + +  L F  T + +   F     I    + I  +  PD GR
Sbjct: 8   GGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPD-GR 66

Query: 155 SKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV--------GTVTDRNESVGGGPS 203
             G  F+ F   + A+ A  + +   L  R +++          V +R  S  G  S
Sbjct: 67  PTGDAFVLFACEEYAQNA-LRKHKDLLGKRYIELFRSTAAEVQQVLNRFSSASGPSS 122

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 56.4 bits (136), Expect = 3e-10
 Identities = 17/106 (16%), Positives = 32/106 (30%), Gaps = 4/106 (3%)

Query: 11  PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVR---LITCNKTRRFKGIAYIEFKD 67
             + +   +    L       ++  FF     +   +   L       R  G A++ F  
Sbjct: 18  LSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFAC 77

Query: 68  PESVPLAMGLNGQKLLGIPIIVQP-TQAEKNRAGNTLPNLQPRGTG 112
            E    A+  +   L    I +   T AE  +  N   +     +G
Sbjct: 78  EEYAQNALRKHKDLLGKRYIELFRSTAAEVQQVLNRFSSASGPSSG 123

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 59.8 bits (144), Expect = 9e-11
 Identities = 17/84 (20%), Positives = 36/84 (42%), Gaps = 4/84 (4%)

Query: 17  RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
           R+++           D++E+    G+V ++++      + FKG  ++ F   ES    + 
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRR-TLHKAFKGSIFVVFDSIESAKKFVE 168

Query: 77  LNGQKLLGIPIIVQPTQ---AEKN 97
             GQK     +++       A+KN
Sbjct: 169 TPGQKYKETDLLILFKDDYFAKKN 192

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 59.8 bits (144), Expect = 9e-11
 Identities = 19/79 (24%), Positives = 31/79 (39%), Gaps = 2/79 (2%)

Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
             +YI     + T D ++   E  G++ NIQ+         KG  F+ F S + AKK  E
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE 168

Query: 175 QLNGFELAGRPMKVGTVTD 193
                +     + +    D
Sbjct: 169 TPGQ-KYKETDLLILFKDD 186

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 55.6 bits (134), Expect = 4e-10
 Identities = 13/36 (36%), Positives = 19/36 (52%)

Query: 270 TQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
           T+   L NM  P    +     EI +DV +EC+K+G
Sbjct: 5   TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYG 40

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 41.3 bits (97), Expect = 4e-05
 Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 3/65 (4%)

Query: 126 ITEDMLRGIFEPFGKIDNIQL--MVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG 183
           I ED+ R     +G + +I++   VD       G  F+ F S  D +KA + L G + A 
Sbjct: 28  IVEDV-RDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFAN 86

Query: 184 RPMKV 188
           R +  
Sbjct: 87  RVVVT 91

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 55.3 bits (133), Expect = 5e-10
 Identities = 22/96 (22%), Positives = 38/96 (39%), Gaps = 10/96 (10%)

Query: 97  NRAGNTLPNLQPRGTGGPMR-LYIGSL-HFNITEDMLRGIFEPFGKIDNIQLMVDPDTGR 154
            +     P+ +        R +++ +L H   ++  +  + EP+GKI N  LM      R
Sbjct: 7   GKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM------R 60

Query: 155 SKGYGFITFHSADDAKKAQE--QLNGFELAGRPMKV 188
            K   FI   + +DA    +          GR +KV
Sbjct: 61  MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV 96

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 55.4 bits (133), Expect = 6e-10
 Identities = 19/90 (21%), Positives = 32/90 (35%), Gaps = 11/90 (12%)

Query: 110 GTGGPMR---LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPD--TGRSKGYGFITFH 164
           G+ G      +++G L  +I ED +   F  FG +                KGY F+ F 
Sbjct: 1   GSSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60

Query: 165 ---SADDAKKAQEQLNG---FELAGRPMKV 188
              S      A  + +G     ++   +K 
Sbjct: 61  EESSVQALIDACLEEDGKLYLCVSSPTIKD 90

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 41.9 bits (98), Expect = 3e-05
 Identities = 13/68 (19%), Positives = 23/68 (33%), Gaps = 2/68 (2%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLI--TCNKTRRFKGIAYIEFKD 67
          S     +R +F   L   I   ++   F   G +                KG A++ F++
Sbjct: 2  SSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQE 61

Query: 68 PESVPLAM 75
            SV   +
Sbjct: 62 ESSVQALI 69

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 55.6 bits (133), Expect = 4e-09
 Identities = 20/91 (21%), Positives = 34/91 (37%), Gaps = 15/91 (16%)

Query: 117 LYIGSLHFNIT---------EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
           LY+G +   +          E  +R +F   G ID I+ +       SK  GF+ F    
Sbjct: 137 LYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV------ESKNCGFVKFKYQA 190

Query: 168 DAKKAQEQLNGFELAGRPMKVGTVTDRNESV 198
           +A+ A+E ++   L     K          +
Sbjct: 191 NAEFAKEAMSNQTLLLPSDKEWDDRREGTGL 221

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} PDB: 3us5_A 2dny_A Length = 118

 Score = 49.8 bits (119), Expect = 6e-08
 Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 5/52 (9%)

Query: 254 NSSTPQVSSSTAPPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
           +S+   V         +   +L NM DP        D ++  +V EEC K G
Sbjct: 4   SSARHMVMQKLLRKQESTVMVLRNMVDPKD-----IDDDLEGEVTEECGKFG 50

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104

 Score = 49.1 bits (117), Expect = 9e-08
 Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 128 EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMK 187
           E++   + E +G+++ + +  D       G  ++ F   +DA+KA   LN     G+P+ 
Sbjct: 41  EEVFTEMEEKYGEVEEMNV-CDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99

Query: 188 V 188
            
Sbjct: 100 A 100

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 48.9 bits (116), Expect = 1e-07
 Identities = 25/100 (25%), Positives = 40/100 (40%), Gaps = 10/100 (10%)

Query: 91  PTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDP 150
            +     R GN      P G    + L I +  + IT D+L  +  P GK+  I      
Sbjct: 5   SSGKRITRPGN---TDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRI-----V 56

Query: 151 DTGRSKGYGFITFHSADDAKKAQEQLNGFELAGR--PMKV 188
              R+     + F S   A+KA+  LNG ++      +K+
Sbjct: 57  IFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKI 96

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A Length = 105

 Score = 46.0 bits (109), Expect = 8e-07
 Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 5/40 (12%)

Query: 266 PPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
               T+  LL NM           D ++  +  EEC K+G
Sbjct: 4   GKCPTKVVLLRNMVGAGEV-----DEDLEVETKEECEKYG 38

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 45.2 bits (107), Expect = 2e-06
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 10/88 (11%)

Query: 105 NLQPRGTGGPMR-LYIGSLHFNI-TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFIT 162
           +   +G     R ++I            L  + EPFG I N  ++            FI 
Sbjct: 5   SSGQKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL------NKINEAFIE 58

Query: 163 FHSADDAKKAQE--QLNGFELAGRPMKV 188
             + +DA+ A +        + G+P++V
Sbjct: 59  MATTEDAQAAVDYYTTTPALVFGKPVRV 86

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 44.2 bits (104), Expect = 4e-06
 Identities = 14/95 (14%), Positives = 38/95 (40%), Gaps = 7/95 (7%)

Query: 110 GTGGPMRLYIGSLHFNITED----MLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS 165
            +G    + + ++ + ++      +L+  F   GK+ +++L    D    +    +   +
Sbjct: 5   SSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTD---YQLKAVVQMEN 61

Query: 166 ADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGG 200
             DA  A   L+ +++  + + V   T  +    G
Sbjct: 62  LQDAIGAVNSLHRYKIGSKKILVSLATGASGPSSG 96

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 41.1 bits (96), Expect = 5e-05
 Identities = 19/103 (18%), Positives = 38/103 (36%), Gaps = 7/103 (6%)

Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           G+ G + + +  L   + +++L   FE   +     ++      R    G +TF    DA
Sbjct: 4   GSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVL---SWQRLGCGGVLTFREPADA 60

Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNES---VGGGPSNLDTDE 209
           ++   Q +  EL G  + +     R  +   + G P       
Sbjct: 61  ERVLAQAD-HELHGAQLSLRPAPPRAPARLLLQGLPPGTSGPS 102

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 37.6 bits (87), Expect = 8e-04
 Identities = 11/106 (10%), Positives = 29/106 (27%), Gaps = 6/106 (5%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
           S        +    L   +    L  +F +  +     +++  +         + F++P 
Sbjct: 2   SSGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCG---GVLTFREPA 58

Query: 70  SVPLAMGLNGQKLLGIPIIVQPTQAEKNRA---GNTLPNLQPRGTG 112
                +     +L G  + ++P               P      +G
Sbjct: 59  DAERVLAQADHELHGAQLSLRPAPPRAPARLLLQGLPPGTSGPSSG 104

>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* Length = 345

 Score = 42.8 bits (100), Expect = 1e-04
 Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 8/71 (11%)

Query: 117 LYI--GSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           L +  G L   ++ + L  + E  G +D + +        +K Y F  + + +++K+A  
Sbjct: 21  LVVANGGLGNGVSRNQLLPVLEKCGLVDALLM------PPNKPYSFARYRTTEESKRAYV 74

Query: 175 QLNGFELAGRP 185
            LNG E+    
Sbjct: 75  TLNGKEVVDDL 85

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 39.4 bits (91), Expect = 2e-04
 Identities = 15/79 (18%), Positives = 35/79 (44%), Gaps = 7/79 (8%)

Query: 125 NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGR 184
             ++D+L  + + +G++ N+ L     + +  G   + F +   A+ A +   G  L   
Sbjct: 28  GYSKDVLLRLLQKYGEVLNLVL-----SSKKPGTAVVEFATVKAAELAVQNEVG--LVDN 80

Query: 185 PMKVGTVTDRNESVGGGPS 203
           P+K+  +  + +   G  S
Sbjct: 81  PLKISWLEGQPQDASGPSS 99

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	370
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	100.0
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	100.0
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.98
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.98
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.97
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.97
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.97
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.96
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.96
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.96
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.96
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.89
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.84
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.83
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.81
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.81
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.8
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.8
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.79
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.78
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.77
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.77
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.76
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.76
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.76
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.76
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.76
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.76
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.75
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.75
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.75
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.75
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.75
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.75
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.75
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.75
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.75
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.74
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.74
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.74
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.74
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.74
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.74
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.74
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.74
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.74
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.74
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.74
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.73
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.73
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.73
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.73
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.73
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.73
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.73
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.73
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.73
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.73
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.73
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.73
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.73
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.73
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.73
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.73
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.73
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.73
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.73
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.73
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.73
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.72
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.72
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.72
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.72
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.72
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.72
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.72
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.72
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.72
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.72
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.72
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.72
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.72
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.72
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.72
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.72
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.72
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.72
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.72
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.71
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.71
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.71
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.71
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.71
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.71
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.71
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.71
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.71
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.71
2div_A	99	TRNA selenocysteine associated protein; structural	99.71
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.71
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.71
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.71
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.71
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.71
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.71
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.71
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.71
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.71
2div_A	99	TRNA selenocysteine associated protein; structural	99.71
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.71
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.7
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.7
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.7
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.7
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.7
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.7
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.7
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.7
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.7
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.7
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.7
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.7
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.7
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.7
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.7
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.7
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.7
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.7
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.7
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.7
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.7
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.69
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.69
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.69
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.69
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.69
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.69
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.69
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.69
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.69
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.69
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.69
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.69
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.69
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.69
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.69
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.69
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.69
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.69
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.69
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.69
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.69
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.68
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.68
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.68
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.68
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.68
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.68
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.68
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.68
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.68
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.68
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.68
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.68
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.68
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.68
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.68
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.68
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.68
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.68
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.68
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.68
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.68
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.68
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.67
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.67
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.67
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.67
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.67
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.67
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.67
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.67
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.67
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.67
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.67
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.67
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.67
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.67
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.67
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.67
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.67
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.67
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.67
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.67
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.67
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.66
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.66
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.66
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.66
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.66
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.66
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.66
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.66
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.66
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.66
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.66
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.66
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.66
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.66
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.65
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.65
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.65
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.65
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.65
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.65
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.65
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.65
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.65
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.65
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.65
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.65
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.65
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.65
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.65
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.65
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.64
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.64
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.64
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.64
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.64
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.64
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.64
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.64
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.64
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.64
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.64
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.63
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.63
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.63
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.63
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.63
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.63
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.63
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.63
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.63
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.63
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.63
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.63
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.62
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.62
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.62
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.62
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.62
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.62
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.62
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.42
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.62
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.62
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.62
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.62
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.62
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.61
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.61
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.61
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.61
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.61
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.61
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.61
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.61
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.61
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.61
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.61
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.6
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.6
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.6
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.6
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.6
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.6
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.6
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.6
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.6
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.6
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.6
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.38
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.59
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.59
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.59
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.59
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.59
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.59
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.59
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.59
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.58
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.58
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.58
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.58
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.58
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.58
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.58
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.58
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.57
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.57
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.57
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.57
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.57
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.57
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.56
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.56
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.56
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.56
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.56
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.56
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.56
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.56
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.55
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.55
1x5p_A	97	Negative elongation factor E; structure genomics,	99.55
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.55
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.55
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.55
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.55
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.55
1x5p_A	97	Negative elongation factor E; structure genomics,	99.54
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.54
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.54
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.54
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.53
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.53
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.53
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.52
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.52
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.52
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.52
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.51
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.5
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.5
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.5
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.5
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.49
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.49
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.48
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.48
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.48
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.48
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.46
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.44
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.43
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.41
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.39
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.39
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.38
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.34
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.34
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.32
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.3
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.29
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.25
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.2
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.19
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.16
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.15
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.15
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.13
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.89
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.89
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.79
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.7
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.67
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.64
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.62
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.55
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.53
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.26
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.06
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.66
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.25
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.16
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.09
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.01
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.97
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.94
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.73
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.56
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.48
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.43
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.31
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	95.93
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	94.97
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	94.81
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	94.29
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	90.99

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=8e-35  Score=259.10  Aligned_cols=174  Identities=28%  Similarity=0.448  Sum_probs=151.7

Q ss_pred             CCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCee
Q psy2983           8 DLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIP   86 (370)
Q Consensus         8 ~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~   86 (370)
                      .+.....+.++|||+|||.++|+++|+++|++||+|.+|++++|+.+++++|||||+|.+.++|.+|++ +++..+.|+.
T Consensus         7 ~p~~p~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~   86 (213)
T 4f02_A            7 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKP   86 (213)
T ss_dssp             --------CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcc
Confidence            334445678999999999999999999999999999999999999999999999999999999999995 9999999999


Q ss_pred             EEEecccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCH
Q psy2983          87 IIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA  166 (370)
Q Consensus        87 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~  166 (370)
                      +++.++........           ....+|||+|||+.+++++|+++|++||.|..++++.+.  +.++|||||+|.+.
T Consensus        87 i~~~~~~~~~~~~~-----------~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~  153 (213)
T 4f02_A           87 VRIMWSQRDPSLRK-----------SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQ  153 (213)
T ss_dssp             CEEEECCCCTHHHH-----------HCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSH
T ss_pred             cccccccccccccc-----------cccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCH
Confidence            99988764332211           123689999999999999999999999999999999884  55899999999999


Q ss_pred             HHHHHHHHHhCCceeCCeeEEEEEeecC
Q psy2983         167 DDAKKAQEQLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       167 ~~a~~A~~~l~g~~i~g~~l~V~~~~~~  194 (370)
                      ++|.+|++.|||..|.|++|+|.++.++
T Consensus       154 ~~a~~Ai~~lng~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          154 EAAERAIEKMNGMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             HHHHHHHHHHTTCEETTEECEEEECCCH
T ss_pred             HHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            9999999999999999999999998654

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=100.00  E-value=3.6e-34  Score=250.71  Aligned_cols=180  Identities=23%  Similarity=0.416  Sum_probs=155.1

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIV   89 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v   89 (370)
                      +....+.++|||+|||.++|+++|+++|+.||.|.++.+++++.++.++|||||+|.+.++|.+|++.++..+.|+.|.|
T Consensus         7 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v   86 (196)
T 1l3k_A            7 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEP   86 (196)
T ss_dssp             -CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeee
Confidence            33456789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHH
Q psy2983          90 QPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA  169 (370)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a  169 (370)
                      .++........       +......++|||+|||+.+++++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|
T Consensus        87 ~~~~~~~~~~~-------~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A  159 (196)
T 1l3k_A           87 KRAVSREDSQR-------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV  159 (196)
T ss_dssp             EECCC------------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHH
T ss_pred             ecccCcccccc-------cccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHH
Confidence            98765432211       11223457999999999999999999999999999999999988999999999999999999


Q ss_pred             HHHHHHhCCceeCCeeEEEEEeecCCCC
Q psy2983         170 KKAQEQLNGFELAGRPMKVGTVTDRNES  197 (370)
Q Consensus       170 ~~A~~~l~g~~i~g~~l~V~~~~~~~~~  197 (370)
                      .+|+.. +|..+.|+.|.|.++.++...
T Consensus       160 ~~A~~~-~~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          160 DKIVIQ-KYHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             HHHHHC-SCCEETTEECEEEECC-----
T ss_pred             HHHHHh-CCcEECCEEEEEEecCChhHh
Confidence            999995 899999999999998776554

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.6e-33  Score=239.63  Aligned_cols=164  Identities=24%  Similarity=0.532  Sum_probs=151.0

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHh-hccCCccCCeeEEEeccccc
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAE   95 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~i~g~~l~v~~~~~~   95 (370)
                      |+|||+|||.++|+++|+++|+.||+|.++.+++++. ++++|||||+|.+.++|..|+ .++|..+.|++|.|.++...
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC--CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCC-CCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            7899999999999999999999999999999999875 678999999999999999999 59999999999999987643


Q ss_pred             ccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHH
Q psy2983          96 KNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ  175 (370)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~  175 (370)
                      ..           .......+|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..
T Consensus        80 ~~-----------~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~  148 (166)
T 3md3_A           80 QQ-----------SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS  148 (166)
T ss_dssp             CC-----------CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHH
T ss_pred             CC-----------CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHH
Confidence            22           1233467999999999999999999999999999999999988999999999999999999999999


Q ss_pred             hCCceeCCeeEEEEEee
Q psy2983         176 LNGFELAGRPMKVGTVT  192 (370)
Q Consensus       176 l~g~~i~g~~l~V~~~~  192 (370)
                      |||..+.|++|+|.++.
T Consensus       149 l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          149 MQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             HTTCEETTEECEEEESC
T ss_pred             hCCCccCCcEEEEEecC
Confidence            99999999999999975

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=100.00  E-value=1.9e-33  Score=239.86  Aligned_cols=164  Identities=25%  Similarity=0.417  Sum_probs=152.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      ++++|||+|||.++++++|+++|+.||+|.++.+++++.+++++|||||+|.+.++|..|++ ++|..+.|++|.|.++.
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            46899999999999999999999999999999999999999999999999999999999996 99999999999999886


Q ss_pred             ccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHH
Q psy2983          94 AEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ  173 (370)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~  173 (370)
                      ....             .....+|||+|||..+++++|+++|++||.|..+.+..+..+|.++|||||+|.+.++|.+|+
T Consensus        82 ~~~~-------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~  148 (168)
T 1b7f_A           82 PGGE-------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI  148 (168)
T ss_dssp             CCSS-------------TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH
T ss_pred             CCcc-------------cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHH
Confidence            4321             223578999999999999999999999999999999999889999999999999999999999


Q ss_pred             HHhCCceeCC--eeEEEEEe
Q psy2983         174 EQLNGFELAG--RPMKVGTV  191 (370)
Q Consensus       174 ~~l~g~~i~g--~~l~V~~~  191 (370)
                      ..|||..+.|  ++|+|.++
T Consensus       149 ~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          149 SALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHHTTCCCTTCSSCCEEEEC
T ss_pred             HHhcCCEecCCCeEEEEEeC
Confidence            9999999987  99999875

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=100.00  E-value=3.2e-33  Score=237.97  Aligned_cols=164  Identities=26%  Similarity=0.448  Sum_probs=151.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      .+++|||+|||.++++++|+++|+.||+|.++.+++++.+++++|||||+|.+.++|..|++ ++|..+.|++|.|.++.
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            36899999999999999999999999999999999999899999999999999999999996 99999999999999886


Q ss_pred             ccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHH
Q psy2983          94 AEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ  173 (370)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~  173 (370)
                      +....             ....+|||+|||..+++++|+++|++||.|..+++..+..+|.++|||||+|.+.++|.+|+
T Consensus        81 ~~~~~-------------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~  147 (167)
T 1fxl_A           81 PSSAS-------------IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI  147 (167)
T ss_dssp             CCCGG-------------GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH
T ss_pred             CCccc-------------CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHH
Confidence            44321             23468999999999999999999999999999999999889999999999999999999999


Q ss_pred             HHhCCceeCCee--EEEEEe
Q psy2983         174 EQLNGFELAGRP--MKVGTV  191 (370)
Q Consensus       174 ~~l~g~~i~g~~--l~V~~~  191 (370)
                      ..|||..+.|+.  |+|.++
T Consensus       148 ~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          148 KGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHHTTCCCTTCSSCCEEEEC
T ss_pred             HHhcCCccCCCccceEEEeC
Confidence            999999999975  777764

>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=100.00  E-value=3.8e-34  Score=244.13  Aligned_cols=166  Identities=23%  Similarity=0.463  Sum_probs=152.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEeccc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~~   93 (370)
                      +++++|||+|||.++|+++|+++|+.||+|.++.+++++.+++++|||||+|.+.++|..|++ ++..+.|+.|.+.++.
T Consensus         1 k~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK-TQHILDGKVIDPKRAI   79 (167)
T ss_dssp             CGGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH-SCCEETTEECCCEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh-cccccCCeEccccccc
Confidence            467999999999999999999999999999999999999999999999999999999999997 3678999999988876


Q ss_pred             ccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHH
Q psy2983          94 AEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ  173 (370)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~  173 (370)
                      .....             ....+|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+
T Consensus        80 ~~~~~-------------~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~  146 (167)
T 2cjk_A           80 PRDEQ-------------DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC  146 (167)
T ss_dssp             CHHHH-------------HHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHH
T ss_pred             chhhc-------------cCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHH
Confidence            44322             12468999999999999999999999999999999999889999999999999999999999


Q ss_pred             HHhCCceeCCeeEEEEEeecC
Q psy2983         174 EQLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       174 ~~l~g~~i~g~~l~V~~~~~~  194 (370)
                      + ++|..+.|++|+|.++.++
T Consensus       147 ~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          147 Q-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             H-CSEECSSSSCEEEEECCCC
T ss_pred             h-CCCEEeCCeEEEEeecCCC
Confidence            9 8999999999999998775

>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=100.00  E-value=8e-33  Score=256.61  Aligned_cols=208  Identities=23%  Similarity=0.343  Sum_probs=185.9

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      .+++++|||+|||.++|+++|+++|+.|| |.++.+      ++++|||||+|.+.++|..|++ ++|..+.|++|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~------~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~   91 (284)
T 3smz_A           19 FRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL   91 (284)
T ss_dssp             HHCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE------ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEe
Confidence            45789999999999999999999999999 999887      4568999999999999999995 999999999999987


Q ss_pred             ccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHH
Q psy2983          92 TQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK  171 (370)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~  171 (370)
                      +.                   ...+|||+|||+.+++++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|.+
T Consensus        92 ~~-------------------~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~  152 (284)
T 3smz_A           92 QP-------------------TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR  152 (284)
T ss_dssp             CC-------------------CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHH
T ss_pred             cC-------------------CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHH
Confidence            43                   23689999999999999999999999999999999998899999999999999999999


Q ss_pred             HHHHhCCceeCCeeEEEEEeecCCC----------CcCCCCCCC-CHHHHHHhcccCCceeeeeeeeccc---cCCC---
Q psy2983         172 AQEQLNGFELAGRPMKVGTVTDRNE----------SVGGGPSNL-DTDEMERAGVDLGATGRLQLMFKLA---EGTG---  234 (370)
Q Consensus       172 A~~~l~g~~i~g~~l~V~~~~~~~~----------~~~~~~~~~-~~~~l~~~~~~~g~~~~~~l~~~~~---~~~~---  234 (370)
                      |+..|+|..+.|+.|.|.++.+...          .++++|..+ ++++++..|..+|.+..+.++.+..   ++++   
T Consensus       153 A~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~  232 (284)
T 3smz_A          153 AKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLE  232 (284)
T ss_dssp             HHHHHTTCEETTEECEEEECCGGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEE
T ss_pred             HHHHhCCCEeCCcEEEEEECCCCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEE
Confidence            9999999999999999999876543          256889995 8999999999999999999887632   3344   


Q ss_pred             CCChHHHHHHHh
Q psy2983         235 LELPPAAASALN  246 (370)
Q Consensus       235 ~~~~~~a~~a~~  246 (370)
                      |..+.+|..|+.
T Consensus       233 f~~~~~A~~A~~  244 (284)
T 3smz_A          233 YETAEMAEEAQQ  244 (284)
T ss_dssp             CSSHHHHHHHHH
T ss_pred             eCCHHHHHHHHH
Confidence            778888888776

>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=100.00  E-value=2.9e-33  Score=260.58  Aligned_cols=217  Identities=17%  Similarity=0.238  Sum_probs=180.9

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIV   89 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v   89 (370)
                      +...++.++|||+|||.++|+++|+++|+.||+|.+|.++++..+  ++|||||+|.+.++|.+|++++|..+.|++|.|
T Consensus        35 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v  112 (292)
T 2ghp_A           35 LTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAITKTHKVVGQNEIIV  112 (292)
T ss_dssp             -------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHTTTTCEETTEECEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC--CcEEEEEEECCHHHHHHHHHhCCcEeCCcEEEE
Confidence            445678999999999999999999999999999999999998754  479999999999999999999999999999999


Q ss_pred             ecccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCC-ceeeEEEeecCCCCCcccEEEEEECCHHH
Q psy2983          90 QPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFG-KIDNIQLMVDPDTGRSKGYGFITFHSADD  168 (370)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G-~i~~v~~~~~~~~g~~~g~afV~f~~~~~  168 (370)
                      .++.                    .++|||+|||+.+++++|+++|++|| .|..+.++.+. .|.++|||||+|.+.++
T Consensus       113 ~~~~--------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~-~~~~~g~afV~f~~~~~  171 (292)
T 2ghp_A          113 SHLT--------------------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRRFAYIDVTSKED  171 (292)
T ss_dssp             EECC--------------------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHH
T ss_pred             EECC--------------------CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCC-CCCcceEEEEEECCHHH
Confidence            8752                    46899999999999999999999999 99999999886 48899999999999999


Q ss_pred             HHHHHHHhCCceeCCeeEEEEEeecCCC--------------CcCCCCCC-CCHHHHHHhcccCCceeeeeeeeccc---
Q psy2983         169 AKKAQEQLNGFELAGRPMKVGTVTDRNE--------------SVGGGPSN-LDTDEMERAGVDLGATGRLQLMFKLA---  230 (370)
Q Consensus       169 a~~A~~~l~g~~i~g~~l~V~~~~~~~~--------------~~~~~~~~-~~~~~l~~~~~~~g~~~~~~l~~~~~---  230 (370)
                      |.+|+..|+|..+.|+.|.|.++.+...              .+++++.. +++++|+..|..||.+..+.++.+..   
T Consensus       172 a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg  251 (292)
T 2ghp_A          172 ARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHS  251 (292)
T ss_dssp             HHHHHHHHTTCEETTEECEEEECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---
T ss_pred             HHHHHHHhCCCEeCCcEEEEEECCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCC
Confidence            9999999999999999999999765432              15567888 99999999999999999999887543   


Q ss_pred             --cCCC---CCChHHHHHHHhhhc
Q psy2983         231 --EGTG---LELPPAAASALNLAQ  249 (370)
Q Consensus       231 --~~~~---~~~~~~a~~a~~~~~  249 (370)
                        ++++   |..+.+|..|+.+.+
T Consensus       252 ~~~g~afV~F~~~~~A~~A~~l~g  275 (292)
T 2ghp_A          252 FNNCCAFMVFENKDSAERALQMNR  275 (292)
T ss_dssp             CCCEEEEEEESSHHHHHHHGGGTT
T ss_pred             CCceEEEEEeCCHHHHHHHHHhcC
Confidence              3444   677888888774433

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=100.00  E-value=2e-32  Score=243.28  Aligned_cols=183  Identities=25%  Similarity=0.446  Sum_probs=157.0

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      ..+.++|||+|||.++|+++|+++|+.||+|.++.++++..+++++|||||+|.+.++|.+|++ ++|..+.|+.|.|.+
T Consensus        25 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~  104 (216)
T 2qfj_A           25 LAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGR  104 (216)
T ss_dssp             HHHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEEC
T ss_pred             cCcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEec
Confidence            4567899999999999999999999999999999999999899999999999999999999997 999999999999988


Q ss_pred             ccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHH
Q psy2983          92 TQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK  171 (370)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~  171 (370)
                      +...........  .........++|||+|||..+++++|+++|++||.|..+++..++.+|.++|||||+|.+.++|.+
T Consensus       105 ~~~~~~~~~~~~--~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~  182 (216)
T 2qfj_A          105 PSNIGQAQPIID--QLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQD  182 (216)
T ss_dssp             CSCCGGGHHHHH--HHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHH
T ss_pred             CCCccccchhhh--hhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHH
Confidence            764332110000  000011234789999999999999999999999999999999998899999999999999999999


Q ss_pred             HHHHhCCceeCCeeEEEEEeecCCCC
Q psy2983         172 AQEQLNGFELAGRPMKVGTVTDRNES  197 (370)
Q Consensus       172 A~~~l~g~~i~g~~l~V~~~~~~~~~  197 (370)
                      |+..|||..|+|+.|+|.++.++..+
T Consensus       183 A~~~l~g~~~~g~~i~V~~a~~~~~~  208 (216)
T 2qfj_A          183 AVSSMNLFDLGGQYLRVGKAVTPPMP  208 (216)
T ss_dssp             HHHHHTTCBCSSSBCEEEECSSCSST
T ss_pred             HHHHccCCEeCCcEEEEEEecCCCCC
Confidence            99999999999999999998876554

>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=100.00  E-value=4.1e-32  Score=233.01  Aligned_cols=164  Identities=27%  Similarity=0.478  Sum_probs=147.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCC--CeecEEEEEecCCCChHHHhh-ccCCccC---CeeEE
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTR--RFKGIAYIEFKDPESVPLAMG-LNGQKLL---GIPII   88 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~--~~kg~afVeF~~~e~A~~Al~-l~g~~i~---g~~l~   88 (370)
                      ++++|||+|||.++|+++|+++|++||+|.++++++++.++  +++|||||+|.+.++|.+|++ ++|..+.   ++++.
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            57899999999999999999999999999999999999887  899999999999999999996 9998776   67777


Q ss_pred             EecccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHH
Q psy2983          89 VQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADD  168 (370)
Q Consensus        89 v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~  168 (370)
                      +.++......            ....++|||+|||+.+++++|+++|++||.|..+.++.++ +|.++|||||+|.+.++
T Consensus        82 ~~~~~~~~~~------------~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~  148 (175)
T 3nmr_A           82 MKPADSEKNN------------AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAM  148 (175)
T ss_dssp             EEECGGGCCS------------CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHH
T ss_pred             Eccccccccc------------cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHH
Confidence            7776543221            2245789999999999999999999999999999999996 69999999999999999


Q ss_pred             HHHHHHHhCCceeC---CeeEEEEEe
Q psy2983         169 AKKAQEQLNGFELA---GRPMKVGTV  191 (370)
Q Consensus       169 a~~A~~~l~g~~i~---g~~l~V~~~  191 (370)
                      |.+|+..|||..+.   +++|+|.++
T Consensus       149 A~~A~~~l~g~~~~~g~~~~l~V~~a  174 (175)
T 3nmr_A          149 AQTAIKAMHQAQTMEGCSSPMVVKFA  174 (175)
T ss_dssp             HHHHHHHHTTSCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHhcCCcccCCCCCCeEEEec
Confidence            99999999998776   499999986

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.98  E-value=3.7e-32  Score=232.94  Aligned_cols=159  Identities=25%  Similarity=0.475  Sum_probs=144.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcC----C-------CeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCcc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSV----G-------KVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKL   82 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~----G-------~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i   82 (370)
                      +++++|||+|||.++|+++|+++|++|    |       .|.++.+.      +++|||||+|.+.++|.+|++++|..+
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~~~~~~~~   75 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAMAFDGIIF   75 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHGGGTTCEE
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHHHhCCcEe
Confidence            467999999999999999999999999    6       77777664      347999999999999999999999999


Q ss_pred             CCeeEEEecccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEE
Q psy2983          83 LGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFIT  162 (370)
Q Consensus        83 ~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~  162 (370)
                      .|++|.|.++.....             .....+|||+|||..+++++|+++|++||.|..+.+..++.+|.++|||||+
T Consensus        76 ~g~~i~v~~~~~~~~-------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~  142 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQP-------------LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCE  142 (172)
T ss_dssp             TTEECEEECCSSCCC-------------CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEE
T ss_pred             cCceeeecCCcccCC-------------CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEE
Confidence            999999988754321             1235789999999999999999999999999999999998899999999999


Q ss_pred             ECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         163 FHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       163 f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      |.+.++|.+|+..|||..+.|++|+|.++
T Consensus       143 f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          143 YVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             ESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             eCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            99999999999999999999999999986

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.98  E-value=1.1e-31  Score=235.16  Aligned_cols=177  Identities=22%  Similarity=0.409  Sum_probs=150.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcC----C-------CeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCcc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSV----G-------KVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKL   82 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~----G-------~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i   82 (370)
                      +.+|+|||+|||.++|+++|+++|+.|    |       .|.++.+      ++++|||||+|.+.++|.+|++++|..+
T Consensus         2 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al~l~g~~~   75 (198)
T 2yh0_A            2 AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAMAFDGIIF   75 (198)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHGGGTTEEE
T ss_pred             CceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHHHhcCCEE
Confidence            467999999999999999999999999    5       5666655      4558999999999999999999999999


Q ss_pred             CCeeEEEecccccccccCCCCC-------CCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCc
Q psy2983          83 LGIPIIVQPTQAEKNRAGNTLP-------NLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRS  155 (370)
Q Consensus        83 ~g~~l~v~~~~~~~~~~~~~~~-------~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~  155 (370)
                      .|++|.|.++............       ..........++|||+|||..+++++|+++|++||.|..+.+..++.+|.+
T Consensus        76 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~  155 (198)
T 2yh0_A           76 QGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLS  155 (198)
T ss_dssp             TTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSE
T ss_pred             cCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCc
Confidence            9999999988654322211100       011122345689999999999999999999999999999999999889999


Q ss_pred             ccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecCCC
Q psy2983         156 KGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNE  196 (370)
Q Consensus       156 ~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~~~  196 (370)
                      +|||||+|.+.++|.+|+..|||..+.|+.|+|.++.++..
T Consensus       156 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          156 KGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             EEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             ceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            99999999999999999999999999999999999877643

>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=99.97  E-value=2.5e-32  Score=234.88  Aligned_cols=167  Identities=26%  Similarity=0.398  Sum_probs=147.6

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEe
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQ   90 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~   90 (370)
                      ...++.++|||+|||.++|+++|+++|+.||.+.. .++.+..+++++|||||+|.+.++|.+|++++|..+.|++|.|.
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~   86 (175)
T 1fje_B            8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLE   86 (175)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEe
Confidence            35678899999999999999999999999998766 34555567888999999999999999999999999999999999


Q ss_pred             cccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHH
Q psy2983          91 PTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAK  170 (370)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~  170 (370)
                      ++......           ......+|||+|||..+++++|+++|++||.|..+     ..+|.++|||||+|.+.++|.
T Consensus        87 ~~~~~~~~-----------~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~  150 (175)
T 1fje_B           87 KPKGRDSK-----------KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAE  150 (175)
T ss_dssp             CCCCSSCS-----------TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHH
T ss_pred             cCCCcccc-----------ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHH
Confidence            98654221           12345799999999999999999999999988766     358999999999999999999


Q ss_pred             HHHHHhCCceeCCeeEEEEEeecC
Q psy2983         171 KAQEQLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       171 ~A~~~l~g~~i~g~~l~V~~~~~~  194 (370)
                      +|+..|||..+.|+.|+|.++.++
T Consensus       151 ~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          151 KNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             HHHHHHTEEEETTEEEEEEECSSC
T ss_pred             HHHHHhCCCEECCeEEEEEecCCC
Confidence            999999999999999999998765

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.97  E-value=3.8e-30  Score=238.56  Aligned_cols=172  Identities=20%  Similarity=0.273  Sum_probs=157.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHh-hccCCccCCeeEEEecc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQPT   92 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~i~g~~l~v~~~   92 (370)
                      ...++|||+|||..+++++|+++|+.||.|.++.++++..+|.++|||||+|.+.++|.+|+ .++|..+.|++|.|.++
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a  172 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT  172 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            35689999999999999999999999999999999999999999999999999999999999 59999999999999998


Q ss_pred             cccccccCCCCCCCCCCCCCCCceEEEecCCCCC-CHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHH
Q psy2983          93 QAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI-TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK  171 (370)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~-t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~  171 (370)
                      .......          ......+|||+|||..+ ++++|+++|++||.|..+.++.+. +|.++|+|||+|.+.++|.+
T Consensus       173 ~~~~~~~----------~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~  241 (284)
T 3smz_A          173 DAGQLTP----------ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEE  241 (284)
T ss_dssp             CGGGCCT----------TTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHH
T ss_pred             CCCCCCc----------ccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHH
Confidence            7653221          12345789999999995 999999999999999999999986 89999999999999999999


Q ss_pred             HHHHhCCceeCCeeEEEEEeecCCC
Q psy2983         172 AQEQLNGFELAGRPMKVGTVTDRNE  196 (370)
Q Consensus       172 A~~~l~g~~i~g~~l~V~~~~~~~~  196 (370)
                      |+..|||..+.|++|+|.++.++..
T Consensus       242 A~~~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          242 AQQQADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             HHHHHTTCEETTEECEEEECCSSSC
T ss_pred             HHHHhCCCccCCeEEEEEEecCCCc
Confidence            9999999999999999999876544

>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=99.97  E-value=4.3e-30  Score=227.03  Aligned_cols=170  Identities=18%  Similarity=0.289  Sum_probs=140.5

Q ss_pred             CCCeEEEcCCC-CCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          15 DARTIFCMQLS-QRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        15 ~~r~v~V~nLp-~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      ++++|||+||| ..+++++|+++|++||.|.+|+++++.     +|||||+|.+.++|..|++ |+|..+.|++|+|.++
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            57899999999 899999999999999999999998753     7999999999999999996 9999999999999987


Q ss_pred             cccccccCC--CC-----------C----CC-------CCCCCCCCceEEEecCCCCCCHHHHHhcccCCCce--eeEEE
Q psy2983          93 QAEKNRAGN--TL-----------P----NL-------QPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKI--DNIQL  146 (370)
Q Consensus        93 ~~~~~~~~~--~~-----------~----~~-------~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i--~~v~~  146 (370)
                      +........  ..           .    ..       ......+.++|||+|||+.+++++|+++|++||.|  .++++
T Consensus        78 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~  157 (205)
T 3tyt_A           78 KQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKV  157 (205)
T ss_dssp             SCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEE
T ss_pred             cCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE
Confidence            643211000  00           0    00       00112345789999999999999999999999999  89998


Q ss_pred             eecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCe----eEEEEEe
Q psy2983         147 MVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGR----PMKVGTV  191 (370)
Q Consensus       147 ~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~----~l~V~~~  191 (370)
                      +.+.  |.++|+|||+|.+.++|.+|+..|||..+.|+    ++.|+++
T Consensus       158 ~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          158 FSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             EcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            8774  56679999999999999999999999999876    5666654

>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=99.97  E-value=1.4e-29  Score=234.45  Aligned_cols=174  Identities=22%  Similarity=0.406  Sum_probs=146.4

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHH----HHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHh-hccCCccCCe
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLE----EFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGI   85 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~----~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~i~g~   85 (370)
                      ++.+++++|||+|||.++++++|+    ++|+.||.|.+|.+.+   +++++|||||+|.+.++|.+|+ .++|..+.|+
T Consensus         4 ~~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   80 (282)
T 3pgw_A            4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK   80 (282)
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCc
Confidence            356789999999999999999966    8999999999999876   5788999999999999999999 5999999999


Q ss_pred             eEEEecccccccccCCCCC-------------------------------------------------------------
Q psy2983          86 PIIVQPTQAEKNRAGNTLP-------------------------------------------------------------  104 (370)
Q Consensus        86 ~l~v~~~~~~~~~~~~~~~-------------------------------------------------------------  104 (370)
                      .|+|.++............                                                             
T Consensus        81 ~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~  160 (282)
T 3pgw_A           81 PMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQ  160 (282)
T ss_pred             EEEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCC
Confidence            9999887643321000000                                                             


Q ss_pred             ----------------C---------------------CCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEe
Q psy2983         105 ----------------N---------------------LQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLM  147 (370)
Q Consensus       105 ----------------~---------------------~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~  147 (370)
                                      .                     .........++|||+|||..+++++|+++|++||.|..++++
T Consensus       161 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~  240 (282)
T 3pgw_A          161 PPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV  240 (282)
T ss_pred             CCCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEe
Confidence                            0                     000112245789999999999999999999999999999998


Q ss_pred             ecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeC-CeeEEEEEee
Q psy2983         148 VDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELA-GRPMKVGTVT  192 (370)
Q Consensus       148 ~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~-g~~l~V~~~~  192 (370)
                      .+.     +|||||+|.+.++|.+|+..|||..+. |+.|+|.+++
T Consensus       241 ~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          241 PGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             cCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            653     689999999999999999999999999 9999999975

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.96  E-value=9.6e-30  Score=236.77  Aligned_cols=172  Identities=20%  Similarity=0.357  Sum_probs=145.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCC-CeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVG-KVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G-~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      ..++|||+|||..+++++|+++|+.|| .|.++.++++.. +.++|||||+|.+.++|.+|++ ++|..+.|++|.|.++
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  194 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            578999999999999999999999999 999999998876 7789999999999999999997 9999999999999988


Q ss_pred             cccccccCCCCCCCCCCCCCCCceEEEecCCCC-CCHHHHHhcccCCCceeeEEEeecCC-CCCcccEEEEEECCHHHHH
Q psy2983          93 QAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFN-ITEDMLRGIFEPFGKIDNIQLMVDPD-TGRSKGYGFITFHSADDAK  170 (370)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~-~t~e~l~~~f~~~G~i~~v~~~~~~~-~g~~~g~afV~f~~~~~a~  170 (370)
                      .+.......      ........+|||+|||.. +++++|+++|++||.|..++++.+.. +|.++|||||+|.+.++|.
T Consensus       195 ~~~~~~~~~------~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~  268 (292)
T 2ghp_A          195 NPLEKSKRT------DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE  268 (292)
T ss_dssp             CCC---------------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHH
T ss_pred             CCCcccccc------cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHH
Confidence            654332211      122345679999999999 99999999999999999999999875 4999999999999999999


Q ss_pred             HHHHHhCCceeCCeeEEEEEeecC
Q psy2983         171 KAQEQLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       171 ~A~~~l~g~~i~g~~l~V~~~~~~  194 (370)
                      +|+ .|||..+.|+.|+|.++.++
T Consensus       269 ~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          269 RAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             HHG-GGTTEEETTEEEEEEECCCC
T ss_pred             HHH-HhcCCEECCcEEEEEEecCC
Confidence            999 99999999999999998765

>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=99.96  E-value=2.5e-29  Score=226.06  Aligned_cols=174  Identities=19%  Similarity=0.302  Sum_probs=146.4

Q ss_pred             cccCCCCeEEEcCCCC-CCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEE
Q psy2983          11 PEERDARTIFCMQLSQ-RIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPII   88 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~-~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~   88 (370)
                      ....++++|||+|||. ++++++|+++|+.||.|.+|++++++     +|||||+|.+.++|.+|++ ++|..+.|++|.
T Consensus        29 ~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~  103 (229)
T 2adc_A           29 LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIR  103 (229)
T ss_dssp             GGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            3456789999999999 99999999999999999999998865     6899999999999999996 999999999999


Q ss_pred             EecccccccccCCCC---------------CCC-------CCCCCCCCceEEEecCCCCCCHHHHHhcccCCC-ceeeEE
Q psy2983          89 VQPTQAEKNRAGNTL---------------PNL-------QPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFG-KIDNIQ  145 (370)
Q Consensus        89 v~~~~~~~~~~~~~~---------------~~~-------~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G-~i~~v~  145 (370)
                      |.++...........               ...       ......+..+|||+|||..+++++|+++|++|| .|..++
T Consensus       104 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~  183 (229)
T 2adc_A          104 ITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFK  183 (229)
T ss_dssp             EECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEE
T ss_pred             EEEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEE
Confidence            998764321110000               000       001123458899999999999999999999999 999999


Q ss_pred             EeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeC-CeeEEEEEeecC
Q psy2983         146 LMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELA-GRPMKVGTVTDR  194 (370)
Q Consensus       146 ~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~-g~~l~V~~~~~~  194 (370)
                      ++.+     .+|||||+|.+.++|.+|+..|||..+. |+.|+|.+++++
T Consensus       184 i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          184 FFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             ECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             EEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            9653     3789999999999999999999999999 999999998764

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.96  E-value=1.6e-29  Score=221.79  Aligned_cols=170  Identities=19%  Similarity=0.309  Sum_probs=144.0

Q ss_pred             CCCeEEEcCCCC-CCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          15 DARTIFCMQLSQ-RIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        15 ~~r~v~V~nLp~-~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      .+++|||+|||. ++++++|+++|+.||.|.++.+++++     +|||||+|.+.++|.+|++ ++|..+.|++|.|.++
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a   76 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   76 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEEC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEe
Confidence            468999999999 99999999999999999999998764     6899999999999999996 9999999999999887


Q ss_pred             cccccccCCC----------------------CCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCC-ceeeEEEeec
Q psy2983          93 QAEKNRAGNT----------------------LPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFG-KIDNIQLMVD  149 (370)
Q Consensus        93 ~~~~~~~~~~----------------------~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G-~i~~v~~~~~  149 (370)
                      ..........                      ..........+..+|||+|||..+++++|+++|++|| .|..++++.+
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~  156 (198)
T 1qm9_A           77 KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK  156 (198)
T ss_dssp             CCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST
T ss_pred             cCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC
Confidence            6432111100                      0000011123468999999999999999999999999 9999999754


Q ss_pred             CCCCCcccEEEEEECCHHHHHHHHHHhCCceeC-CeeEEEEEeecC
Q psy2983         150 PDTGRSKGYGFITFHSADDAKKAQEQLNGFELA-GRPMKVGTVTDR  194 (370)
Q Consensus       150 ~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~-g~~l~V~~~~~~  194 (370)
                      .     +|+|||+|.+.++|.+|+..|||..+. |++|+|.++.++
T Consensus       157 ~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          157 D-----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             T-----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             C-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            2     789999999999999999999999999 999999998764

>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=99.96  E-value=1.4e-28  Score=225.54  Aligned_cols=160  Identities=24%  Similarity=0.412  Sum_probs=144.2

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPII   88 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~   88 (370)
                      .....+.++|||+|||.++|+++|+++|+.||.|.+|.+.+      ++|||||+|.+.++|..|+. ++|..+.|+.|.
T Consensus        16 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~   89 (261)
T 3sde_A           16 EKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR------DRGFGFIRLESRTLAEIAKAELDGTILKSRPLR   89 (261)
T ss_dssp             CCSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCcEEEEEECCHHHHHHHHHHcCCcEECCceeE
Confidence            33446678999999999999999999999999999999854      37999999999999999996 999999999999


Q ss_pred             EecccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHH
Q psy2983          89 VQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADD  168 (370)
Q Consensus        89 v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~  168 (370)
                      |.++..                   ..+|||+|||+.+++++|+++|++||.|..+.++.+ .+|.++|||||+|.+.++
T Consensus        90 v~~a~~-------------------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~  149 (261)
T 3sde_A           90 IRFATH-------------------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPP  149 (261)
T ss_dssp             EEECCC-------------------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHH
T ss_pred             eeeccc-------------------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHH
Confidence            998752                   358999999999999999999999999999999999 599999999999999999


Q ss_pred             HHHHHHHhC-CceeC---CeeEEEEEeecCC
Q psy2983         169 AKKAQEQLN-GFELA---GRPMKVGTVTDRN  195 (370)
Q Consensus       169 a~~A~~~l~-g~~i~---g~~l~V~~~~~~~  195 (370)
                      |.+|+..|| +..+.   +++|.|.++....
T Consensus       150 A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          150 ARKALERCGDGAFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             HHHHHHHHHHSCEESSSSCCBCEEEECCCEE
T ss_pred             HHHHHHHhcCCeEEecCCCceEEEeeccccC
Confidence            999999994 55555   9999999986543

>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=99.89  E-value=4.5e-23  Score=174.39  Aligned_cols=151  Identities=21%  Similarity=0.329  Sum_probs=116.3

Q ss_pred             EEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecccccccccCCCCCCCCCCCCCCCceEEEecCC
Q psy2983          45 DVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLH  123 (370)
Q Consensus        45 ~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp  123 (370)
                      ++.++.+..  +++|||||+|.+.++|++|++ +++....+....+..........................+|||+|||
T Consensus         2 ~~kl~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~   79 (158)
T 2kn4_A            2 QYKLILNGK--TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLT   79 (158)
T ss_dssp             EEEEEEECS--SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCC
T ss_pred             cEEEEecCc--cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCC
Confidence            456777664  689999999999999999995 55443333333333222221111111111222233456899999999


Q ss_pred             CCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecCCCC
Q psy2983         124 FNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNES  197 (370)
Q Consensus       124 ~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~~~~  197 (370)
                      +.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..+.|++|+|.++.++...
T Consensus        80 ~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  153 (158)
T 2kn4_A           80 YRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  153 (158)
T ss_dssp             TTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSCC
T ss_pred             CCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            99999999999999999999999999889999999999999999999999999999999999999999876543

>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=99.84  E-value=3.4e-21  Score=154.12  Aligned_cols=109  Identities=20%  Similarity=0.315  Sum_probs=73.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      .+.+|||+|||.++|+++|+++|++||.|.+++++++.  +.++|||||+|.+.++|.+|++ |+|..+.|++|.|.++.
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            46789999999999999999999999999999999986  4589999999999999999995 99999999999999876


Q ss_pred             ccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHH
Q psy2983          94 AEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDM  130 (370)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~  130 (370)
                      ....+....     ........+|||+|||+++|++.
T Consensus        82 ~~~~~~~~~-----~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           82 SRKEREAEL-----GARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             CCCC---------------------------------
T ss_pred             Ccccccccc-----ccccCCCCceEeCCCCCCccccc
Confidence            543322211     11122345799999999999864

>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=99.83  E-value=7.6e-21  Score=159.29  Aligned_cols=135  Identities=18%  Similarity=0.283  Sum_probs=113.2

Q ss_pred             CCeecEEEEEecCCCChHHHhh-c-cCCccCCeeEEEecccccccccCC---CCCCCCCCCCCCCceEEEecCCCCCCHH
Q psy2983          55 RRFKGIAYIEFKDPESVPLAMG-L-NGQKLLGIPIIVQPTQAEKNRAGN---TLPNLQPRGTGGPMRLYIGSLHFNITED  129 (370)
Q Consensus        55 ~~~kg~afVeF~~~e~A~~Al~-l-~g~~i~g~~l~v~~~~~~~~~~~~---~~~~~~~~~~~~~~~l~V~nlp~~~t~e  129 (370)
                      ...+|+++|+|.+.++|++|++ + +|..+.| .+.+.++.........   .............++|||+|||+.++++
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~   88 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKT   88 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCH
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHH
Confidence            4678999999999999999995 8 9999999 9999887653322211   1111223334566899999999999999


Q ss_pred             HHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecCC
Q psy2983         130 MLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRN  195 (370)
Q Consensus       130 ~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~~  195 (370)
                      +|+++|++||.|..++++.+     ++|||||+|.+.++|.+|+..|||..+.|++|+|.++.++.
T Consensus        89 ~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           89 ELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             HHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             HHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            99999999999999999876     58999999999999999999999999999999999987753

>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=99.81  E-value=1.2e-19  Score=140.96  Aligned_cols=81  Identities=33%  Similarity=0.605  Sum_probs=77.6

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ...+|||+|||+++|+++|+++|++||.|.++++++|+.+|.++|||||+|.+.++|.+|++.|||..+.|++|+|.+++
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             c
Q psy2983         193 D  193 (370)
Q Consensus       193 ~  193 (370)
                      |
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            5

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.81  E-value=2.4e-19  Score=158.93  Aligned_cols=134  Identities=26%  Similarity=0.379  Sum_probs=119.2

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      +.++|||+|||+++++++|+++|++||.|.+|++++|+.+|+++|||||+|.+.++|.+|+..+++..+.|+.+++.++.
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            44789999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             cCC---------CCcCCCCCCCCHHHHHHhcccCCceeeeeeeecc--ccCCC---CCChHHHHHHHh
Q psy2983         193 DRN---------ESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKL--AEGTG---LELPPAAASALN  246 (370)
Q Consensus       193 ~~~---------~~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~--~~~~~---~~~~~~a~~a~~  246 (370)
                      ...         ..+++++..+++++|+..|..+|.+..+.++.+.  +++++   |..+.+|..|+.
T Consensus        94 ~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~  161 (213)
T 4f02_A           94 RDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIE  161 (213)
T ss_dssp             CCTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHH
T ss_pred             ccccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHH
Confidence            443         2377899999999999999999999999998763  34455   567888888775

>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=99.80  E-value=4.9e-19  Score=149.86  Aligned_cols=133  Identities=28%  Similarity=0.476  Sum_probs=118.5

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|+|..+.|+.|+|.++.+
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            46899999999999999999999999999999999988999999999999999999999999999999999999999876


Q ss_pred             CCC-------CcCCCCCCCCHHHHHHhcccCCceeeeeeeecc----ccCCC---CCChHHHHHHHh
Q psy2983         194 RNE-------SVGGGPSNLDTDEMERAGVDLGATGRLQLMFKL----AEGTG---LELPPAAASALN  246 (370)
Q Consensus       194 ~~~-------~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~----~~~~~---~~~~~~a~~a~~  246 (370)
                      ...       .+++++..+++++++..|..+|.+..+.++.+.    .++++   |..+.+|..|+.
T Consensus        82 ~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~  148 (167)
T 1fxl_A           82 SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK  148 (167)
T ss_dssp             CCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH
T ss_pred             CcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHH
Confidence            543       367899999999999999999999998887764    23444   567788877766

>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=99.80  E-value=7.6e-19  Score=149.07  Aligned_cols=134  Identities=25%  Similarity=0.386  Sum_probs=119.2

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      +.++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|+|..+.|++|+|.++.
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            35789999999999999999999999999999999998899999999999999999999999999999999999999987


Q ss_pred             cCCCC-------cCCCCCCCCHHHHHHhcccCCceeeeeeeeccc----cCCC---CCChHHHHHHHh
Q psy2983         193 DRNES-------VGGGPSNLDTDEMERAGVDLGATGRLQLMFKLA----EGTG---LELPPAAASALN  246 (370)
Q Consensus       193 ~~~~~-------~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~~----~~~~---~~~~~~a~~a~~  246 (370)
                      +....       +.+++..+++++++..|..+|.+..+.++.+..    ++++   |..+.+|..|+.
T Consensus        82 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~  149 (168)
T 1b7f_A           82 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS  149 (168)
T ss_dssp             CCSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH
T ss_pred             CCcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHH
Confidence            65443       668999999999999999999999998887642    2344   677888888776

>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=99.79  E-value=1.5e-19  Score=140.51  Aligned_cols=81  Identities=22%  Similarity=0.372  Sum_probs=76.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      -+.++|||+|||.++|+++|+++|++||+|.++++++|+.+|+++|||||+|.+.++|.+|++ |+|..+.|++|+|.++
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~A   96 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA   96 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            356789999999999999999999999999999999999999999999999999999999995 9999999999999987


Q ss_pred             cc
Q psy2983          93 QA   94 (370)
Q Consensus        93 ~~   94 (370)
                      ++
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            53

>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=99.78  E-value=2.7e-18  Score=149.49  Aligned_cols=136  Identities=23%  Similarity=0.437  Sum_probs=118.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+.. ++..+.|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~   88 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKR   88 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeec
Confidence            34568999999999999999999999999999999999998999999999999999999999985 99999999999999


Q ss_pred             eecCCC-------------CcCCCCCCCCHHHHHHhcccCCceeeeeeeecc----ccCCC---CCChHHHHHHHhh
Q psy2983         191 VTDRNE-------------SVGGGPSNLDTDEMERAGVDLGATGRLQLMFKL----AEGTG---LELPPAAASALNL  247 (370)
Q Consensus       191 ~~~~~~-------------~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~----~~~~~---~~~~~~a~~a~~~  247 (370)
                      +.....             .+++++..+++++|+..|..+|.+..+.++.+.    .+|++   |..+..|..|+..
T Consensus        89 ~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~  165 (196)
T 1l3k_A           89 AVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ  165 (196)
T ss_dssp             CCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC
T ss_pred             ccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh
Confidence            865422             266889999999999999999999999998763    23444   6778888888764

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.77  E-value=3.5e-18  Score=144.39  Aligned_cols=131  Identities=29%  Similarity=0.480  Sum_probs=115.2

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecC
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~  194 (370)
                      ++|||+|||.++++++|+++|++||.|.++.++.++ +|.++|||||+|.+.++|.+|+..|+|..+.|+.|+|.++.+.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            479999999999999999999999999999999996 6889999999999999999999999999999999999998655


Q ss_pred             CCC---------cCCCCCCCCHHHHHHhcccCCceeeeeeeecc----ccCCC---CCChHHHHHHHh
Q psy2983         195 NES---------VGGGPSNLDTDEMERAGVDLGATGRLQLMFKL----AEGTG---LELPPAAASALN  246 (370)
Q Consensus       195 ~~~---------~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~----~~~~~---~~~~~~a~~a~~  246 (370)
                      ...         +++++..+++++++..|..+|.+..+.++.+.    ++|++   |..+.+|..|+.
T Consensus        80 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~  147 (166)
T 3md3_A           80 QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD  147 (166)
T ss_dssp             CCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHH
T ss_pred             CCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHH
Confidence            432         66899999999999999999999999998763    23344   677888888876

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.77  E-value=2e-18  Score=136.69  Aligned_cols=82  Identities=17%  Similarity=0.323  Sum_probs=78.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      .++++|||+|||+.+++++|+++|++||.|.+++++.|+.+|+++|||||+|.+.++|.+|++.|||..+.|+.|+|.++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             ec
Q psy2983         192 TD  193 (370)
Q Consensus       192 ~~  193 (370)
                      ..
T Consensus        84 ~~   85 (110)
T 3s8s_A           84 IK   85 (110)
T ss_dssp             ST
T ss_pred             CC
Confidence            54

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.76  E-value=2.5e-19  Score=136.96  Aligned_cols=82  Identities=20%  Similarity=0.348  Sum_probs=75.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCC-CeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-c-cCCccCCeeEEEecc
Q psy2983          16 ARTIFCMQLSQRIRTRDLEEFFSSVG-KVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-L-NGQKLLGIPIIVQPT   92 (370)
Q Consensus        16 ~r~v~V~nLp~~~te~~L~~~f~~~G-~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l-~g~~i~g~~l~v~~~   92 (370)
                      +++|||+|||+++|+++|+++|++|| .|.+|++++|+.++.++|||||+|.+.++|.+|++ + ++..+.|++|.|.++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            58999999999999999999999999 89999999999999999999999999999999996 5 567899999999998


Q ss_pred             ccccc
Q psy2983          93 QAEKN   97 (370)
Q Consensus        93 ~~~~~   97 (370)
                      .+...
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            76543

>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=99.76  E-value=5.2e-18  Score=144.76  Aligned_cols=133  Identities=19%  Similarity=0.371  Sum_probs=115.6

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCC--CcccEEEEEECCHHHHHHHHHHhCCceeC---CeeEEE
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTG--RSKGYGFITFHSADDAKKAQEQLNGFELA---GRPMKV  188 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g--~~~g~afV~f~~~~~a~~A~~~l~g~~i~---g~~l~V  188 (370)
                      .++|||+|||+++++++|+++|++||.|.++++++++.+|  .++|||||+|.+.++|.+|+..|+|..+.   ++.+.+
T Consensus         3 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~   82 (175)
T 3nmr_A            3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQM   82 (175)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEE
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEE
Confidence            5789999999999999999999999999999999998776  89999999999999999999999998876   688888


Q ss_pred             EEeecCCC--------CcCCCCCCCCHHHHHHhcccCCceeeeeeeeccc---cCCC---CCChHHHHHHHh
Q psy2983         189 GTVTDRNE--------SVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLA---EGTG---LELPPAAASALN  246 (370)
Q Consensus       189 ~~~~~~~~--------~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~~---~~~~---~~~~~~a~~a~~  246 (370)
                      .++.....        .+++++..+++++++..|..+|.+.++.++.+..   ++++   |..+..|..|+.
T Consensus        83 ~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~  154 (175)
T 3nmr_A           83 KPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIK  154 (175)
T ss_dssp             EECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHH
T ss_pred             ccccccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHH
Confidence            88765443        2678999999999999999999999999987632   3344   677888888775

>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=99.76  E-value=2.4e-18  Score=130.17  Aligned_cols=83  Identities=30%  Similarity=0.427  Sum_probs=77.2

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIV   89 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v   89 (370)
                      ++...+.++|||+|||..+++++|+++|++||.|.++.+++++.+++++|||||+|.+.++|.+|+++++..++|+.|.|
T Consensus         5 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v   84 (87)
T 3s7r_A            5 SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDP   84 (87)
T ss_dssp             --CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEE
Confidence            45567889999999999999999999999999999999999999999999999999999999999998999999999999


Q ss_pred             ecc
Q psy2983          90 QPT   92 (370)
Q Consensus        90 ~~~   92 (370)
                      +++
T Consensus        85 ~~A   87 (87)
T 3s7r_A           85 KKA   87 (87)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            764

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.76  E-value=4.6e-19  Score=135.51  Aligned_cols=82  Identities=22%  Similarity=0.428  Sum_probs=76.5

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCC-ceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHh-CCceeCCeeEEEEEee
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFG-KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL-NGFELAGRPMKVGTVT  192 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G-~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l-~g~~i~g~~l~V~~~~  192 (370)
                      ++|||+|||+++|+++|+++|++|| .|.++++++|+.+|.++|||||+|.+.++|.+|++.+ ++..+.|++|+|.++.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            6899999999999999999999999 8999999999999999999999999999999999987 4568999999999988


Q ss_pred             cCCC
Q psy2983         193 DRNE  196 (370)
Q Consensus       193 ~~~~  196 (370)
                      ++..
T Consensus        82 ~~~~   85 (91)
T 2lxi_A           82 PKPK   85 (91)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7654

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.76  E-value=1.3e-18  Score=137.71  Aligned_cols=83  Identities=18%  Similarity=0.285  Sum_probs=78.4

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      ..+.++|||+|||.++++++|+++|++||.|.++.+++|+.+++++|||||+|.+.++|.+|++ |||..+.|+.|.|.+
T Consensus         3 ~~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~   82 (110)
T 3s8s_A            3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQL   82 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3567999999999999999999999999999999999999999999999999999999999996 999999999999998


Q ss_pred             cccc
Q psy2983          92 TQAE   95 (370)
Q Consensus        92 ~~~~   95 (370)
                      +...
T Consensus        83 a~~~   86 (110)
T 3s8s_A           83 DIKG   86 (110)
T ss_dssp             CSTT
T ss_pred             CCCC
Confidence            7644

>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=99.76  E-value=2.6e-18  Score=137.19  Aligned_cols=82  Identities=34%  Similarity=0.615  Sum_probs=75.2

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      +..+|||+|||+++++++|+++|++||.|.+++++.+.  +.++|||||+|.+.++|.+|++.|+|..+.|+.|+|.++.
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            34689999999999999999999999999999999984  5589999999999999999999999999999999999987


Q ss_pred             cCCC
Q psy2983         193 DRNE  196 (370)
Q Consensus       193 ~~~~  196 (370)
                      ++..
T Consensus        82 ~~~~   85 (115)
T 4f25_A           82 SRKE   85 (115)
T ss_dssp             CCCC
T ss_pred             Cccc
Confidence            6544

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.75  E-value=1.4e-18  Score=133.74  Aligned_cols=80  Identities=20%  Similarity=0.418  Sum_probs=74.8

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCc--eeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCc----eeCCeeEE
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGK--IDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF----ELAGRPMK  187 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~--i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~----~i~g~~l~  187 (370)
                      -.+|||+|||+.+|+++|+++|++||.  +.+|++++|+.+|.++|||||+|.+.++|.+|++.|||.    .++|++|.
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  679999999999999999999999999999999999997    58999999


Q ss_pred             EEEeec
Q psy2983         188 VGTVTD  193 (370)
Q Consensus       188 V~~~~~  193 (370)
                      |.++++
T Consensus        89 V~~Aks   94 (95)
T 2lkz_A           89 VDFAKS   94 (95)
T ss_dssp             EEECCC
T ss_pred             EEEccC
Confidence            999864

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.75  E-value=1e-18  Score=134.52  Aligned_cols=83  Identities=18%  Similarity=0.284  Sum_probs=76.2

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCC--eeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCC----ccCC
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGK--VRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQ----KLLG   84 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~--v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~----~i~g   84 (370)
                      .+..-.||||+|||+.+|+++|+++|++||.  |.+|++++|+.+++++|||||+|.+.++|.+|++ ++|.    .++|
T Consensus         5 ~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G   84 (95)
T 2lkz_A            5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG   84 (95)
T ss_dssp             SSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT
T ss_pred             cCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC
Confidence            4567789999999999999999999999995  6799999999999999999999999999999996 8886    4899


Q ss_pred             eeEEEecccc
Q psy2983          85 IPIIVQPTQA   94 (370)
Q Consensus        85 ~~l~v~~~~~   94 (370)
                      ++|.|.+++.
T Consensus        85 r~i~V~~Aks   94 (95)
T 2lkz_A           85 KTIGVDFAKS   94 (95)
T ss_dssp             EEEEEEECCC
T ss_pred             EEEEEEEccC
Confidence            9999998763

>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=99.75  E-value=6.9e-18  Score=127.53  Aligned_cols=82  Identities=34%  Similarity=0.652  Sum_probs=76.9

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      +.++|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++.
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            45789999999999999999999999999999999998899999999999999999999999999999999999999987


Q ss_pred             cC
Q psy2983         193 DR  194 (370)
Q Consensus       193 ~~  194 (370)
                      ++
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            64

>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=99.75  E-value=9.9e-18  Score=125.48  Aligned_cols=81  Identities=35%  Similarity=0.703  Sum_probs=77.6

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecC
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~  194 (370)
                      .+|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++.++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            57999999999999999999999999999999999889999999999999999999999999999999999999998765


Q ss_pred             C
Q psy2983         195 N  195 (370)
Q Consensus       195 ~  195 (370)
                      .
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.75  E-value=7.2e-18  Score=149.05  Aligned_cols=133  Identities=29%  Similarity=0.484  Sum_probs=115.2

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .++|||+|||.++++++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|.+|++.|+|..+.|+.|+|.++..
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            36899999999999999999999999999999999988999999999999999999999999999999999999988754


Q ss_pred             CC------------------CCcCCCCCCCCHHHHHHhcccCCceeeeeeeeccc----cCCC---CCChHHHHHHHh
Q psy2983         194 RN------------------ESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLA----EGTG---LELPPAAASALN  246 (370)
Q Consensus       194 ~~------------------~~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~~----~~~~---~~~~~~a~~a~~  246 (370)
                      ..                  ..+++++..+++++|+..|..+|.+..+.++.+..    ++++   |.....|..|+.
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~  185 (216)
T 2qfj_A          108 IGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS  185 (216)
T ss_dssp             CGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH
T ss_pred             ccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHH
Confidence            43                  23678999999999999999999999999987632    3444   677888888877

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=1.1e-17  Score=128.63  Aligned_cols=86  Identities=74%  Similarity=1.205  Sum_probs=81.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      .++++|||+|||..+++++|+++|++||.|..+.+..++.++.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            35689999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy2983         192 TDRNES  197 (370)
Q Consensus       192 ~~~~~~  197 (370)
                      .++...
T Consensus        83 ~~~~~~   88 (95)
T 2dnz_A           83 TERLDG   88 (95)
T ss_dssp             SCCCCC
T ss_pred             ccccCC
Confidence            876654

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=2.1e-17  Score=129.16  Aligned_cols=87  Identities=31%  Similarity=0.510  Sum_probs=81.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            45568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2983         191 VTDRNES  197 (370)
Q Consensus       191 ~~~~~~~  197 (370)
                      +.++...
T Consensus        92 a~~~~~~   98 (103)
T 2cq0_A           92 AKPSTNS   98 (103)
T ss_dssp             SSCCCCS
T ss_pred             CCCCCCC
Confidence            8776543

>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=99.75  E-value=3.7e-18  Score=134.78  Aligned_cols=91  Identities=25%  Similarity=0.430  Sum_probs=83.9

Q ss_pred             CCCCCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccC
Q psy2983           5 YSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLL   83 (370)
Q Consensus         5 ~~~~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~   83 (370)
                      ....+++...+.++|||+|||..+++++|+++|+.||+|.++.+++++.+++++|||||+|.+.++|.+|++ ++|..+.
T Consensus        15 ~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~   94 (108)
T 2jrs_A           15 MANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELA   94 (108)
T ss_dssp             SCCSSCCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSS
T ss_pred             cccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            445556677888999999999999999999999999999999999999999999999999999999999996 9999999


Q ss_pred             CeeEEEeccccc
Q psy2983          84 GIPIIVQPTQAE   95 (370)
Q Consensus        84 g~~l~v~~~~~~   95 (370)
                      |++|.|.++...
T Consensus        95 g~~l~V~~a~~k  106 (108)
T 2jrs_A           95 GRPMKVGHVTER  106 (108)
T ss_dssp             SSCCEEECSCSS
T ss_pred             CEEEEEEEcccC
Confidence            999999988654

>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=99.75  E-value=1.2e-17  Score=129.43  Aligned_cols=87  Identities=28%  Similarity=0.526  Sum_probs=81.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ...++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   85 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             ecCCCCc
Q psy2983         192 TDRNESV  198 (370)
Q Consensus       192 ~~~~~~~  198 (370)
                      .++....
T Consensus        86 ~~~~~~~   92 (99)
T 1whw_A           86 TIKKEAS   92 (99)
T ss_dssp             CCCSTTC
T ss_pred             CCCcccc
Confidence            8876643

>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=99.74  E-value=1.9e-18  Score=137.68  Aligned_cols=93  Identities=72%  Similarity=1.151  Sum_probs=83.9

Q ss_pred             CCCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCee
Q psy2983           7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIP   86 (370)
Q Consensus         7 ~~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~   86 (370)
                      ++..+.....++|||+|||..+++++|+++|+.||.|.+|.+++++.++.++|||||+|.+.++|.+|+.++|..|.|+.
T Consensus        16 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~   95 (114)
T 2cq4_A           16 DNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVP   95 (114)
T ss_dssp             CCCCTTHHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEE
T ss_pred             CccCcccCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeE
Confidence            33444556779999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeccccccccc
Q psy2983          87 IIVQPTQAEKNRA   99 (370)
Q Consensus        87 l~v~~~~~~~~~~   99 (370)
                      |.|.++.....+.
T Consensus        96 l~V~~a~~~~~~~  108 (114)
T 2cq4_A           96 IIVQASQAEKNRL  108 (114)
T ss_dssp             EEEEEHHHHHHHH
T ss_pred             EEEEecCCCccCC
Confidence            9999987665443

>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=99.74  E-value=9.4e-18  Score=142.71  Aligned_cols=134  Identities=25%  Similarity=0.334  Sum_probs=80.5

Q ss_pred             EEecCCCChHHHhh-ccCCccC--CeeEEEecccccccccC-------CCCCCCCCCCCCCCceEEEecCCCCCCHHHHH
Q psy2983          63 IEFKDPESVPLAMG-LNGQKLL--GIPIIVQPTQAEKNRAG-------NTLPNLQPRGTGGPMRLYIGSLHFNITEDMLR  132 (370)
Q Consensus        63 VeF~~~e~A~~Al~-l~g~~i~--g~~l~v~~~~~~~~~~~-------~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~  132 (370)
                      .+|.+.++|..++. +++....  |+...............       .......+......++|||+|||+.+++++|+
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            78999999999995 7776554  55555443221110000       00011122233456789999999999999999


Q ss_pred             hcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecCCC
Q psy2983         133 GIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNE  196 (370)
Q Consensus       133 ~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~~~  196 (370)
                      ++|++||.|..|.++.++.+|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++.++..
T Consensus        91 ~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  154 (165)
T 1rk8_A           91 EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP  154 (165)
T ss_dssp             HHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC-
T ss_pred             HHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCC
Confidence            9999999999999999988999999999999999999999999999999999999999877554

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=3.6e-18  Score=134.17  Aligned_cols=89  Identities=22%  Similarity=0.395  Sum_probs=81.2

Q ss_pred             CCCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCe
Q psy2983           7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGI   85 (370)
Q Consensus         7 ~~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~   85 (370)
                      ...+....+.++|||+|||..+++++|+++|+.||.|.++.+++++.++.++|||||+|.+.++|.+|++ ++|..+.|+
T Consensus        14 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   93 (106)
T 1p27_B           14 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ   93 (106)
T ss_dssp             -CCBCCBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCc
Confidence            3344456677899999999999999999999999999999999999999999999999999999999996 999999999


Q ss_pred             eEEEeccccc
Q psy2983          86 PIIVQPTQAE   95 (370)
Q Consensus        86 ~l~v~~~~~~   95 (370)
                      .|.|.++...
T Consensus        94 ~l~V~~a~~~  103 (106)
T 1p27_B           94 PISVDWCFVR  103 (106)
T ss_dssp             BCEEEESEES
T ss_pred             EEEEEeecCC
Confidence            9999998754

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.74  E-value=1.6e-17  Score=132.47  Aligned_cols=91  Identities=22%  Similarity=0.314  Sum_probs=83.0

Q ss_pred             CCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCee
Q psy2983           8 DLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIP   86 (370)
Q Consensus         8 ~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~   86 (370)
                      .......+.++|||+|||..+++++|+++|+.||.|.+|.+++++.++.++|||||+|.+.++|.+|++ |+|..|.|+.
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   86 (115)
T 2dgo_A            7 GQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQ   86 (115)
T ss_dssp             SSCCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEE
T ss_pred             cCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            334556788999999999999999999999999999999999999899999999999999999999996 9999999999


Q ss_pred             EEEecccccccc
Q psy2983          87 IIVQPTQAEKNR   98 (370)
Q Consensus        87 l~v~~~~~~~~~   98 (370)
                      |.|.++......
T Consensus        87 l~V~~a~~~~~~   98 (115)
T 2dgo_A           87 IRTNWATRKPPA   98 (115)
T ss_dssp             CEEEESSCCCCC
T ss_pred             EEEEEccCCCCC
Confidence            999998765443

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=8.4e-18  Score=131.40  Aligned_cols=87  Identities=24%  Similarity=0.358  Sum_probs=81.3

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPII   88 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~   88 (370)
                      ++...+.++|||+|||..+++++|+++|+.||.|.++.+++++.+++++|||||+|.+.++|.+|++ |+|..+.|+.|.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2dnm_A            7 GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELR   86 (103)
T ss_dssp             SSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCE
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            4456778999999999999999999999999999999999999999999999999999999999997 999999999999


Q ss_pred             Eecccccc
Q psy2983          89 VQPTQAEK   96 (370)
Q Consensus        89 v~~~~~~~   96 (370)
                      |.++....
T Consensus        87 V~~a~~~~   94 (103)
T 2dnm_A           87 VQVARYGR   94 (103)
T ss_dssp             EEECSSCC
T ss_pred             EEECCcCC
Confidence            99987543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=5.7e-18  Score=131.36  Aligned_cols=86  Identities=22%  Similarity=0.431  Sum_probs=80.4

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEec
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQP   91 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~   91 (370)
                      ...+.++|||+|||..+++++|+++|+.||.|.++.+++++.+++++|||||+|.+.++|.+|+++++..+.|+.|.|.+
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~~   85 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKR   85 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEEE
Confidence            44578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccc
Q psy2983          92 TQAEKN   97 (370)
Q Consensus        92 ~~~~~~   97 (370)
                      +.....
T Consensus        86 a~~~~~   91 (99)
T 2dgs_A           86 AEPRDS   91 (99)
T ss_dssp             CCCCCC
T ss_pred             CCCCcc
Confidence            876543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.9e-17  Score=127.18  Aligned_cols=83  Identities=34%  Similarity=0.590  Sum_probs=78.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ..+.++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..+.|++|+|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            44568999999999999999999999999999999999998999999999999999999999999999999999999998


Q ss_pred             eec
Q psy2983         191 VTD  193 (370)
Q Consensus       191 ~~~  193 (370)
                      +++
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            754

>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=99.74  E-value=1.1e-17  Score=125.86  Aligned_cols=81  Identities=33%  Similarity=0.620  Sum_probs=77.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            35689999999999999999999999999999999999889999999999999999999999999999999999999986


Q ss_pred             e
Q psy2983         192 T  192 (370)
Q Consensus       192 ~  192 (370)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=2.4e-17  Score=126.49  Aligned_cols=82  Identities=32%  Similarity=0.550  Sum_probs=77.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            34567999999999999999999999999999999999988899999999999999999999999999999999999998


Q ss_pred             ee
Q psy2983         191 VT  192 (370)
Q Consensus       191 ~~  192 (370)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            63

>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=99.74  E-value=1.4e-17  Score=128.48  Aligned_cols=83  Identities=34%  Similarity=0.668  Sum_probs=79.0

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .++|||+|||..+++++|+++|++||.|..+++..++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++.+
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            46899999999999999999999999999999999988999999999999999999999999999999999999999877


Q ss_pred             CCC
Q psy2983         194 RNE  196 (370)
Q Consensus       194 ~~~  196 (370)
                      +..
T Consensus        82 ~~~   84 (96)
T 2x1f_A           82 SDI   84 (96)
T ss_dssp             SSG
T ss_pred             CCC
Confidence            654

>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=99.74  E-value=5.1e-18  Score=143.87  Aligned_cols=132  Identities=27%  Similarity=0.500  Sum_probs=115.3

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .++|||+|||+++++++|+++|++||.|.++.+++++.+|.++|||||+|.+.++|.+|+.  ++..+.|+.|.+.++.+
T Consensus         3 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~~~~   80 (167)
T 2cjk_A            3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKVIDPKRAIP   80 (167)
T ss_dssp             GGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEECCCEECCC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh--cccccCCeEcccccccc
Confidence            4789999999999999999999999999999999998899999999999999999999998  46789999999998764


Q ss_pred             CC-------CCcCCCCCCCCHHHHHHhcccCCceeeeeeeecc----ccCCC---CCChHHHHHHHhh
Q psy2983         194 RN-------ESVGGGPSNLDTDEMERAGVDLGATGRLQLMFKL----AEGTG---LELPPAAASALNL  247 (370)
Q Consensus       194 ~~-------~~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~----~~~~~---~~~~~~a~~a~~~  247 (370)
                      +.       ..+++++..+++++|+..|..+|.+..+.++.+.    ++|++   |..+.+|..|+.+
T Consensus        81 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~  148 (167)
T 2cjk_A           81 RDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN  148 (167)
T ss_dssp             HHHHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHHC
T ss_pred             hhhccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHhC
Confidence            33       2367899999999999999999999999888763    23444   6778888888764

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=2.5e-17  Score=127.67  Aligned_cols=85  Identities=24%  Similarity=0.560  Sum_probs=79.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ...++|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|++ |++..+.|+.|+|.++
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a   86 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRA   86 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEEC
Confidence            456899999999999999999999999999999999998899999999999999999999999 9999999999999999


Q ss_pred             ecCCCC
Q psy2983         192 TDRNES  197 (370)
Q Consensus       192 ~~~~~~  197 (370)
                      .++...
T Consensus        87 ~~~~~~   92 (99)
T 2dgs_A           87 EPRDSK   92 (99)
T ss_dssp             CCCCCC
T ss_pred             CCCccc
Confidence            876554

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.73  E-value=1.7e-18  Score=142.26  Aligned_cols=124  Identities=23%  Similarity=0.385  Sum_probs=82.0

Q ss_pred             EEEEEecCCCChHHHhh-ccCCccCCeeEEEecccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCC
Q psy2983          60 IAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPF  138 (370)
Q Consensus        60 ~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~  138 (370)
                      ++|.+|.+...+..|++ ++|....|+.- ..+.             ..+......++|||+|||+.+++++|+++|++|
T Consensus         6 ~~~~~~~~~~~~~~a~~~~~g~~~~g~~~-~~~~-------------~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~   71 (135)
T 2lea_A            6 HHHHHSSGLVPRGSHMASMTGGQQMGRGS-MSYG-------------RPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKY   71 (135)
T ss_dssp             ------------------------------CCSC-------------CSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGG
T ss_pred             cccccccCCCchhhhhhhccCCCCCCCCC-CCcC-------------CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhc
Confidence            67788888888888885 77766555421 1111             111223345789999999999999999999999


Q ss_pred             CceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecCCCC
Q psy2983         139 GKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNES  197 (370)
Q Consensus       139 G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~~~~  197 (370)
                      |.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++.+....
T Consensus        72 G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~~  130 (135)
T 2lea_A           72 GRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  130 (135)
T ss_dssp             SCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCCC
T ss_pred             CCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence            99999999999889999999999999999999999999999999999999998776543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.7e-17  Score=129.41  Aligned_cols=87  Identities=31%  Similarity=0.552  Sum_probs=81.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ...++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   89 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeC
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             ecCCCCc
Q psy2983         192 TDRNESV  198 (370)
Q Consensus       192 ~~~~~~~  198 (370)
                      .++....
T Consensus        90 ~~~~~~~   96 (102)
T 2cqb_A           90 KPMRIKE   96 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            8766543

>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=99.73  E-value=1.4e-17  Score=131.48  Aligned_cols=88  Identities=77%  Similarity=1.295  Sum_probs=81.7

Q ss_pred             CCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEE
Q psy2983         108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMK  187 (370)
Q Consensus       108 ~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~  187 (370)
                      +....++++|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|+|..+.|+.|+
T Consensus        20 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~   99 (108)
T 2jrs_A           20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMK   99 (108)
T ss_dssp             CCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            34455678999999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             EEEeecCC
Q psy2983         188 VGTVTDRN  195 (370)
Q Consensus       188 V~~~~~~~  195 (370)
                      |.++.++.
T Consensus       100 V~~a~~k~  107 (108)
T 2jrs_A          100 VGHVTERT  107 (108)
T ss_dssp             EECSCSSC
T ss_pred             EEEcccCC
Confidence            99987653

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=3.1e-17  Score=127.42  Aligned_cols=85  Identities=20%  Similarity=0.462  Sum_probs=79.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||..+++++|+++|++||.|..+.+..++ +|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   92 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456789999999999999999999999999999999997 999999999999999999999999999999999999999


Q ss_pred             eecCCC
Q psy2983         191 VTDRNE  196 (370)
Q Consensus       191 ~~~~~~  196 (370)
                      +.++..
T Consensus        93 a~~~~~   98 (100)
T 2do4_A           93 SNSGPS   98 (100)
T ss_dssp             CCCCSC
T ss_pred             CCCCCC
Confidence            877643

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.73  E-value=1.8e-17  Score=128.55  Aligned_cols=83  Identities=29%  Similarity=0.485  Sum_probs=78.0

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHhcccCCCceee--------EEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCcee
Q psy2983         110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDN--------IQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFEL  181 (370)
Q Consensus       110 ~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~--------v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i  181 (370)
                      ......+|||+|||..+++++|+++|++||.|..        ++++.++.+|.++|||||+|.+.++|.+|++.|||..+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            3455689999999999999999999999999999        99999988999999999999999999999999999999


Q ss_pred             CCeeEEEEEee
Q psy2983         182 AGRPMKVGTVT  192 (370)
Q Consensus       182 ~g~~l~V~~~~  192 (370)
                      .|+.|+|.+++
T Consensus        89 ~g~~l~V~~A~   99 (99)
T 2la6_A           89 SGNPIKVSFAT   99 (99)
T ss_dssp             SSSBCEEEECC
T ss_pred             CCcEEEEEecC
Confidence            99999999863

>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=99.73  E-value=2.3e-18  Score=131.30  Aligned_cols=82  Identities=27%  Similarity=0.417  Sum_probs=72.8

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCC--ceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFG--KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G--~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      .+|||+|||+.+++++|+++|++||  .|.+++++.++.+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.
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            4799999999999999999999999  99999999999999999999999999999999999999999999999999987


Q ss_pred             cCCC
Q psy2983         193 DRNE  196 (370)
Q Consensus       193 ~~~~  196 (370)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            6544

>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=99.73  E-value=2.2e-17  Score=129.38  Aligned_cols=88  Identities=28%  Similarity=0.538  Sum_probs=82.0

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEE
Q psy2983         110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG  189 (370)
Q Consensus       110 ~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~  189 (370)
                      .....++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   90 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   90 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            34556899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EeecCCCC
Q psy2983         190 TVTDRNES  197 (370)
Q Consensus       190 ~~~~~~~~  197 (370)
                      ++.++...
T Consensus        91 ~a~~~~~~   98 (105)
T 1x5u_A           91 KASAHNKN   98 (105)
T ss_dssp             ETTTTSCC
T ss_pred             ECCCCCcC
Confidence            98776554

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.73  E-value=5.8e-17  Score=129.20  Aligned_cols=88  Identities=33%  Similarity=0.633  Sum_probs=82.0

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEE
Q psy2983         110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG  189 (370)
Q Consensus       110 ~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~  189 (370)
                      .....++|||+|||..+++++|+++|+.||.|..++++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34556899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EeecCCCC
Q psy2983         190 TVTDRNES  197 (370)
Q Consensus       190 ~~~~~~~~  197 (370)
                      ++.++...
T Consensus        91 ~a~~~~~~   98 (115)
T 2dgo_A           91 WATRKPPA   98 (115)
T ss_dssp             ESSCCCCC
T ss_pred             EccCCCCC
Confidence            98776554

>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=99.73  E-value=8.4e-18  Score=130.36  Aligned_cols=85  Identities=27%  Similarity=0.417  Sum_probs=79.8

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHh-hccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~i~g~~l~v~~   91 (370)
                      ..+.++|||+|||..+++++|+++|+.||+|.++.+++++.+++++|||||+|.+.++|.+|+ .++|..+.|++|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            457899999999999999999999999999999999999989999999999999999999999 5999999999999999


Q ss_pred             cccccc
Q psy2983          92 TQAEKN   97 (370)
Q Consensus        92 ~~~~~~   97 (370)
                      +.....
T Consensus        85 a~~~~~   90 (99)
T 1whw_A           85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             cCCCcc
Confidence            876544

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=9.4e-18  Score=131.11  Aligned_cols=89  Identities=25%  Similarity=0.344  Sum_probs=82.0

Q ss_pred             CCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCee
Q psy2983           8 DLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIP   86 (370)
Q Consensus         8 ~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~   86 (370)
                      .......+.++|||+|||..+++++|+++|++||+|.+|.+++++.++.++|||||+|.+.++|.+|++ ++|..|.|+.
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   86 (103)
T 2cq0_A            7 GPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLI   86 (103)
T ss_dssp             CSCCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEE
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcE
Confidence            334456778999999999999999999999999999999999999999999999999999999999997 9999999999


Q ss_pred             EEEecccccc
Q psy2983          87 IIVQPTQAEK   96 (370)
Q Consensus        87 l~v~~~~~~~   96 (370)
                      |.|.++....
T Consensus        87 l~v~~a~~~~   96 (103)
T 2cq0_A           87 LNVEWAKPST   96 (103)
T ss_dssp             CEEEESSCCC
T ss_pred             EEEEECCCCC
Confidence            9999987654

>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=99.73  E-value=6.1e-18  Score=127.26  Aligned_cols=81  Identities=22%  Similarity=0.436  Sum_probs=76.6

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      ..+.++|||+|||..+++++|+++|++||+|.++.+++++.+++++|||||+|.+.++|.+|++ ++|..+.|++|+|.+
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            3577999999999999999999999999999999999999999999999999999999999994 999999999999987


Q ss_pred             cc
Q psy2983          92 TQ   93 (370)
Q Consensus        92 ~~   93 (370)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            63

>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=99.73  E-value=1.3e-17  Score=131.98  Aligned_cols=91  Identities=24%  Similarity=0.365  Sum_probs=83.8

Q ss_pred             CCCCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-cc------
Q psy2983           6 SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LN------   78 (370)
Q Consensus         6 ~~~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~------   78 (370)
                      +...++...+.++|||+|||..+++++|+++|+.||.|.+|.+++++.++.++|||||+|.+.++|.+|++ ++      
T Consensus         5 ~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~   84 (111)
T 1x4h_A            5 SSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGG   84 (111)
T ss_dssp             CCCCCCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTC
T ss_pred             CCCCCCcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccC
Confidence            44556677789999999999999999999999999999999999999999999999999999999999996 88      


Q ss_pred             CCccCCeeEEEecccccc
Q psy2983          79 GQKLLGIPIIVQPTQAEK   96 (370)
Q Consensus        79 g~~i~g~~l~v~~~~~~~   96 (370)
                      +..+.|++|.|.++....
T Consensus        85 ~~~~~g~~l~v~~a~~~~  102 (111)
T 1x4h_A           85 GLKLDGRQLKVDLAVTRD  102 (111)
T ss_dssp             CEESSSCEEEEECCCCCC
T ss_pred             CcEEcCEEEEEEECCCCc
Confidence            999999999999987653

>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=99.73  E-value=2.2e-17  Score=145.39  Aligned_cols=129  Identities=15%  Similarity=0.232  Sum_probs=108.7

Q ss_pred             CCceEEEecCC-CCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         113 GPMRLYIGSLH-FNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       113 ~~~~l~V~nlp-~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      +..+|||+||| ..+++++|+++|++||.|.++++++++     +|||||+|.+.++|.+|++.|||..+.|++|+|.++
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            35789999999 899999999999999999999998653     799999999999999999999999999999999987


Q ss_pred             ecCC--------------------------------------------CCcCCCCCCCCHHHHHHhcccCCce--eeeee
Q psy2983         192 TDRN--------------------------------------------ESVGGGPSNLDTDEMERAGVDLGAT--GRLQL  225 (370)
Q Consensus       192 ~~~~--------------------------------------------~~~~~~~~~~~~~~l~~~~~~~g~~--~~~~l  225 (370)
                      +...                                            ..+++++..+++++|+..|..+|.+  .++.+
T Consensus        78 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~  157 (205)
T 3tyt_A           78 KQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKV  157 (205)
T ss_dssp             SCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEE
T ss_pred             cCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE
Confidence            5211                                            0134677889999999999999998  78888


Q ss_pred             eeccc--cCCC---CCChHHHHHHHh
Q psy2983         226 MFKLA--EGTG---LELPPAAASALN  246 (370)
Q Consensus       226 ~~~~~--~~~~---~~~~~~a~~a~~  246 (370)
                      +.+..  +++|   |...+.|..|+.
T Consensus       158 ~~~~~~~~g~gfV~f~~~~~A~~Ai~  183 (205)
T 3tyt_A          158 FSGKSERSSSGLLEWDSKSDALETLG  183 (205)
T ss_dssp             CSCCSSSSEEEEEECSSHHHHHHHHH
T ss_pred             EcCCCCCceEEEEEeCCHHHHHHHHH
Confidence            76532  2455   677888877765

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.73  E-value=2e-17  Score=129.32  Aligned_cols=88  Identities=24%  Similarity=0.400  Sum_probs=80.7

Q ss_pred             CCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEE
Q psy2983           9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPII   88 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~   88 (370)
                      .+....+.++|||+|||..+++++|+++|+.|| |.+|.+++++.+++++|||||+|.+.++|.+|++++|..+.|++|.
T Consensus         8 ~~~~~~~~~~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            8 KELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLR   86 (103)
T ss_dssp             CCCCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECE
T ss_pred             CCCCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEE
Confidence            344456789999999999999999999999997 9999999999999999999999999999999999999999999999


Q ss_pred             Eeccccccc
Q psy2983          89 VQPTQAEKN   97 (370)
Q Consensus        89 v~~~~~~~~   97 (370)
                      |.++.....
T Consensus        87 V~~a~~~~~   95 (103)
T 2dng_A           87 VDIAEGRKQ   95 (103)
T ss_dssp             EEECCCCCC
T ss_pred             EEEecCCCC
Confidence            999876543

>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=99.73  E-value=6.7e-18  Score=127.61  Aligned_cols=81  Identities=23%  Similarity=0.313  Sum_probs=75.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      .+.++|||+|||.++++++|+++|+.||.|.++.+++++.+++++|||||+|.+.++|.+|++ ++|..+.|+.|.|.++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            467899999999999999999999999999999999999899999999999999999999996 9999999999999987


Q ss_pred             cc
Q psy2983          93 QA   94 (370)
Q Consensus        93 ~~   94 (370)
                      ..
T Consensus        84 ~~   85 (87)
T 3bs9_A           84 TR   85 (87)
T ss_dssp             C-
T ss_pred             CC
Confidence            64

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.2e-17  Score=128.37  Aligned_cols=85  Identities=27%  Similarity=0.371  Sum_probs=79.2

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPII   88 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~   88 (370)
                      .....+.++|||+|||..+++++|+++|+.||+|.++.+++++.+++++|||||+|.+.++|.+|++ ++|..+.|++|.
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (95)
T 2cqc_A            9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR   88 (95)
T ss_dssp             CCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3445678999999999999999999999999999999999999999999999999999999999996 999999999999


Q ss_pred             Eecccc
Q psy2983          89 VQPTQA   94 (370)
Q Consensus        89 v~~~~~   94 (370)
                      |.+++.
T Consensus        89 v~~a~~   94 (95)
T 2cqc_A           89 VSGPSS   94 (95)
T ss_dssp             EECCSC
T ss_pred             EEecCC
Confidence            998753

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.9e-17  Score=129.96  Aligned_cols=84  Identities=32%  Similarity=0.524  Sum_probs=79.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ...++|||+|||..+++++|+++|++||.|..+.+..++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            44578999999999999999999999999999999999989999999999999999999999999999999999999998


Q ss_pred             ecCC
Q psy2983         192 TDRN  195 (370)
Q Consensus       192 ~~~~  195 (370)
                      .++.
T Consensus       101 ~~~~  104 (106)
T 1p27_B          101 FVRG  104 (106)
T ss_dssp             EESS
T ss_pred             cCCC
Confidence            7754

>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=99.73  E-value=9.6e-18  Score=131.49  Aligned_cols=89  Identities=24%  Similarity=0.353  Sum_probs=81.9

Q ss_pred             CCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeE
Q psy2983           9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPI   87 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l   87 (370)
                      .+....+.++|||+|||..+++++|+++|++||.|.++.+++++.+++++|||||+|.+.++|.+|++ |+|..+.|++|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   87 (105)
T 1x5u_A            8 PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPI   87 (105)
T ss_dssp             CCCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBC
T ss_pred             CcccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            34456688999999999999999999999999999999999999899999999999999999999997 99999999999


Q ss_pred             EEeccccccc
Q psy2983          88 IVQPTQAEKN   97 (370)
Q Consensus        88 ~v~~~~~~~~   97 (370)
                      .|.++.....
T Consensus        88 ~v~~a~~~~~   97 (105)
T 1x5u_A           88 RVNKASAHNK   97 (105)
T ss_dssp             EEEETTTTSC
T ss_pred             EEEECCCCCc
Confidence            9999876543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=3.3e-18  Score=133.79  Aligned_cols=82  Identities=17%  Similarity=0.321  Sum_probs=77.0

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecc
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPT   92 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~   92 (370)
                      ..+.++|||+|||.++|+++|+++|++||+|.+|.+++++. ++++|||||+|.+.++|.+|++++|..+.|+.|.|.+.
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFK   86 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEEH
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            44679999999999999999999999999999999999987 99999999999999999999999999999999999987


Q ss_pred             ccc
Q psy2983          93 QAE   95 (370)
Q Consensus        93 ~~~   95 (370)
                      ...
T Consensus        87 ~~~   89 (103)
T 1s79_A           87 DDY   89 (103)
T ss_dssp             HHH
T ss_pred             hHH
Confidence            653

>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=99.73  E-value=3.6e-17  Score=130.42  Aligned_cols=86  Identities=27%  Similarity=0.497  Sum_probs=80.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ...++|||+|||..+++++|+++|++||.|..++++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  102 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK  102 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            45579999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             ecCCCC
Q psy2983         192 TDRNES  197 (370)
Q Consensus       192 ~~~~~~  197 (370)
                      .++...
T Consensus       103 ~~~~~~  108 (115)
T 2cpz_A          103 RSKNDS  108 (115)
T ss_dssp             CCSCCC
T ss_pred             CCCCcC
Confidence            876553

>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=99.72  E-value=9.3e-18  Score=125.63  Aligned_cols=80  Identities=18%  Similarity=0.274  Sum_probs=76.0

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecccc
Q psy2983          16 ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQA   94 (370)
Q Consensus        16 ~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~   94 (370)
                      +.+|||+|||.++++++|+++|++||+|.++.+++++.+++++|||||+|.+.++|.+|++ ++|..+.|++|.|.++..
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            3689999999999999999999999999999999999999999999999999999999996 999999999999999875


Q ss_pred             c
Q psy2983          95 E   95 (370)
Q Consensus        95 ~   95 (370)
                      .
T Consensus        81 ~   81 (83)
T 3md1_A           81 L   81 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=2.4e-17  Score=129.29  Aligned_cols=88  Identities=22%  Similarity=0.360  Sum_probs=81.3

Q ss_pred             CCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEE
Q psy2983           9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPII   88 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~   88 (370)
                      ......+.++|||+|||..+++++|+++|+.||+|.+|.+++++.++.++|||||+|.+.++|.+|++.++..|.|+.|.
T Consensus         9 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~   88 (105)
T 2dh8_A            9 NNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNID   88 (105)
T ss_dssp             CCCCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEB
T ss_pred             CcCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEE
Confidence            34456788999999999999999999999999999999999999999999999999999999999997799999999999


Q ss_pred             Eecccccc
Q psy2983          89 VQPTQAEK   96 (370)
Q Consensus        89 v~~~~~~~   96 (370)
                      |.++....
T Consensus        89 V~~a~~~~   96 (105)
T 2dh8_A           89 PKPCTPRG   96 (105)
T ss_dssp             CCCSCCSS
T ss_pred             EEEccCCC
Confidence            99987554

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=2.4e-17  Score=128.82  Aligned_cols=87  Identities=28%  Similarity=0.616  Sum_probs=81.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ..+.++|||+|||..+++++|+++|++||.|..+.+..++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV   89 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            34568999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2983         191 VTDRNES  197 (370)
Q Consensus       191 ~~~~~~~  197 (370)
                      +.+....
T Consensus        90 a~~~~~~   96 (103)
T 2dnm_A           90 ARYGRRD   96 (103)
T ss_dssp             CSSCCSC
T ss_pred             CCcCCCC
Confidence            8875543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.5e-17  Score=128.13  Aligned_cols=86  Identities=40%  Similarity=0.665  Sum_probs=80.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeE-EEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNI-QLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      .+.++|||+|||..+++++|+++|++||.|..+ +++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345799999999999999999999999999999 9999988999999999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2983         191 VTDRNES  197 (370)
Q Consensus       191 ~~~~~~~  197 (370)
                      +.++...
T Consensus        83 a~~~~~~   89 (96)
T 1x5t_A           83 AFKKDSK   89 (96)
T ss_dssp             SCCCCCC
T ss_pred             ecccCCC
Confidence            8776543

>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=99.72  E-value=1.6e-17  Score=132.45  Aligned_cols=88  Identities=20%  Similarity=0.365  Sum_probs=80.7

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHh-hccCCccCCeeEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPII   88 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~i~g~~l~   88 (370)
                      .....+.++|||+|||..+++++|+++|+.||.|.++.+++++.+++++|||||+|.+.++|.+|+ .|++..|.|+.|+
T Consensus        19 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   98 (115)
T 2cpz_A           19 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLK   98 (115)
T ss_dssp             CCCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CcCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            344557799999999999999999999999999999999999989999999999999999999999 4999999999999


Q ss_pred             Eeccccccc
Q psy2983          89 VQPTQAEKN   97 (370)
Q Consensus        89 v~~~~~~~~   97 (370)
                      |.++.....
T Consensus        99 V~~a~~~~~  107 (115)
T 2cpz_A           99 VQLKRSKND  107 (115)
T ss_dssp             EECCCCSCC
T ss_pred             EEEcCCCCc
Confidence            999876543

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=2.1e-17  Score=127.87  Aligned_cols=86  Identities=28%  Similarity=0.555  Sum_probs=79.3

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCC---CCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPD---TGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV  188 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~---~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V  188 (370)
                      .+.++|||+|||+.+++++|+++|++||.|..+.+..++.   ++.++|||||+|.+.++|.+|+..|||..+.|+.|+|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            3457899999999999999999999999999999998876   5689999999999999999999999999999999999


Q ss_pred             EEeecCCCC
Q psy2983         189 GTVTDRNES  197 (370)
Q Consensus       189 ~~~~~~~~~  197 (370)
                      .++.++...
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            998776554

>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=99.72  E-value=1.6e-17  Score=126.11  Aligned_cols=81  Identities=32%  Similarity=0.485  Sum_probs=77.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEeccc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~~   93 (370)
                      .+.++|||+|||.++++++|+++|+.||.|.++.+++++.+++++|||||+|.+.++|.+|+.++|..+.|+.|.|.++.
T Consensus         4 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEETT
T ss_pred             CcCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEEcc
Confidence            35689999999999999999999999999999999999989999999999999999999999999999999999999876


Q ss_pred             c
Q psy2983          94 A   94 (370)
Q Consensus        94 ~   94 (370)
                      .
T Consensus        84 ~   84 (89)
T 3ucg_A           84 T   84 (89)
T ss_dssp             T
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=99.72  E-value=1.9e-17  Score=128.65  Aligned_cols=85  Identities=24%  Similarity=0.385  Sum_probs=78.6

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPII   88 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~   88 (370)
                      .....+.++|||+|||..+++++|+++|+.||.|.++.++.++ +++++|||||+|.+.++|.+|++ ++|..+.|++|.
T Consensus        11 ~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   89 (100)
T 2do4_A           11 YSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIK   89 (100)
T ss_dssp             CSSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3445678999999999999999999999999999999999998 89999999999999999999995 999999999999


Q ss_pred             Eeccccc
Q psy2983          89 VQPTQAE   95 (370)
Q Consensus        89 v~~~~~~   95 (370)
                      |.++.+.
T Consensus        90 v~~a~~~   96 (100)
T 2do4_A           90 VAISNSG   96 (100)
T ss_dssp             EEECCCC
T ss_pred             EEECCCC
Confidence            9998754

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.72  E-value=1.5e-17  Score=128.94  Aligned_cols=84  Identities=27%  Similarity=0.516  Sum_probs=78.5

Q ss_pred             CCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeE--------EEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccC
Q psy2983           9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRD--------VRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNG   79 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~--------v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g   79 (370)
                      .+......++|||+|||.++++++|+++|++||.|..        +.+++++.+++++|||||+|.+.++|.+|++ ++|
T Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g   85 (99)
T 2la6_A            6 HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDG   85 (99)
T ss_dssp             SCCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCC
Confidence            3445567899999999999999999999999999999        9999999999999999999999999999996 999


Q ss_pred             CccCCeeEEEecc
Q psy2983          80 QKLLGIPIIVQPT   92 (370)
Q Consensus        80 ~~i~g~~l~v~~~   92 (370)
                      ..+.|+.|+|.++
T Consensus        86 ~~~~g~~l~V~~A   98 (99)
T 2la6_A           86 KEFSGNPIKVSFA   98 (99)
T ss_dssp             CBSSSSBCEEEEC
T ss_pred             CEeCCcEEEEEec
Confidence            9999999999876

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=2.6e-17  Score=128.29  Aligned_cols=87  Identities=32%  Similarity=0.674  Sum_probs=81.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2983         191 VTDRNES  197 (370)
Q Consensus       191 ~~~~~~~  197 (370)
                      +.++...
T Consensus        89 a~~~~~~   95 (102)
T 1x5s_A           89 AGKSSDN   95 (102)
T ss_dssp             EECCCCC
T ss_pred             CCCCCCC
Confidence            9876654

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=5.5e-17  Score=128.92  Aligned_cols=88  Identities=24%  Similarity=0.424  Sum_probs=81.5

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHhcccCCCcee--------eEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCcee
Q psy2983         110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKID--------NIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFEL  181 (370)
Q Consensus       110 ~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~--------~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i  181 (370)
                      .....++|||+|||+.+++++|+++|++||.|.        .++++.++.+|.++|||||+|.+.++|.+|+..|||..+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            344568999999999999999999999999999        699999988999999999999999999999999999999


Q ss_pred             CCeeEEEEEeecCCCC
Q psy2983         182 AGRPMKVGTVTDRNES  197 (370)
Q Consensus       182 ~g~~l~V~~~~~~~~~  197 (370)
                      .|+.|+|.++.++...
T Consensus        91 ~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           91 QGSKLKVSLARKKPPM  106 (113)
T ss_dssp             TTEECEEECSSCCCCS
T ss_pred             CCCEEEEEECCCCCCC
Confidence            9999999998876554

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=8.3e-18  Score=131.13  Aligned_cols=88  Identities=22%  Similarity=0.389  Sum_probs=81.2

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPII   88 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~   88 (370)
                      .....+.++|||+|||..+++++|+++|+.||.|.++.+++++.+++++|||||+|.+.++|.+|++ ++|..+.|+.|.
T Consensus         6 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   85 (102)
T 2cqb_A            6 SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR   85 (102)
T ss_dssp             SCSCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCcCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            3445678999999999999999999999999999999999999999999999999999999999995 999999999999


Q ss_pred             Eeccccccc
Q psy2983          89 VQPTQAEKN   97 (370)
Q Consensus        89 v~~~~~~~~   97 (370)
                      |.++.....
T Consensus        86 V~~a~~~~~   94 (102)
T 2cqb_A           86 VNLAKPMRI   94 (102)
T ss_dssp             EEECCCCCC
T ss_pred             EEeCCCCCC
Confidence            999876543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=1.8e-17  Score=127.48  Aligned_cols=84  Identities=27%  Similarity=0.430  Sum_probs=79.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      .++++|||+|||..+++++|+++|++||.|.++.+++++.+++++|||||+|.+.++|.+|++ ++|..+.|++|+|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            467999999999999999999999999999999999999999999999999999999999997 9999999999999998


Q ss_pred             ccccc
Q psy2983          93 QAEKN   97 (370)
Q Consensus        93 ~~~~~   97 (370)
                      .....
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            76543

>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=99.72  E-value=3.7e-17  Score=129.28  Aligned_cols=86  Identities=31%  Similarity=0.500  Sum_probs=80.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  102 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  102 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            34568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eecCCC
Q psy2983         191 VTDRNE  196 (370)
Q Consensus       191 ~~~~~~  196 (370)
                      +.++..
T Consensus       103 a~~~~~  108 (110)
T 1oo0_B          103 CFVKGP  108 (110)
T ss_dssp             SEESSC
T ss_pred             cccCCC
Confidence            877543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=1.9e-17  Score=130.23  Aligned_cols=92  Identities=21%  Similarity=0.429  Sum_probs=83.1

Q ss_pred             CCCCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeee-CCCCCeecEEEEEecCCCChHHHhh-c-cCCcc
Q psy2983           6 SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITC-NKTRRFKGIAYIEFKDPESVPLAMG-L-NGQKL   82 (370)
Q Consensus         6 ~~~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d-~~~~~~kg~afVeF~~~e~A~~Al~-l-~g~~i   82 (370)
                      +...++...+.++|||+|||..+++++|+++|+.||.|..|.++++ +.++.++|||||+|.+.++|.+|++ + ++..+
T Consensus         5 s~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~   84 (107)
T 2cph_A            5 SSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHL   84 (107)
T ss_dssp             CCCSSCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBS
T ss_pred             CCcccccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeE
Confidence            3344556778899999999999999999999999999999999998 7889999999999999999999996 8 99999


Q ss_pred             CCeeEEEeccccccc
Q psy2983          83 LGIPIIVQPTQAEKN   97 (370)
Q Consensus        83 ~g~~l~v~~~~~~~~   97 (370)
                      .|+.|.|.++.....
T Consensus        85 ~g~~l~v~~a~~~~~   99 (107)
T 2cph_A           85 YGRRLVLEWADSEVT   99 (107)
T ss_dssp             SSCBCEEEECCCCCC
T ss_pred             CCCEEEEEeCCCCCC
Confidence            999999999876543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=5.7e-17  Score=127.46  Aligned_cols=87  Identities=24%  Similarity=0.487  Sum_probs=80.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeec-CCCCCcccEEEEEECCHHHHHHHHHHh-CCceeCCeeEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVD-PDTGRSKGYGFITFHSADDAKKAQEQL-NGFELAGRPMKV  188 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~-~~~g~~~g~afV~f~~~~~a~~A~~~l-~g~~i~g~~l~V  188 (370)
                      ....++|||+|||..+++++|+++|++||.|..+.++.+ ..+|.++|||||+|.+.++|.+|+..| |+..+.|+.|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v   91 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   91 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEE
Confidence            345689999999999999999999999999999999998 779999999999999999999999999 999999999999


Q ss_pred             EEeecCCCC
Q psy2983         189 GTVTDRNES  197 (370)
Q Consensus       189 ~~~~~~~~~  197 (370)
                      .++.++...
T Consensus        92 ~~a~~~~~~  100 (107)
T 2cph_A           92 EWADSEVTV  100 (107)
T ss_dssp             EECCCCCCC
T ss_pred             EeCCCCCCC
Confidence            999876554

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.72  E-value=1.1e-16  Score=124.99  Aligned_cols=85  Identities=29%  Similarity=0.569  Sum_probs=79.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ..+.++|||+|||+.+++++|+++|++|| |..++++.++.+|.++|||||+|.+.++|.+|+ .|||..+.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   89 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDI   89 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEE
Confidence            34568999999999999999999999997 999999999989999999999999999999999 7999999999999999


Q ss_pred             eecCCCC
Q psy2983         191 VTDRNES  197 (370)
Q Consensus       191 ~~~~~~~  197 (370)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2dng_A           90 AEGRKQD   96 (103)
T ss_dssp             CCCCCCC
T ss_pred             ecCCCCC
Confidence            8876554

>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=99.72  E-value=1e-17  Score=131.53  Aligned_cols=91  Identities=26%  Similarity=0.445  Sum_probs=82.8

Q ss_pred             CCCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCcc---
Q psy2983           7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL---   82 (370)
Q Consensus         7 ~~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i---   82 (370)
                      ...+....+.++|||+|||..+++++|+++|++||.|.+|.+++++.+++++|||||+|.+.++|.+|++ ++|..+   
T Consensus         4 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~   83 (106)
T 2dgp_A            4 GSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPG   83 (106)
T ss_dssp             CCCSCCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTT
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCC
Confidence            3445566788999999999999999999999999999999999999999999999999999999999996 999987   


Q ss_pred             CCeeEEEeccccccc
Q psy2983          83 LGIPIIVQPTQAEKN   97 (370)
Q Consensus        83 ~g~~l~v~~~~~~~~   97 (370)
                      .|++|.|.++.....
T Consensus        84 ~g~~l~v~~a~~~~~   98 (106)
T 2dgp_A           84 MNRPIQVKPADSESR   98 (106)
T ss_dssp             CSSCCEEEECCCCSC
T ss_pred             CCceEEEEECCcccc
Confidence            899999999876543

>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=99.72  E-value=6.7e-17  Score=126.64  Aligned_cols=85  Identities=31%  Similarity=0.533  Sum_probs=79.3

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCC---eeEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG---RPMKV  188 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g---~~l~V  188 (370)
                      ...++|||+|||+.+++++|+++|++||.|..+.+..++ +|.++|||||+|.+.++|.+|+..|||..+.|   +.|+|
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            456899999999999999999999999999999999997 89999999999999999999999999999998   99999


Q ss_pred             EEeecCCCC
Q psy2983         189 GTVTDRNES  197 (370)
Q Consensus       189 ~~~~~~~~~  197 (370)
                      .++.++...
T Consensus        92 ~~a~~~~~~  100 (105)
T 2dnh_A           92 KFADTDKES  100 (105)
T ss_dssp             EESCSSCCC
T ss_pred             EECccCccc
Confidence            998776543

>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=99.71  E-value=5.2e-17  Score=128.57  Aligned_cols=87  Identities=29%  Similarity=0.574  Sum_probs=81.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhC------CceeCCe
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN------GFELAGR  184 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~------g~~i~g~  184 (370)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..||      +..+.|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~   91 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   91 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCE
Confidence            3456899999999999999999999999999999999999899999999999999999999999999      9999999


Q ss_pred             eEEEEEeecCCCC
Q psy2983         185 PMKVGTVTDRNES  197 (370)
Q Consensus       185 ~l~V~~~~~~~~~  197 (370)
                      .|+|.++.++...
T Consensus        92 ~l~v~~a~~~~~~  104 (111)
T 1x4h_A           92 QLKVDLAVTRDEA  104 (111)
T ss_dssp             EEEEECCCCCCCC
T ss_pred             EEEEEECCCCccC
Confidence            9999998876553

>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=99.71  E-value=3.3e-17  Score=128.60  Aligned_cols=87  Identities=31%  Similarity=0.535  Sum_probs=81.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCcee---CCeeEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFEL---AGRPMK  187 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i---~g~~l~  187 (370)
                      ....++|||+|||..+++++|+++|++||.|..++++.++.+|.++|||||+|.+.++|.+|+..|||..+   .|+.|+
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            44568999999999999999999999999999999999988999999999999999999999999999988   899999


Q ss_pred             EEEeecCCCC
Q psy2983         188 VGTVTDRNES  197 (370)
Q Consensus       188 V~~~~~~~~~  197 (370)
                      |.++.++...
T Consensus        90 v~~a~~~~~~   99 (106)
T 2dgp_A           90 VKPADSESRG   99 (106)
T ss_dssp             EEECCCCSCC
T ss_pred             EEECCccccc
Confidence            9999876554

>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=99.71  E-value=4.2e-17  Score=126.17  Aligned_cols=84  Identities=20%  Similarity=0.308  Sum_probs=78.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ...+.+|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            34568999999999999999999999999999888888888999999999999999999999999999999999999999


Q ss_pred             eecC
Q psy2983         191 VTDR  194 (370)
Q Consensus       191 ~~~~  194 (370)
                      +..+
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8654

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=1.6e-17  Score=127.52  Aligned_cols=84  Identities=27%  Similarity=0.394  Sum_probs=78.1

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPII   88 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~   88 (370)
                      .....+.++|||+|||..+++++|+++|++||+|.++.+++++.+++++|||||+|.+.++|.+|++ ++|..+.|++|.
T Consensus        10 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   89 (94)
T 2e5h_A           10 GGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIK   89 (94)
T ss_dssp             CSCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEE
Confidence            3445678999999999999999999999999999999999999999999999999999999999995 999999999999


Q ss_pred             Eeccc
Q psy2983          89 VQPTQ   93 (370)
Q Consensus        89 v~~~~   93 (370)
                      |.+++
T Consensus        90 v~~ak   94 (94)
T 2e5h_A           90 ASIAI   94 (94)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            98863

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.71  E-value=4e-17  Score=134.65  Aligned_cols=91  Identities=21%  Similarity=0.433  Sum_probs=83.2

Q ss_pred             CCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCee
Q psy2983           8 DLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIP   86 (370)
Q Consensus         8 ~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~   86 (370)
                      ...+.....++|||+|||.++++++|+++|+.||.|.+|.+++++.+++++|||||+|.+.++|.+|++ ++|..+.|+.
T Consensus        34 ~~~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~  113 (139)
T 1u6f_A           34 QMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKR  113 (139)
T ss_dssp             CSSCCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCE
T ss_pred             ccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            344556778999999999999999999999999999999999999999999999999999999999996 9999999999


Q ss_pred             EEEecccccccc
Q psy2983          87 IIVQPTQAEKNR   98 (370)
Q Consensus        87 l~v~~~~~~~~~   98 (370)
                      |.|.++.....+
T Consensus       114 l~v~~a~~~~~~  125 (139)
T 1u6f_A          114 LKVALAASGHQR  125 (139)
T ss_dssp             EEEEESSCCCCC
T ss_pred             EEEEECCCCCCC
Confidence            999998765443

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=1e-16  Score=125.21  Aligned_cols=85  Identities=35%  Similarity=0.652  Sum_probs=79.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||+.+++++|+++|++||.|..+.+..+  +|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            345689999999999999999999999999999999988  899999999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2983         191 VTDRNES  197 (370)
Q Consensus       191 ~~~~~~~  197 (370)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2d9p_A           90 AQRKEER   96 (103)
T ss_dssp             CSSCCCC
T ss_pred             ecccccC
Confidence            9876654

>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=99.71  E-value=1.2e-17  Score=128.88  Aligned_cols=82  Identities=26%  Similarity=0.350  Sum_probs=77.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      ++++|||+|||..+++++|+++|+.||.|.++.+++++.+++++|||||+|.+.++|.+|++ ++|..+.|+.|.|.++.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            46899999999999999999999999999999999999999999999999999999999995 99999999999999987


Q ss_pred             ccc
Q psy2983          94 AEK   96 (370)
Q Consensus        94 ~~~   96 (370)
                      ...
T Consensus        81 ~~~   83 (96)
T 2x1f_A           81 NSD   83 (96)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            543

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.71  E-value=9.9e-18  Score=132.59  Aligned_cols=89  Identities=19%  Similarity=0.315  Sum_probs=81.7

Q ss_pred             CCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCee
Q psy2983           8 DLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIP   86 (370)
Q Consensus         8 ~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~   86 (370)
                      ..+....+.++|||+|||..+++++|+++|+.||.|.++.++.++.++.++|||||+|.+.++|.+|++ ++|..+.|++
T Consensus        18 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~   97 (110)
T 1oo0_B           18 PGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQT   97 (110)
T ss_dssp             CCBCCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcE
Confidence            344556678999999999999999999999999999999999999999999999999999999999996 9999999999


Q ss_pred             EEEecccccc
Q psy2983          87 IIVQPTQAEK   96 (370)
Q Consensus        87 l~v~~~~~~~   96 (370)
                      |.|.++....
T Consensus        98 l~V~~a~~~~  107 (110)
T 1oo0_B           98 IQVDWCFVKG  107 (110)
T ss_dssp             CEEEESEESS
T ss_pred             EEEEEcccCC
Confidence            9999987543

>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=99.71  E-value=4.2e-18  Score=129.82  Aligned_cols=80  Identities=20%  Similarity=0.297  Sum_probs=71.3

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCC--CeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVG--KVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G--~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      .+|||+|||.++|+++|+++|++||  .|.++++++++.+|+++|||||+|.+.++|.+|++ ++|..+.|+.|.|.++.
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            5799999999999999999999999  99999999999999999999999999999999995 99999999999999887


Q ss_pred             ccc
Q psy2983          94 AEK   96 (370)
Q Consensus        94 ~~~   96 (370)
                      +..
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            543

>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=99.71  E-value=3.2e-17  Score=124.05  Aligned_cols=83  Identities=31%  Similarity=0.564  Sum_probs=77.2

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCC-cccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGR-SKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~-~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      .+++|||+|||.++++++|+++|++||.|..+.+..+..++. ++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
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            357899999999999999999999999999999999877666 8999999999999999999999999999999999998


Q ss_pred             ecCC
Q psy2983         192 TDRN  195 (370)
Q Consensus       192 ~~~~  195 (370)
                      .++.
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=2.6e-17  Score=127.62  Aligned_cols=85  Identities=25%  Similarity=0.454  Sum_probs=79.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCcee-eEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCee----E
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKID-NIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRP----M  186 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~-~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~----l  186 (370)
                      ...++|||+|||+.+++++|+++|++||.|. .++++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.    |
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l   86 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRF   86 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEEC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeE
Confidence            4568999999999999999999999999999 9999999889999999999999999999999999999999999    9


Q ss_pred             EEEEeecCCC
Q psy2983         187 KVGTVTDRNE  196 (370)
Q Consensus       187 ~V~~~~~~~~  196 (370)
                      +|.++.+...
T Consensus        87 ~v~~a~~~~~   96 (99)
T 2div_A           87 KLNYATYSGP   96 (99)
T ss_dssp             CEEETTCCSS
T ss_pred             EEeecCCCCC
Confidence            9999876544

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=2e-17  Score=127.96  Aligned_cols=84  Identities=20%  Similarity=0.367  Sum_probs=77.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCC---CCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEE
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNK---TRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIV   89 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~---~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v   89 (370)
                      .+.++|||+|||.++++++|+++|+.||+|..+.+.+++.   +++++|||||+|.+.++|.+|++ |+|..+.|++|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            4679999999999999999999999999999999999886   66899999999999999999997 9999999999999


Q ss_pred             eccccccc
Q psy2983          90 QPTQAEKN   97 (370)
Q Consensus        90 ~~~~~~~~   97 (370)
                      .++.....
T Consensus        83 ~~a~~~~~   90 (98)
T 2cpf_A           83 RISERATK   90 (98)
T ss_dssp             ECSSCSSC
T ss_pred             EEccCCCC
Confidence            99876543

>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=99.71  E-value=2e-17  Score=127.21  Aligned_cols=84  Identities=33%  Similarity=0.535  Sum_probs=76.5

Q ss_pred             CCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeE
Q psy2983           9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPI   87 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l   87 (370)
                      .+....+.++|||+|||..+++++|+++|++||+|.++.+++++. ++++|||||+|.+.++|.+|++ ++|..+.|++|
T Consensus         9 ~~~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   87 (95)
T 2ywk_A            9 FPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPI   87 (95)
T ss_dssp             ---CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEE
Confidence            344566789999999999999999999999999999999999876 8999999999999999999997 99999999999


Q ss_pred             EEeccc
Q psy2983          88 IVQPTQ   93 (370)
Q Consensus        88 ~v~~~~   93 (370)
                      .|.+++
T Consensus        88 ~V~~a~   93 (95)
T 2ywk_A           88 NVSGPS   93 (95)
T ss_dssp             EEECCC
T ss_pred             EEEEcC
Confidence            998875

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.6e-17  Score=129.47  Aligned_cols=86  Identities=24%  Similarity=0.414  Sum_probs=80.0

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHh-hccCCccCCeeEEE
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIV   89 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~i~g~~l~v   89 (370)
                      ....+.++|||+|||..+++++|+++|++||+|.++.+++++.++.++|||||+|.+.++|.+|+ .+++..+.|++|+|
T Consensus         7 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   86 (102)
T 1x5s_A            7 GMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRV   86 (102)
T ss_dssp             CCCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999 59999999999999


Q ss_pred             ecccccc
Q psy2983          90 QPTQAEK   96 (370)
Q Consensus        90 ~~~~~~~   96 (370)
                      .++....
T Consensus        87 ~~a~~~~   93 (102)
T 1x5s_A           87 DQAGKSS   93 (102)
T ss_dssp             EEEECCC
T ss_pred             EECCCCC
Confidence            9987543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.71  E-value=6.4e-18  Score=131.46  Aligned_cols=81  Identities=25%  Similarity=0.393  Sum_probs=77.5

Q ss_pred             CceEEEecCCC------CCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCC-eeE
Q psy2983         114 PMRLYIGSLHF------NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG-RPM  186 (370)
Q Consensus       114 ~~~l~V~nlp~------~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g-~~l  186 (370)
                      .++|||+|||.      .+++++|+++|++||.|.+++++.++.+|+++|||||+|.+.++|.+|+..|||..+.| +.|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l   85 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL   85 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEE
Confidence            47899999999      99999999999999999999999999899999999999999999999999999999999 999


Q ss_pred             EEEEeecC
Q psy2983         187 KVGTVTDR  194 (370)
Q Consensus       187 ~V~~~~~~  194 (370)
                      +|.++.++
T Consensus        86 ~V~~a~~~   93 (100)
T 3ns6_A           86 FLYTMKDV   93 (100)
T ss_dssp             EEEESHHH
T ss_pred             EEEECchh
Confidence            99998664

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.71  E-value=1.7e-17  Score=132.96  Aligned_cols=82  Identities=23%  Similarity=0.366  Sum_probs=77.2

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEE
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIV   89 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v   89 (370)
                      ....+.++|||+|||.++++++|+++|++||.|.++++++++.+++++|||||+|.+.++|.+|++ ++|..+.|+.|+|
T Consensus        35 ~~~~~~~~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           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV  114 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345677999999999999999999999999999999999999999999999999999999999996 9999999999999


Q ss_pred             ecc
Q psy2983          90 QPT   92 (370)
Q Consensus        90 ~~~   92 (370)
                      +++
T Consensus       115 ~~a  117 (118)
T 2khc_A          115 QLK  117 (118)
T ss_dssp             EEC
T ss_pred             Eec
Confidence            876

>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=99.71  E-value=6.1e-17  Score=122.39  Aligned_cols=80  Identities=28%  Similarity=0.614  Sum_probs=74.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|++ +++..+.|+.|+|.+
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            3456899999999999999999999999999999999998899999999999999999999997 688999999999987


Q ss_pred             e
Q psy2983         191 V  191 (370)
Q Consensus       191 ~  191 (370)
                      +
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.71  E-value=1.3e-17  Score=131.80  Aligned_cols=89  Identities=19%  Similarity=0.263  Sum_probs=75.3

Q ss_pred             CCCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCee
Q psy2983           7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIP   86 (370)
Q Consensus         7 ~~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~   86 (370)
                      ....+...+.++|||+|||.++++++|+++|+.||.|.++.+++++.+++++|||||+|.+.++|.+|++..+..+.|+.
T Consensus        16 ~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~   95 (109)
T 2rs2_A           16 PRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKT   95 (109)
T ss_dssp             ----------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEE
T ss_pred             ccccccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEE
Confidence            33445567889999999999999999999999999999999999999999999999999999999999986679999999


Q ss_pred             EEEeccccc
Q psy2983          87 IIVQPTQAE   95 (370)
Q Consensus        87 l~v~~~~~~   95 (370)
                      |.|.++...
T Consensus        96 l~V~~a~~~  104 (109)
T 2rs2_A           96 IDPKVAFPR  104 (109)
T ss_dssp             EEEEECCCC
T ss_pred             EEEEEccCC
Confidence            999988754

>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=99.71  E-value=1.1e-16  Score=125.17  Aligned_cols=84  Identities=24%  Similarity=0.534  Sum_probs=78.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCC-CCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDT-GRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      .++++|||+|||+.+++++|+++|++|| |..+.++.++.+ |.++|||||+|.+.++|.+|+ .||+..+.|+.|+|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEE
Confidence            4568999999999999999999999999 999999999877 999999999999999999999 8999999999999999


Q ss_pred             eecCCCC
Q psy2983         191 VTDRNES  197 (370)
Q Consensus       191 ~~~~~~~  197 (370)
                      +.++...
T Consensus        91 a~~~~~~   97 (104)
T 1wi8_A           91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             ccCCCCC
Confidence            9876654

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.71  E-value=5.9e-17  Score=129.76  Aligned_cols=82  Identities=29%  Similarity=0.508  Sum_probs=77.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||+++++++|+++|++||.|..++++.++.+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.+
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            44568999999999999999999999999999999999988999999999999999999999999999999999999988


Q ss_pred             ee
Q psy2983         191 VT  192 (370)
Q Consensus       191 ~~  192 (370)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            63

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=2e-17  Score=128.26  Aligned_cols=84  Identities=18%  Similarity=0.287  Sum_probs=78.6

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCee-EEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCee---
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVR-DVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIP---   86 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~-~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~---   86 (370)
                      ...++++|||+|||..+++++|+++|++||+|. ++++++++.+++++|||||+|.+.++|.+|++ |+|..+.|+.   
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~   84 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAK   84 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCE
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcce
Confidence            345789999999999999999999999999999 99999999999999999999999999999997 9999999999   


Q ss_pred             -EEEeccccc
Q psy2983          87 -IIVQPTQAE   95 (370)
Q Consensus        87 -l~v~~~~~~   95 (370)
                       |+|.++...
T Consensus        85 ~l~v~~a~~~   94 (99)
T 2div_A           85 RFKLNYATYS   94 (99)
T ss_dssp             ECCEEETTCC
T ss_pred             eEEEeecCCC
Confidence             999887654

>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=99.71  E-value=6.6e-17  Score=126.24  Aligned_cols=88  Identities=19%  Similarity=0.290  Sum_probs=80.2

Q ss_pred             CCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeE
Q psy2983           8 DLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPI   87 (370)
Q Consensus         8 ~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l   87 (370)
                      .......+.++|||+|||..+++++|+++|+.||.|..+.+++++.+++++|||||+|.+.++|.+|++ ++..+.|+.|
T Consensus         7 ~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~l   85 (103)
T 2cqg_A            7 GVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWC   85 (103)
T ss_dssp             SCSCCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEE
T ss_pred             CCCCccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH-cCCeeCCeEE
Confidence            344556778999999999999999999999999999999999999999999999999999999999998 5778999999


Q ss_pred             EEecccccc
Q psy2983          88 IVQPTQAEK   96 (370)
Q Consensus        88 ~v~~~~~~~   96 (370)
                      .|.++....
T Consensus        86 ~v~~a~~~~   94 (103)
T 2cqg_A           86 DCKLPNSKQ   94 (103)
T ss_dssp             EEECCCTTC
T ss_pred             EEEecCCCC
Confidence            999987653

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.70  E-value=7.4e-18  Score=123.76  Aligned_cols=75  Identities=21%  Similarity=0.371  Sum_probs=72.2

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecc
Q psy2983          18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPT   92 (370)
Q Consensus        18 ~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~   92 (370)
                      +|||+|||.++++++|+++|++||+|.++.+++++.+++++|||||+|.+.++|.+|++++|..+.|++|.|+++
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 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEeC
Confidence            599999999999999999999999999999999998999999999999999999999999999999999999864

>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=99.70  E-value=4.5e-17  Score=127.23  Aligned_cols=88  Identities=20%  Similarity=0.418  Sum_probs=79.3

Q ss_pred             CCCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCe
Q psy2983           7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGI   85 (370)
Q Consensus         7 ~~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~   85 (370)
                      ........+.++|||+|||..+++++|+++|++||.|.+|.+++++.+  ++|||||+|.+.++|.+|++ ++|..+.|+
T Consensus         6 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   83 (103)
T 2cqi_A            6 SGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGK   83 (103)
T ss_dssp             CCCCCCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCCCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCC
Confidence            344556778899999999999999999999999999999999998643  68999999999999999997 999999999


Q ss_pred             eEEEecccccc
Q psy2983          86 PIIVQPTQAEK   96 (370)
Q Consensus        86 ~l~v~~~~~~~   96 (370)
                      +|.|.++....
T Consensus        84 ~l~V~~a~~~~   94 (103)
T 2cqi_A           84 EVKVNWATTPS   94 (103)
T ss_dssp             EEEEEECCCTT
T ss_pred             eEEEEECCCCc
Confidence            99999987654

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=8.1e-17  Score=128.60  Aligned_cols=87  Identities=18%  Similarity=0.242  Sum_probs=80.1

Q ss_pred             CCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCee
Q psy2983           8 DLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIP   86 (370)
Q Consensus         8 ~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~   86 (370)
                      ..+....+.++|||+|||..+++++|+++|+.||.|.++++++++.+++++|||||+|.+.++|.+|++ +++ .+.|++
T Consensus         9 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~   87 (116)
T 2cqd_A            9 HGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRK   87 (116)
T ss_dssp             CCCCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEE
T ss_pred             CCCcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEE
Confidence            345566788999999999999999999999999999999999999999999999999999999999996 777 899999


Q ss_pred             EEEeccccc
Q psy2983          87 IIVQPTQAE   95 (370)
Q Consensus        87 l~v~~~~~~   95 (370)
                      |.|.++...
T Consensus        88 l~V~~a~~~   96 (116)
T 2cqd_A           88 ANVNLAYLG   96 (116)
T ss_dssp             CEEEESTTT
T ss_pred             EEEEEcccC
Confidence            999998654

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.70  E-value=5.9e-17  Score=123.75  Aligned_cols=84  Identities=27%  Similarity=0.553  Sum_probs=78.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      .+.++|||+|||..+++++|+++|++||.|..+.+..+  +|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45689999999999999999999999999999999875  8999999999999999999999999999999999999998


Q ss_pred             ecCCCC
Q psy2983         192 TDRNES  197 (370)
Q Consensus       192 ~~~~~~  197 (370)
                      .+....
T Consensus        84 ~~~~~~   89 (92)
T 2dgv_A           84 RNASGP   89 (92)
T ss_dssp             SCCSSC
T ss_pred             CCCCCC
Confidence            776553

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=1.8e-17  Score=127.75  Aligned_cols=83  Identities=27%  Similarity=0.366  Sum_probs=78.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEE-EEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDV-RLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v-~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      .+.++|||+|||..+++++|+++|+.||.|.++ .+++++.++.++|||||+|.+.++|.+|++ ++|..+.|++|.|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            467999999999999999999999999999999 999998999999999999999999999997 999999999999999


Q ss_pred             ccccc
Q psy2983          92 TQAEK   96 (370)
Q Consensus        92 ~~~~~   96 (370)
                      +....
T Consensus        83 a~~~~   87 (96)
T 1x5t_A           83 AFKKD   87 (96)
T ss_dssp             SCCCC
T ss_pred             ecccC
Confidence            87654

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.70  E-value=6.9e-18  Score=131.30  Aligned_cols=82  Identities=16%  Similarity=0.226  Sum_probs=77.4

Q ss_pred             CCCCeEEEcCCCC------CCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCC-e
Q psy2983          14 RDARTIFCMQLSQ------RIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLG-I   85 (370)
Q Consensus        14 ~~~r~v~V~nLp~------~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g-~   85 (370)
                      ..+++|||+|||.      ++++++|+++|++||+|.++.+++++.+++++|||||+|.+.++|.+|++ ++|..+.| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            4568999999999      99999999999999999999999999999999999999999999999995 99999999 9


Q ss_pred             eEEEeccccc
Q psy2983          86 PIIVQPTQAE   95 (370)
Q Consensus        86 ~l~v~~~~~~   95 (370)
                      +|.|.++.+.
T Consensus        84 ~l~V~~a~~~   93 (100)
T 3ns6_A           84 RLFLYTMKDV   93 (100)
T ss_dssp             BCEEEESHHH
T ss_pred             EEEEEECchh
Confidence            9999988653

>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=99.70  E-value=5.5e-18  Score=135.20  Aligned_cols=103  Identities=19%  Similarity=0.331  Sum_probs=91.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      ..+++|||+|||..+++++|+++|+.||.|.++.++++   +.++|||||+|.+.++|.+|++ ++|..+.|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            46789999999999999999999999999999999876   4458999999999999999997 9999999999999998


Q ss_pred             cccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCc
Q psy2983          93 QAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGK  140 (370)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~  140 (370)
                      ......                     .+++...++++|.++|++||.
T Consensus        83 ~~~~~~---------------------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           83 NANRAF---------------------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             CHHHHT---------------------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             cCChhh---------------------hhhhHhHhHHHHHHHHHHhCC
Confidence            765332                     456677889999999999984

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=4.3e-17  Score=127.35  Aligned_cols=87  Identities=21%  Similarity=0.369  Sum_probs=79.4

Q ss_pred             CCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeE
Q psy2983           9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPI   87 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l   87 (370)
                      ......+.++|||+|||..+++++|+++|+.||.|.++.++++  ++.++|||||+|.+.++|.+|++ |+|..+.|++|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   85 (103)
T 2d9p_A            8 DRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPL   85 (103)
T ss_dssp             CCCCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEE
Confidence            3344568899999999999999999999999999999999998  78999999999999999999996 99999999999


Q ss_pred             EEeccccccc
Q psy2983          88 IVQPTQAEKN   97 (370)
Q Consensus        88 ~v~~~~~~~~   97 (370)
                      .|.++.....
T Consensus        86 ~V~~a~~~~~   95 (103)
T 2d9p_A           86 YVALAQRKEE   95 (103)
T ss_dssp             EEEECSSCCC
T ss_pred             EEEEeccccc
Confidence            9999876544

>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=99.70  E-value=3.2e-17  Score=128.37  Aligned_cols=86  Identities=27%  Similarity=0.395  Sum_probs=79.3

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCC-CCeecEEEEEecCCCChHHHhhccCCccCCeeEEE
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKT-RRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIV   89 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~-~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v   89 (370)
                      ....+.++|||+|||..+++++|+++|+.|| |.+|.+++++.+ ++++|||||+|.+.++|.+|+.+++..+.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V   88 (104)
T 1wi8_A           10 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRV   88 (104)
T ss_dssp             CCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEEE
Confidence            3445779999999999999999999999999 999999999987 89999999999999999999999999999999999


Q ss_pred             eccccccc
Q psy2983          90 QPTQAEKN   97 (370)
Q Consensus        90 ~~~~~~~~   97 (370)
                      .++.....
T Consensus        89 ~~a~~~~~   96 (104)
T 1wi8_A           89 DVADQAQD   96 (104)
T ss_dssp             EECCCCCC
T ss_pred             EEccCCCC
Confidence            99876543

>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=99.70  E-value=7.6e-18  Score=131.79  Aligned_cols=85  Identities=31%  Similarity=0.499  Sum_probs=79.5

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      ...+.++|||+|||..+++++|+++|+.||.|.++.+++++.++.++|||||+|.+.++|.+|++ ++|..+.|+.|.|.
T Consensus         4 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   83 (104)
T 1p1t_A            4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVD   83 (104)
T ss_dssp             SHHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEE
T ss_pred             cCCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            44567999999999999999999999999999999999999999999999999999999999996 99999999999999


Q ss_pred             cccccc
Q psy2983          91 PTQAEK   96 (370)
Q Consensus        91 ~~~~~~   96 (370)
                      ++....
T Consensus        84 ~a~~~~   89 (104)
T 1p1t_A           84 NAASEK   89 (104)
T ss_dssp             ETTCTT
T ss_pred             eCCCcc
Confidence            987544

>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=99.70  E-value=1.7e-17  Score=135.18  Aligned_cols=87  Identities=26%  Similarity=0.368  Sum_probs=80.6

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPII   88 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~   88 (370)
                      .....+.++|||+|||..+++++|+++|++||+|.+|.+++++.+++++|||||+|.+.++|.+|++ ++|..|.|++|.
T Consensus        40 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~  119 (129)
T 2kxn_B           40 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR  119 (129)
T ss_dssp             SSCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3445678999999999999999999999999999999999999999999999999999999999996 999999999999


Q ss_pred             Eecccccc
Q psy2983          89 VQPTQAEK   96 (370)
Q Consensus        89 v~~~~~~~   96 (370)
                      |.++....
T Consensus       120 V~~a~~~~  127 (129)
T 2kxn_B          120 VDFSITKR  127 (129)
T ss_dssp             ESCCSSSS
T ss_pred             EEEecCCC
Confidence            99987543

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.70  E-value=9.5e-18  Score=130.61  Aligned_cols=99  Identities=24%  Similarity=0.348  Sum_probs=82.3

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccccc
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQAE   95 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~~   95 (370)
                      ++|||+|||.++|+++|+++|++||+|.++.++++     ++|||||+|.+.++|.+|++ ++|..+.|+.|.|.++...
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            48999999999999999999999999999999886     58999999999999999996 9999999999999998765


Q ss_pred             ccccCCCCCCCCCCCCCCCceEEEecCC
Q psy2983          96 KNRAGNTLPNLQPRGTGGPMRLYIGSLH  123 (370)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~l~V~nlp  123 (370)
                      ........   .+.......+||||||+
T Consensus        76 ~~~~~~~~---~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           76 PRRSRFDR---PPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CCSSCCCS---CCCSCCCCSCCCSCCCC
T ss_pred             CCcccCCC---CCccccCCCceecCCCC
Confidence            43322111   11122345689999997

>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=99.70  E-value=1.1e-16  Score=125.87  Aligned_cols=81  Identities=32%  Similarity=0.550  Sum_probs=77.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ..+.++|||+|||+.+++++|+++|++||.|..+.++.+. +|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            4556899999999999999999999999999999999998 999999999999999999999999999999999999998


Q ss_pred             ee
Q psy2983         191 VT  192 (370)
Q Consensus       191 ~~  192 (370)
                      +.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>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=99.70  E-value=6.2e-17  Score=124.40  Aligned_cols=82  Identities=26%  Similarity=0.555  Sum_probs=76.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||+.+++++|+++|++||.|..+++..++ +|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            3456899999999999999999999999999999999997 499999999999999999999999999999999999998


Q ss_pred             eec
Q psy2983         191 VTD  193 (370)
Q Consensus       191 ~~~  193 (370)
                      +..
T Consensus        92 a~~   94 (95)
T 2ywk_A           92 PSS   94 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            653

>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=99.70  E-value=7e-17  Score=129.07  Aligned_cols=85  Identities=35%  Similarity=0.636  Sum_probs=79.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ..+++|||+|||.++++++|+++|++||.|..+.+..+. +|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            445799999999999999999999999999999999997 9999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy2983         192 TDRNES  197 (370)
Q Consensus       192 ~~~~~~  197 (370)
                      .++...
T Consensus        84 ~~~~~~   89 (116)
T 2fy1_A           84 KKPSFQ   89 (116)
T ss_dssp             CCSSCS
T ss_pred             CCCCCC
Confidence            876554

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=1.8e-17  Score=124.80  Aligned_cols=80  Identities=31%  Similarity=0.505  Sum_probs=75.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      .++++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.+++.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            34679999999999999999999999999999999999889999999999999999999999999999999999988764

>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=99.70  E-value=6.1e-17  Score=122.80  Aligned_cols=80  Identities=21%  Similarity=0.498  Sum_probs=76.2

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .++|||+|||+.+++++|+++|++||.|..+++..++.+|.++|||||+|.+.++|.+|+ .|||..+.|+.|+|.++.+
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            368999999999999999999999999999999999889999999999999999999999 8999999999999999765


Q ss_pred             C
Q psy2983         194 R  194 (370)
Q Consensus       194 ~  194 (370)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=1.2e-16  Score=127.05  Aligned_cols=86  Identities=23%  Similarity=0.359  Sum_probs=78.9

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPII   88 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~   88 (370)
                      .+..+..++|||+|||..+++++|+++|+.||.|.++.+++++ +++++|||||+|.+.++|.+|++ |+|..+.|+.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   87 (114)
T 2do0_A            9 LQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMH   87 (114)
T ss_dssp             CCCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEE
Confidence            4455678999999999999999999999999999999999987 58999999999999999999997 999999999999


Q ss_pred             Eecccccc
Q psy2983          89 VQPTQAEK   96 (370)
Q Consensus        89 v~~~~~~~   96 (370)
                      |.++....
T Consensus        88 v~~a~~~~   95 (114)
T 2do0_A           88 VKMDERAL   95 (114)
T ss_dssp             EEECSCCC
T ss_pred             EEEcccCC
Confidence            99886543

>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=99.70  E-value=1.8e-17  Score=132.12  Aligned_cols=86  Identities=17%  Similarity=0.205  Sum_probs=79.5

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCe-eEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKV-RDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPII   88 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v-~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~   88 (370)
                      .....+.++|||+|||.++|+++|+++|+.||.| .+|.+++++ +++++|||||+|.+.++|.+|+++++..|.|+.|.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~   87 (114)
T 2cpy_A            9 GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERLHRKKLNGREAF   87 (114)
T ss_dssp             CSCCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEE
T ss_pred             CCCCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEE
Confidence            3456678999999999999999999999999999 899999998 89999999999999999999998899999999999


Q ss_pred             Eecccccc
Q psy2983          89 VQPTQAEK   96 (370)
Q Consensus        89 v~~~~~~~   96 (370)
                      |.++....
T Consensus        88 v~~a~~~~   95 (114)
T 2cpy_A           88 VHVVTLED   95 (114)
T ss_dssp             EEEECHHH
T ss_pred             EEECCHHH
Confidence            99887554

>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=99.70  E-value=3.3e-16  Score=122.27  Aligned_cols=85  Identities=34%  Similarity=0.658  Sum_probs=77.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||+.+++++|+++|++||.|..++++.+.  +.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~--~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   89 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC--CCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456899999999999999999999999999999999885  34899999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2983         191 VTDRNES  197 (370)
Q Consensus       191 ~~~~~~~  197 (370)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2cq3_A           90 ATARVMT   96 (103)
T ss_dssp             CCSSCCC
T ss_pred             cccCCCC
Confidence            9876554

>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=99.70  E-value=5.8e-17  Score=132.01  Aligned_cols=85  Identities=33%  Similarity=0.575  Sum_probs=80.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ..+.++|||+|||+.+++++|+++|++||.|..++++.++.+|.++|||||+|.+.++|.+|+..|+|..|.|+.|+|.+
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~  122 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF  122 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            44568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eecCC
Q psy2983         191 VTDRN  195 (370)
Q Consensus       191 ~~~~~  195 (370)
                      +.++.
T Consensus       123 a~~~~  127 (129)
T 2kxn_B          123 SITKR  127 (129)
T ss_dssp             CSSSS
T ss_pred             ecCCC
Confidence            87654

>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=99.69  E-value=4.5e-17  Score=125.19  Aligned_cols=81  Identities=21%  Similarity=0.346  Sum_probs=75.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      .++.+|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            34589999999999999999999999999999999998889999999999999999999999999999999999999886


Q ss_pred             e
Q psy2983         192 T  192 (370)
Q Consensus       192 ~  192 (370)
                      .
T Consensus        93 ~   93 (95)
T 2ek1_A           93 S   93 (95)
T ss_dssp             C
T ss_pred             c
Confidence            4

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=3.5e-17  Score=130.05  Aligned_cols=88  Identities=23%  Similarity=0.432  Sum_probs=81.1

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCee--------EEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCC
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVR--------DVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQ   80 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~--------~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~   80 (370)
                      +....+.++|||+|||..+++++|+++|+.||.|.        .+.++.++.+++++|||||+|.+.++|.+|++ |+|.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   88 (113)
T 2cpe_A            9 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   88 (113)
T ss_dssp             CCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             cccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCC
Confidence            34567889999999999999999999999999999        69999999999999999999999999999996 9999


Q ss_pred             ccCCeeEEEeccccccc
Q psy2983          81 KLLGIPIIVQPTQAEKN   97 (370)
Q Consensus        81 ~i~g~~l~v~~~~~~~~   97 (370)
                      .|.|+.|.|.++.....
T Consensus        89 ~~~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           89 DFQGSKLKVSLARKKPP  105 (113)
T ss_dssp             EETTEECEEECSSCCCC
T ss_pred             ccCCCEEEEEECCCCCC
Confidence            99999999999876543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.69  E-value=4.8e-17  Score=126.82  Aligned_cols=85  Identities=21%  Similarity=0.377  Sum_probs=78.5

Q ss_pred             CCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEE
Q psy2983           9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPII   88 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~   88 (370)
                      +++....+++|||+|||..+++++|+++|+.||.|.++.+++++ +++++|||||+|.+.++|.+|++ ++..++|+.|.
T Consensus         2 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~-~~~~~~g~~l~   79 (102)
T 2xs2_A            2 LPEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKLK   79 (102)
T ss_dssp             CCCCEEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT-CCCEETTEECE
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh-CCCeECCEEEE
Confidence            34556678999999999999999999999999999999999998 89999999999999999999999 99999999999


Q ss_pred             Eeccccc
Q psy2983          89 VQPTQAE   95 (370)
Q Consensus        89 v~~~~~~   95 (370)
                      |.++...
T Consensus        80 v~~a~~~   86 (102)
T 2xs2_A           80 LGPAIRK   86 (102)
T ss_dssp             EEEEEEC
T ss_pred             EEECCcC
Confidence            9887654

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=2.8e-17  Score=131.27  Aligned_cols=87  Identities=20%  Similarity=0.328  Sum_probs=80.1

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEe
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQ   90 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~   90 (370)
                      ....+.++|||+|||..+++++|+++|+.||.|..|.+++++.+++++|||||+|.+.++|.+|++.++..|.|+.|.|.
T Consensus        22 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~  101 (116)
T 1x4b_A           22 REKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPK  101 (116)
T ss_dssp             CHHHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEE
T ss_pred             cccCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEE
Confidence            33456699999999999999999999999999999999999999999999999999999999999889999999999999


Q ss_pred             ccccccc
Q psy2983          91 PTQAEKN   97 (370)
Q Consensus        91 ~~~~~~~   97 (370)
                      ++.....
T Consensus       102 ~a~~~~~  108 (116)
T 1x4b_A          102 RAVAREE  108 (116)
T ss_dssp             CCSSCCC
T ss_pred             ECCCCcc
Confidence            9876543

>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=99.69  E-value=2.2e-16  Score=145.60  Aligned_cols=81  Identities=26%  Similarity=0.502  Sum_probs=73.9

Q ss_pred             CCCceEEEecCCCCCCHHHHH----hcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMK  187 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~----~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~  187 (370)
                      .+.++|||+|||+.+++++|+    ++|++||.|..|++.+   +|+++|||||+|.+.++|.+|+..|||..+.|+.|+
T Consensus         7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   83 (282)
T 3pgw_A            7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   83 (282)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEE
Confidence            446899999999999999977    8999999999998874   788999999999999999999999999999999999


Q ss_pred             EEEeecCC
Q psy2983         188 VGTVTDRN  195 (370)
Q Consensus       188 V~~~~~~~  195 (370)
                      |.++....
T Consensus        84 v~~a~~~~   91 (282)
T 3pgw_A           84 IQYAKTDS   91 (282)
T ss_pred             EEEeccCc
Confidence            99986543

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.69  E-value=5.5e-17  Score=129.70  Aligned_cols=84  Identities=25%  Similarity=0.417  Sum_probs=78.1

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      ..+.++|||+|||.++++++|+++|+.||.|.+|.++.+. +++++|||||+|.+.++|.+|++ ++|..+.|+.|.|.+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4567999999999999999999999999999999999998 89999999999999999999996 999999999999999


Q ss_pred             cccccc
Q psy2983          92 TQAEKN   97 (370)
Q Consensus        92 ~~~~~~   97 (370)
                      +.....
T Consensus        83 a~~~~~   88 (116)
T 2fy1_A           83 AKKPSF   88 (116)
T ss_dssp             CCCSSC
T ss_pred             CCCCCC
Confidence            876543

>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=99.69  E-value=8.2e-17  Score=126.13  Aligned_cols=84  Identities=18%  Similarity=0.368  Sum_probs=77.7

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCC---eeEE
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLG---IPII   88 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g---~~l~   88 (370)
                      ..+.++|||+|||..+++++|+++|+.||.|.++.+++++ ++.++|||||+|.+.++|.+|++ |+|..+.|   ++|.
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            3568999999999999999999999999999999999987 79999999999999999999996 99999998   9999


Q ss_pred             Eeccccccc
Q psy2983          89 VQPTQAEKN   97 (370)
Q Consensus        89 v~~~~~~~~   97 (370)
                      |.++.....
T Consensus        91 V~~a~~~~~   99 (105)
T 2dnh_A           91 VKFADTDKE   99 (105)
T ss_dssp             EEESCSSCC
T ss_pred             EEECccCcc
Confidence            999876543

>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=99.69  E-value=2.3e-17  Score=124.81  Aligned_cols=82  Identities=22%  Similarity=0.408  Sum_probs=75.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCC-eecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRR-FKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~-~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      ...++|||+|||.++++++|+++|++||.|.++.++.+..++. ++|||||+|.+.++|.+|++ ++|..+.|+.|.|.+
T Consensus         2 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   81 (88)
T 4a8x_A            2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATA   81 (88)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEE
Confidence            3568999999999999999999999999999999999987766 89999999999999999997 999999999999998


Q ss_pred             cccc
Q psy2983          92 TQAE   95 (370)
Q Consensus        92 ~~~~   95 (370)
                      +.+.
T Consensus        82 a~~~   85 (88)
T 4a8x_A           82 VLAP   85 (88)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            7643

>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=99.69  E-value=2.8e-16  Score=122.68  Aligned_cols=85  Identities=26%  Similarity=0.489  Sum_probs=77.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||+.+++++|+++|++||.|..++++.+.  +.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~--~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCC--CSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecC--CCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            3456899999999999999999999999999999999885  33689999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2983         191 VTDRNES  197 (370)
Q Consensus       191 ~~~~~~~  197 (370)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2cqi_A           90 ATTPSSQ   96 (103)
T ss_dssp             CCCTTCC
T ss_pred             CCCCccc
Confidence            9876554

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.69  E-value=5.6e-17  Score=136.46  Aligned_cols=82  Identities=24%  Similarity=0.417  Sum_probs=77.1

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCC--ceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFG--KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G--~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ..++|||+|||+.+++++|+++|++||  .|..++++.|+.+|.++|||||+|.+.++|.+|+..|||..|.|+.|+|.+
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            457999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             eecC
Q psy2983         191 VTDR  194 (370)
Q Consensus       191 ~~~~  194 (370)
                      +.++
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            8653

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=6.2e-17  Score=126.59  Aligned_cols=85  Identities=19%  Similarity=0.258  Sum_probs=78.7

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhc-CCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCc-cCCeeEE
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSS-VGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQK-LLGIPII   88 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~-~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~-i~g~~l~   88 (370)
                      ...+.++|||+|||.++|+++|+++|+. ||.|.++.+++++ +++++|||||+|.+.++|.+|++ ++|.. +.|++|.
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~   83 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVR   83 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEE
Confidence            3457799999999999999999999999 9999999999998 89999999999999999999996 99999 9999999


Q ss_pred             Eeccccccc
Q psy2983          89 VQPTQAEKN   97 (370)
Q Consensus        89 v~~~~~~~~   97 (370)
                      |.++.....
T Consensus        84 v~~a~~~~~   92 (104)
T 2dhg_A           84 LSVAIPKAS   92 (104)
T ss_dssp             CCBCCCCCS
T ss_pred             EEEccCCCc
Confidence            999865543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=2.1e-16  Score=126.19  Aligned_cols=85  Identities=29%  Similarity=0.536  Sum_probs=79.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||+.+++++|+++|++||.|..++++.++.++.++|||||+|.+.++|.+|+..+++ .+.|+.|+|.+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~   92 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   92 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEE
Confidence            44568999999999999999999999999999999999988999999999999999999999999998 89999999999


Q ss_pred             eecCCC
Q psy2983         191 VTDRNE  196 (370)
Q Consensus       191 ~~~~~~  196 (370)
                      +.....
T Consensus        93 a~~~~~   98 (116)
T 2cqd_A           93 AYLGAK   98 (116)
T ss_dssp             STTTCC
T ss_pred             cccCCC
Confidence            866544

>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=99.69  E-value=7.2e-18  Score=131.16  Aligned_cols=87  Identities=26%  Similarity=0.366  Sum_probs=74.3

Q ss_pred             CCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeC-CCCCeecEEEEEecCCCChHHHhhccCCccCCee
Q psy2983           8 DLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCN-KTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIP   86 (370)
Q Consensus         8 ~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~-~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~   86 (370)
                      ..+......++|||+|||.++++++|+++|+.|| |.++.+++++ .+++++|||||+|.+.++|.+|++++|..+.|+.
T Consensus        11 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~   89 (100)
T 2j76_E           11 RSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRR   89 (100)
T ss_dssp             ---------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBC
T ss_pred             CCcCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeE
Confidence            3445567889999999999999999999999999 9999999998 5899999999999999999999999999999999


Q ss_pred             EEEeccccc
Q psy2983          87 IIVQPTQAE   95 (370)
Q Consensus        87 l~v~~~~~~   95 (370)
                      |.|.++...
T Consensus        90 l~V~~a~~~   98 (100)
T 2j76_E           90 IRVDVADQA   98 (100)
T ss_dssp             CCCEECCCS
T ss_pred             EEEEeccCC
Confidence            999987643

>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=99.69  E-value=1.3e-16  Score=122.97  Aligned_cols=82  Identities=16%  Similarity=0.336  Sum_probs=75.6

Q ss_pred             CCCceEEEecCCCCCCHHHHH----hcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMK  187 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~----~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~  187 (370)
                      ....+|||+|||+.+++++|+    ++|++||.|.+++++.++.+   +|||||+|.+.++|.+|+..|||..+.|+.|+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~   83 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKIL   83 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            345799999999999999999    99999999999999988654   88999999999999999999999999999999


Q ss_pred             EEEeecCCC
Q psy2983         188 VGTVTDRNE  196 (370)
Q Consensus       188 V~~~~~~~~  196 (370)
                      |.++.++..
T Consensus        84 V~~a~~~~~   92 (96)
T 2dgx_A           84 VSLATGASG   92 (96)
T ss_dssp             EEECCCSSC
T ss_pred             EEEcCCCCC
Confidence            999877654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.69  E-value=2.4e-17  Score=134.74  Aligned_cols=90  Identities=18%  Similarity=0.224  Sum_probs=81.0

Q ss_pred             CCCCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeE--EEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCC--
Q psy2983           6 SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRD--VRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQ--   80 (370)
Q Consensus         6 ~~~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~--v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~--   80 (370)
                      +...+......++|||+|||..+|+++|+++|++||.|..  |++++|+.+++++|||||+|.+. +|.+|+. ++|.  
T Consensus        13 ~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~   91 (131)
T 2m2b_A           13 QGSEPSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHP   91 (131)
T ss_dssp             CCCCCCCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCC
T ss_pred             CCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCC
Confidence            3344555678899999999999999999999999999976  99999999999999999999999 9999995 9999  


Q ss_pred             --ccCCeeEEEecccccc
Q psy2983          81 --KLLGIPIIVQPTQAEK   96 (370)
Q Consensus        81 --~i~g~~l~v~~~~~~~   96 (370)
                        .+.|+.|.|.++....
T Consensus        92 ~~~~~gr~l~V~~a~~~~  109 (131)
T 2m2b_A           92 PLTIDGKTINVEFAKGSK  109 (131)
T ss_dssp             SCCGGGCCCCCEECCCSC
T ss_pred             CccCCCEEEEEEECCCCC
Confidence              9999999999887643

>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=99.69  E-value=1.1e-16  Score=124.96  Aligned_cols=89  Identities=24%  Similarity=0.383  Sum_probs=79.4

Q ss_pred             CCCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCe
Q psy2983           7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGI   85 (370)
Q Consensus         7 ~~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~   85 (370)
                      ...++...+.++|||+|||..+++++|+++|+.||.|.+|.++++..  .++|||||+|.+.++|.+|++ ++|..|.|+
T Consensus         6 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   83 (103)
T 2cq3_A            6 SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGR   83 (103)
T ss_dssp             CCCSCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            34455667889999999999999999999999999999999998864  378999999999999999996 999999999


Q ss_pred             eEEEeccccccc
Q psy2983          86 PIIVQPTQAEKN   97 (370)
Q Consensus        86 ~l~v~~~~~~~~   97 (370)
                      .|.|.++.....
T Consensus        84 ~l~v~~a~~~~~   95 (103)
T 2cq3_A           84 KIEVNNATARVM   95 (103)
T ss_dssp             ECEEEECCSSCC
T ss_pred             EEEEEEcccCCC
Confidence            999999876543

>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=99.69  E-value=2.4e-17  Score=161.08  Aligned_cols=165  Identities=21%  Similarity=0.352  Sum_probs=111.6

Q ss_pred             HHHHHhhcCCCeeEEEEe----eeC-CCCCeecEE--EEEecCCCChHHHhh-ccCCccCCeeEE--Eeccccc--cccc
Q psy2983          32 DLEEFFSSVGKVRDVRLI----TCN-KTRRFKGIA--YIEFKDPESVPLAMG-LNGQKLLGIPII--VQPTQAE--KNRA   99 (370)
Q Consensus        32 ~L~~~f~~~G~v~~v~i~----~d~-~~~~~kg~a--fVeF~~~e~A~~Al~-l~g~~i~g~~l~--v~~~~~~--~~~~   99 (370)
                      .|.++|.++|+|..+..+    .+. .+....|++  |++|....++..++. .+.....++.-.  .......  ....
T Consensus         8 ~L~~lF~p~pPl~~~~P~~~~p~~~~~~~~~~gia~~~~~f~~~~~~~~~~~~e~~~~~~~~~~~~k~~~~~~~~~~~~~   87 (437)
T 3pgw_S            8 NLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELK   87 (437)
T ss_pred             cHHHhcCCCCCCcCCCCcccccccccCCCCcccHHHHHHhhcCcccccccccccCHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            378999999999877332    222 122223344  888888777665552 222221111000  0000000  0000


Q ss_pred             CCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCc
Q psy2983         100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF  179 (370)
Q Consensus       100 ~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~  179 (370)
                      .............+..+|||+|||+.+|+++|+++|++||.|..|.|+.+..+|.++|||||+|.+.++|.+|+..|||.
T Consensus        88 ~~~p~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~  167 (437)
T 3pgw_S           88 MWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGK  167 (437)
T ss_pred             hcCCcccccccCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCC
Confidence            00000111112334579999999999999999999999999999999999889999999999999999999999999999


Q ss_pred             eeCCeeEEEEEeecCCC
Q psy2983         180 ELAGRPMKVGTVTDRNE  196 (370)
Q Consensus       180 ~i~g~~l~V~~~~~~~~  196 (370)
                      .|.|+.|.|.++.+...
T Consensus       168 ~i~gr~i~V~~a~~~~~  184 (437)
T 3pgw_S          168 KIDGRRVLVDVERGRTV  184 (437)
T ss_pred             EECCEEEEEEEeCCCCC
Confidence            99999999999876543

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.1e-16  Score=125.36  Aligned_cols=86  Identities=24%  Similarity=0.500  Sum_probs=80.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+.. ++..+.|+.|+|.+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKP   91 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEE
Confidence            44568999999999999999999999999999999999988999999999999999999999998 99999999999999


Q ss_pred             eecCCCC
Q psy2983         191 VTDRNES  197 (370)
Q Consensus       191 ~~~~~~~  197 (370)
                      +.++...
T Consensus        92 a~~~~~~   98 (105)
T 2dh8_A           92 CTPRGMQ   98 (105)
T ss_dssp             SCCSSCC
T ss_pred             ccCCCCC
Confidence            8876654

>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=99.69  E-value=2.3e-16  Score=144.04  Aligned_cols=131  Identities=27%  Similarity=0.454  Sum_probs=114.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||+++|+++|+++|++||.|..+.+.++      +|||||+|.+.++|.+|+..|+|..+.|+.|+|.+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~   92 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            345679999999999999999999999999999998643      79999999999999999999999999999999999


Q ss_pred             eecCCC-CcCCCCCCCCHHHHHHhcccCCceeeeeeeecc---ccCCC---CCChHHHHHHHhh
Q psy2983         191 VTDRNE-SVGGGPSNLDTDEMERAGVDLGATGRLQLMFKL---AEGTG---LELPPAAASALNL  247 (370)
Q Consensus       191 ~~~~~~-~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~---~~~~~---~~~~~~a~~a~~~  247 (370)
                      +.+... .+++++..+++++++..|..+|.+..+.++.+.   ++|++   |..+.+|..|+..
T Consensus        93 a~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~  156 (261)
T 3sde_A           93 ATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALER  156 (261)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHH
T ss_pred             cccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHH
Confidence            876443 578999999999999999999999999988772   23444   6778888777764

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.69  E-value=1.5e-16  Score=131.10  Aligned_cols=88  Identities=28%  Similarity=0.563  Sum_probs=81.9

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEE
Q psy2983         110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG  189 (370)
Q Consensus       110 ~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~  189 (370)
                      .....++|||+|||..+++++|+++|+.||.|..++++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34456899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EeecCCCC
Q psy2983         190 TVTDRNES  197 (370)
Q Consensus       190 ~~~~~~~~  197 (370)
                      ++.++...
T Consensus       118 ~a~~~~~~  125 (139)
T 1u6f_A          118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             ECCCCCCC
Confidence            98876554

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=4e-17  Score=127.55  Aligned_cols=79  Identities=25%  Similarity=0.257  Sum_probs=74.5

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ..++|||+|||+++|+++|+++|++||.|..+.++.++. |.++|||||+|.+.++|.+|+. ++|..+.|+.|.|.++.
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   87 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEch
Confidence            357899999999999999999999999999999999986 9999999999999999999999 89999999999999865


Q ss_pred             c
Q psy2983         193 D  193 (370)
Q Consensus       193 ~  193 (370)
                      +
T Consensus        88 ~   88 (103)
T 1s79_A           88 D   88 (103)
T ss_dssp             H
T ss_pred             H
Confidence            4

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.68  E-value=4.3e-17  Score=137.13  Aligned_cols=80  Identities=20%  Similarity=0.282  Sum_probs=75.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCC--CeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVG--KVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G--~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      ..++|||+|||..+|+++|+++|+.||  .|.+|++++|+.+|+++|||||+|.+.++|.+|++ |+|..|.|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            568999999999999999999999999  99999999999999999999999999999999996 899999999999998


Q ss_pred             ccc
Q psy2983          92 TQA   94 (370)
Q Consensus        92 ~~~   94 (370)
                      +..
T Consensus       134 a~~  136 (156)
T 3n9u_C          134 ATR  136 (156)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            864

>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=99.68  E-value=4e-17  Score=127.42  Aligned_cols=82  Identities=18%  Similarity=0.224  Sum_probs=75.2

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEec
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQP   91 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~   91 (370)
                      .....++|||+|||+++|+++|+++|++||.+ +|.+++++ +++++|||||+|.+.++|.+|+++++..+.|+.|.|.+
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~   88 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFL   88 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEE
Confidence            44677899999999999999999999999955 99999998 89999999999999999999999999999999999987


Q ss_pred             cccc
Q psy2983          92 TQAE   95 (370)
Q Consensus        92 ~~~~   95 (370)
                      +...
T Consensus        89 ~~~~   92 (102)
T 1wez_A           89 NSTA   92 (102)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            6543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.68  E-value=3.2e-16  Score=126.67  Aligned_cols=86  Identities=28%  Similarity=0.501  Sum_probs=80.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||..+++++|+++|++||.|..+.+..+. +|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            4456899999999999999999999999999999999997 999999999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2983         191 VTDRNES  197 (370)
Q Consensus       191 ~~~~~~~  197 (370)
                      +.+....
T Consensus       111 a~~~~~~  117 (124)
T 2kt5_A          111 VASQIDL  117 (124)
T ss_dssp             ECCTTCC
T ss_pred             eCCCCCC
Confidence            8775543

>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=99.68  E-value=5.6e-17  Score=129.14  Aligned_cols=82  Identities=23%  Similarity=0.410  Sum_probs=77.2

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ..++|||+|||..+++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|.+|+ .|||..+.|+.|+|.++.
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            3478999999999999999999999999999999999888999999999999999999999 899999999999999986


Q ss_pred             cCC
Q psy2983         193 DRN  195 (370)
Q Consensus       193 ~~~  195 (370)
                      ++.
T Consensus       103 ~~~  105 (114)
T 2cq4_A          103 AEK  105 (114)
T ss_dssp             HHH
T ss_pred             CCc
Confidence            543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.68  E-value=5.2e-17  Score=130.21  Aligned_cols=85  Identities=21%  Similarity=0.272  Sum_probs=78.5

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCC---eeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCee
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGK---VRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIP   86 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~---v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~   86 (370)
                      .+...+.++|||+|||.++|+++|+++|+.||.   |.+|++++++. ++++|||||+|.+.++|.+|+++++..|.|+.
T Consensus        11 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~   89 (118)
T 2db1_A           11 GPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALKKDRESMGHRY   89 (118)
T ss_dssp             SSCBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGGGTTEEETTEE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeE
Confidence            344567899999999999999999999999999   89999999987 99999999999999999999999999999999


Q ss_pred             EEEeccccc
Q psy2983          87 IIVQPTQAE   95 (370)
Q Consensus        87 l~v~~~~~~   95 (370)
                      |.|.++...
T Consensus        90 i~V~~a~~~   98 (118)
T 2db1_A           90 IEVFKSHRT   98 (118)
T ss_dssp             EEEEEECHH
T ss_pred             EEEEECCHH
Confidence            999887644

>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=99.68  E-value=3.9e-17  Score=127.00  Aligned_cols=83  Identities=25%  Similarity=0.542  Sum_probs=75.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecC-CCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDP-DTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG  189 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~-~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~  189 (370)
                      ....++|||+|||..+++++|+++|++|| |..++++.++ .+|+++|||||+|.+.++|.+|+ .|+|..+.|+.|+|.
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 9999999997 58999999999999999999999 799999999999999


Q ss_pred             EeecCC
Q psy2983         190 TVTDRN  195 (370)
Q Consensus       190 ~~~~~~  195 (370)
                      ++.++.
T Consensus        94 ~a~~~~   99 (100)
T 2j76_E           94 VADQAQ   99 (100)
T ss_dssp             ECCCSC
T ss_pred             eccCCC
Confidence            987653

>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=99.68  E-value=1.2e-16  Score=129.50  Aligned_cols=87  Identities=31%  Similarity=0.512  Sum_probs=81.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   98 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   98 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            34568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2983         191 VTDRNES  197 (370)
Q Consensus       191 ~~~~~~~  197 (370)
                      +.++...
T Consensus        99 a~~~~~~  105 (126)
T 3ex7_B           99 CFVRGPP  105 (126)
T ss_dssp             SEESSSC
T ss_pred             ecCCCCC
Confidence            9876554

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=1.2e-16  Score=124.85  Aligned_cols=85  Identities=26%  Similarity=0.527  Sum_probs=79.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccC-CCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCce-eCCeeEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEP-FGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFE-LAGRPMKVG  189 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~-~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~-i~g~~l~V~  189 (370)
                      ....+|||+|||+.+++++|+++|++ ||.|..+.++.+. +|.++|||||+|.+.++|.+|+..|||.. +.|+.|+|.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~   85 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            34578999999999999999999999 9999999999998 99999999999999999999999999999 999999999


Q ss_pred             EeecCCCC
Q psy2983         190 TVTDRNES  197 (370)
Q Consensus       190 ~~~~~~~~  197 (370)
                      ++.++...
T Consensus        86 ~a~~~~~~   93 (104)
T 2dhg_A           86 VAIPKASR   93 (104)
T ss_dssp             BCCCCCSC
T ss_pred             EccCCCcC
Confidence            98766554

>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=99.68  E-value=4e-17  Score=139.58  Aligned_cols=133  Identities=23%  Similarity=0.335  Sum_probs=109.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||..+++++|+++|+.||.+.. .++.+..+|.++|||||+|.+.++|.+|++ |+|..+.|+.|+|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~   87 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEec
Confidence            345689999999999999999999999998776 334444588999999999999999999995 999999999999999


Q ss_pred             eecCCC---------CcCCCCCCCCHHHHHHhcccCCceeeeeeeeccccCCC---CCChHHHHHHHh
Q psy2983         191 VTDRNE---------SVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLAEGTG---LELPPAAASALN  246 (370)
Q Consensus       191 ~~~~~~---------~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~~~~~~---~~~~~~a~~a~~  246 (370)
                      +.++..         .+++++..+++++|+..|..+|.+..+ .....+++++   |..+.+|..|+.
T Consensus        88 ~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-~~~~~~~g~afV~f~~~~~A~~A~~  154 (175)
T 1fje_B           88 PKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-SQDGKSKGIAYIEFKSEADAEKNLE  154 (175)
T ss_dssp             CCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-CSSSSCCSEEEEECSSHHHHHHHHH
T ss_pred             CCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-cCCCCCceEEEEEECCHHHHHHHHH
Confidence            875433         267899999999999999999988665 1112344554   678888888877

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.68  E-value=1.1e-16  Score=125.55  Aligned_cols=84  Identities=18%  Similarity=0.187  Sum_probs=75.7

Q ss_pred             CCcccCCCCeEEEcCCCCCC------cHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCc
Q psy2983           9 LSPEERDARTIFCMQLSQRI------RTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQK   81 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~------te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~   81 (370)
                      ++.....+++|||+|||..+      ++++|+++|++||.|.++.++  +.+|+++|||||+|.+.++|.+|++ |+|..
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~   85 (105)
T 2nlw_A            8 PQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYK   85 (105)
T ss_dssp             CCSCCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEE
T ss_pred             CCCCCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcc
Confidence            34455668999999999999      889999999999999999988  4678999999999999999999996 99999


Q ss_pred             cCCe-eEEEecccc
Q psy2983          82 LLGI-PIIVQPTQA   94 (370)
Q Consensus        82 i~g~-~l~v~~~~~   94 (370)
                      +.|+ +|.|.++..
T Consensus        86 ~~g~~~l~V~~a~~   99 (105)
T 2nlw_A           86 LDKQHTFRVNLFTD   99 (105)
T ss_dssp             CSTTCEEEEECSCC
T ss_pred             cCCCceEEEEEcch
Confidence            9998 999998764

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.68  E-value=2.8e-17  Score=120.65  Aligned_cols=75  Identities=33%  Similarity=0.636  Sum_probs=72.0

Q ss_pred             eEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       116 ~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      +|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|++ |+|..+.|++|+|.++
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            58999999999999999999999999999999998899999999999999999999998 9999999999999864

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=2.9e-16  Score=119.71  Aligned_cols=81  Identities=22%  Similarity=0.337  Sum_probs=76.3

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ....+|||+|||+.+++++|+++|++| .|..++++.+ .+|.++|||||+|.+.++|.+|+. |||..+.|+.|+|.++
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEE
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEEC
Confidence            446799999999999999999999999 9999999999 699999999999999999999999 9999999999999998


Q ss_pred             ecCC
Q psy2983         192 TDRN  195 (370)
Q Consensus       192 ~~~~  195 (370)
                      .++.
T Consensus        85 ~~~~   88 (91)
T 2dgw_A           85 KSGP   88 (91)
T ss_dssp             SSCC
T ss_pred             CcCC
Confidence            7764

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1e-17  Score=126.10  Aligned_cols=80  Identities=16%  Similarity=0.283  Sum_probs=75.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      .+.++|||+|||..+++++|+++|++||.|.++.+++++.+++++|||||+|.+.++|.+|++ ++|..+.|+.+++.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            467999999999999999999999999999999999999999999999999999999999996 9999999999988765


Q ss_pred             c
Q psy2983          93 Q   93 (370)
Q Consensus        93 ~   93 (370)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.68  E-value=4.4e-17  Score=132.08  Aligned_cols=89  Identities=22%  Similarity=0.380  Sum_probs=81.7

Q ss_pred             CCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeE
Q psy2983           9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPI   87 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l   87 (370)
                      .++...+.++|||+|||..+|+++|+++|+.||.|.+|.++.++.++.++|||||+|.+.++|.+|++ |+|..|.|+.|
T Consensus        15 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   94 (126)
T 3ex7_B           15 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPI   94 (126)
T ss_dssp             CBCCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEE
Confidence            34556678899999999999999999999999999999999999899999999999999999999995 99999999999


Q ss_pred             EEeccccccc
Q psy2983          88 IVQPTQAEKN   97 (370)
Q Consensus        88 ~v~~~~~~~~   97 (370)
                      .|.++.....
T Consensus        95 ~v~~a~~~~~  104 (126)
T 3ex7_B           95 SVDWCFVRGP  104 (126)
T ss_dssp             EEEESEESSS
T ss_pred             EEEEecCCCC
Confidence            9999876543

>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=99.68  E-value=5e-16  Score=121.23  Aligned_cols=85  Identities=25%  Similarity=0.389  Sum_probs=78.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+.  ++..+.|+.|+|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEEC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEe
Confidence            4456789999999999999999999999999999999998899999999999999999999998  57899999999999


Q ss_pred             eecCCCC
Q psy2983         191 VTDRNES  197 (370)
Q Consensus       191 ~~~~~~~  197 (370)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2cqg_A           90 PNSKQSQ   96 (103)
T ss_dssp             CCTTCCC
T ss_pred             cCCCCcC
Confidence            9876554

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=6.3e-16  Score=122.92  Aligned_cols=84  Identities=24%  Similarity=0.377  Sum_probs=77.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ...++|||+|||+.+++++|+++|++||.|..+.++.++ +|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   91 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD   91 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEc
Confidence            345799999999999999999999999999999999997 6999999999999999999999999999999999999998


Q ss_pred             ecCCC
Q psy2983         192 TDRNE  196 (370)
Q Consensus       192 ~~~~~  196 (370)
                      .....
T Consensus        92 ~~~~~   96 (114)
T 2do0_A           92 ERALP   96 (114)
T ss_dssp             SCCCC
T ss_pred             ccCCC
Confidence            65433

>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=99.68  E-value=7.5e-17  Score=126.81  Aligned_cols=82  Identities=21%  Similarity=0.310  Sum_probs=76.8

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEE
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIV   89 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v   89 (370)
                      +...+.++|||+|||..+++++|+++|+.||.|.++.++++. +++++|||||+|.+.++|.+|++ |+|..+.|+.|.|
T Consensus        24 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V  102 (107)
T 3ulh_A           24 AGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI  102 (107)
T ss_dssp             CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            445678999999999999999999999999999999999998 89999999999999999999997 9999999999999


Q ss_pred             eccc
Q psy2983          90 QPTQ   93 (370)
Q Consensus        90 ~~~~   93 (370)
                      .++.
T Consensus       103 ~~a~  106 (107)
T 3ulh_A          103 QLVT  106 (107)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            8764

>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=99.68  E-value=1.8e-17  Score=121.64  Aligned_cols=75  Identities=25%  Similarity=0.359  Sum_probs=71.6

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecc
Q psy2983          18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPT   92 (370)
Q Consensus        18 ~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~   92 (370)
                      +|||+|||.++++++|+++|++||+|.++.+++++.+++++|||||+|.+.++|.+|+++++..+.|+.|.|+++
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEC
Confidence            699999999999999999999999999999999999999999999999999999999999999999999988763

>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=99.68  E-value=8.7e-17  Score=125.92  Aligned_cols=85  Identities=18%  Similarity=0.205  Sum_probs=77.2

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeE-EEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRD-VRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPII   88 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~-v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~   88 (370)
                      .+.....++|||+|||..+|+++|+++|++||.|.+ |.++.+ .+++++|||||+|.+.++|.+|++.++..+.|+.|.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~   87 (104)
T 1wg5_A            9 SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIE   87 (104)
T ss_dssp             CSSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEE
Confidence            344567899999999999999999999999999987 888888 789999999999999999999998899999999999


Q ss_pred             Eeccccc
Q psy2983          89 VQPTQAE   95 (370)
Q Consensus        89 v~~~~~~   95 (370)
                      |.++...
T Consensus        88 v~~~~~~   94 (104)
T 1wg5_A           88 IFKSSRA   94 (104)
T ss_dssp             EEEECTT
T ss_pred             EEECCHH
Confidence            9887543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.68  E-value=1.7e-16  Score=125.30  Aligned_cols=85  Identities=29%  Similarity=0.527  Sum_probs=76.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..+ +..+.|+.|+|.+
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~  100 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKV  100 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEE
Confidence            345679999999999999999999999999999999999889999999999999999999999975 6999999999999


Q ss_pred             eecCCC
Q psy2983         191 VTDRNE  196 (370)
Q Consensus       191 ~~~~~~  196 (370)
                      +.++..
T Consensus       101 a~~~~~  106 (109)
T 2rs2_A          101 AFPRRA  106 (109)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            877644

>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=99.68  E-value=4.5e-16  Score=123.33  Aligned_cols=85  Identities=18%  Similarity=0.281  Sum_probs=77.4

Q ss_pred             CCCceEEEecCCCCCCHHHHH---hcccCCCceeeEEEeecCCCC---CcccEEEEEECCHHHHHHHHHHhCCceeCCee
Q psy2983         112 GGPMRLYIGSLHFNITEDMLR---GIFEPFGKIDNIQLMVDPDTG---RSKGYGFITFHSADDAKKAQEQLNGFELAGRP  185 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~---~~f~~~G~i~~v~~~~~~~~g---~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~  185 (370)
                      ...++|||+|||+.+++++|+   ++|++||.|..+.+..+..++   .++|||||+|.+.++|.+|+..|||..+.|+.
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            345789999999999999999   999999999999999887644   56699999999999999999999999999999


Q ss_pred             EEEEEeecCCC
Q psy2983         186 MKVGTVTDRNE  196 (370)
Q Consensus       186 l~V~~~~~~~~  196 (370)
                      |+|.++.++..
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            99999887654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.68  E-value=5.6e-17  Score=132.50  Aligned_cols=87  Identities=16%  Similarity=0.381  Sum_probs=80.0

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHhcccCCCceee--EEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCc----eeCC
Q psy2983         110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDN--IQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF----ELAG  183 (370)
Q Consensus       110 ~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~--v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~----~i~g  183 (370)
                      .....++|||+|||+.+++++|+++|++||.|..  |+++.|+.+|.++|||||+|.+. +|.+|+..|||.    .+.|
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            3455689999999999999999999999999977  99999998999999999999999 999999999999    9999


Q ss_pred             eeEEEEEeecCCCC
Q psy2983         184 RPMKVGTVTDRNES  197 (370)
Q Consensus       184 ~~l~V~~~~~~~~~  197 (370)
                      +.|+|.++.+....
T Consensus        98 r~l~V~~a~~~~~~  111 (131)
T 2m2b_A           98 KTINVEFAKGSKRD  111 (131)
T ss_dssp             CCCCCEECCCSCCC
T ss_pred             EEEEEEECCCCCCC
Confidence            99999998775443

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=1.2e-16  Score=121.85  Aligned_cols=82  Identities=17%  Similarity=0.254  Sum_probs=76.7

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEec
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQP   91 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~   91 (370)
                      .....++|||+|||.++++++|+++|+.| .|.++.++++ .+++++|||||+|.+.++|.+|++++|..+.|+.|.|.+
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEEE
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEEE
Confidence            34577999999999999999999999999 9999999999 789999999999999999999999999999999999998


Q ss_pred             cccc
Q psy2983          92 TQAE   95 (370)
Q Consensus        92 ~~~~   95 (370)
                      +...
T Consensus        84 a~~~   87 (91)
T 2dgw_A           84 EKSG   87 (91)
T ss_dssp             ESSC
T ss_pred             CCcC
Confidence            7654

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.8e-16  Score=125.20  Aligned_cols=83  Identities=35%  Similarity=0.686  Sum_probs=76.4

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEE
Q psy2983         110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG  189 (370)
Q Consensus       110 ~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~  189 (370)
                      .....++|||+|||..+++++|+++|++||.|..+++..+.  +.++|||||+|.+.++|.+|+..|||..+.|+.|+|.
T Consensus        25 ~~~~~~~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           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34456899999999999999999999999999999999884  4589999999999999999999999999999999999


Q ss_pred             EeecC
Q psy2983         190 TVTDR  194 (370)
Q Consensus       190 ~~~~~  194 (370)
                      ++.++
T Consensus       103 ~a~~~  107 (109)
T 2err_A          103 NATAR  107 (109)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            98765

>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=99.67  E-value=6.5e-17  Score=126.43  Aligned_cols=83  Identities=30%  Similarity=0.655  Sum_probs=78.2

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .++|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++.+
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            46899999999999999999999999999999999988999999999999999999999999999999999999999766


Q ss_pred             CCC
Q psy2983         194 RNE  196 (370)
Q Consensus       194 ~~~  196 (370)
                      +..
T Consensus        88 ~~~   90 (104)
T 1p1t_A           88 EKN   90 (104)
T ss_dssp             TTH
T ss_pred             ccc
Confidence            433

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=9.4e-17  Score=125.08  Aligned_cols=80  Identities=20%  Similarity=0.311  Sum_probs=72.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhC--CceeCCeeEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN--GFELAGRPMKVG  189 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~--g~~i~g~~l~V~  189 (370)
                      .+..+|||+|||+++++++|+++|++||.|.++.++++      +|||||+|.+.++|.+|++.|+  +..+.|++|+|.
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   87 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ   87 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            34579999999999999999999999999999999865      7999999999999999999886  478999999999


Q ss_pred             EeecCCCC
Q psy2983         190 TVTDRNES  197 (370)
Q Consensus       190 ~~~~~~~~  197 (370)
                      ++.++...
T Consensus        88 ~A~~~~~~   95 (105)
T 1sjq_A           88 FSNHKELK   95 (105)
T ss_dssp             CCSSSSCC
T ss_pred             EcCCCCCC
Confidence            98776554

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.67  E-value=4.7e-17  Score=119.97  Aligned_cols=75  Identities=21%  Similarity=0.347  Sum_probs=71.1

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      ++|||+|||.++++++|+++|++||+|.++.+++++.+++++|||||+|.+.++|.+|++ ++ ..+.|++|.|+++
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            579999999999999999999999999999999999999999999999999999999997 66 9999999999875

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.67  E-value=1.7e-16  Score=122.40  Aligned_cols=78  Identities=22%  Similarity=0.237  Sum_probs=70.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCce--eCCeeEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFE--LAGRPMKVG  189 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~--i~g~~l~V~  189 (370)
                      .++++|||+|||+++++++|+++|++||.|.++.++++      +|+|||+|.+.++|.+|+..|++..  +.|++|+|.
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~   92 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN   92 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEE
Confidence            45678999999999999999999999999999998743      7899999999999999999999875  789999999


Q ss_pred             EeecCC
Q psy2983         190 TVTDRN  195 (370)
Q Consensus       190 ~~~~~~  195 (370)
                      +++.+.
T Consensus        93 ~S~~k~   98 (100)
T 3r27_A           93 YSTSQK   98 (100)
T ss_dssp             ECSCSC
T ss_pred             eccccc
Confidence            987653

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.67  E-value=1e-16  Score=119.50  Aligned_cols=72  Identities=21%  Similarity=0.299  Sum_probs=68.3

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      +.-|||+||++.+|+++|+++|.+||+|.++++..      ++|||||+|.+.++|.+|++.||+..+.|++|+|.++
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 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            45799999999999999999999999999999864      5999999999999999999999999999999999886

>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=99.67  E-value=6.8e-16  Score=122.74  Aligned_cols=83  Identities=24%  Similarity=0.505  Sum_probs=77.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCcee--------C
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFEL--------A  182 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i--------~  182 (370)
                      ....++|||+|||+.+++++|+++|++||.|..++++.++ +|.++|||||+|.+.++|.+|+..|||..+        .
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            3456899999999999999999999999999999999997 999999999999999999999999999999        5


Q ss_pred             CeeEEEEEeecC
Q psy2983         183 GRPMKVGTVTDR  194 (370)
Q Consensus       183 g~~l~V~~~~~~  194 (370)
                      +++|.|.++.++
T Consensus       101 ~~~l~v~~a~p~  112 (114)
T 1x5o_A          101 TEPLLCKFSGPS  112 (114)
T ss_dssp             SSCBEEEECCCS
T ss_pred             CCceeEEccCCC
Confidence            788999998754

>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=99.67  E-value=6.1e-17  Score=125.24  Aligned_cols=83  Identities=12%  Similarity=0.167  Sum_probs=77.2

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHh-hccCCccCCeeEEEe
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQ   90 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~i~g~~l~v~   90 (370)
                      .....++|||+|||..+++++|+++|+.||.|..+.++.++.+++++|||||+|.+.++|.+|+ .++|..|.|+.|.|.
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   90 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV   90 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            4456789999999999999999999999999999889999999999999999999999999999 599999999999999


Q ss_pred             cccc
Q psy2983          91 PTQA   94 (370)
Q Consensus        91 ~~~~   94 (370)
                      ++..
T Consensus        91 ~a~~   94 (98)
T 2cqp_A           91 LGSG   94 (98)
T ss_dssp             ESSC
T ss_pred             EcCC
Confidence            8753

>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=99.67  E-value=5.8e-17  Score=129.21  Aligned_cols=105  Identities=21%  Similarity=0.338  Sum_probs=89.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ...++|||+|||..+++++|+++|++||.|..+.++.+   +.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            34579999999999999999999999999999999855   556999999999999999999999999999999999998


Q ss_pred             ecCCCCcCCCCCCCCHHHHHHhcccCCce
Q psy2983         192 TDRNESVGGGPSNLDTDEMERAGVDLGAT  220 (370)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  220 (370)
                      .++... ..++....++++++.+..+|..
T Consensus        83 ~~~~~~-~~~~~~~~~~~l~~~~~~~g~~  110 (115)
T 3lqv_A           83 NANRAF-QKMDTKKKEEQLKLLKEKYGIN  110 (115)
T ss_dssp             CHHHHT-TTSCHHHHHHHHHHHHHHHCCC
T ss_pred             cCChhh-hhhhHhHhHHHHHHHHHHhCCC
Confidence            765543 3344556677888888877754

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.67  E-value=1.1e-16  Score=122.13  Aligned_cols=83  Identities=25%  Similarity=0.309  Sum_probs=76.1

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      ...+.++|||+|||..+++++|+++|++||.|..+.+.++  +++++|||||+|.+.++|.+|++ ++|..+.|+.|.|.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   81 (92)
T 2dgv_A            4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVR   81 (92)
T ss_dssp             SSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3457899999999999999999999999999999999884  68899999999999999999996 99999999999999


Q ss_pred             cccccc
Q psy2983          91 PTQAEK   96 (370)
Q Consensus        91 ~~~~~~   96 (370)
                      ++....
T Consensus        82 ~a~~~~   87 (92)
T 2dgv_A           82 IDRNAS   87 (92)
T ss_dssp             ECSCCS
T ss_pred             EcCCCC
Confidence            887543

>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=99.67  E-value=2.8e-17  Score=125.03  Aligned_cols=82  Identities=26%  Similarity=0.619  Sum_probs=74.0

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecC
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~  194 (370)
                      ++|||+|||..+++++|+++|++||.|..+.+..++.+|.++|||||+|.+.+ |.+|+..|||..+.|+.|+|.++.+.
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            57999999999999999999999999999999999889999999999999999 99999999999999999999998775


Q ss_pred             CCC
Q psy2983         195 NES  197 (370)
Q Consensus       195 ~~~  197 (370)
                      ...
T Consensus        81 ~~~   83 (90)
T 2ki2_A           81 KSL   83 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            543

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=5.7e-17  Score=126.33  Aligned_cols=79  Identities=20%  Similarity=0.289  Sum_probs=71.1

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-cc--CCccCCeeEE
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LN--GQKLLGIPII   88 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~--g~~i~g~~l~   88 (370)
                      ...+.++|||+|||.++|+++|+++|++||.|.+|+++++      ||||||+|.+.++|..|++ ++  +..+.|++|+
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~   85 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY   85 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            3467899999999999999999999999999999999874      6999999999999999996 65  5789999999


Q ss_pred             Eecccccc
Q psy2983          89 VQPTQAEK   96 (370)
Q Consensus        89 v~~~~~~~   96 (370)
                      |.++....
T Consensus        86 V~~A~~~~   93 (105)
T 1sjq_A           86 IQFSNHKE   93 (105)
T ss_dssp             BCCCSSSS
T ss_pred             EEEcCCCC
Confidence            99987543

>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=99.67  E-value=3.3e-16  Score=121.79  Aligned_cols=79  Identities=20%  Similarity=0.254  Sum_probs=71.3

Q ss_pred             CCCceEEEecCCC-CCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCC--ceeCCeeEEE
Q psy2983         112 GGPMRLYIGSLHF-NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNG--FELAGRPMKV  188 (370)
Q Consensus       112 ~~~~~l~V~nlp~-~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g--~~i~g~~l~V  188 (370)
                      .+.++|||+|||+ .+++++|+++|++||.|.++.++++      +|||||+|.+.++|.+|++.|++  ..+.|++|+|
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   86 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   86 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEE
Confidence            3567999999999 9999999999999999999999865      58999999999999999999986  4599999999


Q ss_pred             EEeecCCC
Q psy2983         189 GTVTDRNE  196 (370)
Q Consensus       189 ~~~~~~~~  196 (370)
                      .++.....
T Consensus        87 ~~a~~~~~   94 (102)
T 1x4d_A           87 HLSQKYKR   94 (102)
T ss_dssp             EEECCCTT
T ss_pred             EECCCCCC
Confidence            99986544

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.67  E-value=7.6e-17  Score=124.38  Aligned_cols=78  Identities=19%  Similarity=0.247  Sum_probs=70.1

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCc--cCCeeEE
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQK--LLGIPII   88 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~--i~g~~l~   88 (370)
                      ...++++|||+|||.++|+++|+++|++||.|.++.+++      +||||||+|.+.++|.+|++ +++..  +.|++|+
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~   90 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAF   90 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEE
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEE
Confidence            345789999999999999999999999999999999875      37899999999999999996 88775  7899999


Q ss_pred             Eeccccc
Q psy2983          89 VQPTQAE   95 (370)
Q Consensus        89 v~~~~~~   95 (370)
                      |++++.+
T Consensus        91 V~~S~~k   97 (100)
T 3r27_A           91 VNYSTSQ   97 (100)
T ss_dssp             EEECSCS
T ss_pred             EEecccc
Confidence            9998754

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.7e-16  Score=126.71  Aligned_cols=84  Identities=35%  Similarity=0.629  Sum_probs=78.9

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ..++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+.. ++..+.|+.|+|.++.
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            347899999999999999999999999999999999988999999999999999999999997 9999999999999988


Q ss_pred             cCCCC
Q psy2983         193 DRNES  197 (370)
Q Consensus       193 ~~~~~  197 (370)
                      ++...
T Consensus       105 ~~~~~  109 (116)
T 1x4b_A          105 AREES  109 (116)
T ss_dssp             SCCCC
T ss_pred             CCccC
Confidence            76554

>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=1.2e-15  Score=118.59  Aligned_cols=81  Identities=20%  Similarity=0.252  Sum_probs=72.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHh--CCceeCCeeEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL--NGFELAGRPMKVG  189 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l--~g~~i~g~~l~V~  189 (370)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++++      +|||||+|.+.++|.+|+..|  ++..+.|++|+|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   86 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   86 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEE
Confidence            34579999999999999999999999999999988754      899999999999999999977  4688999999999


Q ss_pred             EeecCCCCc
Q psy2983         190 TVTDRNESV  198 (370)
Q Consensus       190 ~~~~~~~~~  198 (370)
                      ++..+....
T Consensus        87 ~a~~~~~~~   95 (101)
T 2cq1_A           87 YSNHKELKT   95 (101)
T ss_dssp             ECSCSSCCC
T ss_pred             EcCcccCcC
Confidence            998765543

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.67  E-value=1e-16  Score=129.47  Aligned_cols=82  Identities=28%  Similarity=0.455  Sum_probs=77.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEeccc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~~   93 (370)
                      .+.++|||+|||.++|+++|+++|+.||.|.++.+++++.++.++|||||+|.+.++|.+|++++|..|.|+.|.|.++.
T Consensus        34 ~~~~~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           34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETTEECEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECC
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             cc
Q psy2983          94 AE   95 (370)
Q Consensus        94 ~~   95 (370)
                      ..
T Consensus       114 ~~  115 (124)
T 2jwn_A          114 TN  115 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.67  E-value=4e-16  Score=131.26  Aligned_cols=86  Identities=27%  Similarity=0.414  Sum_probs=80.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|.+|+..||+..|.|+.|+|.+
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34568999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             eecCCC
Q psy2983         191 VTDRNE  196 (370)
Q Consensus       191 ~~~~~~  196 (370)
                      +.+...
T Consensus       116 a~~~~~  121 (156)
T 1h2v_Z          116 DAGFKE  121 (156)
T ss_dssp             ESCCCT
T ss_pred             CCCCCC
Confidence            977554

>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=99.67  E-value=3.7e-17  Score=125.63  Aligned_cols=81  Identities=12%  Similarity=0.171  Sum_probs=74.8

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      ....++|||+|||..+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|.+|++ ++|..+.|++|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            3456899999999999999999999999999999999999999999999999999999999996 999999999999988


Q ss_pred             cc
Q psy2983          92 TQ   93 (370)
Q Consensus        92 ~~   93 (370)
                      +.
T Consensus        92 a~   93 (95)
T 2ek1_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cc
Confidence            65

>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=99.67  E-value=5.6e-17  Score=133.05  Aligned_cols=85  Identities=19%  Similarity=0.242  Sum_probs=78.6

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCC---eeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCee
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGK---VRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIP   86 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~---v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~   86 (370)
                      .+...+.++|||+|||.++|+++|+++|++||.   |.+|.+++|+. ++++|||||+|.+.++|.+|+++++..+.|+.
T Consensus        38 ~~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~  116 (136)
T 2hgl_A           38 GPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALKKDRESMGHRY  116 (136)
T ss_dssp             CSSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHTTTEEESSSSE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCEECCEE
Confidence            345567899999999999999999999999999   89999999987 99999999999999999999999999999999


Q ss_pred             EEEeccccc
Q psy2983          87 IIVQPTQAE   95 (370)
Q Consensus        87 l~v~~~~~~   95 (370)
                      |.|.++...
T Consensus       117 i~V~~a~~~  125 (136)
T 2hgl_A          117 IEVFKSHRT  125 (136)
T ss_dssp             EEEEECCHH
T ss_pred             EEEEECChH
Confidence            999887643

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=5.7e-17  Score=127.88  Aligned_cols=84  Identities=19%  Similarity=0.277  Sum_probs=76.4

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIV   89 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v   89 (370)
                      .+...+.++|||+|||.++|+++|+++|+.| .|.+|.|++|+. |+++|||||+|.+.++|.+|+++++..+.|+.|.|
T Consensus        10 ~~~~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V   87 (109)
T 2dnn_A           10 LPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEV   87 (109)
T ss_dssp             CCCCHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEE
Confidence            3445566899999999999999999999999 899999999876 89999999999999999999999999999999999


Q ss_pred             eccccc
Q psy2983          90 QPTQAE   95 (370)
Q Consensus        90 ~~~~~~   95 (370)
                      ..+...
T Consensus        88 ~~a~~~   93 (109)
T 2dnn_A           88 SPATER   93 (109)
T ss_dssp             EECCHH
T ss_pred             EECCcc
Confidence            877643

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=1.2e-16  Score=126.32  Aligned_cols=85  Identities=25%  Similarity=0.425  Sum_probs=76.9

Q ss_pred             CCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeE
Q psy2983           9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPI   87 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l   87 (370)
                      ........++|||+|||.++++++|+++|++||.|.++.++++.  +.++|||||+|.+.++|.+|++ ++|..+.|+.|
T Consensus        22 ~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   99 (109)
T 2err_A           22 NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKI   99 (109)
T ss_dssp             CCSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEEC
T ss_pred             CccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34456688999999999999999999999999999999999885  3489999999999999999996 99999999999


Q ss_pred             EEeccccc
Q psy2983          88 IVQPTQAE   95 (370)
Q Consensus        88 ~v~~~~~~   95 (370)
                      .|.++...
T Consensus       100 ~V~~a~~~  107 (109)
T 2err_A          100 EVNNATAR  107 (109)
T ss_dssp             EEEECCCS
T ss_pred             EEEECCCC
Confidence            99987643

>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=99.66  E-value=7.2e-17  Score=130.53  Aligned_cols=83  Identities=17%  Similarity=0.266  Sum_probs=76.7

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecc
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPT   92 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~   92 (370)
                      ..+.++|||+|||.++|+++|+++|+.||.|.++.++.+..+++++|||||+|.+.++|.+|++++|..|.|+.|.|.++
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEEC
Confidence            45668999999999999999999999999999877777888999999999999999999999999999999999999987


Q ss_pred             ccc
Q psy2983          93 QAE   95 (370)
Q Consensus        93 ~~~   95 (370)
                      ...
T Consensus       102 ~~~  104 (124)
T 1wel_A          102 TKK  104 (124)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            653

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.66  E-value=1.4e-17  Score=129.70  Aligned_cols=86  Identities=19%  Similarity=0.284  Sum_probs=77.9

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIV   89 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v   89 (370)
                      .......++|||+|||.++|+++|+++|+.||.|.. .++.+..+++++|||||+|.+.++|.+|++++|..+.|+.|.|
T Consensus        11 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V   89 (101)
T 1fj7_A           11 GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKL   89 (101)
T ss_dssp             STTCSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEE
Confidence            344567899999999999999999999999999988 6777777889999999999999999999999999999999999


Q ss_pred             ecccccc
Q psy2983          90 QPTQAEK   96 (370)
Q Consensus        90 ~~~~~~~   96 (370)
                      .++....
T Consensus        90 ~~a~~~~   96 (101)
T 1fj7_A           90 EKPKGRD   96 (101)
T ss_dssp             ECCSCCC
T ss_pred             EEcCCCC
Confidence            9987543

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.66  E-value=5.9e-17  Score=133.07  Aligned_cols=88  Identities=24%  Similarity=0.360  Sum_probs=81.5

Q ss_pred             CCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeE
Q psy2983           9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPI   87 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l   87 (370)
                      .++...+.++|||+|||..+|+++|+++|+.||.|..|.+++++.+++++|||||+|.+.++|.+|++ ++|..+.|++|
T Consensus        40 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l  119 (135)
T 2lea_A           40 PPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL  119 (135)
T ss_dssp             SCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34556778999999999999999999999999999999999999899999999999999999999996 99999999999


Q ss_pred             EEecccccc
Q psy2983          88 IVQPTQAEK   96 (370)
Q Consensus        88 ~v~~~~~~~   96 (370)
                      .|.++....
T Consensus       120 ~V~~a~~~~  128 (135)
T 2lea_A          120 RVQMARYGR  128 (135)
T ss_dssp             EEEECCCCC
T ss_pred             EEEECCCCC
Confidence            999987543

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.66  E-value=7e-17  Score=119.01  Aligned_cols=76  Identities=32%  Similarity=0.594  Sum_probs=72.7

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ++|||+|||+.+++++|+++|++||.|..+.+..++.+|.++|||||+|.+.++|.+|+..++ ..+.|+.|+|.++
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            369999999999999999999999999999999998899999999999999999999999988 9999999999875

>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=99.66  E-value=1e-15  Score=120.73  Aligned_cols=84  Identities=21%  Similarity=0.426  Sum_probs=76.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||..+++++|+++|++||.|..+.+..   ++.++|||||+|.+.++|.+|++.||+..+.|+.|+|.+
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE---CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34568999999999999999999999999999999864   456899999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2983         191 VTDRNES  197 (370)
Q Consensus       191 ~~~~~~~  197 (370)
                      +.++...
T Consensus        96 a~~~~~~  102 (109)
T 1x4a_A           96 PRSGRGT  102 (109)
T ss_dssp             CCCCCCC
T ss_pred             cccCCCC
Confidence            8876554

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=9.5e-16  Score=119.17  Aligned_cols=84  Identities=32%  Similarity=0.525  Sum_probs=75.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||+.+++++|+++|++||.|   +++.+ .+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            3456899999999999999999999999987   56666 5899999999999999999999999999999999999999


Q ss_pred             eecCCCCc
Q psy2983         191 VTDRNESV  198 (370)
Q Consensus       191 ~~~~~~~~  198 (370)
                      +.++....
T Consensus        88 a~~~~~~~   95 (101)
T 2fc9_A           88 QGPRGSPN   95 (101)
T ss_dssp             CSSCCCCC
T ss_pred             cCCCCCCC
Confidence            98775543

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.66  E-value=4.2e-16  Score=128.42  Aligned_cols=81  Identities=33%  Similarity=0.622  Sum_probs=76.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||..+++++|+++|++||.|..++++.++.+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.+
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  139 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL  139 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34568999999999999999999999999999999999988999999999999999999999999999999999999987


Q ss_pred             e
Q psy2983         191 V  191 (370)
Q Consensus       191 ~  191 (370)
                      +
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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=99.66  E-value=3.9e-16  Score=139.78  Aligned_cols=129  Identities=18%  Similarity=0.339  Sum_probs=111.1

Q ss_pred             CCCceEEEecCCC-CCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         112 GGPMRLYIGSLHF-NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       112 ~~~~~l~V~nlp~-~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      .+.++|||+|||+ .+++++|+++|++||.|..++++.++     +|||||+|.+.++|.+|++.|+|..+.|+.|+|.+
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~  106 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL  106 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEEC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            3457999999999 99999999999999999999998774     78999999999999999999999999999999998


Q ss_pred             eecCC------------------------------------------CCcCCCCCCCCHHHHHHhcccCC-ceeeeeeee
Q psy2983         191 VTDRN------------------------------------------ESVGGGPSNLDTDEMERAGVDLG-ATGRLQLMF  227 (370)
Q Consensus       191 ~~~~~------------------------------------------~~~~~~~~~~~~~~l~~~~~~~g-~~~~~~l~~  227 (370)
                      +....                                          ..+.+++..+++++++..|..+| .+..+.++.
T Consensus       107 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~  186 (229)
T 2adc_A          107 SKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ  186 (229)
T ss_dssp             CSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS
T ss_pred             ecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEE
Confidence            86431                                          11557888999999999999999 898888865


Q ss_pred             ccccCCC---CCChHHHHHHHh
Q psy2983         228 KLAEGTG---LELPPAAASALN  246 (370)
Q Consensus       228 ~~~~~~~---~~~~~~a~~a~~  246 (370)
                      + .++++   |..+..|..|+.
T Consensus       187 ~-~~g~afV~f~~~~~A~~Ai~  207 (229)
T 2adc_A          187 K-DRKMALIQMGSVEEAVQALI  207 (229)
T ss_dssp             S-STTCEEEEESSHHHHHHHHH
T ss_pred             C-CCcEEEEEECCHHHHHHHHH
Confidence            3 35555   667888877776

>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=99.66  E-value=3.4e-17  Score=124.59  Aligned_cols=79  Identities=29%  Similarity=0.511  Sum_probs=72.6

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccccc
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQAE   95 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~~   95 (370)
                      ++|||+|||.++++++|+++|++||+|.++.+++++.+++++|||||+|.+.+ |.+|++ ++|..+.|++|.|.++...
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            68999999999999999999999999999999999999999999999999999 999996 9999999999999998754


Q ss_pred             c
Q psy2983          96 K   96 (370)
Q Consensus        96 ~   96 (370)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            3

>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=99.66  E-value=3.2e-16  Score=123.59  Aligned_cols=86  Identities=17%  Similarity=0.312  Sum_probs=78.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCc-eeeEEEe-ecCCCCCcccEEEEEECCHHHHHHHHHHhC--CceeCCeeEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGK-IDNIQLM-VDPDTGRSKGYGFITFHSADDAKKAQEQLN--GFELAGRPMK  187 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~-i~~v~~~-~~~~~g~~~g~afV~f~~~~~a~~A~~~l~--g~~i~g~~l~  187 (370)
                      ...++|||+|||+.+++++|+++|++||. |..+.++ .+..+|.++|||||+|.+.++|.+|+..|+  +..+.|+.|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            34589999999999999999999999998 9999998 788889999999999999999999999996  5999999999


Q ss_pred             EEEeecCCCC
Q psy2983         188 VGTVTDRNES  197 (370)
Q Consensus       188 V~~~~~~~~~  197 (370)
                      |.++.++...
T Consensus        86 V~~a~~~~~~   95 (109)
T 2dis_A           86 VDWAEPEIDV   95 (109)
T ss_dssp             EEESCSSCST
T ss_pred             EEEcCCCCCc
Confidence            9999876553

>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=99.66  E-value=2.5e-16  Score=132.49  Aligned_cols=86  Identities=19%  Similarity=0.226  Sum_probs=80.0

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEE
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIV   89 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v   89 (370)
                      ....+.++|||+|||..+|+++|+++|+.||+|..|.+++++.++.++|||||+|.+.++|.+|++ |++..|.|+.|.|
T Consensus        34 ~~~~~~~~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           34 KLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRT  113 (156)
T ss_dssp             TTTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            334578999999999999999999999999999999999999999999999999999999999997 9999999999999


Q ss_pred             ecccccc
Q psy2983          90 QPTQAEK   96 (370)
Q Consensus        90 ~~~~~~~   96 (370)
                      .++....
T Consensus       114 ~~a~~~~  120 (156)
T 1h2v_Z          114 DWDAGFK  120 (156)
T ss_dssp             EEESCCC
T ss_pred             EECCCCC
Confidence            9987543

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.66  E-value=1.9e-16  Score=130.56  Aligned_cols=82  Identities=22%  Similarity=0.419  Sum_probs=76.7

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEE
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIV   89 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v   89 (370)
                      ....+.++|||+|||..+++++|+++|++||+|.++.+++++.+++++|||||+|.+.++|.+|++ ++|..+.|++|+|
T Consensus        58 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  137 (140)
T 2ku7_A           58 GSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV  137 (140)
T ss_dssp             SSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEE
T ss_pred             CCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            445678999999999999999999999999999999999999999999999999999999999995 9999999999999


Q ss_pred             ecc
Q psy2983          90 QPT   92 (370)
Q Consensus        90 ~~~   92 (370)
                      .++
T Consensus       138 ~~A  140 (140)
T 2ku7_A          138 NLA  140 (140)
T ss_dssp             EC-
T ss_pred             EeC
Confidence            864

>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=99.65  E-value=2.1e-16  Score=124.66  Aligned_cols=85  Identities=19%  Similarity=0.288  Sum_probs=77.3

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCC-eeEEEEe-eeCCCCCeecEEEEEecCCCChHHHhh-cc--CCccCCeeE
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGK-VRDVRLI-TCNKTRRFKGIAYIEFKDPESVPLAMG-LN--GQKLLGIPI   87 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~-v~~v~i~-~d~~~~~~kg~afVeF~~~e~A~~Al~-l~--g~~i~g~~l   87 (370)
                      ..+.++|||+|||..+++++|+++|+.||. |.++.++ .+..+++++|||||+|.+.++|..|++ ++  +..+.|+.|
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l   84 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeE
Confidence            346799999999999999999999999998 9999998 788888999999999999999999996 85  589999999


Q ss_pred             EEeccccccc
Q psy2983          88 IVQPTQAEKN   97 (370)
Q Consensus        88 ~v~~~~~~~~   97 (370)
                      .|.++.....
T Consensus        85 ~V~~a~~~~~   94 (109)
T 2dis_A           85 AVDWAEPEID   94 (109)
T ss_dssp             EEEESCSSCS
T ss_pred             EEEEcCCCCC
Confidence            9999876543

>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=99.65  E-value=2e-16  Score=133.32  Aligned_cols=86  Identities=23%  Similarity=0.337  Sum_probs=79.7

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEE
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIV   89 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v   89 (370)
                      ......++|||+|||..+++++|+++|+.||.|.++.+++++.+++++|||||+|.+.++|.+|++ |+|..+.|++|.|
T Consensus        65 ~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  144 (158)
T 2kn4_A           65 MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV  144 (158)
T ss_dssp             CCCCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            344567999999999999999999999999999999999999999999999999999999999996 9999999999999


Q ss_pred             ecccccc
Q psy2983          90 QPTQAEK   96 (370)
Q Consensus        90 ~~~~~~~   96 (370)
                      .++....
T Consensus       145 ~~a~~~~  151 (158)
T 2kn4_A          145 QMARYGR  151 (158)
T ss_dssp             EEECCSS
T ss_pred             EECCCCC
Confidence            9987543

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.65  E-value=1.3e-16  Score=129.32  Aligned_cols=85  Identities=19%  Similarity=0.371  Sum_probs=74.5

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHH----HHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCC
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLE----EFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLG   84 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~----~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g   84 (370)
                      ++...+.++|||+|||..+++++|+    ++|++||.|.+|.+.+   +++++|||||+|.+.++|..|++ ++|..+.|
T Consensus        23 ~~~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~g   99 (127)
T 2a3j_A           23 PPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQG   99 (127)
T ss_dssp             CCCCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTT
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCC
Confidence            3445678999999999999999876    6999999999987754   57889999999999999999995 99999999


Q ss_pred             eeEEEeccccccc
Q psy2983          85 IPIIVQPTQAEKN   97 (370)
Q Consensus        85 ~~l~v~~~~~~~~   97 (370)
                      ++|.|.++.....
T Consensus       100 r~l~V~~a~~~~~  112 (127)
T 2a3j_A          100 NPLVITFSETPQS  112 (127)
T ss_dssp             SCCEEEECCCCCH
T ss_pred             CEEEEEEccCcch
Confidence            9999999876543

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.65  E-value=3.9e-16  Score=126.06  Aligned_cols=82  Identities=24%  Similarity=0.468  Sum_probs=77.3

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .++|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+ .|||..+.|+.|+|.++.+
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCC
Confidence            478999999999999999999999999999999999889999999999999999999999 7999999999999999876


Q ss_pred             CCC
Q psy2983         194 RNE  196 (370)
Q Consensus       194 ~~~  196 (370)
                      ...
T Consensus       115 ~~~  117 (124)
T 2jwn_A          115 NMP  117 (124)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            544

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.65  E-value=2.6e-16  Score=123.42  Aligned_cols=82  Identities=24%  Similarity=0.408  Sum_probs=75.0

Q ss_pred             CCceEEEecCCCCC------CHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCe-e
Q psy2983         113 GPMRLYIGSLHFNI------TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGR-P  185 (370)
Q Consensus       113 ~~~~l~V~nlp~~~------t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~-~  185 (370)
                      ..++|||+|||+.+      ++++|+++|++||.|..+.+.  ..+|.++|||||+|.+.++|.+|+..|||..+.|+ +
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~   91 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT   91 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCE
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCce
Confidence            45799999999999      789999999999999999988  35899999999999999999999999999999998 9


Q ss_pred             EEEEEeecCCC
Q psy2983         186 MKVGTVTDRNE  196 (370)
Q Consensus       186 l~V~~~~~~~~  196 (370)
                      |+|.++.+...
T Consensus        92 l~V~~a~~~~k  102 (105)
T 2nlw_A           92 FRVNLFTDFDK  102 (105)
T ss_dssp             EEEECSCCCCC
T ss_pred             EEEEEcchHhh
Confidence            99999876543

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=3.9e-16  Score=124.28  Aligned_cols=82  Identities=24%  Similarity=0.349  Sum_probs=76.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCce-eeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKI-DNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG  189 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i-~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~  189 (370)
                      ....++|||+|||+.+++++|+++|++||.| ..++++.++ +|.++|||||+|.+.++|.+|+.. |+..+.|+.|+|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~   89 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            3456899999999999999999999999999 899999998 999999999999999999999996 9999999999999


Q ss_pred             EeecC
Q psy2983         190 TVTDR  194 (370)
Q Consensus       190 ~~~~~  194 (370)
                      ++.++
T Consensus        90 ~a~~~   94 (114)
T 2cpy_A           90 VVTLE   94 (114)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            98653

>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=99.65  E-value=3.1e-16  Score=121.92  Aligned_cols=85  Identities=16%  Similarity=0.242  Sum_probs=74.0

Q ss_pred             CCCCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-c--cCCcc
Q psy2983           6 SDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-L--NGQKL   82 (370)
Q Consensus         6 ~~~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l--~g~~i   82 (370)
                      ++.......++++|||+|||.++++++|+++|++||.|.++.++++      +|||||+|.+.++|..|++ +  ++..+
T Consensus         5 s~~~~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~   78 (101)
T 2cq1_A            5 SSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHL   78 (101)
T ss_dssp             CCCCCCCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEE
T ss_pred             CCCCCccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceE
Confidence            3444455678899999999999999999999999999999988764      7999999999999999996 4  57889


Q ss_pred             CCeeEEEecccccc
Q psy2983          83 LGIPIIVQPTQAEK   96 (370)
Q Consensus        83 ~g~~l~v~~~~~~~   96 (370)
                      .|++|+|.++....
T Consensus        79 ~Gr~l~V~~a~~~~   92 (101)
T 2cq1_A           79 RNQPIYIQYSNHKE   92 (101)
T ss_dssp             TTEECEEEECSCSS
T ss_pred             CCcEEEEEEcCccc
Confidence            99999999987543

>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=99.65  E-value=3.1e-16  Score=122.62  Aligned_cols=83  Identities=14%  Similarity=0.188  Sum_probs=72.3

Q ss_pred             CCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccC--CccCC
Q psy2983           8 DLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNG--QKLLG   84 (370)
Q Consensus         8 ~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g--~~i~g   84 (370)
                      ..+....++++|||+|||.++++++|+++|++||.|.+|.++++      ||||||+|.+.++|.+|++ +++  ..+.|
T Consensus         7 ~~~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~G   80 (104)
T 1wex_A            7 GSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAG   80 (104)
T ss_dssp             CSCCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSS
T ss_pred             CCCCcCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            33445678899999999999999999999999999999998763      7999999999999999996 654  46999


Q ss_pred             eeEEEecccccc
Q psy2983          85 IPIIVQPTQAEK   96 (370)
Q Consensus        85 ~~l~v~~~~~~~   96 (370)
                      ++|+|.++....
T Consensus        81 r~l~V~~a~~~~   92 (104)
T 1wex_A           81 QQAFFNYSTSKR   92 (104)
T ss_dssp             SBCEEEECSSSS
T ss_pred             EEEEEEEccCcc
Confidence            999999987654

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.65  E-value=4.3e-16  Score=125.91  Aligned_cols=83  Identities=19%  Similarity=0.294  Sum_probs=77.9

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      .....++|||+|||..+++++|+++|+.||.|.++.+.+++ +++++|||||+|.+.++|.+|++ ++|..+.|++|.|.
T Consensus        31 ~~~~~~~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           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            45677899999999999999999999999999999999998 89999999999999999999997 99999999999999


Q ss_pred             ccccc
Q psy2983          91 PTQAE   95 (370)
Q Consensus        91 ~~~~~   95 (370)
                      ++...
T Consensus       110 ~a~~~  114 (124)
T 2kt5_A          110 LVASQ  114 (124)
T ss_dssp             EECCT
T ss_pred             EeCCC
Confidence            98654

>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=99.65  E-value=3.9e-16  Score=123.14  Aligned_cols=85  Identities=28%  Similarity=0.473  Sum_probs=75.8

Q ss_pred             CCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHh-hccCCccCCeeE
Q psy2983           9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPI   87 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~i~g~~l   87 (370)
                      ......+.++|||+|||..+++++|+++|++||.|..+.+..+   +.++|||||+|.+.++|.+|+ .|++..+.|+.|
T Consensus        15 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   91 (109)
T 1x4a_A           15 RGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRL   91 (109)
T ss_dssp             SCCCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            3445667899999999999999999999999999999998654   457899999999999999999 599999999999


Q ss_pred             EEecccccc
Q psy2983          88 IVQPTQAEK   96 (370)
Q Consensus        88 ~v~~~~~~~   96 (370)
                      .|.++....
T Consensus        92 ~V~~a~~~~  100 (109)
T 1x4a_A           92 RVEFPRSGR  100 (109)
T ss_dssp             EEECCCCCC
T ss_pred             EEEEcccCC
Confidence            999987643

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=1.9e-16  Score=122.15  Aligned_cols=80  Identities=19%  Similarity=0.264  Sum_probs=73.8

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHH----HHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeE
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLE----EFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPI   87 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~----~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l   87 (370)
                      ..+.++|||+|||..+++++|+    ++|++||.|.++.+++++.+   +|||||+|.+.++|.+|++ ++|..+.|++|
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l   82 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKI   82 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            3466899999999999999999    99999999999999988765   7899999999999999996 99999999999


Q ss_pred             EEeccccc
Q psy2983          88 IVQPTQAE   95 (370)
Q Consensus        88 ~v~~~~~~   95 (370)
                      +|.++...
T Consensus        83 ~V~~a~~~   90 (96)
T 2dgx_A           83 LVSLATGA   90 (96)
T ss_dssp             EEEECCCS
T ss_pred             EEEEcCCC
Confidence            99998654

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.65  E-value=3.9e-16  Score=136.27  Aligned_cols=127  Identities=17%  Similarity=0.326  Sum_probs=110.3

Q ss_pred             CceEEEecCCC-CCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         114 PMRLYIGSLHF-NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       114 ~~~l~V~nlp~-~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      +++|||+|||+ .+++++|+++|++||.|..++++.++     +|||||+|.+.++|.+|+..|||..+.|+.|+|.++.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            46899999999 99999999999999999999998764     7899999999999999999999999999999999886


Q ss_pred             cCC------------------------------------------CCcCCCCCCCCHHHHHHhcccCC-ceeeeeeeecc
Q psy2983         193 DRN------------------------------------------ESVGGGPSNLDTDEMERAGVDLG-ATGRLQLMFKL  229 (370)
Q Consensus       193 ~~~------------------------------------------~~~~~~~~~~~~~~l~~~~~~~g-~~~~~~l~~~~  229 (370)
                      ...                                          ..+++++..+++++++..|..+| .+..+.++.+ 
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-  156 (198)
T 1qm9_A           78 HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-  156 (198)
T ss_dssp             CCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-
T ss_pred             CCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-
Confidence            431                                          11567888999999999999999 8988888654 


Q ss_pred             ccCCC---CCChHHHHHHHh
Q psy2983         230 AEGTG---LELPPAAASALN  246 (370)
Q Consensus       230 ~~~~~---~~~~~~a~~a~~  246 (370)
                      .++++   |..+..|..|+.
T Consensus       157 ~~g~afV~f~~~~~A~~A~~  176 (198)
T 1qm9_A          157 DRKMALIQMGSVEEAVQALI  176 (198)
T ss_dssp             TSSCEEEECSSHHHHHHHHH
T ss_pred             CCcEEEEEeCCHHHHHHHHH
Confidence            35555   678888888776

>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=99.65  E-value=2.5e-16  Score=133.87  Aligned_cols=88  Identities=19%  Similarity=0.321  Sum_probs=80.1

Q ss_pred             CCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeE
Q psy2983           9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPI   87 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l   87 (370)
                      .+....+.++|||+|||..+++++|+++|+.||.|..|.++.++.++.++|||||+|.+.++|..|++ |+|..|.|++|
T Consensus        65 ~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l  144 (165)
T 1rk8_A           65 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTI  144 (165)
T ss_dssp             -CCCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            34456677899999999999999999999999999999999999999999999999999999999996 99999999999


Q ss_pred             EEecccccc
Q psy2983          88 IVQPTQAEK   96 (370)
Q Consensus        88 ~v~~~~~~~   96 (370)
                      .|.++....
T Consensus       145 ~V~~a~~~~  153 (165)
T 1rk8_A          145 QVDWCFVKG  153 (165)
T ss_dssp             EEEESEECC
T ss_pred             EEEEecCCC
Confidence            999987654

>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=99.65  E-value=6.6e-16  Score=120.43  Aligned_cols=83  Identities=17%  Similarity=0.295  Sum_probs=75.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      .....+|||+|||+++++++|+++|++||.+ .++++.++ +|+++|||||+|.+.++|.+|++ +|+..+.|+.|+|..
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~   88 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            3455799999999999999999999999955 99999997 89999999999999999999996 799999999999998


Q ss_pred             eecCCC
Q psy2983         191 VTDRNE  196 (370)
Q Consensus       191 ~~~~~~  196 (370)
                      +.....
T Consensus        89 ~~~~~~   94 (102)
T 1wez_A           89 NSTAGT   94 (102)
T ss_dssp             ECCCCC
T ss_pred             CCCCCC
Confidence            876544

>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=99.65  E-value=1.2e-15  Score=119.38  Aligned_cols=82  Identities=22%  Similarity=0.308  Sum_probs=75.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceee-EEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDN-IQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~-v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....+|||+|||+.+++++|+++|++||.|.. +.++.+ .+|+++|||||+|.+.++|.+|+.. ++..+.|+.|+|.+
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFK   90 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEE
Confidence            44579999999999999999999999999987 888888 6999999999999999999999996 99999999999998


Q ss_pred             eecCC
Q psy2983         191 VTDRN  195 (370)
Q Consensus       191 ~~~~~  195 (370)
                      +..+.
T Consensus        91 ~~~~~   95 (104)
T 1wg5_A           91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            76543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.65  E-value=5.7e-16  Score=124.15  Aligned_cols=80  Identities=16%  Similarity=0.277  Sum_probs=74.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCc---eeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGK---IDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV  188 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~---i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V  188 (370)
                      ...++|||+|||+++++++|+++|+.||.   |..++++.++. |+++|||||+|.+.++|.+|+. +|+..+.|+.|+|
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   92 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV   92 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEE
Confidence            34578999999999999999999999999   89999999975 9999999999999999999999 9999999999999


Q ss_pred             EEeec
Q psy2983         189 GTVTD  193 (370)
Q Consensus       189 ~~~~~  193 (370)
                      .++..
T Consensus        93 ~~a~~   97 (118)
T 2db1_A           93 FKSHR   97 (118)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            98754

>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=99.64  E-value=1e-15  Score=119.70  Aligned_cols=80  Identities=20%  Similarity=0.206  Sum_probs=71.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCc--eeCCeeEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF--ELAGRPMKVG  189 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~--~i~g~~l~V~  189 (370)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++++      +|||||+|.+.++|.+|+..|++.  .+.|++|+|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~   86 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            34579999999999999999999999999999998753      799999999999999999988764  5899999999


Q ss_pred             EeecCCCC
Q psy2983         190 TVTDRNES  197 (370)
Q Consensus       190 ~~~~~~~~  197 (370)
                      ++..+...
T Consensus        87 ~a~~~~~~   94 (104)
T 1wex_A           87 YSTSKRIT   94 (104)
T ss_dssp             ECSSSSCC
T ss_pred             EccCcccc
Confidence            99876554

>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=99.64  E-value=1.9e-16  Score=127.96  Aligned_cols=83  Identities=17%  Similarity=0.249  Sum_probs=75.1

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCee--EEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEE
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVR--DVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPII   88 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~--~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~   88 (370)
                      +.....++|||+|||+++|+++|+++|++| .|.  +|.|++|+. |+++|||||+|.+.++|.+|+++++..|.|+.|.
T Consensus        37 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~  114 (126)
T 2hgm_A           37 ADSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGKHKERIGHRYIE  114 (126)
T ss_dssp             TCSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHCCCEECCEEEE
Confidence            445678999999999999999999999999 566  899999987 9999999999999999999999889999999999


Q ss_pred             Eeccccc
Q psy2983          89 VQPTQAE   95 (370)
Q Consensus        89 v~~~~~~   95 (370)
                      |.++...
T Consensus       115 V~~a~~~  121 (126)
T 2hgm_A          115 VFKSSQE  121 (126)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            9877543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=2.3e-15  Score=117.19  Aligned_cols=84  Identities=29%  Similarity=0.507  Sum_probs=76.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||..+++++|+++|+.|+   .+.++.+..++.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDW   88 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            34568999999999999999999999874   677888888999999999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2983         191 VTDRNES  197 (370)
Q Consensus       191 ~~~~~~~  197 (370)
                      +.++...
T Consensus        89 a~~~~~~   95 (102)
T 2fc8_A           89 AKPKGEG   95 (102)
T ss_dssp             CCCCCSS
T ss_pred             ecCCCCC
Confidence            9887654

>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=99.64  E-value=5.3e-17  Score=127.82  Aligned_cols=85  Identities=19%  Similarity=0.159  Sum_probs=78.2

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCC---eeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCee
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGK---VRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIP   86 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~---v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~   86 (370)
                      .......++|||+|||.++|+++|+++|+.||.   |.+|.+++++. |+++|||||+|.+.++|.+|+++++..+.|+.
T Consensus         5 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~   83 (107)
T 2lmi_A            5 EEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALEKHRMYMGQRY   83 (107)
T ss_dssp             CCCCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHTTTTCCSSSSC
T ss_pred             cCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHHhCcceeCCeE
Confidence            344567899999999999999999999999998   89999999987 99999999999999999999999999999999


Q ss_pred             EEEeccccc
Q psy2983          87 IIVQPTQAE   95 (370)
Q Consensus        87 l~v~~~~~~   95 (370)
                      |.|.++...
T Consensus        84 i~V~~a~~~   92 (107)
T 2lmi_A           84 VEVYEINNE   92 (107)
T ss_dssp             CCCEECCHH
T ss_pred             EEEEECCHH
Confidence            999887653

>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=99.64  E-value=1.3e-15  Score=118.02  Aligned_cols=81  Identities=30%  Similarity=0.534  Sum_probs=74.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ..+.++|||+|||+.+++++|+++|++||.|..+.+.++      +|||||+|.+.++|.+|+..|||..+.|++|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   85 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEE
Confidence            345689999999999999999999999999999998754      78999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2983         191 VTDRNES  197 (370)
Q Consensus       191 ~~~~~~~  197 (370)
                      +.++...
T Consensus        86 a~~~~~~   92 (99)
T 2cpj_A           86 ACHSASL   92 (99)
T ss_dssp             SSCCSCC
T ss_pred             cCCCCCC
Confidence            8876553

>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=99.64  E-value=1.5e-16  Score=123.64  Aligned_cols=79  Identities=18%  Similarity=0.273  Sum_probs=70.2

Q ss_pred             ccCCCCeEEEcCCCC-CCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccC--CccCCeeE
Q psy2983          12 EERDARTIFCMQLSQ-RIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNG--QKLLGIPI   87 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~-~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g--~~i~g~~l   87 (370)
                      ...++++|||+|||. ++|+++|+++|++||.|.+|+++++      +|||||+|.+.++|..|++ +++  ..+.|++|
T Consensus        11 ~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   84 (102)
T 1x4d_A           11 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   84 (102)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEE
Confidence            345789999999999 9999999999999999999999864      5899999999999999996 765  45999999


Q ss_pred             EEecccccc
Q psy2983          88 IVQPTQAEK   96 (370)
Q Consensus        88 ~v~~~~~~~   96 (370)
                      +|.+++...
T Consensus        85 ~V~~a~~~~   93 (102)
T 1x4d_A           85 RVHLSQKYK   93 (102)
T ss_dssp             EEEEECCCT
T ss_pred             EEEECCCCC
Confidence            999987543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.64  E-value=1.2e-16  Score=119.10  Aligned_cols=72  Identities=21%  Similarity=0.258  Sum_probs=66.6

Q ss_pred             CCeEEEcCCCCCC------cHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCe-eE
Q psy2983          16 ARTIFCMQLSQRI------RTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGI-PI   87 (370)
Q Consensus        16 ~r~v~V~nLp~~~------te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~-~l   87 (370)
                      +++|||+|||..+      ++++|+++|++||+|.++.+.  +.+++++|||||+|.+.++|.+|++ ++|..+.|+ +|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            4799999999999      789999999999999999987  4578999999999999999999996 999999999 88


Q ss_pred             EE
Q psy2983          88 IV   89 (370)
Q Consensus        88 ~v   89 (370)
                      +|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            66

>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=99.64  E-value=1.3e-15  Score=129.64  Aligned_cols=126  Identities=25%  Similarity=0.469  Sum_probs=106.5

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCC----C-------ceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeC
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPF----G-------KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELA  182 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~----G-------~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~  182 (370)
                      .++|||+|||+++++++|+++|++|    |       .|..+.+.      .++|||||+|.+.++|.+|+ .|||..+.
T Consensus         4 ~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~-~~~~~~~~   76 (172)
T 2g4b_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (172)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHG-GGTTCEET
T ss_pred             ccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHH-HhCCcEec
Confidence            4789999999999999999999999    6       66666554      44899999999999999999 79999999


Q ss_pred             CeeEEEEEeecCCC-------CcCCCCCCCCHHHHHHhcccCCceeeeeeeeccc----cCCC---CCChHHHHHHHh
Q psy2983         183 GRPMKVGTVTDRNE-------SVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLA----EGTG---LELPPAAASALN  246 (370)
Q Consensus       183 g~~l~V~~~~~~~~-------~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~~----~~~~---~~~~~~a~~a~~  246 (370)
                      |+.|+|.++.+...       .+++++..+++++++..|..+|.+..+.++.+..    +|++   |..+.+|..|+.
T Consensus        77 g~~i~v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~  154 (172)
T 2g4b_A           77 GQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA  154 (172)
T ss_dssp             TEECEEECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHH
T ss_pred             CceeeecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHH
Confidence            99999999865432       3678999999999999999999999999887632    3444   567777777766

>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=99.64  E-value=4e-16  Score=124.49  Aligned_cols=81  Identities=20%  Similarity=0.270  Sum_probs=72.0

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-cc--CCccCCeeE
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LN--GQKLLGIPI   87 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~--g~~i~g~~l   87 (370)
                      ....++++|||+|||.++|+++|+++|++||.|.+|.++++      ||||||+|.+.++|.+|++ ++  +..+.|++|
T Consensus        26 ~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l   99 (119)
T 2ad9_A           26 SAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPI   99 (119)
T ss_dssp             SCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEE
Confidence            34567899999999999999999999999999999999875      7999999999999999996 65  578999999


Q ss_pred             EEeccccccc
Q psy2983          88 IVQPTQAEKN   97 (370)
Q Consensus        88 ~v~~~~~~~~   97 (370)
                      +|.++.....
T Consensus       100 ~V~~a~~k~~  109 (119)
T 2ad9_A          100 YIQFSNHKEL  109 (119)
T ss_dssp             EEEECSSSSC
T ss_pred             EEEEccCCCC
Confidence            9999875543

>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=99.64  E-value=8.6e-16  Score=122.58  Aligned_cols=81  Identities=20%  Similarity=0.313  Sum_probs=72.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCC--ceeCCeeEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNG--FELAGRPMKVG  189 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g--~~i~g~~l~V~  189 (370)
                      .+.++|||+|||+++++++|+++|++||.|.++.++++      +|||||+|.+.++|.+|++.|++  ..+.|++|+|.
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~  102 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ  102 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEE
Confidence            34578999999999999999999999999999999865      79999999999999999998874  68999999999


Q ss_pred             EeecCCCCc
Q psy2983         190 TVTDRNESV  198 (370)
Q Consensus       190 ~~~~~~~~~  198 (370)
                      ++.++....
T Consensus       103 ~a~~k~~~~  111 (119)
T 2ad9_A          103 FSNHKELKT  111 (119)
T ss_dssp             ECSSSSCCC
T ss_pred             EccCCCCCc
Confidence            997765543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=2.4e-15  Score=114.81  Aligned_cols=80  Identities=28%  Similarity=0.464  Sum_probs=72.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||..+++++|+++|++||.|..+.+.        ++||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   78 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--------SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            3456899999999999999999999999999999987        44999999999999999999999999999999999


Q ss_pred             eecCCCCc
Q psy2983         191 VTDRNESV  198 (370)
Q Consensus       191 ~~~~~~~~  198 (370)
                      +.++....
T Consensus        79 a~~~~~~~   86 (92)
T 2dgt_A           79 STSRLRTA   86 (92)
T ss_dssp             SSCCCSCC
T ss_pred             ccCCCCCC
Confidence            98765543

>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=99.63  E-value=6.5e-16  Score=122.88  Aligned_cols=82  Identities=17%  Similarity=0.430  Sum_probs=74.7

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCcc-------
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL-------   82 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i-------   82 (370)
                      +...+.++|||+|||..+++++|+++|+.||.|.++.+++++ ++.++|||||+|.+.++|.+|++ |+|..+       
T Consensus        20 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~   98 (114)
T 1x5o_A           20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVS   98 (114)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCcccc
Confidence            345677999999999999999999999999999999999998 89999999999999999999996 999999       


Q ss_pred             -CCeeEEEeccc
Q psy2983          83 -LGIPIIVQPTQ   93 (370)
Q Consensus        83 -~g~~l~v~~~~   93 (370)
                       .+++|.|.++.
T Consensus        99 ~~~~~l~v~~a~  110 (114)
T 1x5o_A           99 APTEPLLCKFSG  110 (114)
T ss_dssp             CCSSCBEEEECC
T ss_pred             CCCCceeEEccC
Confidence             56778887765

>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=99.63  E-value=2.5e-16  Score=124.83  Aligned_cols=87  Identities=20%  Similarity=0.271  Sum_probs=77.7

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHH---HHhhcCCCeeEEEEeeeCCCC---CeecEEEEEecCCCChHHHhh-ccCCcc
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLE---EFFSSVGKVRDVRLITCNKTR---RFKGIAYIEFKDPESVPLAMG-LNGQKL   82 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~---~~f~~~G~v~~v~i~~d~~~~---~~kg~afVeF~~~e~A~~Al~-l~g~~i   82 (370)
                      .......++|||+|||..+++++|+   ++|++||+|.++.++++..++   +++|||||+|.+.++|.+|++ |+|..+
T Consensus         9 ~~r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~   88 (111)
T 2cpi_A            9 SVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVV   88 (111)
T ss_dssp             CCCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             cccccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEE
Confidence            3445667899999999999999999   999999999999999887654   456999999999999999996 899999


Q ss_pred             CCeeEEEecccccc
Q psy2983          83 LGIPIIVQPTQAEK   96 (370)
Q Consensus        83 ~g~~l~v~~~~~~~   96 (370)
                      .|++|.|.++....
T Consensus        89 ~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           89 DGRTLKASLGTTKY  102 (111)
T ss_dssp             TTEEEEEESCCCCS
T ss_pred             CCEEEEEEeccccc
Confidence            99999999987654

>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=99.63  E-value=3.6e-16  Score=126.41  Aligned_cols=81  Identities=19%  Similarity=0.336  Sum_probs=74.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ....+|||+|||+.+++++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|.+|+. |||..+.|+.|.|.++
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            455899999999999999999999999999986666666799999999999999999999999 9999999999999997


Q ss_pred             ec
Q psy2983         192 TD  193 (370)
Q Consensus       192 ~~  193 (370)
                      ..
T Consensus       102 ~~  103 (124)
T 1wel_A          102 TK  103 (124)
T ss_dssp             CH
T ss_pred             CH
Confidence            65

>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=99.63  E-value=4e-16  Score=127.94  Aligned_cols=80  Identities=16%  Similarity=0.267  Sum_probs=74.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCc---eeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGK---IDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV  188 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~---i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V  188 (370)
                      ....+|||+|||+++|+++|+++|++||.   |..|+++.++. |+++|||||+|.+.++|.+|++ ||+..+.|+.|+|
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V  119 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEV  119 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEE
Confidence            44579999999999999999999999999   89999999985 9999999999999999999999 9999999999999


Q ss_pred             EEeec
Q psy2983         189 GTVTD  193 (370)
Q Consensus       189 ~~~~~  193 (370)
                      .++.+
T Consensus       120 ~~a~~  124 (136)
T 2hgl_A          120 FKSHR  124 (136)
T ss_dssp             EECCH
T ss_pred             EECCh
Confidence            88643

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=1.8e-15  Score=115.05  Aligned_cols=78  Identities=28%  Similarity=0.602  Sum_probs=72.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      .+.++|||+|||..+++++|+++|++||.|..+.+.        +|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   77 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS   77 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECS
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEEC
Confidence            456899999999999999999999999999999987        679999999999999999999999999999999998


Q ss_pred             ecCCCC
Q psy2983         192 TDRNES  197 (370)
Q Consensus       192 ~~~~~~  197 (370)
                      .++...
T Consensus        78 ~~~~~~   83 (90)
T 2dnq_A           78 KNKSKA   83 (90)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            776554

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=7.2e-16  Score=120.03  Aligned_cols=90  Identities=19%  Similarity=0.303  Sum_probs=79.6

Q ss_pred             CCCCCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccC
Q psy2983           5 YSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLL   83 (370)
Q Consensus         5 ~~~~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~   83 (370)
                      .+........+.++|||+|||..+++++|+++|+.|+   .+.++.++.+++++|||||+|.+.++|.+|++ |+|..|.
T Consensus         4 ~s~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~   80 (102)
T 2fc8_A            4 GSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEID   80 (102)
T ss_dssp             CCCTTSSSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCCCCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeEC
Confidence            3445556677889999999999999999999999873   67888898899999999999999999999996 9999999


Q ss_pred             CeeEEEeccccccc
Q psy2983          84 GIPIIVQPTQAEKN   97 (370)
Q Consensus        84 g~~l~v~~~~~~~~   97 (370)
                      |+.|.|.++.....
T Consensus        81 g~~l~V~~a~~~~~   94 (102)
T 2fc8_A           81 GNKVTLDWAKPKGE   94 (102)
T ss_dssp             TEECEEEECCCCCS
T ss_pred             CeEEEEEEecCCCC
Confidence            99999999876543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.63  E-value=1.7e-16  Score=118.31  Aligned_cols=72  Identities=25%  Similarity=0.451  Sum_probs=67.5

Q ss_pred             ceEEEecCCCCC------CHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCe-eEE
Q psy2983         115 MRLYIGSLHFNI------TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGR-PMK  187 (370)
Q Consensus       115 ~~l~V~nlp~~~------t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~-~l~  187 (370)
                      ++|||+|||..+      ++++|+++|++||.|..+.+.+  .+|.++|||||+|.+.++|.+|+..|||..+.|+ +|+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~--~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC--BTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC--CCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            589999999999      7799999999999999999873  5899999999999999999999999999999999 887


Q ss_pred             E
Q psy2983         188 V  188 (370)
Q Consensus       188 V  188 (370)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=4.8e-16  Score=120.84  Aligned_cols=83  Identities=22%  Similarity=0.286  Sum_probs=74.2

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPII   88 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~   88 (370)
                      .+...+.++|||+|||..+++++|+++|++||.|   .++++ .+++++|||||+|.+.++|.+|++ +++..+.|+.|.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   84 (101)
T 2fc9_A            9 STWSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIR   84 (101)
T ss_dssp             CCCSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEE
Confidence            3456788999999999999999999999999987   55666 678899999999999999999997 999999999999


Q ss_pred             Eecccccc
Q psy2983          89 VQPTQAEK   96 (370)
Q Consensus        89 v~~~~~~~   96 (370)
                      |.++....
T Consensus        85 v~~a~~~~   92 (101)
T 2fc9_A           85 LELQGPRG   92 (101)
T ss_dssp             EEECSSCC
T ss_pred             EEEcCCCC
Confidence            99987653

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.63  E-value=1.2e-16  Score=124.38  Aligned_cols=83  Identities=29%  Similarity=0.502  Sum_probs=76.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ...++|||+|||+.+++++|+++|++||.|.. .++.+..+|.++|||||+|.+.++|.+|++ |||..+.|+.|+|.++
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            45689999999999999999999999999988 666776789999999999999999999999 9999999999999998


Q ss_pred             ecCCC
Q psy2983         192 TDRNE  196 (370)
Q Consensus       192 ~~~~~  196 (370)
                      .++..
T Consensus        93 ~~~~~   97 (101)
T 1fj7_A           93 KGRDG   97 (101)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            77654

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.63  E-value=7.2e-16  Score=124.93  Aligned_cols=82  Identities=16%  Similarity=0.321  Sum_probs=73.6

Q ss_pred             CCCceEEEecCCCCCCHHHHH----hcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMK  187 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~----~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~  187 (370)
                      .+.++|||+|||+.+++++|+    ++|++||.|..|.+.   .+|.++|||||+|.+.++|..|+..|||..+.|++|+
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~---~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD---LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC---CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec---cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            345789999999999999876    699999999998774   3688999999999999999999999999999999999


Q ss_pred             EEEeecCCC
Q psy2983         188 VGTVTDRNE  196 (370)
Q Consensus       188 V~~~~~~~~  196 (370)
                      |.++..+..
T Consensus       104 V~~a~~~~~  112 (127)
T 2a3j_A          104 ITFSETPQS  112 (127)
T ss_dssp             EEECCCCCH
T ss_pred             EEEccCcch
Confidence            999877544

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.63  E-value=6.4e-16  Score=122.16  Aligned_cols=79  Identities=18%  Similarity=0.175  Sum_probs=71.3

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCC-ceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFG-KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G-~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....+|||+|||+++++++|+++|++|| .|..+.+..    +.++|||||+|.+.++|.+|++.|||..+.|+.|+|.+
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~  101 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVER  101 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3457999999999999999999999999 899998853    35799999999999999999999999999999999999


Q ss_pred             eecC
Q psy2983         191 VTDR  194 (370)
Q Consensus       191 ~~~~  194 (370)
                      +..+
T Consensus       102 a~~~  105 (111)
T 2jvr_A          102 DDNP  105 (111)
T ss_dssp             SCC-
T ss_pred             CCCC
Confidence            7653

>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=99.63  E-value=5.6e-16  Score=116.43  Aligned_cols=79  Identities=22%  Similarity=0.340  Sum_probs=71.7

Q ss_pred             CCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-c-cCCccCCee
Q psy2983           9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-L-NGQKLLGIP   86 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l-~g~~i~g~~   86 (370)
                      .++.....++|||+|||..+++++|+++|++||.|.++.++++      +|||||+|.+.++|.+|++ + +|..+.|++
T Consensus         5 ~~~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~   78 (85)
T 2ytc_A            5 SSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRR   78 (85)
T ss_dssp             CCCSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEE
T ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCE
Confidence            3455678899999999999999999999999999999999863      7999999999999999997 7 999999999


Q ss_pred             EEEeccc
Q psy2983          87 IIVQPTQ   93 (370)
Q Consensus        87 l~v~~~~   93 (370)
                      |.|.+++
T Consensus        79 l~v~~ak   85 (85)
T 2ytc_A           79 LNVKWGR   85 (85)
T ss_dssp             CCEEECC
T ss_pred             EEEEecC
Confidence            9998763

>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=99.62  E-value=1.9e-16  Score=126.09  Aligned_cols=86  Identities=24%  Similarity=0.383  Sum_probs=73.0

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      ...++++|||+|||..+|+++|+++|+.||.|..+.+..+..+++++|||||+|.+.++|.+|++ |+|..+.|++|.|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~  100 (115)
T 2cpx_A           21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE  100 (115)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34567999999999999999999999999998443332222368889999999999999999996 99999999999999


Q ss_pred             ccccccc
Q psy2983          91 PTQAEKN   97 (370)
Q Consensus        91 ~~~~~~~   97 (370)
                      ++.....
T Consensus       101 ~a~~~~~  107 (115)
T 2cpx_A          101 FGKNKKQ  107 (115)
T ss_dssp             ECCCCSC
T ss_pred             EccCCCC
Confidence            9876543

>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=99.62  E-value=2.4e-15  Score=115.99  Aligned_cols=79  Identities=27%  Similarity=0.474  Sum_probs=72.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeC--CeeEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELA--GRPMKVG  189 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~--g~~l~V~  189 (370)
                      .+.++|||+|||..+++++|+++|++||.|..+.+..+      +|||||+|.+.++|.+|+..|||..+.  |+.|+|.
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            44579999999999999999999999999999988743      789999999999999999999999999  9999999


Q ss_pred             EeecCCC
Q psy2983         190 TVTDRNE  196 (370)
Q Consensus       190 ~~~~~~~  196 (370)
                      ++.++..
T Consensus        89 ~a~~~~~   95 (97)
T 1why_A           89 FAKSGPS   95 (97)
T ss_dssp             ECCCCCC
T ss_pred             ECCCCCC
Confidence            9887643

>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=99.62  E-value=1.1e-15  Score=118.43  Aligned_cols=83  Identities=18%  Similarity=0.248  Sum_probs=74.0

Q ss_pred             CCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCee
Q psy2983           8 DLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIP   86 (370)
Q Consensus         8 ~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~   86 (370)
                      ..+....+.++|||+|||..+++++|+++|++||+|.++.+.++      +|||||+|.+.++|.+|++ ++|..+.|++
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~   80 (99)
T 2cpj_A            7 GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQ   80 (99)
T ss_dssp             CCSCCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBC
T ss_pred             CCCCcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCce
Confidence            33445578899999999999999999999999999999998753      7899999999999999995 9999999999


Q ss_pred             EEEecccccc
Q psy2983          87 IIVQPTQAEK   96 (370)
Q Consensus        87 l~v~~~~~~~   96 (370)
                      |.|.++....
T Consensus        81 l~v~~a~~~~   90 (99)
T 2cpj_A           81 LRVRFACHSA   90 (99)
T ss_dssp             CEEEESSCCS
T ss_pred             EEEEEcCCCC
Confidence            9999987543

>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=99.62  E-value=1.3e-16  Score=116.97  Aligned_cols=75  Identities=25%  Similarity=0.521  Sum_probs=71.4

Q ss_pred             eEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       116 ~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      +|||+|||+.+++++|+++|++||.|..+.+..++.+|.++|||||+|.+.++|.+|+. +++..+.|+.|+|+++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            58999999999999999999999999999999998899999999999999999999999 5999999999999864

>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=99.62  E-value=1.9e-15  Score=113.52  Aligned_cols=75  Identities=32%  Similarity=0.431  Sum_probs=69.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHh-CCceeCCeeEEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL-NGFELAGRPMKVGT  190 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l-~g~~i~g~~l~V~~  190 (370)
                      ...++|||+|||..+++++|+++|++||.|..+.+.++      +|||||+|.+.++|.+|+..| +|..+.|++|+|.+
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~   83 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKW   83 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEE
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEe
Confidence            45578999999999999999999999999999999864      799999999999999999998 99999999999998


Q ss_pred             ee
Q psy2983         191 VT  192 (370)
Q Consensus       191 ~~  192 (370)
                      ++
T Consensus        84 ak   85 (85)
T 2ytc_A           84 GR   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            63

>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=99.62  E-value=3e-16  Score=123.46  Aligned_cols=81  Identities=19%  Similarity=0.310  Sum_probs=75.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCc---eeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGK---IDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMK  187 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~---i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~  187 (370)
                      .....+|||+|||+++++++|+++|+.||.   |..++++.++. |+++|||||+|.+.++|.+|+. +|+..++|+.|+
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            345689999999999999999999999998   89999999975 9999999999999999999999 999999999999


Q ss_pred             EEEeec
Q psy2983         188 VGTVTD  193 (370)
Q Consensus       188 V~~~~~  193 (370)
                      |.++.+
T Consensus        86 V~~a~~   91 (107)
T 2lmi_A           86 VYEINN   91 (107)
T ss_dssp             CEECCH
T ss_pred             EEECCH
Confidence            988654

>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=99.62  E-value=2e-15  Score=119.13  Aligned_cols=81  Identities=22%  Similarity=0.294  Sum_probs=71.8

Q ss_pred             CCCCceEEEecCCCC-CCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhC--CceeCCeeEE
Q psy2983         111 TGGPMRLYIGSLHFN-ITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN--GFELAGRPMK  187 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~-~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~--g~~i~g~~l~  187 (370)
                      ..+.++|||+|||++ +++++|+++|++||.|.++.+++      ++|||||+|.+.++|.+|+..|+  +..+.|++|+
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            345689999999998 99999999999999999999974      37999999999999999999886  4569999999


Q ss_pred             EEEeecCCCC
Q psy2983         188 VGTVTDRNES  197 (370)
Q Consensus       188 V~~~~~~~~~  197 (370)
                      |.++..+...
T Consensus        96 V~~a~~~~~~  105 (112)
T 1x4f_A           96 VDLSEKYKKL  105 (112)
T ss_dssp             EEEECSCSSS
T ss_pred             EEECcccccc
Confidence            9999776554

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.42  E-value=3.2e-17  Score=131.03  Aligned_cols=86  Identities=27%  Similarity=0.534  Sum_probs=79.9

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeE--------EEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCcc
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRD--------VRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL   82 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~--------v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i   82 (370)
                      ...+.++|||+|||..+++++|+++|++||.|..        +.+++++.+++++|||||+|.+.++|.+|++ |+|..+
T Consensus         3 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   82 (116)
T 2lcw_A            3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   82 (116)
Confidence            4567899999999999999999999999999998        9999998889999999999999999999997 999999


Q ss_pred             CCeeEEEeccccccc
Q psy2983          83 LGIPIIVQPTQAEKN   97 (370)
Q Consensus        83 ~g~~l~v~~~~~~~~   97 (370)
                      .|++|.|.++.....
T Consensus        83 ~g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           83 SGNPIKVSFATRRAD   97 (116)
Confidence            999999999876543

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=1.2e-15  Score=120.26  Aligned_cols=77  Identities=25%  Similarity=0.477  Sum_probs=71.7

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      ..+|||+|||+++++++|+++|++| .|..|+++.++ .|+++|||||+|.+.++|.+|+ .+|+..++||.|.|..+.+
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-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT-TCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC-CCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            4689999999999999999999999 89999999997 5999999999999999999999 5999999999999987643

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.62  E-value=3.7e-16  Score=116.51  Aligned_cols=74  Identities=18%  Similarity=0.186  Sum_probs=68.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      ..+.-|||+||++.+|+++|+++|.+||+|.++.+..      ++|||||+|.+.++|.+|++ ||+..+.|++|+|..+
T Consensus         5 ~~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            5 WGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            3567899999999999999999999999999999864      58999999999999999996 9999999999999887


Q ss_pred             c
Q psy2983          93 Q   93 (370)
Q Consensus        93 ~   93 (370)
                      .
T Consensus        79 ~   79 (89)
T 2wbr_A           79 S   79 (89)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=1.2e-15  Score=116.06  Aligned_cols=77  Identities=21%  Similarity=0.396  Sum_probs=70.9

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      ..+.++|||+|||.++++++|+++|++||.|.++.+.        +|||||+|.+.++|.+|++ +++..+.|++|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEE
Confidence            4578999999999999999999999999999999986        5899999999999999995 999999999999999


Q ss_pred             cccccc
Q psy2983          92 TQAEKN   97 (370)
Q Consensus        92 ~~~~~~   97 (370)
                      +.....
T Consensus        77 a~~~~~   82 (90)
T 2dnq_A           77 SKNKSK   82 (90)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            876543

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=2.6e-16  Score=126.77  Aligned_cols=80  Identities=16%  Similarity=0.131  Sum_probs=73.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCe----eEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEE
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKV----RDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIV   89 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v----~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v   89 (370)
                      .+.++|||+|||+++|+++|+++|++||.|    .+|.|+++ .+++++|||||+|.+.++|.+|++.++..+.|+.|.|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~V   99 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIEL   99 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEE
Confidence            567899999999999999999999999975    68999998 4899999999999999999999988999999999999


Q ss_pred             ecccc
Q psy2983          90 QPTQA   94 (370)
Q Consensus        90 ~~~~~   94 (370)
                      ..+..
T Consensus       100 ~~a~~  104 (123)
T 2dha_A          100 FRSTA  104 (123)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            87654

>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=99.62  E-value=6.3e-16  Score=119.17  Aligned_cols=82  Identities=26%  Similarity=0.504  Sum_probs=74.9

Q ss_pred             CCCceEEEecCCCCCCHHHHH----hcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMK  187 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~----~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~  187 (370)
                      .+.++|||+|||..+++++|+    ++|++||.|..+.+..   +|.++|||||+|.+.++|.+|+..|||..+.|+.|+
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            345799999999999999999    9999999999998862   678899999999999999999999999999999999


Q ss_pred             EEEeecCCC
Q psy2983         188 VGTVTDRNE  196 (370)
Q Consensus       188 V~~~~~~~~  196 (370)
                      |.++.++..
T Consensus        83 v~~a~~~~~   91 (97)
T 1nu4_A           83 IQYAKTDSD   91 (97)
T ss_dssp             EEECSSCCT
T ss_pred             EEEccCCCc
Confidence            999877543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.61  E-value=1.1e-15  Score=117.58  Aligned_cols=80  Identities=34%  Similarity=0.515  Sum_probs=73.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ...++|||+|||+.+++++|+++|++||.|..+     ..+|.++|||||+|.+.++|.+|+..|+|..+.|+.|+|.++
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   88 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            456899999999999999999999999988776     247899999999999999999999999999999999999998


Q ss_pred             ecCCC
Q psy2983         192 TDRNE  196 (370)
Q Consensus       192 ~~~~~  196 (370)
                      .++..
T Consensus        89 ~~~~~   93 (96)
T 1fjc_A           89 GEKGG   93 (96)
T ss_dssp             SSSCC
T ss_pred             CCCCC
Confidence            77654

>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=1.8e-15  Score=119.18  Aligned_cols=79  Identities=28%  Similarity=0.595  Sum_probs=71.9

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEE
Q psy2983         110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG  189 (370)
Q Consensus       110 ~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~  189 (370)
                      .....++|||+|||..+++++|+++|++||.|..+.+.        +|||||+|.+.++|.+|+..|||..+.|+.|+|.
T Consensus        27 ~~~~~~~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           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34556899999999999999999999999999999987        7899999999999999999999999999999999


Q ss_pred             EeecCCC
Q psy2983         190 TVTDRNE  196 (370)
Q Consensus       190 ~~~~~~~  196 (370)
                      ++.++..
T Consensus        99 ~a~~~~~  105 (108)
T 2jvo_A           99 YSKLPAK  105 (108)
T ss_dssp             SCSCCC-
T ss_pred             EecCCCC
Confidence            9876543

>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=99.61  E-value=1.2e-15  Score=136.47  Aligned_cols=81  Identities=20%  Similarity=0.301  Sum_probs=75.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCC--CeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVG--KVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G--~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      ..++|||+|||..+|+++|+++|+.||  .|.+|+|++|+.+++++|||||+|.+.++|.+||+ |++..|.|+.|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            567899999999999999999999999  99999999999999999999999999999999997 999999999999998


Q ss_pred             cccc
Q psy2983          92 TQAE   95 (370)
Q Consensus        92 ~~~~   95 (370)
                      +...
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            7643

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=1.3e-15  Score=117.48  Aligned_cols=79  Identities=16%  Similarity=0.331  Sum_probs=71.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ...++|||+|||+.+++++|+++|++||.|. +.++.    +.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            4467999999999999999999999999996 66663    467999999999999999999999999999999999998


Q ss_pred             ecCC
Q psy2983         192 TDRN  195 (370)
Q Consensus       192 ~~~~  195 (370)
                      .++.
T Consensus        92 ~~~~   95 (97)
T 2e5j_A           92 RQQR   95 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7754

>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=99.61  E-value=6.4e-16  Score=123.05  Aligned_cols=86  Identities=26%  Similarity=0.374  Sum_probs=74.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      .+.++|||+|||..+++++|+++|++||.|..+.+..+..+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
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            45689999999999999999999999999854333222238899999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy2983         192 TDRNES  197 (370)
Q Consensus       192 ~~~~~~  197 (370)
                      .++...
T Consensus       103 ~~~~~~  108 (115)
T 2cpx_A          103 KNKKQR  108 (115)
T ss_dssp             CCCSCC
T ss_pred             cCCCCC
Confidence            876554

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.61  E-value=3.1e-15  Score=117.81  Aligned_cols=79  Identities=18%  Similarity=0.215  Sum_probs=73.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCC-----eeE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG-----RPM  186 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g-----~~l  186 (370)
                      ....+|||+|||+.+++++|+++|++||.|..+.++.+       |||||+|.+.++|.+|++.|||..+.|     +.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            44689999999999999999999999999999999865       899999999999999999999999999     999


Q ss_pred             EEEEeecCCCC
Q psy2983         187 KVGTVTDRNES  197 (370)
Q Consensus       187 ~V~~~~~~~~~  197 (370)
                      +|.++.++...
T Consensus        86 ~V~~a~~~~~~   96 (108)
T 1x4c_A           86 RVKVDGPRSPS   96 (108)
T ss_dssp             EEEESSCCSCC
T ss_pred             EEEeCCCCCCC
Confidence            99998876554

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=9.5e-16  Score=118.32  Aligned_cols=83  Identities=19%  Similarity=0.256  Sum_probs=72.7

Q ss_pred             CCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCee
Q psy2983           8 DLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIP   86 (370)
Q Consensus         8 ~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~   86 (370)
                      .........++|||+|||..+++++|+++|+.||.|. +.++.+    +++|||||+|.+.++|.+|++ |+|..+.|+.
T Consensus        11 ~~~~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   85 (97)
T 2e5j_A           11 PPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDT   85 (97)
T ss_dssp             CCCSSSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSC
T ss_pred             CCCCCCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            3344566789999999999999999999999999997 666654    568999999999999999995 9999999999


Q ss_pred             EEEeccccc
Q psy2983          87 IIVQPTQAE   95 (370)
Q Consensus        87 l~v~~~~~~   95 (370)
                      |.|.++...
T Consensus        86 l~V~~a~~~   94 (97)
T 2e5j_A           86 LRVALARQQ   94 (97)
T ss_dssp             CEEEECCCC
T ss_pred             EEEEEcCCC
Confidence            999988654

>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=99.61  E-value=2.7e-15  Score=118.31  Aligned_cols=81  Identities=26%  Similarity=0.514  Sum_probs=74.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ...++|||+|||..+++++|+++|++||.|..+.+..+      +|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   96 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   96 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEec
Confidence            34579999999999999999999999999999999865      789999999999999999999999999999999999


Q ss_pred             ecCCCCc
Q psy2983         192 TDRNESV  198 (370)
Q Consensus       192 ~~~~~~~  198 (370)
                      .++....
T Consensus        97 ~~~~~~~  103 (109)
T 1x4g_A           97 KESPDMT  103 (109)
T ss_dssp             CCCCSSC
T ss_pred             CCCCCCC
Confidence            8766543

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.61  E-value=2.2e-15  Score=118.67  Aligned_cols=79  Identities=20%  Similarity=0.275  Sum_probs=72.6

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCC-----
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLG-----   84 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g-----   84 (370)
                      +..+..++|||+|||.++++++|+++|++||.|..+.++.+       |||||+|.+.++|.+|++ |+|..|.|     
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~   82 (108)
T 1x4c_A           10 PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGET   82 (108)
T ss_dssp             CCCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcc
Confidence            44567899999999999999999999999999999999875       899999999999999997 99999999     


Q ss_pred             eeEEEecccccc
Q psy2983          85 IPIIVQPTQAEK   96 (370)
Q Consensus        85 ~~l~v~~~~~~~   96 (370)
                      +.|.|.++....
T Consensus        83 ~~i~V~~a~~~~   94 (108)
T 1x4c_A           83 AYIRVKVDGPRS   94 (108)
T ss_dssp             EEEEEEESSCCS
T ss_pred             eEEEEEeCCCCC
Confidence            999999987644

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.61  E-value=1.6e-15  Score=117.80  Aligned_cols=76  Identities=28%  Similarity=0.433  Sum_probs=70.5

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ..++|||+|||..+++++|+++|++||.|..+++.      .++|||||+|.+.++|.+|+..|||..+.|+.|+|.++.
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            35799999999999999999999999999999987      348999999999999999999999999999999999876


Q ss_pred             cC
Q psy2983         193 DR  194 (370)
Q Consensus       193 ~~  194 (370)
                      ++
T Consensus       100 ~~  101 (101)
T 2la4_A          100 ER  101 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.61  E-value=1.3e-15  Score=121.12  Aligned_cols=77  Identities=19%  Similarity=0.285  Sum_probs=70.7

Q ss_pred             ceEEEecC----CCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECC----HHH----HHHHHH--HhCCce
Q psy2983         115 MRLYIGSL----HFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS----ADD----AKKAQE--QLNGFE  180 (370)
Q Consensus       115 ~~l~V~nl----p~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~----~~~----a~~A~~--~l~g~~  180 (370)
                      .+|||+||    |+.+++++|+++|++||+|.++.++.|+.||.++|||||+|.+    +++    |.+|+.  .|+|..
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    9999999999999999999999999999999999999999996    433    888988  789999


Q ss_pred             eCCeeEEEEEe
Q psy2983         181 LAGRPMKVGTV  191 (370)
Q Consensus       181 i~g~~l~V~~~  191 (370)
                      |.|++|+|...
T Consensus        83 I~Gr~irV~ln   93 (136)
T 2j8a_A           83 IMGFKFEVILN   93 (136)
T ss_dssp             ETTEEEEEEEC
T ss_pred             ecCcEEEEEEC
Confidence            99999999874

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.60  E-value=4e-16  Score=120.12  Aligned_cols=82  Identities=30%  Similarity=0.417  Sum_probs=73.1

Q ss_pred             CCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeE
Q psy2983           9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPI   87 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l   87 (370)
                      .+...++.++|||+|||..+++++|+++|+.||.|..+     ..++.++|||||+|.+.++|.+|++ ++|..+.|++|
T Consensus         9 ~~~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   83 (96)
T 1fjc_A            9 TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV   83 (96)
T ss_dssp             TTSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEE
T ss_pred             ccccCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            34456678999999999999999999999999988766     3458899999999999999999997 99999999999


Q ss_pred             EEeccccc
Q psy2983          88 IVQPTQAE   95 (370)
Q Consensus        88 ~v~~~~~~   95 (370)
                      .|.++...
T Consensus        84 ~v~~a~~~   91 (96)
T 1fjc_A           84 SLYYTGEK   91 (96)
T ss_dssp             EEEECSSS
T ss_pred             EEEEcCCC
Confidence            99998654

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=4.1e-15  Score=113.06  Aligned_cols=78  Identities=29%  Similarity=0.541  Sum_probs=71.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ...++|||+|||+.+++++|+++|++||.|..+.+.        +|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   78 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS   78 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            456789999999999999999999999999999987        449999999999999999999999999999999998


Q ss_pred             ecCCCC
Q psy2983         192 TDRNES  197 (370)
Q Consensus       192 ~~~~~~  197 (370)
                      .++...
T Consensus        79 ~~~~~~   84 (90)
T 2dnp_A           79 TKGQKK   84 (90)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            776543

>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=99.60  E-value=3.1e-16  Score=120.94  Aligned_cols=83  Identities=25%  Similarity=0.520  Sum_probs=73.5

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHH----HHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCe
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLE----EFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGI   85 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~----~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~   85 (370)
                      +...++++|||+|||.++++++|+    ++|++||.|.++.+.+   ++.++|||||+|.+.++|..|++ ++|..+.|+
T Consensus         3 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   79 (97)
T 1nu4_A            3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK   79 (97)
T ss_dssp             ---CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCc
Confidence            345688999999999999999999    9999999999998874   46788999999999999999996 999999999


Q ss_pred             eEEEecccccc
Q psy2983          86 PIIVQPTQAEK   96 (370)
Q Consensus        86 ~l~v~~~~~~~   96 (370)
                      +|.|.++....
T Consensus        80 ~l~v~~a~~~~   90 (97)
T 1nu4_A           80 PMRIQYAKTDS   90 (97)
T ss_dssp             ECEEEECSSCC
T ss_pred             EEEEEEccCCC
Confidence            99999987643

>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=99.60  E-value=4.5e-15  Score=114.55  Aligned_cols=76  Identities=26%  Similarity=0.491  Sum_probs=70.3

Q ss_pred             CCCCceEEEecCCC-CCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEE
Q psy2983         111 TGGPMRLYIGSLHF-NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG  189 (370)
Q Consensus       111 ~~~~~~l~V~nlp~-~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~  189 (370)
                      ....++|||+|||. .+++++|+++|++||.|..+.+.        +|||||+|.+.++|.+|+..|||..+.|+.|+|.
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   90 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE   90 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34568999999998 99999999999999999999883        7899999999999999999999999999999999


Q ss_pred             EeecC
Q psy2983         190 TVTDR  194 (370)
Q Consensus       190 ~~~~~  194 (370)
                      ++..+
T Consensus        91 ~a~~~   95 (97)
T 2xnq_A           91 VSSSN   95 (97)
T ss_dssp             ECCCC
T ss_pred             ecCCC
Confidence            98664

>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=99.60  E-value=9.2e-16  Score=121.06  Aligned_cols=81  Identities=17%  Similarity=0.212  Sum_probs=71.3

Q ss_pred             CcccCCCCeEEEcCCCCC-CcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-cc--CCccCCe
Q psy2983          10 SPEERDARTIFCMQLSQR-IRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LN--GQKLLGI   85 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~-~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~--g~~i~g~   85 (370)
                      .....++++|||+|||.+ +++++|+++|++||.|.+|++++      ++|||||+|.+.++|..|++ ++  +..+.|+
T Consensus        19 ~~~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr   92 (112)
T 1x4f_A           19 DQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGR   92 (112)
T ss_dssp             CCSSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSS
T ss_pred             cccCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCE
Confidence            344678899999999998 99999999999999999999964      37999999999999999996 64  5679999


Q ss_pred             eEEEecccccc
Q psy2983          86 PIIVQPTQAEK   96 (370)
Q Consensus        86 ~l~v~~~~~~~   96 (370)
                      +|+|.+++...
T Consensus        93 ~l~V~~a~~~~  103 (112)
T 1x4f_A           93 CVKVDLSEKYK  103 (112)
T ss_dssp             CCEEEEECSCS
T ss_pred             EEEEEECcccc
Confidence            99999987544

>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=99.60  E-value=2.6e-16  Score=129.48  Aligned_cols=124  Identities=13%  Similarity=0.137  Sum_probs=74.2

Q ss_pred             cEEEEEecCCCChHHHhhccCCccCCeeEEEecccccccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCC
Q psy2983          59 GIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPF  138 (370)
Q Consensus        59 g~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~  138 (370)
                      |+||.+|..++.+..++.--.....|...--....           ...........+|||+|||+++++++|+++|++|
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~gg~~~g~~~g~-----------~~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~   70 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSGD-----------SEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPL   70 (139)
T ss_dssp             ------------------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSC
T ss_pred             CcccccccCccccchhcccchhccCCCCCCCCCCC-----------cccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhc
Confidence            67888888888777666311111222211000000           0011123345789999999999999999999999


Q ss_pred             CceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecCCC
Q psy2983         139 GKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNE  196 (370)
Q Consensus       139 G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~~~  196 (370)
                      | +..|.++.|+. |+++|||||+|.+.++|.+|+ .+|+..+.|+.|+|..+.....
T Consensus        71 G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~~  125 (139)
T 2hgn_A           71 N-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGA  125 (139)
T ss_dssp             C-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSCC
T ss_pred             C-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCCC
Confidence            9 67999999974 999999999999999999999 6899999999999988766543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.60  E-value=1e-15  Score=119.21  Aligned_cols=81  Identities=27%  Similarity=0.657  Sum_probs=75.5

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      .+++|||+|||+.+++++|+++|++||.|..+.++.++ +|.++|||||+|.+.++|.+|+.  ++..+.|+.|.|.++.
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~   84 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECC
Confidence            45789999999999999999999999999999999998 99999999999999999999999  9999999999999987


Q ss_pred             cCCC
Q psy2983         193 DRNE  196 (370)
Q Consensus       193 ~~~~  196 (370)
                      .+..
T Consensus        85 ~~~~   88 (102)
T 2xs2_A           85 RKQN   88 (102)
T ss_dssp             ECC-
T ss_pred             cCcc
Confidence            6543

>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=99.60  E-value=1.5e-15  Score=117.35  Aligned_cols=79  Identities=19%  Similarity=0.352  Sum_probs=69.4

Q ss_pred             CCCcccCCCCeEEEcCCCC-CCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCe
Q psy2983           8 DLSPEERDARTIFCMQLSQ-RIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGI   85 (370)
Q Consensus         8 ~~~~~~~~~r~v~V~nLp~-~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~   85 (370)
                      ......+++++|||+|||. ++++++|+++|+.||.|.++.+.        +|||||+|.+.++|.+|++ ++|..+.|+
T Consensus        14 ~~~~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   85 (97)
T 2xnq_A           14 LVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGK   85 (97)
T ss_dssp             -----CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTE
T ss_pred             cccCCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            3344567889999999998 99999999999999999999883        6899999999999999996 999999999


Q ss_pred             eEEEecccc
Q psy2983          86 PIIVQPTQA   94 (370)
Q Consensus        86 ~l~v~~~~~   94 (370)
                      .|.|.++..
T Consensus        86 ~l~V~~a~~   94 (97)
T 2xnq_A           86 KLILEVSSS   94 (97)
T ss_dssp             ECEEEECCC
T ss_pred             EEEEEecCC
Confidence            999998764

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=1.3e-14  Score=112.34  Aligned_cols=79  Identities=25%  Similarity=0.523  Sum_probs=71.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCC--CceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPF--GKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV  188 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~--G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V  188 (370)
                      ....++|||+|||+.+++++|+++|++|  |.|..+.+.        +|||||+|.+.++|.+|+..|||..+.|+.|+|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            3456899999999999999999999999  899988764        679999999999999999999999999999999


Q ss_pred             EEeecCCCC
Q psy2983         189 GTVTDRNES  197 (370)
Q Consensus       189 ~~~~~~~~~  197 (370)
                      .++.++...
T Consensus        84 ~~a~~~~~~   92 (99)
T 2cpd_A           84 TLAKPVDKD   92 (99)
T ss_dssp             ECCCCCCCC
T ss_pred             EECCCCCCC
Confidence            998876543

>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=99.60  E-value=1.3e-15  Score=117.56  Aligned_cols=78  Identities=15%  Similarity=0.266  Sum_probs=71.4

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccC--CeeEE
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLL--GIPII   88 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~--g~~l~   88 (370)
                      ...+.++|||+|||..+++++|+++|++||.|.++.+.++      +|||||+|.+.++|.+|++ ++|..+.  |++|.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~   86 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR   86 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEE
Confidence            4456799999999999999999999999999999998753      6899999999999999996 9999999  99999


Q ss_pred             Eeccccc
Q psy2983          89 VQPTQAE   95 (370)
Q Consensus        89 v~~~~~~   95 (370)
                      |.++...
T Consensus        87 V~~a~~~   93 (97)
T 1why_A           87 VDFAKSG   93 (97)
T ss_dssp             EEECCCC
T ss_pred             EEECCCC
Confidence            9998764

>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=99.60  E-value=1.1e-15  Score=136.62  Aligned_cols=82  Identities=28%  Similarity=0.437  Sum_probs=77.0

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCC--ceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFG--KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G--~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ...+|||+|||+.+++++|+++|++||  .|..|+|+.|+.+|+++|||||+|.+.++|.+|++.||+..|.|+.|+|.+
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            456899999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             eecC
Q psy2983         191 VTDR  194 (370)
Q Consensus       191 ~~~~  194 (370)
                      +.+.
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            8653

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.38  E-value=7.5e-17  Score=128.83  Aligned_cols=85  Identities=29%  Similarity=0.487  Sum_probs=79.3

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceee--------EEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCe
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDN--------IQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGR  184 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~--------v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~  184 (370)
                      +.++|||+|||..+++++|+++|++||.|..        +.++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   85 (116)
T 2lcw_A            6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGN   85 (116)
Confidence            4578999999999999999999999999998        89999988999999999999999999999999999999999


Q ss_pred             eEEEEEeecCCCC
Q psy2983         185 PMKVGTVTDRNES  197 (370)
Q Consensus       185 ~l~V~~~~~~~~~  197 (370)
                      .|+|.++.++...
T Consensus        86 ~l~V~~a~~~~~~   98 (116)
T 2lcw_A           86 PIKVSFATRRADF   98 (116)
Confidence            9999998776543

>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=99.59  E-value=7e-15  Score=114.72  Aligned_cols=78  Identities=29%  Similarity=0.556  Sum_probs=71.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++        +|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            456789999999999999999999999999999886        559999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy2983         192 TDRNES  197 (370)
Q Consensus       192 ~~~~~~  197 (370)
                      .++...
T Consensus        81 ~~~~~~   86 (103)
T 2dgu_A           81 KPPDQK   86 (103)
T ss_dssp             CCCCCC
T ss_pred             CCCccc
Confidence            776554

>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=99.59  E-value=2.2e-16  Score=129.95  Aligned_cols=83  Identities=18%  Similarity=0.191  Sum_probs=73.8

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEe
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQ   90 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~   90 (370)
                      ......++|||+|||.++|+++|+++|++|| |.+|.|++|+. ++++|||||+|.+.++|.+|+++++..+.|+.|.|.
T Consensus        41 ~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~  118 (139)
T 2hgn_A           41 VQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELF  118 (139)
T ss_dssp             ----CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEE
Confidence            3456778999999999999999999999999 67999999976 999999999999999999999999999999999998


Q ss_pred             ccccc
Q psy2983          91 PTQAE   95 (370)
Q Consensus        91 ~~~~~   95 (370)
                      .+...
T Consensus       119 ~a~~~  123 (139)
T 2hgn_A          119 LNSTT  123 (139)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            77643

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=2.9e-15  Score=114.86  Aligned_cols=78  Identities=19%  Similarity=0.345  Sum_probs=70.0

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecc
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPT   92 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~   92 (370)
                      .+..++|||+|||..+++++|+++|+.||.|.+|  +.++.+++   ||||+|.+.++|.+|++++|..+.|+.|.|.++
T Consensus         5 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHTCSCCEETTEECCCBCS
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHhcCCeEECCEEEEEEEC
Confidence            4567899999999999999999999999999987  66665554   999999999999999999999999999999877


Q ss_pred             ccc
Q psy2983          93 QAE   95 (370)
Q Consensus        93 ~~~   95 (370)
                      ...
T Consensus        80 ~~~   82 (94)
T 2e5g_A           80 EQK   82 (94)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            543

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.59  E-value=1.6e-15  Score=119.55  Aligned_cols=78  Identities=22%  Similarity=0.502  Sum_probs=70.8

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEE
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIV   89 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v   89 (370)
                      ......++|||+|||.++++++|+++|++||.|.++.+.        +|||||+|.+.++|.+|++ |+|..+.|+.|.|
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   97 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEV   97 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            445678999999999999999999999999999999987        6899999999999999996 9999999999999


Q ss_pred             ecccccc
Q psy2983          90 QPTQAEK   96 (370)
Q Consensus        90 ~~~~~~~   96 (370)
                      .++....
T Consensus        98 ~~a~~~~  104 (108)
T 2jvo_A           98 VYSKLPA  104 (108)
T ss_dssp             ESCSCCC
T ss_pred             EEecCCC
Confidence            9987543

>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=99.59  E-value=2.6e-15  Score=118.60  Aligned_cols=76  Identities=24%  Similarity=0.489  Sum_probs=70.3

Q ss_pred             CCceEEEecCCCC-CCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         113 GPMRLYIGSLHFN-ITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       113 ~~~~l~V~nlp~~-~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ..++|||+|||+. +++++|+++|++||.|..+.+        ++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   97 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA   97 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEES
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            3479999999999 999999999999999999988        4889999999999999999999999999999999998


Q ss_pred             ecCCC
Q psy2983         192 TDRNE  196 (370)
Q Consensus       192 ~~~~~  196 (370)
                      .++..
T Consensus        98 ~~~~~  102 (110)
T 1wf1_A           98 GEPKP  102 (110)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            75444

>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=99.59  E-value=1.9e-15  Score=119.16  Aligned_cols=80  Identities=19%  Similarity=0.388  Sum_probs=73.0

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      .....++|||+|||..+++++|+++|+.||.|.++.++++      +|||||+|.+.++|.+|++ |+|..+.|++|.|.
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   94 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY   94 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            3467899999999999999999999999999999999875      6899999999999999994 99999999999999


Q ss_pred             ccccccc
Q psy2983          91 PTQAEKN   97 (370)
Q Consensus        91 ~~~~~~~   97 (370)
                      ++.....
T Consensus        95 ~a~~~~~  101 (109)
T 1x4g_A           95 WGKESPD  101 (109)
T ss_dssp             CCCCCCS
T ss_pred             ecCCCCC
Confidence            9876543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=3.2e-15  Score=114.15  Aligned_cols=78  Identities=15%  Similarity=0.290  Sum_probs=71.2

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEE
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIV   89 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v   89 (370)
                      ....+.++|||+|||..+++++|+++|++||.|.++.+++        +||||+|.+.++|.+|++ ++|..+.|+.|.|
T Consensus         5 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   76 (92)
T 2dgt_A            5 SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHV   76 (92)
T ss_dssp             CCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEE
Confidence            4456789999999999999999999999999999999863        499999999999999995 9999999999999


Q ss_pred             ecccccc
Q psy2983          90 QPTQAEK   96 (370)
Q Consensus        90 ~~~~~~~   96 (370)
                      .++....
T Consensus        77 ~~a~~~~   83 (92)
T 2dgt_A           77 QLSTSRL   83 (92)
T ss_dssp             EESSCCC
T ss_pred             EEccCCC
Confidence            9987654

>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=99.59  E-value=5e-15  Score=117.00  Aligned_cols=75  Identities=23%  Similarity=0.433  Sum_probs=68.8

Q ss_pred             cCCCCeEEEcCCCCC-CcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHh-hccCCccCCeeEEEe
Q psy2983          13 ERDARTIFCMQLSQR-IRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQ   90 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~-~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~i~g~~l~v~   90 (370)
                      ....++|||+|||.. +++++|+++|++||+|.++.+        ++|||||+|.+.++|.+|+ .|+|..+.|+.|.|.
T Consensus        24 ~~~~~~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           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDIN   95 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            345689999999999 999999999999999999988        4799999999999999999 599999999999999


Q ss_pred             ccccc
Q psy2983          91 PTQAE   95 (370)
Q Consensus        91 ~~~~~   95 (370)
                      ++...
T Consensus        96 ~a~~~  100 (110)
T 1wf1_A           96 MAGEP  100 (110)
T ss_dssp             ESCCC
T ss_pred             ECCCC
Confidence            98643

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.58  E-value=4.4e-15  Score=115.87  Aligned_cols=78  Identities=26%  Similarity=0.438  Sum_probs=70.8

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      ..+.++|||+|||..+|+++|+++|++||.|.++.++        ++||||+|.+.++|.+|++ |++..+.|+.|.|.+
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   79 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVF   79 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEE
Confidence            4567999999999999999999999999999999886        4699999999999999997 999999999999999


Q ss_pred             ccccccc
Q psy2983          92 TQAEKNR   98 (370)
Q Consensus        92 ~~~~~~~   98 (370)
                      +......
T Consensus        80 a~~~~~~   86 (103)
T 2dgu_A           80 AKPPDQK   86 (103)
T ss_dssp             CCCCCCC
T ss_pred             cCCCccc
Confidence            8765443

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.58  E-value=1.4e-15  Score=118.20  Aligned_cols=76  Identities=16%  Similarity=0.220  Sum_probs=69.5

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      ....++|||+|||.++++++|+++|+.||.|.++++.      +++|||||+|.+.++|.+|++ ++|..+.|+.|.|.+
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   97 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGW   97 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCB
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEe
Confidence            3457899999999999999999999999999999987      347999999999999999995 999999999999988


Q ss_pred             ccc
Q psy2983          92 TQA   94 (370)
Q Consensus        92 ~~~   94 (370)
                      +..
T Consensus        98 a~~  100 (101)
T 2la4_A           98 GKE  100 (101)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            753

>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=99.58  E-value=1.4e-15  Score=114.63  Aligned_cols=74  Identities=22%  Similarity=0.411  Sum_probs=68.5

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcC----C-------CeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCc
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSV----G-------KVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQK   81 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~----G-------~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~   81 (370)
                      .++.++|||+|||.++++++|+++|++|    |       .|.++.+.++      +|||||+|.+.++|.+|+.++|..
T Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~~l~g~~   76 (87)
T 2hzc_A            3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAMAFDGII   76 (87)
T ss_dssp             SGGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHGGGTTCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHHhcCCCE
Confidence            4678999999999999999999999999    8       8999988654      799999999999999999999999


Q ss_pred             cCCeeEEEecc
Q psy2983          82 LLGIPIIVQPT   92 (370)
Q Consensus        82 i~g~~l~v~~~   92 (370)
                      +.|+.|.|+++
T Consensus        77 ~~g~~l~V~rp   87 (87)
T 2hzc_A           77 FQGQSLKIRRP   87 (87)
T ss_dssp             ETTEECEEECC
T ss_pred             ECCeEEEEeCC
Confidence            99999999763

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.58  E-value=1.8e-15  Score=117.55  Aligned_cols=78  Identities=23%  Similarity=0.467  Sum_probs=72.6

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecC
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~  194 (370)
                      ++|||+|||+.+++++|+++|++||.|..+.+..+     ++|||||+|.+.++|.+|+..|||..+.|+.|+|.++.++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            37999999999999999999999999999999866     6899999999999999999999999999999999998776


Q ss_pred             CCC
Q psy2983         195 NES  197 (370)
Q Consensus       195 ~~~  197 (370)
                      ...
T Consensus        76 ~~~   78 (101)
T 2hvz_A           76 PRR   78 (101)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            543

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.58  E-value=1.1e-15  Score=120.81  Aligned_cols=79  Identities=22%  Similarity=0.230  Sum_probs=70.5

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCC-CeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEE
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVG-KVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIV   89 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G-~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v   89 (370)
                      ..+..++|||+|||.++++++|+++|++|| .|..+.+..    +.++|||||+|.+.++|.+|++ ++|..+.|+.|.|
T Consensus        24 ~p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V   99 (111)
T 2jvr_A           24 LPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV   99 (111)
T ss_dssp             -CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            345678999999999999999999999999 899998854    2468999999999999999995 9999999999999


Q ss_pred             ecccc
Q psy2983          90 QPTQA   94 (370)
Q Consensus        90 ~~~~~   94 (370)
                      .++..
T Consensus       100 ~~a~~  104 (111)
T 2jvr_A          100 ERDDN  104 (111)
T ss_dssp             EESCC
T ss_pred             EECCC
Confidence            98764

>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=99.58  E-value=4.9e-15  Score=113.27  Aligned_cols=79  Identities=32%  Similarity=0.495  Sum_probs=70.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCc-eeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCC-ceeCCeeEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGK-IDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNG-FELAGRPMKVG  189 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~-i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g-~~i~g~~l~V~  189 (370)
                      .+.++|||+|||+.+++++|+++|++||. |..+.+.       ++|||||+|.+.++|.+|+..||| ..+.|+.|+|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            44578999999999999999999999999 6666553       478999999999999999999999 99999999999


Q ss_pred             EeecCCCC
Q psy2983         190 TVTDRNES  197 (370)
Q Consensus       190 ~~~~~~~~  197 (370)
                      ++.++...
T Consensus        79 ~a~~~~~~   86 (93)
T 2cqh_A           79 YSVSKKLR   86 (93)
T ss_dssp             ECCCCCCC
T ss_pred             EccCcccc
Confidence            99876553

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.58  E-value=5.6e-15  Score=113.74  Aligned_cols=78  Identities=26%  Similarity=0.471  Sum_probs=71.2

Q ss_pred             CCCceEEEecCCC-CCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         112 GGPMRLYIGSLHF-NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       112 ~~~~~l~V~nlp~-~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      .+.++|||+|||+ .+++++|+++|++||.|..+.+.        +|||||+|.+.++|.+|+..|||..+.|++|+|.+
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   79 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEV   79 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            4568999999998 99999999999999999999984        78999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2983         191 VTDRNES  197 (370)
Q Consensus       191 ~~~~~~~  197 (370)
                      +.++...
T Consensus        80 a~~~~~~   86 (96)
T 2kvi_A           80 SSSNARP   86 (96)
T ss_dssp             EECCCC-
T ss_pred             cCcCCCC
Confidence            9776554

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=8.7e-15  Score=113.27  Aligned_cols=79  Identities=25%  Similarity=0.398  Sum_probs=71.0

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcC--CCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCee
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSV--GKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIP   86 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~--G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~   86 (370)
                      .....+.++|||+|||..+++++|+++|++|  |.|..+.+.        +|||||+|.+.++|.+|++ ++|..+.|+.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (99)
T 2cpd_A            9 EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSP   80 (99)
T ss_dssp             CSCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEE
T ss_pred             ccccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            3445678999999999999999999999999  899998764        5799999999999999997 9999999999


Q ss_pred             EEEecccccc
Q psy2983          87 IIVQPTQAEK   96 (370)
Q Consensus        87 l~v~~~~~~~   96 (370)
                      |.|.++....
T Consensus        81 l~v~~a~~~~   90 (99)
T 2cpd_A           81 IEVTLAKPVD   90 (99)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEECCCCC
Confidence            9999987543

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.57  E-value=6.8e-15  Score=128.00  Aligned_cols=126  Identities=24%  Similarity=0.449  Sum_probs=104.1

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCC-----------ceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeC
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFG-----------KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELA  182 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G-----------~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~  182 (370)
                      .++|||+|||+++++++|+++|++||           .|..+.+      +.++|||||+|.+.++|.+|+ .|||..+.
T Consensus         4 ~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~~   76 (198)
T 2yh0_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (198)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEET
T ss_pred             eeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEEc
Confidence            47899999999999999999999994           4544444      456899999999999999999 79999999


Q ss_pred             CeeEEEEEeecCCC---------------------------CcCCCCCCCCHHHHHHhcccCCceeeeeeeeccc----c
Q psy2983         183 GRPMKVGTVTDRNE---------------------------SVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLA----E  231 (370)
Q Consensus       183 g~~l~V~~~~~~~~---------------------------~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~~----~  231 (370)
                      |+.|+|.++.+...                           .+++++..+++++++..|..+|.+..+.++.+..    +
T Consensus        77 g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~  156 (198)
T 2yh0_A           77 GQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSK  156 (198)
T ss_dssp             TEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEE
T ss_pred             CceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcc
Confidence            99999998765311                           1557888999999999999999999998887632    3


Q ss_pred             CCC---CCChHHHHHHHh
Q psy2983         232 GTG---LELPPAAASALN  246 (370)
Q Consensus       232 ~~~---~~~~~~a~~a~~  246 (370)
                      +++   |..+..|..|+.
T Consensus       157 g~afV~f~~~~~a~~A~~  174 (198)
T 2yh0_A          157 GYAFCEYVDINVTDQAIA  174 (198)
T ss_dssp             EEEEEEESSSSHHHHHHH
T ss_pred             eEEEEEECCHHHHHHHHH
Confidence            444   567777777766

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.57  E-value=4.5e-15  Score=117.54  Aligned_cols=76  Identities=14%  Similarity=0.129  Sum_probs=70.4

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .++|||+|||+.+++++|+++|++||.|..+.+.+      ++|||||+|.+.++|.+|+..|||..+.|+.|+|.++..
T Consensus        10 ~~~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           10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            46899999999999999999999999999998864      478999999999999999999999999999999999876


Q ss_pred             CC
Q psy2983         194 RN  195 (370)
Q Consensus       194 ~~  195 (370)
                      ..
T Consensus        84 ~~   85 (111)
T 1whx_A           84 GV   85 (111)
T ss_dssp             TT
T ss_pred             Cc
Confidence            43

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.57  E-value=7.5e-15  Score=116.79  Aligned_cols=77  Identities=12%  Similarity=0.179  Sum_probs=69.9

Q ss_pred             CeEEEcCC----CCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecC----CCC----hHHHhh---ccCCc
Q psy2983          17 RTIFCMQL----SQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKD----PES----VPLAMG---LNGQK   81 (370)
Q Consensus        17 r~v~V~nL----p~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~----~e~----A~~Al~---l~g~~   81 (370)
                      ..|||+||    |+.+++.+|+++|+.||+|.++.++.|+.||+++|||||+|.+    +++    |.+|+.   ++|..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    9999999999999999999999999999999999999999997    666    778874   79999


Q ss_pred             cCCeeEEEeccc
Q psy2983          82 LLGIPIIVQPTQ   93 (370)
Q Consensus        82 i~g~~l~v~~~~   93 (370)
                      |.|++|+|....
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999998654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.57  E-value=1.4e-14  Score=116.98  Aligned_cols=81  Identities=17%  Similarity=0.355  Sum_probs=72.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccE-EEEEECCHHHHHHHHHHhCCceeCC--eeEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGY-GFITFHSADDAKKAQEQLNGFELAG--RPMKV  188 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~-afV~f~~~~~a~~A~~~l~g~~i~g--~~l~V  188 (370)
                      ..-.+|||+||++.+|+++|+++|++||.|.+|.+..+.     +|+ |||+|.+.++|.+|++.|||..|.|  +.|+|
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI  100 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI  100 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEE
Confidence            344679999999999999999999999999999887642     677 9999999999999999999999998  99999


Q ss_pred             EEeecCCCC
Q psy2983         189 GTVTDRNES  197 (370)
Q Consensus       189 ~~~~~~~~~  197 (370)
                      .++++....
T Consensus       101 ~~ak~~~l~  109 (130)
T 3zzy_A          101 DFSKLTSLN  109 (130)
T ss_dssp             EECSCSSCC
T ss_pred             EecCCCcee
Confidence            998876543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=3.7e-15  Score=113.26  Aligned_cols=77  Identities=19%  Similarity=0.388  Sum_probs=70.5

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      ...+.++|||+|||.++|+++|+++|++||.|.++.+++        +||||+|.+.++|.+|++ ++|..+.|++|.|.
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   76 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVE   76 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            356789999999999999999999999999999999873        499999999999999996 99999999999999


Q ss_pred             cccccc
Q psy2983          91 PTQAEK   96 (370)
Q Consensus        91 ~~~~~~   96 (370)
                      ++....
T Consensus        77 ~a~~~~   82 (90)
T 2dnp_A           77 LSTKGQ   82 (90)
T ss_dssp             ESCCCC
T ss_pred             ECCCCC
Confidence            987653

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.57  E-value=5.8e-15  Score=126.77  Aligned_cols=85  Identities=28%  Similarity=0.515  Sum_probs=79.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      .....+|||+|||+.+++++|+++|++||.|..|.+..+. +|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
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~~  163 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456899999999999999999999999999999999997 899999999999999999999999999999999999999


Q ss_pred             eecCCC
Q psy2983         191 VTDRNE  196 (370)
Q Consensus       191 ~~~~~~  196 (370)
                      +.....
T Consensus       164 a~~~~~  169 (177)
T 2f3j_A          164 VASQID  169 (177)
T ss_dssp             ESSGGG
T ss_pred             ecCCCC
Confidence            876443

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=2.3e-15  Score=121.17  Aligned_cols=79  Identities=22%  Similarity=0.315  Sum_probs=72.2

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCce----eeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEE
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKI----DNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV  188 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i----~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V  188 (370)
                      ...+|||+|||+++|+++|+++|++||.|    ..|.++.+. +|+++|||||+|.+.++|.+|+.. |+..+.||.|.|
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V   99 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIEL   99 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEE
Confidence            34789999999999999999999999975    689999994 899999999999999999999995 999999999999


Q ss_pred             EEeec
Q psy2983         189 GTVTD  193 (370)
Q Consensus       189 ~~~~~  193 (370)
                      ..+.+
T Consensus       100 ~~a~~  104 (123)
T 2dha_A          100 FRSTA  104 (123)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            87643

>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=99.56  E-value=1.1e-14  Score=110.15  Aligned_cols=76  Identities=13%  Similarity=0.291  Sum_probs=69.8

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ..++|||+|||+.+++++|+++|++| .|..+++.      .++|||||+|.+.++|.+|+..|||..+.|++|+|.++.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            35789999999999999999999999 99999884      569999999999999999999999999999999999976


Q ss_pred             cCC
Q psy2983         193 DRN  195 (370)
Q Consensus       193 ~~~  195 (370)
                      ...
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            543

>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=99.56  E-value=4.1e-15  Score=120.10  Aligned_cols=79  Identities=25%  Similarity=0.346  Sum_probs=71.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCcee--eEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKID--NIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG  189 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~--~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~  189 (370)
                      ....+|||+|||+++++++|+++|++| .|.  .|.++.|+. |+++|||||+|.+.++|.+|+. +++..+.|+.|.|.
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~  116 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVF  116 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEE
Confidence            345789999999999999999999999 566  899999975 9999999999999999999999 58899999999998


Q ss_pred             Eeec
Q psy2983         190 TVTD  193 (370)
Q Consensus       190 ~~~~  193 (370)
                      .+..
T Consensus       117 ~a~~  120 (126)
T 2hgm_A          117 KSSQ  120 (126)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            8754

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=9.3e-15  Score=112.36  Aligned_cols=80  Identities=25%  Similarity=0.420  Sum_probs=71.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeE-EEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNI-QLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ...++|||+|||+.+++++|+++|++||.|..+ .++.++.+    |.|||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~----~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET----AVVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSS----EEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCC----CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            345789999999999999999999999999999 47777543    3499999999999999999999999999999999


Q ss_pred             eecCC
Q psy2983         191 VTDRN  195 (370)
Q Consensus       191 ~~~~~  195 (370)
                      +.++.
T Consensus        89 a~~~~   93 (96)
T 2e44_A           89 IPDEM   93 (96)
T ss_dssp             CCCCC
T ss_pred             cCccc
Confidence            88763

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.56  E-value=3.6e-15  Score=124.55  Aligned_cols=82  Identities=24%  Similarity=0.366  Sum_probs=74.4

Q ss_pred             CCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeE
Q psy2983           9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPI   87 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l   87 (370)
                      ........++|||+|||..+|+++|+++|++||.|.+++++++     ++|||||+|.+.++|..|++ ++|..+.|++|
T Consensus        66 ~~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l  140 (150)
T 2i2y_A           66 HRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRV  140 (150)
T ss_dssp             CSSSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCC
T ss_pred             cccCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            3445567899999999999999999999999999999999876     47999999999999999996 99999999999


Q ss_pred             EEeccccc
Q psy2983          88 IVQPTQAE   95 (370)
Q Consensus        88 ~v~~~~~~   95 (370)
                      .|.++...
T Consensus       141 ~v~~a~~~  148 (150)
T 2i2y_A          141 RVELSNGE  148 (150)
T ss_dssp             EEEECCCC
T ss_pred             EEEEcCCC
Confidence            99987653

>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=99.56  E-value=1.3e-15  Score=120.61  Aligned_cols=77  Identities=22%  Similarity=0.261  Sum_probs=70.3

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      ..+..++|||+|||..+++++|+++|++||.|.+|.+.+      ++|||||+|.+.++|..|++ |+|..+.|++|.|.
T Consensus         6 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   79 (111)
T 1whx_A            6 SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLE   79 (111)
T ss_dssp             TSEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            345678999999999999999999999999999998864      47899999999999999996 99999999999999


Q ss_pred             cccc
Q psy2983          91 PTQA   94 (370)
Q Consensus        91 ~~~~   94 (370)
                      ++..
T Consensus        80 ~a~~   83 (111)
T 1whx_A           80 WAPI   83 (111)
T ss_dssp             EEET
T ss_pred             ECCC
Confidence            8764

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=2e-14  Score=110.19  Aligned_cols=78  Identities=14%  Similarity=0.349  Sum_probs=69.5

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ..++|||+|||+.+++++|+++|++||.|..|  +.++.+|.   ||||+|.+.++|.+|+. |||..+.|+.|+|.++.
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~   80 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPRE   80 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECC
Confidence            45799999999999999999999999999987  55655655   99999999999999999 99999999999999876


Q ss_pred             cCCC
Q psy2983         193 DRNE  196 (370)
Q Consensus       193 ~~~~  196 (370)
                      ++..
T Consensus        81 ~~~~   84 (94)
T 2e5g_A           81 QKEF   84 (94)
T ss_dssp             CSCC
T ss_pred             cCCC
Confidence            5544

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=3.7e-15  Score=113.95  Aligned_cols=78  Identities=21%  Similarity=0.314  Sum_probs=68.9

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCC-eeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccC-CccCCeeEEE
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGK-VRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNG-QKLLGIPIIV   89 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~-v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g-~~i~g~~l~v   89 (370)
                      ....++|||+|||.++|+++|+++|++||. |..+.+.       ++|||||+|.+.++|.+|++ ++| ..+.|++|.|
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v   77 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEV   77 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEE
Confidence            356799999999999999999999999999 6666552       47999999999999999996 999 9999999999


Q ss_pred             eccccccc
Q psy2983          90 QPTQAEKN   97 (370)
Q Consensus        90 ~~~~~~~~   97 (370)
                      .++.....
T Consensus        78 ~~a~~~~~   85 (93)
T 2cqh_A           78 DYSVSKKL   85 (93)
T ss_dssp             EECCCCCC
T ss_pred             EEccCccc
Confidence            99876543

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=1.7e-14  Score=108.54  Aligned_cols=75  Identities=25%  Similarity=0.346  Sum_probs=66.9

Q ss_pred             Cce-EEEecCCCCCCHHH----HHhcccCC-CceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEE
Q psy2983         114 PMR-LYIGSLHFNITEDM----LRGIFEPF-GKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMK  187 (370)
Q Consensus       114 ~~~-l~V~nlp~~~t~e~----l~~~f~~~-G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~  187 (370)
                      +.+ |||+|||+.+++++    |+++|++| |.|..|       +|   |+|||+|.+.++|.+|++.|+|..+.||+|+
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~   77 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRII   77 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEE
Confidence            445 99999999999988    55899999 599887       33   9999999999999999999999999999999


Q ss_pred             EEEeecCCCCc
Q psy2983         188 VGTVTDRNESV  198 (370)
Q Consensus       188 V~~~~~~~~~~  198 (370)
                      |.+++.+...+
T Consensus        78 v~~A~~~sd~~   88 (96)
T 2diu_A           78 VSFTPKNRELC   88 (96)
T ss_dssp             EESSCCSCCCC
T ss_pred             EEecCCCccee
Confidence            99998877654

>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=99.55  E-value=2.7e-15  Score=124.26  Aligned_cols=84  Identities=27%  Similarity=0.429  Sum_probs=72.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeE------EEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCee
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNI------QLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRP  185 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v------~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~  185 (370)
                      .+.++|||+|||+.+++++|+++|++||.|..+      .+.. ..+|.++|||||+|.+.++|.+|+..|||..+.|+.
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRL-MKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEE-EEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEe-ccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            345799999999999999999999999998774      1111 137899999999999999999999999999999999


Q ss_pred             EEEEEeecCCC
Q psy2983         186 MKVGTVTDRNE  196 (370)
Q Consensus       186 l~V~~~~~~~~  196 (370)
                      |+|.++.+...
T Consensus       122 l~V~~a~~~~~  132 (143)
T 3egn_A          122 MVVQFARSARP  132 (143)
T ss_dssp             CEEEECCCSCC
T ss_pred             EEEEECCCCCC
Confidence            99999876543

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=4.2e-14  Score=108.96  Aligned_cols=78  Identities=26%  Similarity=0.485  Sum_probs=70.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|+  .+++++|+++|++||.|..+.+.      .++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~   83 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   83 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            345679999995  89999999999999999999884      4589999999999999999999999999999999999


Q ss_pred             eecCCC
Q psy2983         191 VTDRNE  196 (370)
Q Consensus       191 ~~~~~~  196 (370)
                      +.++..
T Consensus        84 a~~~~~   89 (97)
T 1x5p_A           84 ARKQPM   89 (97)
T ss_dssp             CSSCCC
T ss_pred             CCCCCC
Confidence            877654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.55  E-value=5e-14  Score=113.22  Aligned_cols=77  Identities=26%  Similarity=0.396  Sum_probs=68.9

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccE-EEEEECCHHHHHHHHHHhCCceeCC--eeEEEEEe
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGY-GFITFHSADDAKKAQEQLNGFELAG--RPMKVGTV  191 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~-afV~f~~~~~a~~A~~~l~g~~i~g--~~l~V~~~  191 (370)
                      ..|||+||++.+++++|+++|++||.|.+|.++..      .|| |||+|.+.++|..|+..|||..|.|  +.|+|.++
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            46789999999999999999999999999998642      276 9999999999999999999999987  68999998


Q ss_pred             ecCCCC
Q psy2983         192 TDRNES  197 (370)
Q Consensus       192 ~~~~~~  197 (370)
                      +++...
T Consensus       100 k~~~l~  105 (124)
T 2e5i_A          100 RPTRLN  105 (124)
T ss_dssp             SCSCCC
T ss_pred             cCCcce
Confidence            876543

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.55  E-value=3.2e-15  Score=115.13  Aligned_cols=76  Identities=20%  Similarity=0.380  Sum_probs=68.4

Q ss_pred             ccCCCCeEEEcCCCC-CCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEE
Q psy2983          12 EERDARTIFCMQLSQ-RIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIV   89 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~-~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v   89 (370)
                      ...+.++|||+|||. .+++++|+++|++||+|.++.+.        +|||||+|.+.++|..|++ ++|..+.|++|.|
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   77 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLIL   77 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCE
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            346789999999998 99999999999999999999883        6899999999999999996 9999999999999


Q ss_pred             eccccc
Q psy2983          90 QPTQAE   95 (370)
Q Consensus        90 ~~~~~~   95 (370)
                      .++...
T Consensus        78 ~~a~~~   83 (96)
T 2kvi_A           78 EVSSSN   83 (96)
T ss_dssp             EEEECC
T ss_pred             EEcCcC
Confidence            988654

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=6.3e-15  Score=117.22  Aligned_cols=77  Identities=18%  Similarity=0.220  Sum_probs=66.2

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCC---CCeecEEEEEecCCCChHHHhh-ccCCccCCeeE
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKT---RRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPI   87 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~---~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l   87 (370)
                      ..+.+++|||+|||.++++++|+++|++||+|. +.++.+..+   |+++|||||+|.+.++|.+|++ ++  .++|+.+
T Consensus         4 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~   80 (114)
T 2dnl_A            4 GSSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLY   80 (114)
T ss_dssp             SSSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEE
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEE
Confidence            456789999999999999999999999999999 888888777   7899999999999999999996 53  2566666


Q ss_pred             EEec
Q psy2983          88 IVQP   91 (370)
Q Consensus        88 ~v~~   91 (370)
                      .+..
T Consensus        81 ~~~~   84 (114)
T 2dnl_A           81 LCVS   84 (114)
T ss_dssp             EEEC
T ss_pred             Eecc
Confidence            5543

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.55  E-value=6.3e-15  Score=126.55  Aligned_cols=82  Identities=20%  Similarity=0.300  Sum_probs=76.8

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      ....++|||+|||..+++++|+++|+.||.|..|.+..+. ++.++|||||+|.+.++|.+|++ ++|..+.|++|.|.+
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~~  163 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4557899999999999999999999999999999999998 89999999999999999999996 999999999999999


Q ss_pred             cccc
Q psy2983          92 TQAE   95 (370)
Q Consensus        92 ~~~~   95 (370)
                      +...
T Consensus       164 a~~~  167 (177)
T 2f3j_A          164 VASQ  167 (177)
T ss_dssp             ESSG
T ss_pred             ecCC
Confidence            8654

>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=99.55  E-value=1.2e-14  Score=121.92  Aligned_cols=82  Identities=17%  Similarity=0.317  Sum_probs=72.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCC--eeEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG--RPMKVG  189 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g--~~l~V~  189 (370)
                      ....+|||+||++.+++++|+++|++||.|.+|.+..+    .++|||||+|.+.++|.+|++.|||..|.|  +.|+|.
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~  119 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  119 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEE
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEE
Confidence            33467999999999999999999999999999998744    257899999999999999999999999966  999999


Q ss_pred             EeecCCCC
Q psy2983         190 TVTDRNES  197 (370)
Q Consensus       190 ~~~~~~~~  197 (370)
                      +++++...
T Consensus       120 ~Ak~~~l~  127 (164)
T 1sjr_A          120 FSKLTSLN  127 (164)
T ss_dssp             ECSSSSCC
T ss_pred             EecCCccc
Confidence            99876443

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=1.9e-14  Score=110.89  Aligned_cols=82  Identities=18%  Similarity=0.299  Sum_probs=71.8

Q ss_pred             CCCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHh-hccCCccCCe
Q psy2983           7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGI   85 (370)
Q Consensus         7 ~~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~i~g~   85 (370)
                      .......++.++|||+||  ++|+++|+++|++||.|.++.+.      +++|||||+|.+.++|.+|+ .|+|..+.|+
T Consensus         6 ~~~~~~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~   77 (97)
T 1x5p_A            6 SGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESV   77 (97)
T ss_dssp             SSCCCCCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTE
T ss_pred             CCccCCCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            334445567899999996  89999999999999999999883      45799999999999999999 4999999999


Q ss_pred             eEEEecccccc
Q psy2983          86 PIIVQPTQAEK   96 (370)
Q Consensus        86 ~l~v~~~~~~~   96 (370)
                      +|.|.++....
T Consensus        78 ~l~v~~a~~~~   88 (97)
T 1x5p_A           78 QLKVNIARKQP   88 (97)
T ss_dssp             EEEEECCSSCC
T ss_pred             EEEEEECCCCC
Confidence            99999987653

>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=6.8e-15  Score=113.12  Aligned_cols=81  Identities=17%  Similarity=0.295  Sum_probs=71.8

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEE-EEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEE
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDV-RLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPII   88 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v-~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~   88 (370)
                      +.....++|||+|||..+++++|+++|+.||.|.++ .++.++.++    .|||+|.+.++|..|++ ++|..+.|++|.
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   85 (96)
T 2e44_A           10 PKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLK   85 (96)
T ss_dssp             CCCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCE
T ss_pred             CCCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            344567999999999999999999999999999999 488776543    39999999999999996 999999999999


Q ss_pred             Eeccccc
Q psy2983          89 VQPTQAE   95 (370)
Q Consensus        89 v~~~~~~   95 (370)
                      |.++.+.
T Consensus        86 V~~a~~~   92 (96)
T 2e44_A           86 VAYIPDE   92 (96)
T ss_dssp             EEECCCC
T ss_pred             EEEcCcc
Confidence            9988754

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=1.2e-14  Score=114.73  Aligned_cols=77  Identities=22%  Similarity=0.389  Sum_probs=68.9

Q ss_pred             CCceEEE--ecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCcee-----CCee
Q psy2983         113 GPMRLYI--GSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFEL-----AGRP  185 (370)
Q Consensus       113 ~~~~l~V--~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i-----~g~~  185 (370)
                      +.++|||  +||++.+++++|+++|++||.|..+.+..      .+|||||+|.+.++|.+|++.|||.++     .|++
T Consensus        24 pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~   97 (114)
T 2cq2_A           24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   97 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcE
Confidence            4578999  77999999999999999999999988753      278999999999999999999999998     6899


Q ss_pred             EEEEEeecCC
Q psy2983         186 MKVGTVTDRN  195 (370)
Q Consensus       186 l~V~~~~~~~  195 (370)
                      |.|.++....
T Consensus        98 l~v~~a~~~p  107 (114)
T 2cq2_A           98 LYLNFVEKVQ  107 (114)
T ss_dssp             CEEEEESCCC
T ss_pred             EEEEecccCc
Confidence            9999986543

>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=99.54  E-value=6.5e-15  Score=111.80  Aligned_cols=79  Identities=19%  Similarity=0.405  Sum_probs=62.1

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEe
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQ   90 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~   90 (370)
                      ....+..+|||+|||.++|+++|+++|++||+|.++.++++     ++|||||+|.+.++|.++... ...+.|+.|.|.
T Consensus         6 ~~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~~~~~-~~~~~g~~v~v~   79 (89)
T 3d2w_A            6 HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCGE-DLIIKGISVHIS   79 (89)
T ss_dssp             -----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHHHTTC-EEEETTEEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHHHcCC-CcccCCEEEEEE
Confidence            34567799999999999999999999999999999999874     689999999999999843321 234569999998


Q ss_pred             ccccc
Q psy2983          91 PTQAE   95 (370)
Q Consensus        91 ~~~~~   95 (370)
                      ++.+.
T Consensus        80 ~a~~k   84 (89)
T 3d2w_A           80 NAEPK   84 (89)
T ss_dssp             ECC--
T ss_pred             EcCCC
Confidence            87654

>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=99.53  E-value=5.8e-15  Score=111.74  Aligned_cols=76  Identities=16%  Similarity=0.255  Sum_probs=69.4

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      .+..++|||+|||..+++++|+++|++| .|.++.+.      +++|||||+|.+.++|.+|++ ++|..+.|++|+|.+
T Consensus         2 s~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   74 (88)
T 1wg1_A            2 SSGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQL   74 (88)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEE
Confidence            3567999999999999999999999999 99999884      568999999999999999996 999999999999998


Q ss_pred             cccc
Q psy2983          92 TQAE   95 (370)
Q Consensus        92 ~~~~   95 (370)
                      +...
T Consensus        75 a~~~   78 (88)
T 1wg1_A           75 QPTD   78 (88)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            7543

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.53  E-value=2.9e-14  Score=108.21  Aligned_cols=76  Identities=16%  Similarity=0.396  Sum_probs=62.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCce--eCCeeEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFE--LAGRPMKVG  189 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~--i~g~~l~V~  189 (370)
                      ..+.+|||+|||+++++++|+++|++||.|.+++++.+     ++|||||+|.+.++|.+    +++..  +.|+.|.|.
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~   79 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHIS   79 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEE
Confidence            44579999999999999999999999999999999864     69999999999999983    56655  459999999


Q ss_pred             EeecCCC
Q psy2983         190 TVTDRNE  196 (370)
Q Consensus       190 ~~~~~~~  196 (370)
                      ++.++..
T Consensus        80 ~a~~k~~   86 (89)
T 3d2w_A           80 NAEPKHN   86 (89)
T ss_dssp             ECC----
T ss_pred             EcCCCCc
Confidence            9876543

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.53  E-value=1.8e-15  Score=125.38  Aligned_cols=84  Identities=24%  Similarity=0.397  Sum_probs=71.9

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEE-----eeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCee
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRL-----ITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIP   86 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i-----~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~   86 (370)
                      ..++++|||+|||..+|+++|+++|+.||.|..+.+     ++...+++++|||||+|.+.++|.+|++ ++|..+.|++
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            457799999999999999999999999999876410     1112357889999999999999999997 9999999999


Q ss_pred             EEEecccccc
Q psy2983          87 IIVQPTQAEK   96 (370)
Q Consensus        87 l~v~~~~~~~   96 (370)
                      |.|.++....
T Consensus       122 l~V~~a~~~~  131 (143)
T 3egn_A          122 MVVQFARSAR  131 (143)
T ss_dssp             CEEEECCCSC
T ss_pred             EEEEECCCCC
Confidence            9999987543

>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=99.52  E-value=1.1e-14  Score=126.82  Aligned_cols=81  Identities=17%  Similarity=0.314  Sum_probs=74.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEeccc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~~   93 (370)
                      ...++|||+|||.++|+++|+++|++||+|.+|++.++.. ++++|||||+|.+.++|.+|++..+..+.|++|.|.+..
T Consensus       107 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~-~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~  185 (193)
T 2voo_A          107 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD  185 (193)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTT-CCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETT
T ss_pred             cccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCC-CCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhH
Confidence            4569999999999999999999999999999999998864 889999999999999999999877779999999999876


Q ss_pred             cc
Q psy2983          94 AE   95 (370)
Q Consensus        94 ~~   95 (370)
                      ..
T Consensus       186 ~y  187 (193)
T 2voo_A          186 DY  187 (193)
T ss_dssp             TC
T ss_pred             HH
Confidence            54

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.52  E-value=4e-14  Score=112.52  Aligned_cols=76  Identities=21%  Similarity=0.402  Sum_probs=65.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCC---CCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDT---GRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV  188 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~---g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V  188 (370)
                      ...++|||+|||+.+++++|+++|++||.|. +.++.+..+   |+++|||||+|.+.++|.+|++.|+  .+.|+.+.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            3457899999999999999999999999999 888887766   7999999999999999999999883  356666655


Q ss_pred             EE
Q psy2983         189 GT  190 (370)
Q Consensus       189 ~~  190 (370)
                      ..
T Consensus        83 ~~   84 (114)
T 2dnl_A           83 VS   84 (114)
T ss_dssp             EC
T ss_pred             cc
Confidence            43

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=2.7e-14  Score=107.50  Aligned_cols=76  Identities=21%  Similarity=0.323  Sum_probs=66.1

Q ss_pred             cCCCCe-EEEcCCCCCCcHHH----HHHHhhcC-CCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCe
Q psy2983          13 ERDART-IFCMQLSQRIRTRD----LEEFFSSV-GKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGI   85 (370)
Q Consensus        13 ~~~~r~-v~V~nLp~~~te~~----L~~~f~~~-G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~   85 (370)
                      ..++.| |||+|||.++++++    |+++|++| |+|.+|       ++   |+|||+|.+.++|.+|++ |+|..+.|+
T Consensus         5 ~~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr   74 (96)
T 2diu_A            5 SSGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGN   74 (96)
T ss_dssp             CCCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSS
T ss_pred             CCCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCc
Confidence            345667 99999999999988    55899999 599998       23   999999999999999995 999999999


Q ss_pred             eEEEecccccccc
Q psy2983          86 PIIVQPTQAEKNR   98 (370)
Q Consensus        86 ~l~v~~~~~~~~~   98 (370)
                      +|+|++++.....
T Consensus        75 ~i~v~~A~~~sd~   87 (96)
T 2diu_A           75 RIIVSFTPKNREL   87 (96)
T ss_dssp             CCEEESSCCSCCC
T ss_pred             eEEEEecCCCcce
Confidence            9999999866543

>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=99.52  E-value=8.6e-15  Score=110.73  Aligned_cols=77  Identities=22%  Similarity=0.403  Sum_probs=66.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEeccc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~~   93 (370)
                      ..+++|||+|||.++++++|+++|++||+|.++.++++     ++|||||+|.+.++|++|+.. +..+.|++|.|.++.
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~-~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE-DLIIKGISVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC-EEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC-CceeCCEEEEEEecC
Confidence            46799999999999999999999999999999998764     589999999999999876543 455689999999887


Q ss_pred             ccc
Q psy2983          94 AEK   96 (370)
Q Consensus        94 ~~~   96 (370)
                      +..
T Consensus        77 ~~~   79 (88)
T 1wf0_A           77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.51  E-value=8.3e-14  Score=108.93  Aligned_cols=81  Identities=20%  Similarity=0.180  Sum_probs=71.8

Q ss_pred             CCceEEEecCCC-----CCCHHHHHhcccCCCceeeEEEeecCCC-CCcccEEEEEECCHHHHHHHHHHhCCceeCCeeE
Q psy2983         113 GPMRLYIGSLHF-----NITEDMLRGIFEPFGKIDNIQLMVDPDT-GRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM  186 (370)
Q Consensus       113 ~~~~l~V~nlp~-----~~t~e~l~~~f~~~G~i~~v~~~~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l  186 (370)
                      ++++|+|.|+..     +-++++|++.|++||.|.++.++.++.+ +.++|+|||+|.+.++|.+|+..|||..+.||.|
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i   86 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV   86 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEE
Confidence            457899999963     2378999999999999999999988654 6899999999999999999999999999999999


Q ss_pred             EEEEeec
Q psy2983         187 KVGTVTD  193 (370)
Q Consensus       187 ~V~~~~~  193 (370)
                      +|.++..
T Consensus        87 ~v~~a~~   93 (105)
T 2pe8_A           87 KACFYNL   93 (105)
T ss_dssp             EEEECCH
T ss_pred             EEEEcCH
Confidence            9999754

>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=99.50  E-value=1.2e-14  Score=114.71  Aligned_cols=78  Identities=14%  Similarity=0.213  Sum_probs=68.5

Q ss_pred             cccCCCCeEEE--cCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCcc-----
Q psy2983          11 PEERDARTIFC--MQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL-----   82 (370)
Q Consensus        11 ~~~~~~r~v~V--~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i-----   82 (370)
                      ....++++|||  +|||.++++++|+++|++||.|.+|.+..      .+|||||+|.+.++|.+|++ |||..+     
T Consensus        20 ~~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg   93 (114)
T 2cq2_A           20 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLG   93 (114)
T ss_dssp             CCSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTS
T ss_pred             CCCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccC
Confidence            34457899999  77999999999999999999999998753      27899999999999999996 999988     


Q ss_pred             CCeeEEEecccc
Q psy2983          83 LGIPIIVQPTQA   94 (370)
Q Consensus        83 ~g~~l~v~~~~~   94 (370)
                      .|++|+|.+...
T Consensus        94 ~g~~l~v~~a~~  105 (114)
T 2cq2_A           94 QKITLYLNFVEK  105 (114)
T ss_dssp             CEEECEEEEESC
T ss_pred             CCcEEEEEeccc
Confidence            688999987754

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.50  E-value=3.2e-14  Score=107.17  Aligned_cols=71  Identities=30%  Similarity=0.641  Sum_probs=65.9

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCC----C-------ceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCcee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPF----G-------KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFEL  181 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~----G-------~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i  181 (370)
                      ..++|||+|||+.+++++|+++|++|    |       .|.++++.++      +|||||+|.+.++|.+|+ .|||..+
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~~   77 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGIIF   77 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            35799999999999999999999999    8       8999988754      799999999999999999 8999999


Q ss_pred             CCeeEEEEE
Q psy2983         182 AGRPMKVGT  190 (370)
Q Consensus       182 ~g~~l~V~~  190 (370)
                      .|+.|+|++
T Consensus        78 ~g~~l~V~r   86 (87)
T 2hzc_A           78 QGQSLKIRR   86 (87)
T ss_dssp             TTEECEEEC
T ss_pred             CCeEEEEeC
Confidence            999999975

>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=99.50  E-value=3.3e-14  Score=138.77  Aligned_cols=83  Identities=17%  Similarity=0.386  Sum_probs=78.0

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      ..+.++|||+|||..+|+++|.++|+.||.|..|.|+.+..++.++|||||+|.+.++|.+||+ |+|..|.|+.|.|.+
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~  178 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  178 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4556899999999999999999999999999999999999999999999999999999999995 999999999999998


Q ss_pred             cccc
Q psy2983          92 TQAE   95 (370)
Q Consensus        92 ~~~~   95 (370)
                      +...
T Consensus       179 a~~~  182 (437)
T 3pgw_S          179 ERGR  182 (437)
T ss_pred             eCCC
Confidence            8754

>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=99.50  E-value=2.6e-14  Score=113.89  Aligned_cols=75  Identities=17%  Similarity=0.236  Sum_probs=66.0

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCee-----EE
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRP-----MK  187 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~-----l~  187 (370)
                      ...+|||+|||+.+++++|+++|++||.|..+.++.+       |||||+|.+.++|.+|++.|||..|.|+.     |+
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~   87 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   87 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEE
Confidence            3578999999999999999999999999999999754       89999999999999999999999999998     66


Q ss_pred             EEEeecC
Q psy2983         188 VGTVTDR  194 (370)
Q Consensus       188 V~~~~~~  194 (370)
                      |....++
T Consensus        88 v~~~~~~   94 (115)
T 3beg_B           88 VKVDGPR   94 (115)
T ss_dssp             EEECC--
T ss_pred             eccCCCC
Confidence            6665543

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.49  E-value=1.2e-14  Score=115.79  Aligned_cols=76  Identities=20%  Similarity=0.255  Sum_probs=64.3

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCee----
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIP----   86 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~----   86 (370)
                      ..+..++|||+|||.++++++|+++|++||+|..+.++.+       |||||+|.+.++|.+|++ |+|..|.|+.    
T Consensus        12 ~~r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~   84 (115)
T 3beg_B           12 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETA   84 (115)
T ss_dssp             -----CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeE
Confidence            3467799999999999999999999999999999999764       899999999999999996 9999999998    


Q ss_pred             -EEEecccc
Q psy2983          87 -IIVQPTQA   94 (370)
Q Consensus        87 -l~v~~~~~   94 (370)
                       +.|.....
T Consensus        85 ~i~v~~~~~   93 (115)
T 3beg_B           85 YIRVKVDGP   93 (115)
T ss_dssp             BCEEEECC-
T ss_pred             EEEeccCCC
Confidence             55555443

>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=99.49  E-value=4.1e-14  Score=106.95  Aligned_cols=78  Identities=19%  Similarity=0.420  Sum_probs=66.2

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ..++|||+|||+.+++++|+++|++||.|..++++.+     ++|||||+|.+.++|.+|..  .+..+.|+.|+|.++.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEecC
Confidence            4579999999999999999999999999999999755     68999999999999976432  1345589999999987


Q ss_pred             cCCCC
Q psy2983         193 DRNES  197 (370)
Q Consensus       193 ~~~~~  197 (370)
                      ++...
T Consensus        77 ~~~~~   81 (88)
T 1wf0_A           77 PKHNS   81 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76554

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.48  E-value=5.4e-14  Score=113.60  Aligned_cols=77  Identities=22%  Similarity=0.290  Sum_probs=68.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecE-EEEEecCCCChHHHhh-ccCCccCC--eeEEE
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI-AYIEFKDPESVPLAMG-LNGQKLLG--IPIIV   89 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~-afVeF~~~e~A~~Al~-l~g~~i~g--~~l~v   89 (370)
                      ..-.+|||+||++.+|+++|+++|++||.|.+|.+..+.     +|+ |||+|.+.++|.+|++ |+|..|.|  +.|+|
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI  100 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI  100 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEE
Confidence            344567899999999999999999999999999887643     577 9999999999999996 99999998  89999


Q ss_pred             eccccc
Q psy2983          90 QPTQAE   95 (370)
Q Consensus        90 ~~~~~~   95 (370)
                      ++++..
T Consensus       101 ~~ak~~  106 (130)
T 3zzy_A          101 DFSKLT  106 (130)
T ss_dssp             EECSCS
T ss_pred             EecCCC
Confidence            998754

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.48  E-value=7.3e-14  Score=109.27  Aligned_cols=84  Identities=17%  Similarity=0.122  Sum_probs=73.6

Q ss_pred             cCCCCeEEEcCCCC-----CCcHHHHHHHhhcCCCeeEEEEeeeCCC-CCeecEEEEEecCCCChHHHhh-ccCCccCCe
Q psy2983          13 ERDARTIFCMQLSQ-----RIRTRDLEEFFSSVGKVRDVRLITCNKT-RRFKGIAYIEFKDPESVPLAMG-LNGQKLLGI   85 (370)
Q Consensus        13 ~~~~r~v~V~nLp~-----~~te~~L~~~f~~~G~v~~v~i~~d~~~-~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~   85 (370)
                      ..++++|+|+||..     +-++++|++.|++||.|.++.+++++.+ ++++|||||+|.+.++|.+|++ |||..+.|+
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            35789999999963     2378999999999999999999998754 6889999999999999999995 999999999


Q ss_pred             eEEEecccccc
Q psy2983          86 PIIVQPTQAEK   96 (370)
Q Consensus        86 ~l~v~~~~~~~   96 (370)
                      .|.|.++....
T Consensus        85 ~i~v~~a~~~~   95 (105)
T 2pe8_A           85 VVKACFYNLDK   95 (105)
T ss_dssp             ECEEEECCHHH
T ss_pred             EEEEEEcCHHH
Confidence            99999887543

>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=99.48  E-value=6.5e-14  Score=117.40  Aligned_cols=78  Identities=21%  Similarity=0.231  Sum_probs=69.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCC--eeEEEe
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLG--IPIIVQ   90 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g--~~l~v~   90 (370)
                      ....+|||+|||..+|+++|+++|++||.|.+|.+..+    .++|||||+|.+.++|..|++ |+|..|.|  ++|+|.
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~  119 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  119 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEE
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEE
Confidence            34466899999999999999999999999999998653    247899999999999999996 99999965  999999


Q ss_pred             ccccc
Q psy2983          91 PTQAE   95 (370)
Q Consensus        91 ~~~~~   95 (370)
                      +++..
T Consensus       120 ~Ak~~  124 (164)
T 1sjr_A          120 FSKLT  124 (164)
T ss_dssp             ECSSS
T ss_pred             EecCC
Confidence            98764

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.46  E-value=1.7e-13  Score=119.23  Aligned_cols=78  Identities=26%  Similarity=0.262  Sum_probs=72.0

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .++|||+|||+.+++++|+++|++||.|..+++.++. +|.++|||||+|.+.++|.+|+..+ +..+.|+.|.|.+..+
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            4789999999999999999999999999999999986 6999999999999999999999855 5699999999998654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.43  E-value=3.3e-13  Score=108.40  Aligned_cols=76  Identities=20%  Similarity=0.299  Sum_probs=66.1

Q ss_pred             CCCe--EEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecE-EEEEecCCCChHHHhh-ccCCccCC--eeEE
Q psy2983          15 DART--IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI-AYIEFKDPESVPLAMG-LNGQKLLG--IPII   88 (370)
Q Consensus        15 ~~r~--v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~-afVeF~~~e~A~~Al~-l~g~~i~g--~~l~   88 (370)
                      ++++  |||+|||..+|+++|+++|++||.|.+|++.. +     .|| |||+|.+.++|..|++ |+|..|.|  ++|+
T Consensus        22 ps~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~   95 (124)
T 2e5i_A           22 GNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLK   95 (124)
T ss_dssp             CCSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEE
T ss_pred             CCcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEE
Confidence            3444  67999999999999999999999999999865 2     275 9999999999999996 99999988  6899


Q ss_pred             Eecccccc
Q psy2983          89 VQPTQAEK   96 (370)
Q Consensus        89 v~~~~~~~   96 (370)
                      |.+++...
T Consensus        96 V~~Ak~~~  103 (124)
T 2e5i_A           96 IEYARPTR  103 (124)
T ss_dssp             EECCSCSC
T ss_pred             EEEecCCc
Confidence            99887543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.41  E-value=2.6e-13  Score=121.18  Aligned_cols=80  Identities=25%  Similarity=0.438  Sum_probs=70.2

Q ss_pred             CCCceEEEecCCCCC---------CHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCcee-
Q psy2983         112 GGPMRLYIGSLHFNI---------TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFEL-  181 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~---------t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i-  181 (370)
                      ...++|||+|||..+         ++++|+++|++||.|.+|+++.+      +|||||+|.+.++|..|++.|+|..+ 
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l~  205 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTLL  205 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCCC
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEEe
Confidence            356899999999998         79999999999999999999853      89999999999999999999999999 


Q ss_pred             -----------CCeeEEEEEeecCCCC
Q psy2983         182 -----------AGRPMKVGTVTDRNES  197 (370)
Q Consensus       182 -----------~g~~l~V~~~~~~~~~  197 (370)
                                 .|+.|.|.|+.+...+
T Consensus       206 ~~~~~e~~~~~~gr~L~V~wA~~~pnp  232 (240)
T 3u1l_A          206 LPSDKEWDDRREGTGLLVKWANEDPDP  232 (240)
T ss_dssp             CTTSTTGGGGGGSCCCEEEECC-----
T ss_pred             ccccccccccCCCCEEEEEEccCCCCH
Confidence                       8999999999876543

>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=99.39  E-value=9e-13  Score=103.03  Aligned_cols=81  Identities=20%  Similarity=0.212  Sum_probs=70.2

Q ss_pred             CCceEEEecC--CCCCC--------HHHHHhcccCCCceeeEEEeecCCC--CCcccEEEEEECCHHHHHHHHHHhCCce
Q psy2983         113 GPMRLYIGSL--HFNIT--------EDMLRGIFEPFGKIDNIQLMVDPDT--GRSKGYGFITFHSADDAKKAQEQLNGFE  180 (370)
Q Consensus       113 ~~~~l~V~nl--p~~~t--------~e~l~~~f~~~G~i~~v~~~~~~~~--g~~~g~afV~f~~~~~a~~A~~~l~g~~  180 (370)
                      +++.|.+.|+  |..+.        +++|++.|++||.|.++.++++..+  +.++|+|||+|.+.++|.+|+..|||..
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            4578999998  33443        3799999999999999999988654  3689999999999999999999999999


Q ss_pred             eCCeeEEEEEeec
Q psy2983         181 LAGRPMKVGTVTD  193 (370)
Q Consensus       181 i~g~~l~V~~~~~  193 (370)
                      +.||.|+|.+...
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            9999999998654

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.39  E-value=2.8e-13  Score=121.00  Aligned_cols=81  Identities=16%  Similarity=0.345  Sum_probs=70.2

Q ss_pred             cccCCCCeEEEcCCCCCC---------cHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCC
Q psy2983          11 PEERDARTIFCMQLSQRI---------RTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQ   80 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~---------te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~   80 (370)
                      ...+..++|||+|||..+         ++++|+++|++||+|.+|+++.      ++|||||+|.+.++|+.|++ |+|.
T Consensus       129 s~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~  202 (240)
T 3u1l_A          129 SFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQ  202 (240)
T ss_dssp             --CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             ccccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhCCC
Confidence            345688999999999998         7999999999999999999985      37999999999999999995 9999


Q ss_pred             cc------------CCeeEEEeccccccc
Q psy2983          81 KL------------LGIPIIVQPTQAEKN   97 (370)
Q Consensus        81 ~i------------~g~~l~v~~~~~~~~   97 (370)
                      .+            .|+.|.|.++....+
T Consensus       203 ~l~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          203 TLLLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCCCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             EEeccccccccccCCCCEEEEEEccCCCC
Confidence            99            899999999986544

>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=99.38  E-value=4.7e-12  Score=100.16  Aligned_cols=83  Identities=18%  Similarity=0.308  Sum_probs=70.5

Q ss_pred             CCCCceEEEecCCCCCC-----------HHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCc
Q psy2983         111 TGGPMRLYIGSLHFNIT-----------EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF  179 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t-----------~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~  179 (370)
                      +.+.++|+|.||.....           +++|+++|++||.|..+.+ .++   .++|||||+|.+.++|.+|+..|||.
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~   87 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGR   87 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCC
Confidence            34568899999954432           5899999999999999965 443   37999999999999999999999999


Q ss_pred             eeCCeeEEEEEeecCCCC
Q psy2983         180 ELAGRPMKVGTVTDRNES  197 (370)
Q Consensus       180 ~i~g~~l~V~~~~~~~~~  197 (370)
                      .+.|++|+|.++.++...
T Consensus        88 ~~~gr~l~v~~a~~~~~~  105 (112)
T 2dit_A           88 WFGGRQITAQAWDGTTDY  105 (112)
T ss_dssp             EETTEECEEEECCSCCCS
T ss_pred             EECCcEEEEEEeCCCCCc
Confidence            999999999998776543

>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=99.34  E-value=3.8e-13  Score=105.03  Aligned_cols=72  Identities=18%  Similarity=0.365  Sum_probs=64.0

Q ss_pred             EecCCCCCCHHHHHhcc------------cCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeE
Q psy2983         119 IGSLHFNITEDMLRGIF------------EPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM  186 (370)
Q Consensus       119 V~nlp~~~t~e~l~~~f------------~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l  186 (370)
                      +.|||..+++++|++.|            ++||.|.++.+.++. +|.++|||||+|.+.++|.+|+..|||..+.||+|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56777777887777666            999999999999886 58999999999999999999999999999999999


Q ss_pred             EEEEe
Q psy2983         187 KVGTV  191 (370)
Q Consensus       187 ~V~~~  191 (370)
                      +|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99875

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.34  E-value=2.8e-12  Score=101.41  Aligned_cols=81  Identities=23%  Similarity=0.364  Sum_probs=68.9

Q ss_pred             cccCCCCeEEEcCCCCCCc-----------HHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-cc
Q psy2983          11 PEERDARTIFCMQLSQRIR-----------TRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LN   78 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~t-----------e~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~   78 (370)
                      ....++++|+|+||....+           +++|+++|++||.|.+|.+ .++   .++|||||+|.+.++|.+|++ |+
T Consensus        10 ~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~ln   85 (112)
T 2dit_A           10 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLD   85 (112)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHST
T ss_pred             CCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcC
Confidence            3556899999999954332           6899999999999999965 544   368999999999999999995 99


Q ss_pred             CCccCCeeEEEeccccc
Q psy2983          79 GQKLLGIPIIVQPTQAE   95 (370)
Q Consensus        79 g~~i~g~~l~v~~~~~~   95 (370)
                      |..+.|++|.|.++...
T Consensus        86 g~~~~gr~l~v~~a~~~  102 (112)
T 2dit_A           86 GRWFGGRQITAQAWDGT  102 (112)
T ss_dssp             TCEETTEECEEEECCSC
T ss_pred             CCEECCcEEEEEEeCCC
Confidence            99999999999997654

>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=99.32  E-value=4.6e-12  Score=101.02  Aligned_cols=80  Identities=19%  Similarity=0.253  Sum_probs=69.7

Q ss_pred             CceEEEecCCC--CC---CHHHHHhcccCCCceeeEEEeecCC----CCCcccEEEEEECCHHHHHHHHHHhCCceeCCe
Q psy2983         114 PMRLYIGSLHF--NI---TEDMLRGIFEPFGKIDNIQLMVDPD----TGRSKGYGFITFHSADDAKKAQEQLNGFELAGR  184 (370)
Q Consensus       114 ~~~l~V~nlp~--~~---t~e~l~~~f~~~G~i~~v~~~~~~~----~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~  184 (370)
                      +++|++.|+-.  ++   .+++|++.|++||.|.++.++.+..    ++.++|++||+|.+.++|.+|+..|||..+.||
T Consensus        20 s~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~GR   99 (118)
T 3ue2_A           20 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR   99 (118)
T ss_dssp             CCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            46899999842  22   3689999999999999999998864    457889999999999999999999999999999


Q ss_pred             eEEEEEeec
Q psy2983         185 PMKVGTVTD  193 (370)
Q Consensus       185 ~l~V~~~~~  193 (370)
                      .|+|.+...
T Consensus       100 ~i~v~~~~~  108 (118)
T 3ue2_A          100 KVVAEVYDQ  108 (118)
T ss_dssp             ECEEEEECH
T ss_pred             EEEEEEcCh
Confidence            999998643

>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=99.30  E-value=1.5e-12  Score=101.71  Aligned_cols=82  Identities=16%  Similarity=0.240  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCC--CCCCc--------HHHHHHHhhcCCCeeEEEEeeeCCC--CCeecEEEEEecCCCChHHHhh-ccCC
Q psy2983          14 RDARTIFCMQL--SQRIR--------TRDLEEFFSSVGKVRDVRLITCNKT--RRFKGIAYIEFKDPESVPLAMG-LNGQ   80 (370)
Q Consensus        14 ~~~r~v~V~nL--p~~~t--------e~~L~~~f~~~G~v~~v~i~~d~~~--~~~kg~afVeF~~~e~A~~Al~-l~g~   80 (370)
                      .+++.|.+.|+  |..+.        +++|++.|++||+|.+|.|++++.+  ++++|+|||+|.+.++|.+|++ |||.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            47899999999  44443        4799999999999999999988765  3679999999999999999995 9999


Q ss_pred             ccCCeeEEEeccccc
Q psy2983          81 KLLGIPIIVQPTQAE   95 (370)
Q Consensus        81 ~i~g~~l~v~~~~~~   95 (370)
                      .+.|++|.+.+....
T Consensus        83 ~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           83 KFANRVVVTKYCDPD   97 (105)
T ss_dssp             EETTEECEEEEECHH
T ss_pred             EeCCCEEEEEEeCHH
Confidence            999999999887643

>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=99.29  E-value=4e-12  Score=101.34  Aligned_cols=82  Identities=16%  Similarity=0.240  Sum_probs=71.5

Q ss_pred             CCCCeEEEcCCCC--CC---cHHHHHHHhhcCCCeeEEEEeeeCC----CCCeecEEEEEecCCCChHHHhh-ccCCccC
Q psy2983          14 RDARTIFCMQLSQ--RI---RTRDLEEFFSSVGKVRDVRLITCNK----TRRFKGIAYIEFKDPESVPLAMG-LNGQKLL   83 (370)
Q Consensus        14 ~~~r~v~V~nLp~--~~---te~~L~~~f~~~G~v~~v~i~~d~~----~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~   83 (370)
                      .++++|+++|+-.  ++   -++||++.|++||+|.+|.|++++.    +++++|+|||+|.+.++|.+|++ |||..+.
T Consensus        18 ~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~   97 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA   97 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            3789999999942  22   3799999999999999999999865    46788999999999999999995 9999999


Q ss_pred             CeeEEEeccccc
Q psy2983          84 GIPIIVQPTQAE   95 (370)
Q Consensus        84 g~~l~v~~~~~~   95 (370)
                      |+.|.+.+....
T Consensus        98 GR~i~v~~~~~~  109 (118)
T 3ue2_A           98 GRKVVAEVYDQE  109 (118)
T ss_dssp             TEECEEEEECHH
T ss_pred             CcEEEEEEcChH
Confidence            999999887643

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.25  E-value=1.2e-12  Score=102.23  Aligned_cols=71  Identities=20%  Similarity=0.347  Sum_probs=61.3

Q ss_pred             EcCCCCCCcHHHHHHHh------------hcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeE
Q psy2983          21 CMQLSQRIRTRDLEEFF------------SSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPI   87 (370)
Q Consensus        21 V~nLp~~~te~~L~~~f------------~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l   87 (370)
                      +.|||..+++++|++.|            ++||+|.++.++++.. ++++|||||+|.+.++|.+|++ |+|..+.|++|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            45666677777777666            9999999999998764 7899999999999999999995 99999999999


Q ss_pred             EEecc
Q psy2983          88 IVQPT   92 (370)
Q Consensus        88 ~v~~~   92 (370)
                      .|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99875

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.20  E-value=1.2e-10  Score=89.89  Aligned_cols=66  Identities=20%  Similarity=0.392  Sum_probs=58.1

Q ss_pred             CCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecCCC
Q psy2983         124 FNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNE  196 (370)
Q Consensus       124 ~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~~~  196 (370)
                      ..+++++|+++|++||.|..+.++     +.++|||||+|.+.++|..|+..+++  +.|++|+|.++.++..
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCC
Confidence            568999999999999999999987     46799999999999999999997544  6799999999876644

>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=99.19  E-value=2.2e-11  Score=96.41  Aligned_cols=46  Identities=61%  Similarity=1.039  Sum_probs=42.6

Q ss_pred             CCCCCceEEeecCCCCCCCCCchhhHHhHHHHHHHHhhcCceeeEE
Q psy2983         266 PPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHGVGASTV  311 (370)
Q Consensus       266 ~~~ps~vl~L~Nm~~~~~l~~d~~~~ei~eDv~~Ec~kyG~~~~~~  311 (370)
                      ++.||+||+|.|||+++++.|+++|+||++||++||+|||.+..+.
T Consensus         3 ~p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~   48 (114)
T 3s6e_A            3 QPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIY   48 (114)
T ss_dssp             CCCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEE
T ss_pred             CCCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEE
Confidence            5678999999999999999999999999999999999999986644

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.16  E-value=1.1e-10  Score=90.17  Aligned_cols=76  Identities=16%  Similarity=0.157  Sum_probs=63.5

Q ss_pred             CCCeEEEcCCC-------CCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeE
Q psy2983          15 DARTIFCMQLS-------QRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPI   87 (370)
Q Consensus        15 ~~r~v~V~nLp-------~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l   87 (370)
                      ..++|.|.-.+       ..+++++|+++|++||.|.+|.++     ++++|||||+|.+.++|..|++. +..+.|++|
T Consensus         9 ~~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~-~~~~~g~~l   82 (100)
T 2d9o_A            9 GTPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQN-EVGLVDNPL   82 (100)
T ss_dssp             SSCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHT-CCBCSSSBC
T ss_pred             ccceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHh-cCCCCCCeE
Confidence            36778887665       458999999999999999999987     36789999999999999999963 344679999


Q ss_pred             EEecccccc
Q psy2983          88 IVQPTQAEK   96 (370)
Q Consensus        88 ~v~~~~~~~   96 (370)
                      .|.++....
T Consensus        83 ~V~~a~~~~   91 (100)
T 2d9o_A           83 KISWLEGQP   91 (100)
T ss_dssp             EEECSSCCC
T ss_pred             EEEEccCCC
Confidence            999976543

>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=99.15  E-value=1.7e-10  Score=91.19  Aligned_cols=76  Identities=16%  Similarity=0.168  Sum_probs=64.6

Q ss_pred             CCceEEEecCCCCC----------CHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeC
Q psy2983         113 GPMRLYIGSLHFNI----------TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELA  182 (370)
Q Consensus       113 ~~~~l~V~nlp~~~----------t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~  182 (370)
                      +++.|.+.|+=..-          .+++|++.|++||.|.++.+.++.    ++|+|||+|.+.++|.+|+..|||..+.
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            45688898873221          136899999999999999986552    5899999999999999999999999999


Q ss_pred             CeeEEEEEee
Q psy2983         183 GRPMKVGTVT  192 (370)
Q Consensus       183 g~~l~V~~~~  192 (370)
                      ||.|+|.++.
T Consensus        82 GR~i~v~~~~   91 (114)
T 3s6e_A           82 GKMITAAYVP   91 (114)
T ss_dssp             TEECEEEEEC
T ss_pred             CEEEEEEEEc
Confidence            9999999964

>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=99.15  E-value=6.2e-11  Score=111.35  Aligned_cols=75  Identities=23%  Similarity=0.420  Sum_probs=64.3

Q ss_pred             CCCCceEEEec--CCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeC---Ce-
Q psy2983         111 TGGPMRLYIGS--LHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELA---GR-  184 (370)
Q Consensus       111 ~~~~~~l~V~n--lp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~---g~-  184 (370)
                      ..+..+|||+|  |+..+++++|+++|++||.|.+|.+..      +||||||+|.+.++|.+|++.|||.++.   |+ 
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            34557999999  578999999999999999999987742      4799999999999999999999999883   44 


Q ss_pred             -eEEEEEe
Q psy2983         185 -PMKVGTV  191 (370)
Q Consensus       185 -~l~V~~~  191 (370)
                       .+.+.++
T Consensus        89 ~~ly~~~~   96 (345)
T 3tht_A           89 ITLYLNFV   96 (345)
T ss_dssp             EECEEEEC
T ss_pred             eEEEEEEe
Confidence             5777776

>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=99.13  E-value=4.1e-11  Score=112.54  Aligned_cols=80  Identities=14%  Similarity=0.262  Sum_probs=66.9

Q ss_pred             CCCcccCCCCeEEEcC--CCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccC-
Q psy2983           8 DLSPEERDARTIFCMQ--LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLL-   83 (370)
Q Consensus         8 ~~~~~~~~~r~v~V~n--Lp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~-   83 (370)
                      .+.-...++++|||+|  |+..+|+++|+++|++||.|.+|.+..      +||||||+|.+.++|.+|++ |||..+. 
T Consensus        10 ~v~~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~   83 (345)
T 3tht_A           10 GIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVD   83 (345)
T ss_dssp             TCCCCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEEC
T ss_pred             CceecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCcccc
Confidence            3445567899999999  578999999999999999999987743      47999999999999999996 9999873 


Q ss_pred             --Ce--eEEEeccc
Q psy2983          84 --GI--PIIVQPTQ   93 (370)
Q Consensus        84 --g~--~l~v~~~~   93 (370)
                        |+  .+++.+..
T Consensus        84 ~~g~~~~ly~~~~~   97 (345)
T 3tht_A           84 DLGQKITLYLNFVE   97 (345)
T ss_dssp             TTSCEEECEEEECS
T ss_pred             ccCCceEEEEEEee
Confidence              44  56676654

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.89  E-value=6.4e-09  Score=77.46  Aligned_cols=73  Identities=23%  Similarity=0.315  Sum_probs=61.9

Q ss_pred             CceEEEecCC----CCCCH----HHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCee
Q psy2983         114 PMRLYIGSLH----FNITE----DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRP  185 (370)
Q Consensus       114 ~~~l~V~nlp----~~~t~----e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~  185 (370)
                      ..+|+|...|    ..+-+    .+|.+.|++||.|..+++..+.        +||+|.+.++|.+|++ |||..+.||.
T Consensus         7 d~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~Gr~   77 (91)
T 2dnr_A            7 GGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLNRT   77 (91)
T ss_dssp             SCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETTEE
T ss_pred             CCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCCeE
Confidence            3578888776    23333    6899999999999999998763        8999999999999999 9999999999


Q ss_pred             EEEEEeecCC
Q psy2983         186 MKVGTVTDRN  195 (370)
Q Consensus       186 l~V~~~~~~~  195 (370)
                      |+|+.+.+.-
T Consensus        78 LkV~lkt~dW   87 (91)
T 2dnr_A           78 ITIALKSPSG   87 (91)
T ss_dssp             EEEEECCCSS
T ss_pred             EEEEeCCCCc
Confidence            9999987643

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.89  E-value=5.5e-09  Score=82.86  Aligned_cols=75  Identities=17%  Similarity=0.197  Sum_probs=66.1

Q ss_pred             CCCCceEEEecCCCC-CCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECC-HHHHHHHHHHhC--CceeCCeeE
Q psy2983         111 TGGPMRLYIGSLHFN-ITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS-ADDAKKAQEQLN--GFELAGRPM  186 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~-~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~-~~~a~~A~~~l~--g~~i~g~~l  186 (370)
                      ......|||+||++. ++.++|+++|++||.|..|.+..+..      .|||+|.+ .++|..|+..|+  +..|.|..+
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~   88 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEV   88 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEE
Confidence            345678999999999 99999999999999999999987753      59999999 899999999995  788899888


Q ss_pred             EEEEe
Q psy2983         187 KVGTV  191 (370)
Q Consensus       187 ~V~~~  191 (370)
                      ++...
T Consensus        89 ~~evL   93 (121)
T 1owx_A           89 TWEVL   93 (121)
T ss_dssp             EEEEC
T ss_pred             EEEEC
Confidence            88764

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.79  E-value=8e-09  Score=76.94  Aligned_cols=73  Identities=22%  Similarity=0.330  Sum_probs=61.8

Q ss_pred             CCCeEEEcCCCC----CCcH----HHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCee
Q psy2983          15 DARTIFCMQLSQ----RIRT----RDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIP   86 (370)
Q Consensus        15 ~~r~v~V~nLp~----~~te----~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~   86 (370)
                      +.-||+|.-.|.    ++-.    .+|.+.|.+||.|..++++.++        +||+|.+.++|.+|++|+|..+.|+.
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~mnG~~v~Gr~   77 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLSLNGKELLNRT   77 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGGGTTCEETTEE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHhcCCeEeCCeE
Confidence            446788887762    3333    6789999999999999998864        89999999999999999999999999


Q ss_pred             EEEeccccc
Q psy2983          87 IIVQPTQAE   95 (370)
Q Consensus        87 l~v~~~~~~   95 (370)
                      |+|+...+.
T Consensus        78 LkV~lkt~d   86 (91)
T 2dnr_A           78 ITIALKSPS   86 (91)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEeCCCC
Confidence            999887643

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.70  E-value=1.4e-08  Score=80.45  Aligned_cols=74  Identities=14%  Similarity=0.097  Sum_probs=64.0

Q ss_pred             CCCCeEEEcCCCCC-CcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecC-CCChHHHhh-c--cCCccCCeeEE
Q psy2983          14 RDARTIFCMQLSQR-IRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKD-PESVPLAMG-L--NGQKLLGIPII   88 (370)
Q Consensus        14 ~~~r~v~V~nLp~~-~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~-~e~A~~Al~-l--~g~~i~g~~l~   88 (370)
                      .....|||+||+.. ++.++|+++|++||+|..|.+.++..      .|||+|.+ .++|..|+. +  .+..|.|..+.
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~   89 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   89 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEE
Confidence            46788999999999 99999999999999999999988653      49999999 688998885 6  57889998888


Q ss_pred             Eeccc
Q psy2983          89 VQPTQ   93 (370)
Q Consensus        89 v~~~~   93 (370)
                      +....
T Consensus        90 ~evL~   94 (121)
T 1owx_A           90 WEVLE   94 (121)
T ss_dssp             EEECC
T ss_pred             EEECC
Confidence            86544

>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=98.67  E-value=3.1e-08  Score=87.65  Aligned_cols=67  Identities=21%  Similarity=0.254  Sum_probs=60.3

Q ss_pred             CCHHHHHhcccCCCceeeEEEeecCC----CCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         126 ITEDMLRGIFEPFGKIDNIQLMVDPD----TGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       126 ~t~e~l~~~f~~~G~i~~v~~~~~~~----~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      -.+++|++.|++||.|.++.+..+..    ++.++|++||+|.+.++|.+|+..|||..+.||.|.+.+..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            45689999999999999999986543    45899999999999999999999999999999999999854

>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=98.64  E-value=3.3e-08  Score=73.99  Aligned_cols=72  Identities=18%  Similarity=0.205  Sum_probs=61.5

Q ss_pred             CCCCeEEEcCCCCC-----CcH----HHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCC
Q psy2983          14 RDARTIFCMQLSQR-----IRT----RDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLG   84 (370)
Q Consensus        14 ~~~r~v~V~nLp~~-----~te----~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g   84 (370)
                      ++.-||+|.-++..     +-.    .+|.+.|..||.|..++++.|+        +||+|.+.++|.+|++|+|..+.|
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~ldG~~v~G   84 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLDVDGMKVKG   84 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHHGGGSEETT
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHhcCCeeeCC
Confidence            35578999988743     222    5688999999999999998864        999999999999999999999999


Q ss_pred             eeEEEeccc
Q psy2983          85 IPIIVQPTQ   93 (370)
Q Consensus        85 ~~l~v~~~~   93 (370)
                      +.|+|+...
T Consensus        85 r~L~V~~k~   93 (95)
T 1ufw_A           85 RAVKISGPS   93 (95)
T ss_dssp             EEEEEECCC
T ss_pred             eEEEEeccC
Confidence            999998754

>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=98.62  E-value=3.8e-08  Score=73.63  Aligned_cols=70  Identities=14%  Similarity=0.219  Sum_probs=60.0

Q ss_pred             CCceEEEecCCCC-----CCH----HHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCC
Q psy2983         113 GPMRLYIGSLHFN-----ITE----DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG  183 (370)
Q Consensus       113 ~~~~l~V~nlp~~-----~t~----e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g  183 (370)
                      +..+|+|..++..     +-+    .+|.+.|.+||.|..+++..|.        +||+|.+.++|.+|+. |||..+.|
T Consensus        14 pD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v~G   84 (95)
T 1ufw_A           14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKVKG   84 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEETT
T ss_pred             CCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeeeCC
Confidence            3468999988743     322    5799999999999999998763        9999999999999999 99999999


Q ss_pred             eeEEEEEe
Q psy2983         184 RPMKVGTV  191 (370)
Q Consensus       184 ~~l~V~~~  191 (370)
                      |.|+|+..
T Consensus        85 r~L~V~~k   92 (95)
T 1ufw_A           85 RAVKISGP   92 (95)
T ss_dssp             EEEEEECC
T ss_pred             eEEEEecc
Confidence            99999874

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.55  E-value=2.2e-07  Score=70.88  Aligned_cols=72  Identities=21%  Similarity=0.250  Sum_probs=66.4

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCC-----CceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEE
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPF-----GKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMK  187 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~-----G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~  187 (370)
                      ..++|-+-|||..+++..|+.+++++     |.+.++.+..|      -|-|+|+|.+...|-+|.-.|+|.+|.|++|+
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD------H~GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD------FNGAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT------TTEEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC------CCceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            35789999999999999999999999     99999999877      45699999999999999999999999999999


Q ss_pred             EEE
Q psy2983         188 VGT  190 (370)
Q Consensus       188 V~~  190 (370)
                      +.-
T Consensus        94 ~gT   96 (117)
T 2l9w_A           94 SGT   96 (117)
T ss_dssp             EEC
T ss_pred             ecC
Confidence            964

>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=98.53  E-value=1.8e-07  Score=82.69  Aligned_cols=82  Identities=15%  Similarity=0.191  Sum_probs=67.3

Q ss_pred             CCCCeEEEcCCC-----CCCcHHHHHHHhhcCCCeeEEEEeeeCCC----CCeecEEEEEecCCCChHHHhh-ccCCccC
Q psy2983          14 RDARTIFCMQLS-----QRIRTRDLEEFFSSVGKVRDVRLITCNKT----RRFKGIAYIEFKDPESVPLAMG-LNGQKLL   83 (370)
Q Consensus        14 ~~~r~v~V~nLp-----~~~te~~L~~~f~~~G~v~~v~i~~d~~~----~~~kg~afVeF~~~e~A~~Al~-l~g~~i~   83 (370)
                      ..++.+.+.|+-     ..-.+++|++.|++||.|.++.+.++..+    ++++|++||+|.+.++|.+|++ |+|..+.
T Consensus       122 ~~s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~  201 (222)
T 3dxb_A          122 MESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA  201 (222)
T ss_dssp             CBCSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSS
T ss_pred             cccccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceEC
Confidence            344556666653     22457899999999999999999866543    4899999999999999999996 9999999


Q ss_pred             CeeEEEeccccc
Q psy2983          84 GIPIIVQPTQAE   95 (370)
Q Consensus        84 g~~l~v~~~~~~   95 (370)
                      ||.|.+.+....
T Consensus       202 gr~i~~~~~~~~  213 (222)
T 3dxb_A          202 GRKVVAEVYDQE  213 (222)
T ss_dssp             SSBCEEEECCHH
T ss_pred             CeEEEEEEcCHH
Confidence            999999887643

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.26  E-value=1.1e-06  Score=67.01  Aligned_cols=72  Identities=21%  Similarity=0.244  Sum_probs=65.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcC-----CCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHh-hccCCccCCeeEE
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSV-----GKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPII   88 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~-----G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~i~g~~l~   88 (370)
                      ..|+|-+-|||..++...|+.+++++     |.+..+.+..|.      +-|+|+|.+...|-+|. +|+|..|.|+.|+
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            47999999999999999999999999     999999998875      45999999999999988 7999999999999


Q ss_pred             Eecc
Q psy2983          89 VQPT   92 (370)
Q Consensus        89 v~~~   92 (370)
                      +.-.
T Consensus        94 ~gTv   97 (117)
T 2l9w_A           94 SGTI   97 (117)
T ss_dssp             EECH
T ss_pred             ecCH
Confidence            8543

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.06  E-value=1.1e-05  Score=61.04  Aligned_cols=89  Identities=16%  Similarity=0.265  Sum_probs=73.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhc-----CCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEE
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSS-----VGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPII   88 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~-----~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~   88 (370)
                      ...++|.|.|||+.+.++.|.-+|+.     -|+|.++....        +-|+|+|.+.+.|++.|+.....++|.+|.
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~~H~L~~~~Ls   77 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQADHELHGAQLS   77 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCSCCBSSSSBCE
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCCcceecCeEEE
Confidence            35688999999999999999999997     26899987643        459999999999999999888999999999


Q ss_pred             EecccccccccCCCCCCCCCCCCCCCceEEEecCCCCCC
Q psy2983          89 VQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNIT  127 (370)
Q Consensus        89 v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t  127 (370)
                      |.+...                 ..+.+|++.+||+.++
T Consensus        78 V~P~~~-----------------~~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           78 LRPAPP-----------------RAPARLLLQGLPPGTS   99 (104)
T ss_dssp             EEECCC-----------------CCCCCCCCCSCCCCCC
T ss_pred             EEcCCC-----------------CCcceEeeecCCCCCC
Confidence            976432                 2245788999988765

>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=97.66  E-value=0.00012  Score=55.61  Aligned_cols=76  Identities=18%  Similarity=0.210  Sum_probs=64.3

Q ss_pred             CCCceEEEecCCCCC-C----HHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeE
Q psy2983         112 GGPMRLYIGSLHFNI-T----EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM  186 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~-t----~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l  186 (370)
                      ..+++|+|.||+..+ .    .+.++++|..|+++.....++.      -.-..|.|.++++|.+|...||+..+.|+.+
T Consensus         3 ~~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS------FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~   76 (104)
T 1wey_A            3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc------ceEEEEEeCChHHHHHHHHHhccceecCcee
Confidence            456789999998765 2    2678999999999988887754      2247899999999999999999999999999


Q ss_pred             EEEEeec
Q psy2983         187 KVGTVTD  193 (370)
Q Consensus       187 ~V~~~~~  193 (370)
                      +|-++.+
T Consensus        77 r~YFgq~   83 (104)
T 1wey_A           77 KLYFAQT   83 (104)
T ss_dssp             EEECCCC
T ss_pred             EEEecCC
Confidence            9999874

>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=97.25  E-value=0.0014  Score=48.86  Aligned_cols=69  Identities=14%  Similarity=0.316  Sum_probs=57.4

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCC--cccEEEEEECCHHHHHHHHHHhCCceeCC
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGR--SKGYGFITFHSADDAKKAQEQLNGFELAG  183 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~--~~g~afV~f~~~~~a~~A~~~l~g~~i~g  183 (370)
                      .+|.|++||+.+|++++.+.+.+...+....+.....+.+  .-.-|+|.|.+.+++..-...++|+.+.+
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            4799999999999999999999998887777766544332  22359999999999999999999998864

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.16  E-value=0.0016  Score=48.66  Aligned_cols=55  Identities=18%  Similarity=0.312  Sum_probs=46.9

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhC
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN  177 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~  177 (370)
                      .+.+++ ++|+.+...||.++|++||.| .|+.+-|.       -|||.|.+++.|..|+..+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            456677 999999999999999999955 57777663       79999999999999999763

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.09  E-value=0.0077  Score=45.49  Aligned_cols=74  Identities=22%  Similarity=0.303  Sum_probs=61.3

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccC-----CCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEE
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEP-----FGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMK  187 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~-----~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~  187 (370)
                      ...+|.|.|||..+.++.|.-+|++     -|.|..++...        +-|+|+|.+.+.|++.++ -..+.+.+.+|.
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~-k~~H~L~~~~Ls   77 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLA-QADHELHGAQLS   77 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHT-CSCCBSSSSBCE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhc-CCcceecCeEEE
Confidence            3478999999999999999999987     26898888753        469999999999999987 347888999999


Q ss_pred             EEEeecCC
Q psy2983         188 VGTVTDRN  195 (370)
Q Consensus       188 V~~~~~~~  195 (370)
                      |....++.
T Consensus        78 V~P~~~~~   85 (104)
T 2dhx_A           78 LRPAPPRA   85 (104)
T ss_dssp             EEECCCCC
T ss_pred             EEcCCCCC
Confidence            97755443

>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=97.01  E-value=0.0012  Score=49.09  Aligned_cols=68  Identities=18%  Similarity=0.326  Sum_probs=53.1

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCC--CeecEEEEEecCCCChHHHhh-ccCCccCC
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTR--RFKGIAYIEFKDPESVPLAMG-LNGQKLLG   84 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~--~~kg~afVeF~~~e~A~~Al~-l~g~~i~g   84 (370)
                      .+|-|++||+++||+++.+.+.....+.-........+.  ..-.-|||.|.+.+++....+ ++|..|.+
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            479999999999999999999998877666555433221  223469999999999988885 89888743

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=96.97  E-value=0.0037  Score=47.42  Aligned_cols=74  Identities=16%  Similarity=0.217  Sum_probs=60.7

Q ss_pred             CCCeEEEcCCCCCC-cH----HHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHh-hccCCccCCeeEE
Q psy2983          15 DARTIFCMQLSQRI-RT----RDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPII   88 (370)
Q Consensus        15 ~~r~v~V~nLp~~~-te----~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~i~g~~l~   88 (370)
                      -..+|+|.||+..+ ..    +.++++|..|+++......+.=      +-..|.|.++++|.+|- +|++..++|+.++
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCceeE
Confidence            35789999999765 32    5678899999998887776532      34789999999999999 5999999999999


Q ss_pred             Eecccc
Q psy2983          89 VQPTQA   94 (370)
Q Consensus        89 v~~~~~   94 (370)
                      +-..+.
T Consensus        78 ~YFgq~   83 (104)
T 1wey_A           78 LYFAQT   83 (104)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            988763

>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=96.94  E-value=0.0013  Score=51.23  Aligned_cols=72  Identities=15%  Similarity=0.134  Sum_probs=59.0

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCC-eeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLG-IPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g-~~l~v~~   91 (370)
                      ....+-|.|-+.|+.. ...|...|++||.|.+....      ....+-.|.|.+..+|++||..||..+.| ..|-|.+
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~------~~~NWihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV~p   93 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKP   93 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEE
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC------CCCCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEEEE
Confidence            4456789999999984 77888999999999987751      22468999999999999999999999985 4555555

>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=96.73  E-value=0.0015  Score=48.75  Aligned_cols=57  Identities=21%  Similarity=0.476  Sum_probs=46.1

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG   76 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~   76 (370)
                      ......+.+++ ++|+.+...||.++|++||.|. |+.+-|.       .|||.|.+++.|..|+.
T Consensus        11 ~~p~r~HVf~l-~FP~ewKt~DI~~lFs~fggv~-I~WidDT-------sAlvvf~~~~~a~~al~   67 (100)
T 1whv_A           11 LQPKRDHVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCCCCCSEEEE-ECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHH
T ss_pred             CCCCCCeEEEE-eCChhhhhHHHHHHhhccCCEE-EEEEcCC-------eEEEEecCHHHHHHHHH
Confidence            33344566777 9999999999999999999554 5556553       59999999999999996

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.56  E-value=0.0017  Score=62.92  Aligned_cols=65  Identities=15%  Similarity=0.184  Sum_probs=47.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCC
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLG   84 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g   84 (370)
                      ...|+|+|. .|..+++.+|.++|++||+|.++.+-.+.     .-||.|||.+.+++..+++..+....+
T Consensus        51 qa~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~~~~~p~~~  115 (464)
T 3pq1_A           51 QAQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQNGTHTPXXX  115 (464)
T ss_dssp             HHHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHSSCCCCCCB
T ss_pred             HhcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHhccCCCccc
Confidence            456999998 79999999999999999999998776543     369999999999999888655544443

>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=96.48  E-value=0.0026  Score=47.61  Aligned_cols=51  Identities=24%  Similarity=0.483  Sum_probs=42.4

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG   76 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~   76 (370)
                      +.++| ++|+.+...||.++|++||. ..|..+-|.       .|||.|.+++.|..|+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~   57 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVKIAVN   57 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEETT-------EEEEEEEEECHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHH
Confidence            45666 99999999999999999993 335555543       59999999999999996

>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=96.43  E-value=0.0042  Score=46.49  Aligned_cols=54  Identities=20%  Similarity=0.332  Sum_probs=46.2

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhC
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN  177 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~  177 (370)
                      +.++| ++|+.+...||.++|++||.| .|+.+-|.       -|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            45666 999999999999999999944 67777663       79999999999999999775

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.31  E-value=0.008  Score=45.04  Aligned_cols=70  Identities=16%  Similarity=0.255  Sum_probs=52.1

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCC--cccEEEEEECCHHHHHHHHHHhCCceeCC
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGR--SKGYGFITFHSADDAKKAQEQLNGFELAG  183 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~--~~g~afV~f~~~~~a~~A~~~l~g~~i~g  183 (370)
                      +.+|.|+.||+.+|++++.+.+++.-.+....+.....+.+  .-.-|+|.|.+.++...-.+..+|..+.+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D   80 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLD   80 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEEC
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEe
Confidence            46899999999999999999988765544333332222211  12248999999999999999999988754

>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=95.93  E-value=0.025  Score=44.03  Aligned_cols=72  Identities=14%  Similarity=0.117  Sum_probs=57.4

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCC-eeEEEEEe
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG-RPMKVGTV  191 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g-~~l~V~~~  191 (370)
                      ...-|.|-+.|... ...+...|++||.|.+....    .  ....-.|.|.+..+|++|+. .||..+.| -.|-|.+.
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~----~--~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS----N--TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC----S--SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC----C--CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            35679999999885 56778889999999887752    1  24589999999999999999 79999985 56666654


Q ss_pred             e
Q psy2983         192 T  192 (370)
Q Consensus       192 ~  192 (370)
                      .
T Consensus        95 ~   95 (119)
T 1wwh_A           95 I   95 (119)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=94.97  E-value=0.0082  Score=44.98  Aligned_cols=71  Identities=17%  Similarity=0.341  Sum_probs=48.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCC--CCeecEEEEEecCCCChHHHhh-ccCCccCC
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKT--RRFKGIAYIEFKDPESVPLAMG-LNGQKLLG   84 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~--~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g   84 (370)
                      -.+-+|-|+.||+++||+++.+.++..-.+.-........+  ...-.-|||.|.+.++.....+ .+|..|.+
T Consensus         7 ~~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D   80 (97)
T 2l08_A            7 HHSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLD   80 (97)
T ss_dssp             CCCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEEC
T ss_pred             ccceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEe
Confidence            35678999999999999998888877534322211111111  1112459999999999998885 88887743

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=94.81  E-value=0.014  Score=56.63  Aligned_cols=54  Identities=19%  Similarity=0.228  Sum_probs=41.5

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHH
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE  174 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~  174 (370)
                      +.|+|. .|..+++.+|.++|++||+|.++.+.++.     .-||.|||.+.+++..++.
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHh
Confidence            579998 69999999999999999999999887653     3599999999999987765

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=94.29  E-value=0.024  Score=44.80  Aligned_cols=78  Identities=15%  Similarity=0.234  Sum_probs=55.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeE-EEEeee-----------CCCC--CeecEEEEEecCCCChHHHhhccCC
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRD-VRLITC-----------NKTR--RFKGIAYIEFKDPESVPLAMGLNGQ   80 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~-v~i~~d-----------~~~~--~~kg~afVeF~~~e~A~~Al~l~g~   80 (370)
                      ...-|.|-+.|+. ....+.+.|++||.|.+ +...+.           ++-.  ....+..|.|.+..+|.+||..||.
T Consensus         6 ~e~~VtVFGFp~~-~~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~   84 (132)
T 3p3d_A            6 GELAILVFGYPET-MANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGA   84 (132)
T ss_dssp             --CEEEEECCCGG-GHHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTC
T ss_pred             CceEEEEEecCHH-HHHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCe
Confidence            3456889999765 55667889999999866 211110           0000  1356889999999999999999999


Q ss_pred             ccCCeeEEEeccc
Q psy2983          81 KLLGIPIIVQPTQ   93 (370)
Q Consensus        81 ~i~g~~l~v~~~~   93 (370)
                      .|.|..|-|.+..
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            9999866666554

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=90.99  E-value=0.24  Score=39.09  Aligned_cols=75  Identities=17%  Similarity=0.232  Sum_probs=53.5

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceee-EEEeecC------------CCC-CcccEEEEEECCHHHHHHHHHHhCCce
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDN-IQLMVDP------------DTG-RSKGYGFITFHSADDAKKAQEQLNGFE  180 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~-v~~~~~~------------~~g-~~~g~afV~f~~~~~a~~A~~~l~g~~  180 (370)
                      .-|.|-+.|+... ..+.+.|++||.|.+ +....+.            ..+ ...+.-.|+|.+..+|.+|+. -||..
T Consensus         8 ~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAV   85 (132)
T ss_dssp             CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCE
T ss_pred             eEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeE
Confidence            4577888876655 556678999999866 2221100            000 134578999999999999999 79999


Q ss_pred             eCCeeEEEEEe
Q psy2983         181 LAGRPMKVGTV  191 (370)
Q Consensus       181 i~g~~l~V~~~  191 (370)
                      |.|.-|-|.+.
T Consensus        86 i~G~mIGV~Py   96 (132)
T 3p3d_A           86 FNGVLLGVIPY   96 (132)
T ss_dssp             ETTEECEEEEC
T ss_pred             eCcEEEEEEEC
Confidence            99987777664

---

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	370
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-31
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	9e-09
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-24
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	4e-15
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	4e-21
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-12
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	8e-21
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	7e-12
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-19
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-08
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-19
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-11
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-19
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-09
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-19
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-11
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	8e-19
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	5e-11
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-18
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	9e-11
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	4e-18
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-09
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	4e-18
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	4e-09
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	8e-18
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-11
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-17
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	4e-09
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-17
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-08
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-17
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-09
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	6e-17
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-09
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	7e-17
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-06
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	9e-17
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	4e-10
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	9e-17
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-12
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	9e-17
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-10
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-16
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-11
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-16
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-09
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-16
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-08
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-16
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	9e-09
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	6e-16
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-07
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	6e-16
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	6e-07
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-16
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-09
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	8e-16
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-05
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-15
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	3e-09
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-15
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	9e-11
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-15
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-09
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-15
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-07
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-15
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-15
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	5e-10
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	4e-15
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-07
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:) 4e-15
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-05
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	8e-15
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-07
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	9e-15
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	8e-06
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-14
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-14
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-06
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-14
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-14
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-14
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	6e-09
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	3e-14
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	4e-14
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	5e-14
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-05
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	6e-14
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	4e-07
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	9e-14
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-09
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-13
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	4e-06
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-13
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	7e-06
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	4e-13
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	5e-13
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	8e-13
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	9e-13
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	4e-06
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	0.001
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-12
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-12
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-12
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	9e-05
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-12
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	6e-12
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	0.001
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	6e-12
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-11
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-11
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	3e-11
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	3e-11
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	1e-06
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-11
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	8e-04
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	1e-10
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	5e-04
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-10
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	0.001
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-10
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	1e-09
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	2e-06
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-09
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-09
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	9e-08
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-09
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-05
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-08
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	9e-08
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-07
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	1e-07
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	4e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-07
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	2e-07
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	1e-06
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	1e-06
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-06
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	3e-06
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	3e-06
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	1e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-05

>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 =  114 bits (285), Expect = 4e-31
 Identities = 43/185 (23%), Positives = 73/185 (39%), Gaps = 8/185 (4%)

Query: 12  EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
           E    R +F   LS       L   F   G + D  ++    T+R +G  ++ +   E V
Sbjct: 2   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61

Query: 72  PLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDML 131
             AM             V     E  RA +   + +P       ++++G +  +  E  L
Sbjct: 62  DAAMNARPH-------KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 114

Query: 132 RGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV 191
           R  FE +GKI+ I++M D  +G+ +G+ F+TF   D   K         + G   +V   
Sbjct: 115 RDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA 173

Query: 192 TDRNE 196
             + E
Sbjct: 174 LSKQE 178

>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 = 52.3 bits (124), Expect = 9e-09
 Identities = 16/83 (19%), Positives = 37/83 (44%)

Query: 17  RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
           + IF   + +      L ++F   GK+  + ++T   + + +G A++ F D +SV   + 
Sbjct: 98  KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 157

Query: 77  LNGQKLLGIPIIVQPTQAEKNRA 99
                + G    V+   +++  A
Sbjct: 158 QKYHTVNGHNCEVRKALSKQEMA 180

>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 = 94.3 bits (234), Expect = 1e-24
 Identities = 67/92 (72%), Positives = 82/92 (89%)

Query: 7   DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
           D+LSPEERDART+FCMQL+ RIR RDLE+FFS+VGKVRDVR+I+   +RR KGIAY+EF 
Sbjct: 9   DNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFC 68

Query: 67  DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNR 98
           + +SVPLA+GL GQ+LLG+PIIVQ +QAEKNR
Sbjct: 69  EIQSVPLAIGLTGQRLLGVPIIVQASQAEKNR 100

>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 = 68.5 bits (167), Expect = 4e-15
 Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            ++   L   I    L   F   GK+ +++++ D ++ RSKG  ++ F        A   
Sbjct: 20  TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG- 78

Query: 176 LNGFELAGRPMKV 188
           L G  L G P+ V
Sbjct: 79  LTGQRLLGVPIIV 91

>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 = 84.2 bits (208), Expect = 4e-21
 Identities = 27/72 (37%), Positives = 44/72 (61%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LY+G LH ++TE ML   F P G I +I++  D  T RS GY ++ F    DA++A + +
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 177 NGFELAGRPMKV 188
           N   + G+P+++
Sbjct: 63  NFDVIKGKPVRI 74

>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 = 60.3 bits (146), Expect = 2e-12
 Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 3/81 (3%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
          +++   L   +    L E FS  G +  +R+     TRR  G AY+ F+ P     A+  
Sbjct: 2  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 77 LNGQKLLGIPIIVQPTQAEKN 97
          +N   + G P+ +    ++++
Sbjct: 62 MNFDVIKGKPVRIMW--SQRD 80

>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 = 83.8 bits (207), Expect = 8e-21
 Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPD-TGRSKGYGFITFHSADDAKKAQE 174
           ++ + ++ F   +  +R +F  FG++  ++L      TG  +G+GF+ F +  DAKKA  
Sbjct: 10  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 69

Query: 175 QL-NGFELAGRPMKV 188
            L +   L GR + +
Sbjct: 70  ALCHSTHLYGRRLVL 84

>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 = 58.8 bits (142), Expect = 7e-12
 Identities = 17/91 (18%), Positives = 39/91 (42%), Gaps = 3/91 (3%)

Query: 11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLIT-CNKTRRFKGIAYIEFKDPE 69
          P+++    I    +  +   R++ E FS+ G+++ VRL      T   +G  +++F   +
Sbjct: 3  PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 62

Query: 70 SVPLAMG--LNGQKLLGIPIIVQPTQAEKNR 98
              A     +   L G  ++++   +E   
Sbjct: 63 DAKKAFNALCHSTHLYGRRLVLEWADSEVTV 93

>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 = 80.9 bits (199), Expect = 1e-19
 Identities = 28/94 (29%), Positives = 50/94 (53%)

Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           G+ G  RL++ +L +  +E+ L  +F  +G +  +   +D  T + KG+ F+TF   + A
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
            KA  +++G    GR + V   T + E+   GPS
Sbjct: 64  VKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPS 97

>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 = 49.7 bits (118), Expect = 1e-08
 Identities = 23/86 (26%), Positives = 41/86 (47%), Gaps = 1/86 (1%)

Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
           +  +F   LS      DLE+ FS+ G + ++     + T++ KG A++ F  PE    A
Sbjct: 7  GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66

Query: 75 M-GLNGQKLLGIPIIVQPTQAEKNRA 99
             ++GQ   G  + V P+  +K  +
Sbjct: 67 YAEVDGQVFQGRMLHVLPSTIKKEAS 92

>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 = 79.3 bits (195), Expect = 3e-19
 Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +++IG L +  T++ LR  F  FG++    +M DP T RS+G+GF+TF       K    
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA- 60

Query: 176 LNGFELAGRPMKV 188
            +  EL  + +  
Sbjct: 61  QSRHELDSKTIDP 73

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.5 bits (136), Expect = 4e-11
 Identities = 16/72 (22%), Positives = 32/72 (44%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLN 78
          +F   LS +     L E+F   G+V++  ++    T+R +G  ++ F D   V   +  +
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 79 GQKLLGIPIIVQ 90
            +L    I  +
Sbjct: 63 RHELDSKTIDPK 74

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 79.6 bits (196), Expect = 3e-19
 Identities = 22/73 (30%), Positives = 38/73 (52%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            LY+G+L F  TE+ +  +F   G I  I + +D     + G+ F+ ++S  DA+ A   
Sbjct: 9   TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 176 LNGFELAGRPMKV 188
           +NG  L  R ++ 
Sbjct: 69  INGTRLDDRIIRT 81

>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 = 51.9 bits (124), Expect = 2e-09
 Identities = 15/78 (19%), Positives = 30/78 (38%), Gaps = 1/78 (1%)

Query: 14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
          + + T++   LS       + E FS  G ++ + +      +   G  ++E+        
Sbjct: 5  KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 64

Query: 74 AM-GLNGQKLLGIPIIVQ 90
          AM  +NG +L    I   
Sbjct: 65 AMRYINGTRLDDRIIRTD 82

>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 = 78.9 bits (194), Expect = 4e-19
 Identities = 22/82 (26%), Positives = 40/82 (48%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L+IG L   + +D ++ +   FG +    L+ D  TG SKGY F  +   +   +A   
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 176 LNGFELAGRPMKVGTVTDRNES 197
           LNG +L  + + V   +   ++
Sbjct: 63  LNGMQLGDKKLLVQRASVGAKN 84

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 4e-11
 Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 1/85 (1%)

Query: 16 ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM 75
          A  +F   L   +    ++E  +S G ++   L+  + T   KG A+ E+ D      A+
Sbjct: 1  AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60

Query: 76 -GLNGQKLLGIPIIVQPTQAEKNRA 99
           GLNG +L    ++VQ        A
Sbjct: 61 AGLNGMQLGDKKLLVQRASVGAKNA 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 = 78.1 bits (192), Expect = 8e-19
 Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            LY+ +L   IT+D L  IF  +G I    ++ D  TGR +G  F+ ++  ++A++A   
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 176 LNGFELAG--RPMKV 188
           LN     G  +P+ V
Sbjct: 68  LNNVIPEGGSQPLSV 82

>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 = 56.1 bits (135), Expect = 5e-11
 Identities = 17/82 (20%), Positives = 32/82 (39%), Gaps = 3/82 (3%)

Query: 12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
          E      ++   L + I    L+  F   G +    ++    T R +G+A++ +   E  
Sbjct: 2  ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 61

Query: 72 PLAM-GLNGQKLLGI--PIIVQ 90
            A+  LN     G   P+ V+
Sbjct: 62 QEAISALNNVIPEGGSQPLSVR 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 = 77.0 bits (189), Expect = 2e-18
 Identities = 27/93 (29%), Positives = 51/93 (54%), Gaps = 7/93 (7%)

Query: 113 GPM-------RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS 165
           GP+        +Y+G L   ++E +L  +F   G + N  +  D  TG+ +GYGF+ F S
Sbjct: 1   GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 60

Query: 166 ADDAKKAQEQLNGFELAGRPMKVGTVTDRNESV 198
            +DA  A + ++  +L G+P++V   +  N+++
Sbjct: 61  EEDADYAIKIMDMIKLYGKPIRVNKASAHNKNL 93

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 9e-11
 Identities = 21/88 (23%), Positives = 35/88 (39%), Gaps = 1/88 (1%)

Query: 11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
           E     T++   L +++    L E F   G V +  +     T + +G  ++EF   E 
Sbjct: 4  SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 63

Query: 71 VPLAM-GLNGQKLLGIPIIVQPTQAEKN 97
             A+  ++  KL G PI V    A   
Sbjct: 64 ADYAIKIMDMIKLYGKPIRVNKASAHNK 91

>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 = 76.2 bits (187), Expect = 4e-18
 Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 3/75 (4%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPD---TGRSKGYGFITFHSADDAKKAQ 173
           L+I +L+F+ TE+ L+G+F   G I +  +    +      S G+GF+ +   + A+KA 
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 174 EQLNGFELAGRPMKV 188
           +QL G  + G  ++V
Sbjct: 61  KQLQGHTVDGHKLEV 75

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.0 bits (124), Expect = 2e-09
 Identities = 18/85 (21%), Positives = 33/85 (38%), Gaps = 4/85 (4%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLI---TCNKTRRFKGIAYIEFKDPESVPLAM 75
          +F   L+       L+  FS VG ++   +             G  ++E+K PE    A+
Sbjct: 1  LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 76 -GLNGQKLLGIPIIVQPTQAEKNRA 99
            L G  + G  + V+ ++     A
Sbjct: 61 KQLQGHTVDGHKLEVRISERATKPA 85

>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 = 75.8 bits (186), Expect = 4e-18
 Identities = 24/73 (32%), Positives = 40/73 (54%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            L +  L  ++T+  L  +F   G I+  ++M D  TG S GY F+ F S  D+++A + 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 176 LNGFELAGRPMKV 188
           LNG  +  + +KV
Sbjct: 64  LNGITVRNKRLKV 76

>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 = 50.8 bits (121), Expect = 4e-09
 Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 1/77 (1%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
           +    L Q +  R+L   F ++G +   R++   KT    G A+++F        A+  
Sbjct: 4  NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 77 LNGQKLLGIPIIVQPTQ 93
          LNG  +    + V   +
Sbjct: 64 LNGITVRNKRLKVSYAR 80

>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 = 76.2 bits (187), Expect = 8e-18
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 3/72 (4%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LYI +L + IT + +  IF  +G I     +   +T  ++G  ++ +    DAK A + L
Sbjct: 10  LYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNACDHL 66

Query: 177 NGFELAGRPMKV 188
           +GF +  R + V
Sbjct: 67  SGFNVCNRYLVV 78

>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 = 58.5 bits (141), Expect = 2e-11
 Identities = 20/91 (21%), Positives = 36/91 (39%), Gaps = 6/91 (6%)

Query: 9  LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDP 68
          L PE    R ++   L  +I   ++ + F   G +R    I    T   +G AY+ ++D 
Sbjct: 2  LPPEVN--RILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDI 56

Query: 69 ESVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
               A   L+G  +    ++V    A +  
Sbjct: 57 FDAKNACDHLSGFNVCNRYLVVLYYNANRAF 87

>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 = 74.6 bits (183), Expect = 1e-17
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L + +L F +++  ++ +F  FG +    +  D  +GRS G   + F    DA KA +Q
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQ 60

Query: 176 LNGFELAGRPMKV 188
            NG  L GRPM +
Sbjct: 61  YNGVPLDGRPMNI 73

>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 = 50.7 bits (121), Expect = 4e-09
 Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 2/73 (2%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
          +    L   +   D++E F+  G ++   +     + R  G A + F+       AM   
Sbjct: 3  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQY 61

Query: 78 NGQKLLGIPIIVQ 90
          NG  L G P+ +Q
Sbjct: 62 NGVPLDGRPMNIQ 74

>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 = 74.7 bits (183), Expect = 1e-17
 Identities = 28/73 (38%), Positives = 45/73 (61%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            L +  L    TE  LR +F  +G I ++ ++ D  + RS+G+ F+ F + DDAK+A+E+
Sbjct: 11  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 176 LNGFELAGRPMKV 188
            NG EL GR ++V
Sbjct: 71  ANGMELDGRRIRV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.3 bits (117), Expect = 2e-08
 Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
            +    LS     RDL E FS  G + DV ++   ++RR +G A++ F++ +    A  
Sbjct: 10 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 76 GLNGQKLLGIPIIV 89
            NG +L G  I V
Sbjct: 70 RANGMELDGRRIRV 83

>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 = 73.5 bits (180), Expect = 3e-17
 Identities = 22/73 (30%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +++IG L ++ T+  L+  F  FG++ +  L +DP TGRS+G+GF+ F  ++   K  + 
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD- 59

Query: 176 LNGFELAGRPMKV 188
               +L G+ +  
Sbjct: 60  QKEHKLNGKVIDP 72

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.8 bits (121), Expect = 4e-09
 Identities = 24/72 (33%), Positives = 35/72 (48%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLN 78
          +F   LS     +DL+++FS  G+V D  L     T R +G  ++ FK+ ESV   M   
Sbjct: 2  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61

Query: 79 GQKLLGIPIIVQ 90
            KL G  I  +
Sbjct: 62 EHKLNGKVIDPK 73

>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 = 72.7 bits (178), Expect = 6e-17
 Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++G L  +  E+ +R  F  FG++++I+L +D  T + +G+ FITF   +  KK  E+
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 176 LNGFELAGRPMKV 188
                +     ++
Sbjct: 61  -KYHNVGLSKCEI 72

>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 = 50.3 bits (120), Expect = 5e-09
 Identities = 19/72 (26%), Positives = 30/72 (41%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLN 78
          IF   LS       + E+F   G+V  + L   NKT + +G  +I FK+ E V   M   
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 79 GQKLLGIPIIVQ 90
             +      ++
Sbjct: 62 YHNVGLSKCEIK 73

>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 = 72.8 bits (178), Expect = 7e-17
 Identities = 18/79 (22%), Positives = 33/79 (41%)

Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           G  GP  + + ++ F ++ D +   F  +  I     +   + G   G   + F S D+A
Sbjct: 5   GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEA 64

Query: 170 KKAQEQLNGFELAGRPMKV 188
             A   LN   +  R +K+
Sbjct: 65  TAAVIDLNDRPIGSRKVKL 83

>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 = 42.7 bits (100), Expect = 3e-06
 Identities = 11/82 (13%), Positives = 28/82 (34%), Gaps = 1/82 (1%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
          S  +     I    +   +   ++ +FF     +     +  N+     G A + F+  +
Sbjct: 3  SSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRD 62

Query: 70 SVPLAM-GLNGQKLLGIPIIVQ 90
              A+  LN + +    + + 
Sbjct: 63 EATAAVIDLNDRPIGSRKVKLV 84

>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 = 72.8 bits (178), Expect = 9e-17
 Identities = 27/73 (36%), Positives = 44/73 (60%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            LY+G L   + + +L   F PFG I +IQ+ +D +T + +G+ F+ F  A+DA  A + 
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 176 LNGFELAGRPMKV 188
           +N  EL GR ++V
Sbjct: 67  MNESELFGRTIRV 79

>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 = 53.9 bits (129), Expect = 4e-10
 Identities = 18/83 (21%), Positives = 40/83 (48%), Gaps = 1/83 (1%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
          R ++   L++ +  + L   F   G + D+++    +T + +G A++EF+  E    A+ 
Sbjct: 6  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

Query: 76 GLNGQKLLGIPIIVQPTQAEKNR 98
           +N  +L G  I V   +  + +
Sbjct: 66 NMNESELFGRTIRVNLAKPMRIK 88

>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 = 73.2 bits (179), Expect = 9e-17
 Identities = 29/82 (35%), Positives = 45/82 (54%), Gaps = 1/82 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L+IG L F  TE+ LR  +E +GK+ +  +M DP + RS+G+GF+TF S  +   A   
Sbjct: 22  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA- 80

Query: 176 LNGFELAGRPMKVGTVTDRNES 197
                + GR ++      R ES
Sbjct: 81  ARPHSIDGRVVEPKRAVAREES 102

>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 = 61.2 bits (148), Expect = 2e-12
 Identities = 17/89 (19%), Positives = 33/89 (37%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
             E+   R +F   LS       L  ++   GK+ D  ++    ++R +G  ++ F    
Sbjct: 14  KREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMA 73

Query: 70  SVPLAMGLNGQKLLGIPIIVQPTQAEKNR 98
            V  AM      + G  +  +   A +  
Sbjct: 74  EVDAAMAARPHSIDGRVVEPKRAVAREES 102

>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 = 72.5 bits (177), Expect = 9e-17
 Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 6/85 (7%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQL-----MVDPDTGRSKGYGFITFHSADDAK 170
           RLY+G++ F ITE+ +   F    ++  +       ++     + K + F+ F S D+  
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 171 KAQEQLNGFELAGRPMKVGTVTDRN 195
           +A    +G    G+ +K+    D  
Sbjct: 63  QAM-AFDGIIFQGQSLKIRRPHDYQ 86

>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 = 54.8 bits (131), Expect = 2e-10
 Identities = 13/79 (16%), Positives = 33/79 (41%), Gaps = 5/79 (6%)

Query: 16 ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRL-----ITCNKTRRFKGIAYIEFKDPES 70
          AR ++   +   I    + +FF++  ++  +       +   +  + K  A++EF+  + 
Sbjct: 1  ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 60

Query: 71 VPLAMGLNGQKLLGIPIIV 89
             AM  +G    G  + +
Sbjct: 61 TTQAMAFDGIIFQGQSLKI 79

>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 = 71.6 bits (175), Expect = 2e-16
 Identities = 24/73 (32%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L+IG L F  T++ LR  FE +G + +  +M DP+T RS+G+GF+T+ + ++   A   
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 66

Query: 176 LNGFELAGRPMKV 188
               ++ GR ++ 
Sbjct: 67  ARPHKVDGRVVEP 79

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.1 bits (140), Expect = 1e-11
 Identities = 18/79 (22%), Positives = 30/79 (37%)

Query: 12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
          E    R +F   LS       L   F   G + D  ++    T+R +G  ++ +   E V
Sbjct: 2  EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61

Query: 72 PLAMGLNGQKLLGIPIIVQ 90
            AM     K+ G  +  +
Sbjct: 62 DAAMNARPHKVDGRVVEPK 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 = 71.7 bits (175), Expect = 2e-16
 Identities = 33/81 (40%), Positives = 43/81 (53%), Gaps = 1/81 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQ-LMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++IG+L   I E +L   F  FG I     +M DPDTG SKGY FI F S D +  A E 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 176 LNGFELAGRPMKVGTVTDRNE 196
           +NG  L  RP+ V     ++ 
Sbjct: 61  MNGQYLCNRPITVSYAFKKDS 81

>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 = 3e-09
 Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 2/82 (2%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKV-RDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
          IF   L   I  + L + FS+ G + +  +++    T   KG A+I F   ++   A+  
Sbjct: 1  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 77 LNGQKLLGIPIIVQPTQAEKNR 98
          +NGQ L   PI V     + ++
Sbjct: 61 MNGQYLCNRPITVSYAFKKDSK 82

>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 = 71.3 bits (174), Expect = 2e-16
 Identities = 27/73 (36%), Positives = 43/73 (58%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            L +  L  N+T++  R +F   G+I++ +L+ D  TG+S GYGF+ +    DA+KA   
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 176 LNGFELAGRPMKV 188
           LNG  L  + +KV
Sbjct: 64  LNGLRLQTKTIKV 76

>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 = 48.6 bits (115), Expect = 3e-08
 Identities = 17/78 (21%), Positives = 33/78 (42%), Gaps = 1/78 (1%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
            +    L Q +   +    F S+G++   +L+    T +  G  ++ + DP+    A+ 
Sbjct: 3  TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 76 GLNGQKLLGIPIIVQPTQ 93
           LNG +L    I V   +
Sbjct: 63 TLNGLRLQTKTIKVSYAR 80

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.2 bits (174), Expect = 3e-16
 Identities = 26/75 (34%), Positives = 43/75 (57%), Gaps = 2/75 (2%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            LY+  L   +T+  L  +F  +G+I   +++VD  TG S+G GFI F    +A++A + 
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 176 LNGFELAGR--PMKV 188
           LNG + +G   P+ V
Sbjct: 68  LNGQKPSGATEPITV 82

>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 = 50.0 bits (119), Expect = 9e-09
 Identities = 26/84 (30%), Positives = 42/84 (50%), Gaps = 4/84 (4%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
          S   RDA  ++   L + +  ++LE+ FS  G++   R++    T   +G+ +I F    
Sbjct: 1  SASIRDA-NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRI 59

Query: 70 SVPLAM-GLNGQKLLG--IPIIVQ 90
              A+ GLNGQK  G   PI V+
Sbjct: 60 EAEEAIKGLNGQKPSGATEPITVK 83

>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 = 70.4 bits (172), Expect = 6e-16
 Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 2/81 (2%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            L +  L +  TE  L+  F  FG++  +Q+  D  TG SKG+GF+ F   +   K   Q
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 176 LNGFELAGRPMKVGTVTDRNE 196
            +  +  GR         +  
Sbjct: 70  RHMID--GRWCDCKLPNSKQS 88

>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 = 45.7 bits (108), Expect = 3e-07
 Identities = 17/85 (20%), Positives = 39/85 (45%), Gaps = 1/85 (1%)

Query: 14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
          +    +  + L  +   +DL+E+FS+ G+V  V++    KT   KG  ++ F + E+   
Sbjct: 6  QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVK 65

Query: 74 AMGLNGQKLLGIPIIVQPTQAEKNR 98
           M      + G     +   +++++
Sbjct: 66 VM-SQRHMIDGRWCDCKLPNSKQSQ 89

>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 = 70.5 bits (172), Expect = 6e-16
 Identities = 26/100 (26%), Positives = 49/100 (49%), Gaps = 7/100 (7%)

Query: 105 NLQPRGTGGPMR-------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKG 157
             Q  G  G  +       L+I  L     +  L  +F PFG + + ++ +D  T  SK 
Sbjct: 2   TQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKC 61

Query: 158 YGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNES 197
           +GF+++ +   A+ A + +NGF++  + +KV     +N+S
Sbjct: 62  FGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS 101

>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 = 45.1 bits (106), Expect = 6e-07
 Identities = 18/90 (20%), Positives = 38/90 (42%), Gaps = 1/90 (1%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
             E  +   +F   L Q    +DL + F   G V   ++    +T   K   ++ + +P 
Sbjct: 12  QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPV 71

Query: 70  SVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
           S   A+  +NG ++    + VQ  +++ + 
Sbjct: 72  SAQAAIQSMNGFQIGMKRLKVQLKRSKNDS 101

>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 = 70.3 bits (172), Expect = 7e-16
 Identities = 20/90 (22%), Positives = 43/90 (47%), Gaps = 10/90 (11%)

Query: 116 RLYIGSLH-FNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           R++IG+L+   + +  +  IF  +GKI    +         KG+ F+ + +  +A+ A  
Sbjct: 17  RVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVA 68

Query: 175 QLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
             +G  +AG+ + +    +   +   GPS+
Sbjct: 69  GEDGRMIAGQVLDINLAAEPKVN-RSGPSS 97

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.3 bits (120), Expect = 8e-09
 Identities = 17/95 (17%), Positives = 37/95 (38%), Gaps = 10/95 (10%)

Query: 6  SDDLSPEERDARTIFCMQLSQ-RIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIE 64
          S   +        +F   L+   ++  D+E  FS  GK+    +         KG A+++
Sbjct: 5  SSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQ 56

Query: 65 FKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
          + +  +   A+ G +G+ + G  + +      K  
Sbjct: 57 YVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVN 91

>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 = 70.1 bits (171), Expect = 8e-16
 Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 4/77 (5%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDN--IQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
           RL+IG +      + +        +     I      D  +++G+ F+ + S   A  A+
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 174 EQLNG--FELAGRPMKV 188
            +L     +L G  + V
Sbjct: 63  RKLMPGRIQLWGHQIAV 79

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.8 bits (95), Expect = 2e-05
 Identities = 12/91 (13%), Positives = 36/91 (39%), Gaps = 5/91 (5%)

Query: 18  TIFCMQLSQRIRTRDLEEFFSSVGKVRD--VRLITCNKTRRFKGIAYIEFKDPESVPLA- 74
            +F   + +  +  ++ E  + V +     +   +     + +G A++E++   +  +A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 75  --MGLNGQKLLGIPIIVQPTQAEKNRAGNTL 103
             +     +L G  I V   + E +   + +
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEIDVDEDVM 93

>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 = 69.0 bits (168), Expect = 1e-15
 Identities = 25/73 (34%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++G L  N T + ++  FE FGK+D+  LM D  T R +G+GF+TF S D  +K  E 
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE- 59

Query: 176 LNGFELAGRPMKV 188
           ++  E+  + ++ 
Sbjct: 60  IHFHEINNKMVEC 72

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.9 bits (121), Expect = 3e-09
 Identities = 16/72 (22%), Positives = 31/72 (43%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLN 78
          IF   LS      D++ +F   GKV D  L+    T R +G  ++ F+  + V     ++
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 79 GQKLLGIPIIVQ 90
            ++    +  +
Sbjct: 62 FHEINNKMVECK 73

>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 = 69.7 bits (170), Expect = 1e-15
 Identities = 32/113 (28%), Positives = 53/113 (46%), Gaps = 19/113 (16%)

Query: 87  IIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQL 146
           ++  P  ++K RA  TL                 +L FNITED L+ +FE       +++
Sbjct: 3   MLEDPCTSKKVRAARTL--------------LAKNLSFNITEDELKEVFEDA-----LEI 43

Query: 147 MVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVG 199
            +    G+SKG  +I F S  DA+K  E+  G E+ GR + +    ++  + G
Sbjct: 44  RLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTRG 96

>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 = 55.8 bits (134), Expect = 9e-11
 Identities = 26/92 (28%), Positives = 41/92 (44%), Gaps = 6/92 (6%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
           S + R ART+    LS  I   +L+E F    ++R V     ++  + KGIAYIEFK   
Sbjct: 10  SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEA 64

Query: 70  SVPLAM-GLNGQKLLGIPIIVQPTQAEKNRAG 100
                +    G ++ G  + +  T  +    G
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYYTGEKGGTRG 96

>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 = 68.9 bits (168), Expect = 2e-15
 Identities = 26/73 (35%), Positives = 40/73 (54%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            + + +L  +  E  L+ +F PFG I  I L  D  TG+SKG+ FI+FH  +DA +A   
Sbjct: 10  TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 69

Query: 176 LNGFELAGRPMKV 188
           ++GF      + V
Sbjct: 70  VSGFGYDHLILNV 82

>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 = 51.6 bits (123), Expect = 2e-09
 Identities = 24/89 (26%), Positives = 38/89 (42%), Gaps = 1/89 (1%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
          +    D  TI    LS+  R  DL+E F   G +  + L     T + KG A+I F   E
Sbjct: 2  NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 61

Query: 70 SVPLAM-GLNGQKLLGIPIIVQPTQAEKN 97
              A+ G++G     + + V+  +   N
Sbjct: 62 DAARAIAGVSGFGYDHLILNVEWAKPSTN 90

>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 = 68.6 bits (167), Expect = 2e-15
 Identities = 29/81 (35%), Positives = 52/81 (64%), Gaps = 2/81 (2%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
           P RL++ ++ F   +  LR +F  FGKI +++++ +     SKG+GF+TF ++ DA +A+
Sbjct: 11  PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAR 68

Query: 174 EQLNGFELAGRPMKVGTVTDR 194
           E+L+G  + GR ++V   T R
Sbjct: 69  EKLHGTVVEGRKIEVNNATAR 89

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.6 bits (110), Expect = 2e-07
 Identities = 21/86 (24%), Positives = 33/86 (38%), Gaps = 3/86 (3%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
          S  +   + +    +  R R  DL + F   GK+ DV        R  KG  ++ F++  
Sbjct: 5  SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVE--IIFNERGSKGFGFVTFENSA 62

Query: 70 SVPLAM-GLNGQKLLGIPIIVQPTQA 94
              A   L+G  + G  I V    A
Sbjct: 63 DADRAREKLHGTVVEGRKIEVNNATA 88

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.5 bits (167), Expect = 2e-15
 Identities = 17/84 (20%), Positives = 36/84 (42%), Gaps = 1/84 (1%)

Query: 116 RLYIGSLHFNITEDMLRGI-FEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
            +YI +L+  I +D L+      F +   I  ++   + + +G  F+ F     A  A  
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 175 QLNGFELAGRPMKVGTVTDRNESV 198
            + GF    +PM++      ++ +
Sbjct: 65  SMQGFPFYDKPMRIQYAKTDSDII 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 = 68.1 bits (166), Expect = 3e-15
 Identities = 28/84 (33%), Positives = 45/84 (53%), Gaps = 2/84 (2%)

Query: 113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
           G   ++I +L  +I    L   F  FG I + +++ D +   SKGYGF+ F + + A++A
Sbjct: 7   GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 64

Query: 173 QEQLNGFELAGRPMKVGTVTDRNE 196
            E++NG  L  R + VG    R E
Sbjct: 65  IEKMNGMLLNDRKVFVGRFKSRKE 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 = 53.5 bits (128), Expect = 5e-10
 Identities = 18/90 (20%), Positives = 37/90 (41%), Gaps = 3/90 (3%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
          S  +     IF   L + I  + L + FS+ G +   +++      +     ++ F+  E
Sbjct: 2  SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG--YGFVHFETQE 59

Query: 70 SVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
          +   A+  +NG  L    + V   ++ K R
Sbjct: 60 AAERAIEKMNGMLLNDRKVFVGRFKSRKER 89

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.1 bits (166), Expect = 4e-15
 Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            +Y G +   +T+ ++R  F PFG+I  I++         KGY F+ F + + A  A   
Sbjct: 20  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSFVRFSTHESAAHAIVS 73

Query: 176 LNGFELAGRPMKVG 189
           +NG  + G  +K  
Sbjct: 74  VNGTTIEGHVVKCY 87

>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 = 46.5 bits (110), Expect = 2e-07
 Identities = 14/87 (16%), Positives = 37/87 (42%), Gaps = 7/87 (8%)

Query: 5  YSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIE 64
          + D ++       T++C  ++  +  + + + FS  G++ ++R+            +++ 
Sbjct: 7  FEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVR 60

Query: 65 FKDPESVPLAM-GLNGQKLLGIPIIVQ 90
          F   ES   A+  +NG  + G  +   
Sbjct: 61 FSTHESAAHAIVSVNGTTIEGHVVKCY 87

>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 = 68.1 bits (166), Expect = 4e-15
 Identities = 14/72 (19%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           + +   +    E++   + E +G+++ +  + D       G  ++ F   +DA+KA   L
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMN-VCDNLGDHLVGNVYVKFRREEDAEKAVIDL 88

Query: 177 NGFELAGRPMKV 188
           N     G+P+  
Sbjct: 89  NNRWFNGQPIHA 100

>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 = 40.8 bits (95), Expect = 2e-05
 Identities = 17/91 (18%), Positives = 30/91 (32%), Gaps = 5/91 (5%)

Query: 1   MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
                +D L     D   +   +           E     G+V ++ +   N      G 
Sbjct: 15  NSSQSADGLRSAVSD---VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCD-NLGDHLVGN 70

Query: 61  AYIEFKDPESVPLAM-GLNGQKLLGIPIIVQ 90
            Y++F+  E    A+  LN +   G PI  +
Sbjct: 71  VYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 67.1 bits (163), Expect = 8e-15
 Identities = 27/73 (36%), Positives = 43/73 (58%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            L++ S+H    ED ++  F  +G+I NI L +D  TG SKGY  + + +   A  A+E 
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 68

Query: 176 LNGFELAGRPMKV 188
           LNG E+ G+ ++V
Sbjct: 69  LNGAEIMGQTIQV 81

>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 = 45.5 bits (107), Expect = 3e-07
 Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
          +   +F   + +  +  +++E F   G+++++ L    +T   KG A +E++  +    A
Sbjct: 6  EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 65

Query: 75 M-GLNGQKLLGIPIIVQ 90
             LNG +++G  I V 
Sbjct: 66 KEALNGAEIMGQTIQVD 82

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 66.9 bits (163), Expect = 9e-15
 Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 6/73 (8%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL++G+L  +ITE+ +R +FE +GK   + +  D        +GFI   +   A+ A+ +
Sbjct: 10  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKVE 63

Query: 176 LNGFELAGRPMKV 188
           L+   L G+ ++V
Sbjct: 64  LDNMPLRGKQLRV 76

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.5 bits (97), Expect = 8e-06
 Identities = 13/75 (17%), Positives = 25/75 (33%), Gaps = 7/75 (9%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
            +F   L   I   ++ + F   GK  +V +             +I  +      +A  
Sbjct: 9  SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGF------GFIRLETRTLAEIAKV 62

Query: 76 GLNGQKLLGIPIIVQ 90
           L+   L G  + V+
Sbjct: 63 ELDNMPLRGKQLRVR 77

>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 = 66.6 bits (162), Expect = 1e-14
 Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
           P  LY+G+L  ++TE ++  +F   G   + +++ +     +  Y F+ F+   DA  A 
Sbjct: 8   PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAAL 65

Query: 174 EQLNGFELAGRPMKV 188
             +NG ++ G+ +KV
Sbjct: 66  AAMNGRKILGKEVKV 80

>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 = 66.2 bits (161), Expect = 2e-14
 Identities = 18/94 (19%), Positives = 37/94 (39%), Gaps = 7/94 (7%)

Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           G+ G   +++G    ++TED LR  F  +G + ++ +           + F+TF     A
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQIA 55

Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
           +          + G  + +     ++ S  G  S
Sbjct: 56  QSLCG--EDLIIKGISVHISNAEPKHNSNSGPSS 87

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 1e-06
 Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 6/84 (7%)

Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
           +  +F  + +  +   +L EFFS  G V DV +        F+  A++ F D +     
Sbjct: 4  GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSL 58

Query: 75 MGLNGQKLLGIPIIVQPTQAEKNR 98
           G     + GI + +   + + N 
Sbjct: 59 CG-EDLIIKGISVHISNAEPKHNS 81

>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 = 66.3 bits (161), Expect = 2e-14
 Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 8/81 (9%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKI--------DNIQLMVDPDTGRSKGYGFITFHSAD 167
            +Y+  L+ ++T D L   F+  G +          I + +D +TG+ KG   +++    
Sbjct: 10  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 69

Query: 168 DAKKAQEQLNGFELAGRPMKV 188
            AK A E  +G +  G  +KV
Sbjct: 70  TAKAAVEWFDGKDFQGSKLKV 90

>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 = 46.3 bits (109), Expect = 2e-07
 Identities = 20/97 (20%), Positives = 39/97 (40%), Gaps = 9/97 (9%)

Query: 11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCN--------KTRRFKGIAY 62
           E+ D   I+   L+  +   DL +FF   G V+  +             +T + KG A 
Sbjct: 3  DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 62

Query: 63 IEFKDPESVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
          + ++DP +   A+   +G+   G  + V   + +   
Sbjct: 63 VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 99

>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 = 65.9 bits (160), Expect = 3e-14
 Identities = 20/94 (21%), Positives = 37/94 (39%), Gaps = 2/94 (2%)

Query: 111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAK 170
              P   ++G+L +++TE+ ++  F               +  R KG+G+  F   D   
Sbjct: 12  KSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLL 71

Query: 171 KAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
            A   LN   L  + ++V       +    GPS+
Sbjct: 72  SALS-LNEESLGNKRIRVDVADQAQDK-DSGPSS 103

>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 = 47.4 bits (112), Expect = 1e-07
 Identities = 20/85 (23%), Positives = 33/85 (38%)

Query: 17  RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
            T F   L   +    ++EFF  +           +   R KG  Y EF+D +S+  A+ 
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 77  LNGQKLLGIPIIVQPTQAEKNRAGN 101
           LN + L    I V      +++   
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKDSG 100

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.5 bits (159), Expect = 3e-14
 Identities = 28/82 (34%), Positives = 50/82 (60%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +L++G L F+  E  L  +F  +G+I  + ++ D +T RS+G+GF+TF + DDAK A   
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 176 LNGFELAGRPMKVGTVTDRNES 197
           +NG  + GR ++V      +++
Sbjct: 67  MNGKSVDGRQIRVDQAGKSSDN 88

>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 = 50.5 bits (120), Expect = 6e-09
 Identities = 23/89 (25%), Positives = 43/89 (48%), Gaps = 2/89 (2%)

Query: 13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVP 72
            D   +F   LS     + LE+ FS  G++ +V ++   +T+R +G  ++ F++ +   
Sbjct: 2  ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 61

Query: 73 LAM-GLNGQKLLGIPIIVQPTQA-EKNRA 99
           AM  +NG+ + G  I V        NR+
Sbjct: 62 DAMMAMNGKSVDGRQIRVDQAGKSSDNRS 90

>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 = 65.9 bits (160), Expect = 3e-14
 Identities = 25/74 (33%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
            ++++G L ++ T+  LR  FE FG I+   ++ D  TG+S+GYGF+T      A++A +
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 70

Query: 175 QLNGFELAGRPMKV 188
             N   + GR   V
Sbjct: 71  DPNP-IIDGRKANV 83

>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 = 65.8 bits (160), Expect = 4e-14
 Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 4/79 (5%)

Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           G    +R+ + +L + +T D+L  IF  FG +  I          ++    + +     A
Sbjct: 3   GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSA 58

Query: 170 KKAQEQLNGFELAGRPMKV 188
           + A+  L+G  +      +
Sbjct: 59  QHAKLSLDGQNIYNACCTL 77

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.7 bits (157), Expect = 5e-14
 Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 6/73 (8%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            LY+ +L  + +E+M+   F                  + + Y F+ F + +DA +A + 
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAV------ERVKKIRDYAFVHFSNREDAVEAMKA 63

Query: 176 LNGFELAGRPMKV 188
           LNG  L G P++V
Sbjct: 64  LNGKVLDGSPIEV 76

>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 = 40.8 bits (95), Expect = 1e-05
 Identities = 16/84 (19%), Positives = 34/84 (40%), Gaps = 7/84 (8%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
          + ++   L        +E+ F+++            + ++ +  A++ F + E    AM 
Sbjct: 9  KILYVRNLMLSTSEEMIEKEFNNIKP------GAVERVKKIRDYAFVHFSNREDAVEAMK 62

Query: 76 GLNGQKLLGIPIIVQPTQAEKNRA 99
           LNG+ L G PI V   +     +
Sbjct: 63 ALNGKVLDGSPIEVTLAKPVDKDS 86

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.4 bits (156), Expect = 6e-14
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++++G +  +  E  LR  FE +GKI+ I++M D  +G+ +G+ F+TF   D   K    
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI- 62

Query: 176 LNGFELAGRPMKV 188
                + G   +V
Sbjct: 63  QKYHTVNGHNCEV 75

>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 = 45.1 bits (106), Expect = 4e-07
 Identities = 15/74 (20%), Positives = 33/74 (44%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
          + IF   + +      L ++F   GK+  + ++T   + + +G A++ F D +SV   + 
Sbjct: 3  KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

Query: 77 LNGQKLLGIPIIVQ 90
               + G    V+
Sbjct: 63 QKYHTVNGHNCEVR 76

>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 = 64.3 bits (156), Expect = 9e-14
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 5/82 (6%)

Query: 109 RGTGG--PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA 166
           RG  G    R+Y+G+L  +I    +  +F  +G I +I L           + F+ F   
Sbjct: 7   RGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG---PPFAFVEFEDP 63

Query: 167 DDAKKAQEQLNGFELAGRPMKV 188
            DA+ A    +G++  G  ++V
Sbjct: 64  RDAEDAVYGRDGYDYDGYRLRV 85

>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 = 52.8 bits (126), Expect = 1e-09
 Identities = 23/90 (25%), Positives = 40/90 (44%), Gaps = 4/90 (4%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
           P   +   I+   L   IRT+D+E+ F   G +RD+        R     A++EF+DP 
Sbjct: 8  GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDID---LKNRRGGPPFAFVEFEDPR 64

Query: 70 SVPLAM-GLNGQKLLGIPIIVQPTQAEKNR 98
              A+ G +G    G  + V+  ++ +  
Sbjct: 65 DAEDAVYGRDGYDYDGYRLRVEFPRSGRGT 94

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.9 bits (155), Expect = 1e-13
 Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 7/74 (9%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           +LYIG+L   +T D LR +F            +        GY F+ +   + A +A E 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLP------LAGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 176 LNG-FELAGRPMKV 188
           L+G  EL G+ M+V
Sbjct: 57  LSGKVELHGKIMEV 70

>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 = 42.0 bits (98), Expect = 4e-06
 Identities = 16/84 (19%), Positives = 34/84 (40%), Gaps = 8/84 (9%)

Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-G 76
           ++   LS  +   DL + F               +     G A++++ D      A+  
Sbjct: 3  KLYIGNLSPAVTADDLRQLFGDRKLPLA------GQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 77 LNGQ-KLLGIPIIVQPTQAEKNRA 99
          L+G+ +L G  + V  + ++K R+
Sbjct: 57 LSGKVELHGKIMEVDYSVSKKLRS 80

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 63.7 bits (154), Expect = 1e-13
 Identities = 13/73 (17%), Positives = 32/73 (43%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            L++ +   + T+  +R + +    +     +       S+ + +I   S +DA+   E+
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 176 LNGFELAGRPMKV 188
           LNG ++ G  +  
Sbjct: 63  LNGLKIEGYTLVT 75

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 41.7 bits (97), Expect = 7e-06
 Identities = 12/75 (16%), Positives = 27/75 (36%), Gaps = 1/75 (1%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
           T++          R++ +    +  V     +   +    +  AYI+    E     + 
Sbjct: 2  CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 76 GLNGQKLLGIPIIVQ 90
           LNG K+ G  ++ +
Sbjct: 62 KLNGLKIEGYTLVTK 76

>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 = 62.5 bits (151), Expect = 4e-13
 Identities = 25/95 (26%), Positives = 46/95 (48%), Gaps = 1/95 (1%)

Query: 103 LPNLQPRGTGGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFI 161
           +P       G P + LY+ +L   +TE  L  +F  F +     +     TGR +G  FI
Sbjct: 6   IPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFI 65

Query: 162 TFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
           TF + + A +A   +NG++L G+ + +    ++ +
Sbjct: 66  TFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQ 100

>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 = 62.1 bits (150), Expect = 5e-13
 Identities = 25/88 (28%), Positives = 46/88 (52%), Gaps = 6/88 (6%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            ++I +L F+  E+ L  + + FG +  +++++ PDT  SKG  F  F + + A+K    
Sbjct: 10  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 69

Query: 176 LN------GFELAGRPMKVGTVTDRNES 197
            +      G +L GR +KV     R+E+
Sbjct: 70  ASLEAEGGGLKLDGRQLKVDLAVTRDEA 97

>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 = 43.6 bits (102), Expect = 2e-06
 Identities = 22/98 (22%), Positives = 35/98 (35%), Gaps = 7/98 (7%)

Query: 9  LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDP 68
          L  +  + +T+F   LS       L E     G ++ VR++    T   KG A+ +F   
Sbjct: 1  LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQ 60

Query: 69 ESVPLAM-------GLNGQKLLGIPIIVQPTQAEKNRA 99
          E+    +          G KL G  + V         A
Sbjct: 61 EAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA 98

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 63.0 bits (152), Expect = 8e-13
 Identities = 30/119 (25%), Positives = 58/119 (48%)

Query: 90  QPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVD 149
           Q  Q ++ +  +  P            L +  +   + E  LR +FE +G I++++++ D
Sbjct: 18  QLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCD 77

Query: 150 PDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSNLDTD 208
            +T +S+GYGF+ F S   A++A   LNGF +  + +KV      ++  G   +  D +
Sbjct: 78  RETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGN 136

>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 = 61.5 bits (149), Expect = 9e-13
 Identities = 16/76 (21%), Positives = 26/76 (34%), Gaps = 4/76 (5%)

Query: 113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
            PM      L  N   + LR     FG+I      +        G   ++F   ++A   
Sbjct: 18  HPMDFEDDPLVLNEIREDLRVECSKFGQIRK----LLLFDRHPDGVASVSFRDPEEADYC 73

Query: 173 QEQLNGFELAGRPMKV 188
            + L+G    GR +  
Sbjct: 74  IQTLDGRWFGGRQITA 89

>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 = 42.6 bits (100), Expect = 4e-06
 Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 5/60 (8%)

Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQ 90
          DL    S  G++R + L      R   G+A + F+DPE     +  L+G+   G  I  Q
Sbjct: 35 DLRVECSKFGQIRKLLLFD----RHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQ 90

>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 = 35.7 bits (82), Expect = 0.001
 Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 1/37 (2%)

Query: 269 ATQCFLLANMFDPAT-ETNPTWDVEIRDDVIEECNKH 304
             +  ++ NMF P   E +P    EIR+D+  EC+K 
Sbjct: 7   HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKF 43

>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 = 61.7 bits (149), Expect = 1e-12
 Identities = 28/92 (30%), Positives = 48/92 (52%), Gaps = 5/92 (5%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            +++G++ +  TE+ L+ IF   G + + +L+ D +TG+ KGYGF  +   + A  A   
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 176 LNGFELAGRPMKVGTVTDRNE-----SVGGGP 202
           LNG E +GR ++V             S+G G 
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEELKSLGTGA 101

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.9 bits (147), Expect = 2e-12
 Identities = 32/106 (30%), Positives = 52/106 (49%), Gaps = 6/106 (5%)

Query: 11  PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
             +R  R++F   +        L++ FS VG V   RL+   +T + KG  + E++D E+
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 71  VPLAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPM 115
              AM  LNG++  G  + V    +EKN+       L+  GTG P+
Sbjct: 63  ALSAMRNLNGREFSGRALRVDNAASEKNK-----EELKSLGTGAPV 103

>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 = 59.8 bits (144), Expect = 2e-12
 Identities = 24/71 (33%), Positives = 37/71 (52%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           LYI  L    T+  L  + +P+GKI + + ++D  T + KGYGF+ F S   A+KA   L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 177 NGFELAGRPMK 187
               +  +  K
Sbjct: 61  KASGVQAQMAK 71

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 9e-05
 Identities = 13/67 (19%), Positives = 26/67 (38%), Gaps = 1/67 (1%)

Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
          ++   L      +DL +     GK+   + I    T + KG  +++F  P +   A+  L
Sbjct: 1  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 78 NGQKLLG 84
              +  
Sbjct: 61 KASGVQA 67

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.6 bits (146), Expect = 2e-12
 Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 1/80 (1%)

Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
           +  +I ++ F+IT+  +    E     +N   ++  + G+  G   + F + DDA+K++ 
Sbjct: 9   VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER 68

Query: 175 QLNGFELAGRPMKVGTVTDR 194
            L+  +L GR   V  VT  
Sbjct: 69  -LHRKKLNGREAFVHVVTLE 87

>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 = 59.4 bits (143), Expect = 6e-12
 Identities = 16/84 (19%), Positives = 30/84 (35%), Gaps = 11/84 (13%)

Query: 110 GTGGPMRLYIGSLHFNITEDM-----LRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFH 164
           G+ G   L     + ++  +         +F  + K    Q        +S     I F 
Sbjct: 1   GSSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF------KSFKRVRINFS 54

Query: 165 SADDAKKAQEQLNGFELAGRPMKV 188
           +   A  A+ +L+  E  G+ MK+
Sbjct: 55  NPLSAADARLRLHKTEFLGKEMKL 78

>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 = 35.9 bits (82), Expect = 0.001
 Identities = 13/93 (13%), Positives = 26/93 (27%), Gaps = 12/93 (12%)

Query: 18  TIFCMQLSQRIRT-----RDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVP 72
            +     +  + +        E  F +  K    +               I F +P S  
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAA 60

Query: 73  LAM-GLNGQKLLGIPIIVQPTQAEKNRAGNTLP 104
            A   L+  + LG  + +   Q     + +  P
Sbjct: 61  DARLRLHKTEFLGKEMKLYFAQTLHIGSSHLAP 93

>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 = 59.0 bits (142), Expect = 6e-12
 Identities = 14/95 (14%), Positives = 38/95 (40%), Gaps = 8/95 (8%)

Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
           G+ G   + + +L  +     +  + + +        +      R+K   F+T  + + A
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQA 53

Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
           + A +  + +   G+ + V  +   +  +  GPS+
Sbjct: 54  QNAIQMFHQYSFRGKDLIV-QLQPTDALLCSGPSS 87

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 57.5 bits (138), Expect = 2e-11
 Identities = 15/79 (18%), Positives = 33/79 (41%), Gaps = 6/79 (7%)

Query: 116 RLYIGSLHFNITEDMLRGIFE---PFGKIDNIQLMVDPDTGRS---KGYGFITFHSADDA 169
            +++  L   + +  +    E    FGKI  + +        S       ++T+  ++DA
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 170 KKAQEQLNGFELAGRPMKV 188
            +A + +N   + GR +K 
Sbjct: 70  LRAIQCVNNVVVDGRTLKA 88

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.9 bits (139), Expect = 3e-11
 Identities = 19/104 (18%), Positives = 40/104 (38%), Gaps = 1/104 (0%)

Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
           G++  +     T     + +  L F  +++ +   F     + N   +     GRS G  
Sbjct: 1   GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60

Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
           F+ F S + A+KA  + +   +  R +++   +       G  S
Sbjct: 61  FVQFASQEIAEKA-LKKHKERIGHRYIEIFKSSRAEVRTSGPSS 103

>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 = 57.1 bits (137), Expect = 3e-11
 Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 3/75 (4%)

Query: 116 RLYIGSLHFNIT-EDMLRGIFEPFGKIDNIQLMVD-PDTGRSKGYGFITFHSADDAKKAQ 173
            + I +L   +  E++LR  FE FG I+ I +     +   +    F+ F + D A++A 
Sbjct: 6   EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 174 EQLNGFELAGRPMKV 188
           + +N   L  R + V
Sbjct: 66  Q-MNRSLLGNREISV 79

>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 = 43.6 bits (102), Expect = 2e-06
 Identities = 14/78 (17%), Positives = 26/78 (33%), Gaps = 2/78 (2%)

Query: 15 DARTIFCMQLSQRIRTRDLEE--FFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVP 72
          + R I    LS  +   +L    F       +        +       A++ F++ +S  
Sbjct: 3  EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 62

Query: 73 LAMGLNGQKLLGIPIIVQ 90
           A+ +N   L    I V 
Sbjct: 63 RALQMNRSLLGNREISVS 80

>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 = 57.1 bits (137), Expect = 3e-11
 Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
           P  LYI +L  ++ E  L  + +PFG++ +   ++   +G S+G GF    S +  +   
Sbjct: 18  PTNLYISNLPLSMDEQELENMLKPFGQVIS-TRILRDSSGTSRGVGFARMESTEKCEAVI 76

Query: 174 EQLNGFELAGRPMKVG 189
              NG  +   P    
Sbjct: 77  GHFNGKFIKTPPGVSA 92

>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 = 44.4 bits (104), Expect = 1e-06
 Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 2/84 (2%)

Query: 11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
           +E+D   ++   L   +  ++LE      G+V   R I  + +   +G+ +   +  E 
Sbjct: 13 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTR-ILRDSSGTSRGVGFARMESTEK 71

Query: 71 VPLAM-GLNGQKLLGIPIIVQPTQ 93
              +   NG+ +   P +  PT+
Sbjct: 72 CEAVIGHFNGKFIKTPPGVSAPTE 95

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.5 bits (136), Expect = 6e-11
 Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 2/69 (2%)

Query: 122 LHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGF--ITFHSADDAKKAQEQLNGF 179
             +    + +R     +G + +I++    D     G G   + F S  D +KA + L G 
Sbjct: 22  EEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR 81

Query: 180 ELAGRPMKV 188
           + A R +  
Sbjct: 82  KFANRVVVT 90

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.0 bits (93), Expect = 4e-05
 Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 2/39 (5%)

Query: 266 PPIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKH 304
            P  T+   L NM  P    +     EI +DV +EC+K+
Sbjct: 2   HP--TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKY 38

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.5 bits (84), Expect = 8e-04
 Identities = 13/73 (17%), Positives = 26/73 (35%), Gaps = 3/73 (4%)

Query: 32  DLEEFFSSVGKVRDVRLIT--CNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPII 88
           D+ +  S  G V+ + +            G  ++EF        AM GL G+K     ++
Sbjct: 30  DVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVV 89

Query: 89  VQPTQAEKNRAGN 101
            +    +     +
Sbjct: 90  TKYCDPDSYHRRD 102

>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 = 55.9 bits (134), Expect = 1e-10
 Identities = 13/96 (13%), Positives = 29/96 (30%), Gaps = 7/96 (7%)

Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
           P       R+ +  L  + +   L+      G +    +  D         G + +   +
Sbjct: 9   PPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG-------MGMVEYLRKE 61

Query: 168 DAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
           D + A  +L+  +      +   +    E   G  S
Sbjct: 62  DMEYALRKLDDTKFRSHEGETSYIRVYPERSSGPSS 97

>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 = 36.7 bits (84), Expect = 5e-04
 Identities = 13/91 (14%), Positives = 26/91 (28%), Gaps = 8/91 (8%)

Query: 11  PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
           P  R    +    L      +DL++               C    +  G+  +E+   E 
Sbjct: 10  PTRRSDFRVLVSGLPPSGSWQDLKDHMRE-------AGDVCYADVQKDGMGMVEYLRKED 62

Query: 71  VPLAM-GLNGQKLLGIPIIVQPTQAEKNRAG 100
           +  A+  L+  K           +    R+ 
Sbjct: 63  MEYALRKLDDTKFRSHEGETSYIRVYPERSS 93

>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 = 55.5 bits (133), Expect = 2e-10
 Identities = 15/73 (20%), Positives = 32/73 (43%), Gaps = 7/73 (9%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +  G L   ++ + L  + E  G +D + +  +        Y F  + + +++K+A   L
Sbjct: 23  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKRAYVTL 76

Query: 177 NGFEL-AGRPMKV 188
           NG E+      K+
Sbjct: 77  NGKEVVDDLGQKI 89

>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 = 35.9 bits (82), Expect = 0.001
 Identities = 13/84 (15%), Positives = 26/84 (30%), Gaps = 10/84 (11%)

Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
            +    L   +    L       G V  + +            ++  ++  E    A  
Sbjct: 21 LVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPY------SFARYRTTEESKRAYV 74

Query: 76 GLNGQKLL---GIPIIVQPTQAEK 96
           LNG++++   G  I +     EK
Sbjct: 75 TLNGKEVVDDLGQKITLYLNFVEK 98

>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 = 54.3 bits (130), Expect = 2e-10
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 8/73 (10%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            LY+     ++T  +LRG F PFG I ++ +             F+T+   + A +A  +
Sbjct: 7   TLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAVAE 58

Query: 176 LNGFELAGRPMKV 188
           LNG ++    +KV
Sbjct: 59  LNGTQVESVQLKV 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 = 53.0 bits (126), Expect = 1e-09
 Identities = 21/81 (25%), Positives = 43/81 (53%), Gaps = 2/81 (2%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
           P  L+IG+L+ N +   L+         +++ ++    TG ++ +G++ F SA+D +KA 
Sbjct: 13  PFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKAL 71

Query: 174 EQLNGFELAGRPMKVGTVTDR 194
            +L G ++ G  +K+     R
Sbjct: 72  -ELTGLKVFGNEIKLEKPKGR 91

>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 = 43.4 bits (101), Expect = 2e-06
 Identities = 16/84 (19%), Positives = 34/84 (40%), Gaps = 1/84 (1%)

Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
            E      +F   L+      +L+   S +    D+  +   +T   +   Y++F+  E
Sbjct: 7  GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGYVDFESAE 65

Query: 70 SVPLAMGLNGQKLLGIPIIVQPTQ 93
           +  A+ L G K+ G  I ++  +
Sbjct: 66 DLEKALELTGLKVFGNEIKLEKPK 89

>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 = 20/73 (27%), Positives = 33/73 (45%), Gaps = 6/73 (8%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           RL++G L  N +   L   F+ FG I  I  +          + +I + S D A+ A  +
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYIQYESLDAAQAACAK 72

Query: 176 LNGFELAGRPMKV 188
           + GF L G   ++
Sbjct: 73  MRGFPLGGPDRRL 85

>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 = 52.0 bits (124), Expect = 2e-09
 Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 2/73 (2%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            +YI     + T D ++   E  G++ NIQ M        KG  F+ F S + AKK  E 
Sbjct: 8   SVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDSIESAKKFVE- 65

Query: 176 LNGFELAGRPMKV 188
             G +     + +
Sbjct: 66  TPGQKYKETDLLI 78

>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 = 47.0 bits (111), Expect = 9e-08
 Identities = 14/80 (17%), Positives = 33/80 (41%), Gaps = 1/80 (1%)

Query: 12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
           +   R+++           D++E+    G+V +++ +     + FKG  ++ F   ES 
Sbjct: 2  NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDSIESA 60

Query: 72 PLAMGLNGQKLLGIPIIVQP 91
             +   GQK     +++  
Sbjct: 61 KKFVETPGQKYKETDLLILF 80

>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 = 52.1 bits (124), Expect = 3e-09
 Identities = 17/87 (19%), Positives = 35/87 (40%), Gaps = 4/87 (4%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++  L +  TE+ +   F P   +     +     GR  G   + F + +DA  A    
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLNPMRVH--IEIGPDGRVTGEADVEFATHEDAVAAMA-K 74

Query: 177 NGFELAGRPMKVGTVTDRNESVGGGPS 203
           +   +  R +++   +    + G GPS
Sbjct: 75  DKANMQHRYVELFLNSTA-GTSGSGPS 100

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 5e-05
 Identities = 17/94 (18%), Positives = 32/94 (34%), Gaps = 3/94 (3%)

Query: 10  SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
           S +      +    L  R    D+  FFS +  +R    I  +        A +EF   E
Sbjct: 9   SFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTG--EADVEFATHE 66

Query: 70  SVPLAMGLNGQKLLGIPIIVQP-TQAEKNRAGNT 102
               AM  +   +    + +   + A  + +G +
Sbjct: 67  DAVAAMAKDKANMQHRYVELFLNSTAGTSGSGPS 100

>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 = 49.8 bits (118), Expect = 2e-08
 Identities = 15/77 (19%), Positives = 35/77 (45%), Gaps = 6/77 (7%)

Query: 113 GPMRLYIGSLHF-NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
           G   L + +L+   +T   L  +F  +G +  ++++ +           +     + A+ 
Sbjct: 1   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQL 55

Query: 172 AQEQLNGFELAGRPMKV 188
           A   LNG +L G+P+++
Sbjct: 56  AMSHLNGHKLHGKPIRI 72

>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 = 47.9 bits (113), Expect = 9e-08
 Identities = 18/85 (21%), Positives = 27/85 (31%), Gaps = 7/85 (8%)

Query: 113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS-ADDAKK 171
           G +  + G L      + L  +F   G+I  I  +           G I F   A +A  
Sbjct: 10  GCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA------KEGIILFKEKAKEALG 63

Query: 172 AQEQLNGFELAGRPMKVGTVTDRNE 196
             +  N   L  R  +V       E
Sbjct: 64  KAKDANNGNLQLRNKEVTWEVLEGE 88

>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 = 47.1 bits (111), Expect = 1e-07
 Identities = 14/74 (18%), Positives = 26/74 (35%), Gaps = 8/74 (10%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +++  L  ++ E  L    E FG I  + +M             + F + D AK+     
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEFENIDSAKECVTFA 71

Query: 177 --NGFELAGRPMKV 188
                 +AG+    
Sbjct: 72  ADVPVYIAGQQAFF 85

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.2 bits (111), Expect = 1e-07
 Identities = 15/82 (18%), Positives = 33/82 (40%), Gaps = 1/82 (1%)

Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
              +Y+  L F      +   F+    +++   +     G++ G GF+ F +  D K A 
Sbjct: 18  GFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL 77

Query: 174 EQLNGFELAGRPMKVGTVTDRN 195
              +   +  R ++V  +T + 
Sbjct: 78  C-RHKQYMGNRFIQVHPITKKG 98

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.0 bits (100), Expect = 4e-06
 Identities = 14/88 (15%), Positives = 29/88 (32%)

Query: 11  PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
                   ++   L      + + +FF  +  V D   I      +  G  ++EF++   
Sbjct: 13  SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEAD 72

Query: 71  VPLAMGLNGQKLLGIPIIVQPTQAEKNR 98
              A+  + Q +    I V P   +   
Sbjct: 73  YKAALCRHKQYMGNRFIQVHPITKKGML 100

>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 = 2e-07
 Identities = 12/73 (16%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           L++ ++  +++E+ L+ +F   G +    +       + +    I   S ++A +A   L
Sbjct: 13  LHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVEEAVQALIDL 68

Query: 177 NGFELA-GRPMKV 188
           +  +L     ++V
Sbjct: 69  HNHDLGENHHLRV 81

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 45.6 bits (107), Expect = 2e-07
 Identities = 11/76 (14%), Positives = 29/76 (38%), Gaps = 3/76 (3%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           + + +L  +  ++ +   F+  G I ++ +       ++  +  I F   D A  A  + 
Sbjct: 3   VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGALAAITK- 59

Query: 177 NGFELAGRPMKVGTVT 192
               +    + V  +T
Sbjct: 60  THKVVGQNEIIVSHLT 75

>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 = 43.8 bits (103), Expect = 1e-06
 Identities = 14/79 (17%), Positives = 24/79 (30%), Gaps = 9/79 (11%)

Query: 118 YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN 177
            +          +L   F  +G I    +        +  +  I + S   A+KA    +
Sbjct: 8   TVFGFPQASASYILL-QFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKAL-SKD 59

Query: 178 GFELAGRPM-KVGTVTDRN 195
           G       M  V    D+N
Sbjct: 60  GRIFGESIMIGVKPCIDKN 78

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.7 bits (102), Expect = 1e-06
 Identities = 10/81 (12%), Positives = 26/81 (32%), Gaps = 7/81 (8%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           R+ +  L  + +   L+      G +    +  D         G + F   +D   A  +
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-------TGVVEFVRKEDMTYAVRK 54

Query: 176 LNGFELAGRPMKVGTVTDRNE 196
           L+  +      +   +  + +
Sbjct: 55  LDNTKFRSHEGETAYIRVKVD 75

>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 = 43.1 bits (101), Expect = 2e-06
 Identities = 12/73 (16%), Positives = 24/73 (32%), Gaps = 5/73 (6%)

Query: 117 LYIGSL-HFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
           ++I            L  + EPFG I N  ++   +      +  +       A      
Sbjct: 11  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINE----AFIEMATTEDAQAAVDYYT 66

Query: 176 LNGFELAGRPMKV 188
                + G+P++V
Sbjct: 67  TTPALVFGKPVRV 79

>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 = 42.9 bits (100), Expect = 3e-06
 Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 9/83 (10%)

Query: 109 RGTGGPMR-LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
           +  G P R L+I  L   +TE  +  +  PFGK+ NI ++   +        F+   + +
Sbjct: 2   KMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKN------QAFLELATEE 55

Query: 168 DAKKAQE--QLNGFELAGRPMKV 188
            A             L  +P+ +
Sbjct: 56  AAITMVNYYSAVTPHLRNQPIYI 78

>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 = 42.5 bits (99), Expect = 3e-06
 Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 6/74 (8%)

Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
            L++ +L     E ML  +F  F     ++L+ +          F+ F +   +  A+E 
Sbjct: 10  ILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFTTELQSNAAKEA 64

Query: 176 LNGFEL-AGRPMKV 188
           L GF++     MK+
Sbjct: 65  LQGFKITPTHAMKI 78

>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 = 40.7 bits (94), Expect = 1e-05
 Identities = 12/72 (16%), Positives = 26/72 (36%), Gaps = 7/72 (9%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           + I  L  ++T   +  +   +        +      + KG  F+T  + + A+ A    
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 177 NGFELAGRPMKV 188
           +   L  R + V
Sbjct: 54  HQSRLRERELSV 65

>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 = 41.5 bits (96), Expect = 1e-05
 Identities = 11/72 (15%), Positives = 23/72 (31%), Gaps = 6/72 (8%)

Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
           +   +L        ++  F  FG +  + L              + F    +A+KA   L
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG------ITAIVEFLEPLEARKAFRHL 66

Query: 177 NGFELAGRPMKV 188
              +    P+ +
Sbjct: 67  AYSKFHHVPLYL 78

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	370
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	100.0
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.83
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.81
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.81
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.81
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.8
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.8
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.8
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.8
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.8
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.79
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.79
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.79
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.79
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.79
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.79
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.79
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.79
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.78
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.78
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.78
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.78
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.78
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.78
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.78
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.78
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.78
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.77
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.77
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.77
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.77
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.77
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.77
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.77
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.77
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.77
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.77
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.76
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.76
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.76
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.76
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.76
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.76
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.76
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.76
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.76
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.75
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.75
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.75
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.75
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.75
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.75
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.75
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.75
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.75
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.75
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.75
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.74
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.74
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.74
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.74
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.73
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.73
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.73
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.73
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.73
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.73
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.73
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.73
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.72
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.72
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.72
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.72
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.72
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.71
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.7
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.7
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.7
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.7
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.7
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.7
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.7
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.7
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.7
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.69
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.69
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.69
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.69
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.69
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.69
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.68
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.68
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.68
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.68
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.68
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.68
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.67
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.67
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.67
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.67
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.66
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.66
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.66
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.66
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.66
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.66
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.66
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.66
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.65
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.65
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.65
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.65
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.65
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.64
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.64
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.64
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.64
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.64
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.64
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.64
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.64
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.63
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.63
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.63
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.63
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.63
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.63
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.63
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.62
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.62
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.62
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.62
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.62
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.62
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.62
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.62
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.62
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.61
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.61
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.61
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.6
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.6
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.6
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.59
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.59
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.59
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.59
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.58
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.58
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.58
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.58
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.57
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.55
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.52
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.5
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.49
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	99.43
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	99.37
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.36
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.35
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.34
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.32
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.31
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.29
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.24
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.24
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.2
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.11
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.32
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.22
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.07
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.02
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.9
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.05
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	94.3
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	93.59

>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=100.00  E-value=1.8e-32  Score=235.85  Aligned_cols=172  Identities=23%  Similarity=0.414  Sum_probs=154.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecccc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQA   94 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~~~   94 (370)
                      +.|+|||+|||+.+|+++|+++|++||.|.++.++++..++.++|||||+|.+.++|.+|+...+..+.++.+.+.+...
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhh
Confidence            45899999999999999999999999999999999999999999999999999999999999999999999888877654


Q ss_pred             cccccCCCCCCCCCCCCCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHH
Q psy2983          95 EKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE  174 (370)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~  174 (370)
                      ......       .......++|||+|||+.+++++|+++|+.||.|..+.+..+..+|.++|||||+|.+.++|.+|++
T Consensus        85 ~~~~~~-------~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~  157 (183)
T d1u1qa_          85 REDSQR-------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI  157 (183)
T ss_dssp             TTGGGS-------TTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT
T ss_pred             cccccc-------cccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH
Confidence            433222       1223445789999999999999999999999999999999998899999999999999999999998


Q ss_pred             HhCCceeCCeeEEEEEeecC
Q psy2983         175 QLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       175 ~l~g~~i~g~~l~V~~~~~~  194 (370)
                       +++..+.|+.|+|.++.++
T Consensus       158 -~~~~~~~G~~i~V~~A~~k  176 (183)
T d1u1qa_         158 -QKYHTVNGHNCEVRKALSK  176 (183)
T ss_dssp             -SSCEEETTEEEEEEECCCH
T ss_pred             -hCCCeECCEEEEEEecCCc
Confidence             7999999999999987653

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.2e-21  Score=150.70  Aligned_cols=92  Identities=71%  Similarity=1.123  Sum_probs=84.4

Q ss_pred             CCCCCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCC
Q psy2983           5 YSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLG   84 (370)
Q Consensus         5 ~~~~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g   84 (370)
                      +.++..+.+++.++|||+|||.++++++|+++|+.||+|.+++++++..+|+++|||||+|.+.++|.+|++++|..|.|
T Consensus         7 p~~~~~~~~~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G   86 (101)
T d2cq4a1           7 PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLG   86 (101)
T ss_dssp             CSCCCCTTHHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETT
T ss_pred             CCccCCccccCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECC
Confidence            34455566677899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEecccccc
Q psy2983          85 IPIIVQPTQAEK   96 (370)
Q Consensus        85 ~~l~v~~~~~~~   96 (370)
                      ++|.|+++.+..
T Consensus        87 ~~l~V~~a~~~~   98 (101)
T d2cq4a1          87 VPIIVQASQAEK   98 (101)
T ss_dssp             EEEEEEEHHHHH
T ss_pred             EEEEEEECCCCC
Confidence            999999886554

>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=99.81  E-value=8e-20  Score=136.98  Aligned_cols=82  Identities=33%  Similarity=0.532  Sum_probs=78.1

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ...+|||+|||..+++++|+++|++||.|.+++++.|+.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+.
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            45789999999999999999999999999999999999899999999999999999999999999999999999999987


Q ss_pred             cC
Q psy2983         193 DR  194 (370)
Q Consensus       193 ~~  194 (370)
                      ++
T Consensus        86 ~k   87 (88)
T d1rk8a_          86 VK   87 (88)
T ss_dssp             EC
T ss_pred             CC
Confidence            64

>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=99.81  E-value=1.2e-19  Score=136.62  Aligned_cols=84  Identities=31%  Similarity=0.513  Sum_probs=79.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ....+|||+|||..+++++|+++|++||.|.+++++.++.+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            34578999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             ecCC
Q psy2983         192 TDRN  195 (370)
Q Consensus       192 ~~~~  195 (370)
                      +++.
T Consensus        86 kp~~   89 (90)
T d2cq0a1          86 KPST   89 (90)
T ss_dssp             SCCC
T ss_pred             eCCC
Confidence            7653

>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=99.81  E-value=2.6e-20  Score=138.32  Aligned_cols=80  Identities=21%  Similarity=0.318  Sum_probs=76.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEeccc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~~   93 (370)
                      .+.|+|||+|||.++|+++|+++|+.||+|.++.+++|+.+|+++|||||+|.+.++|.+|+++++..|+|+.|.|+++.
T Consensus         4 e~~~~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           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999998763

>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=99.80  E-value=6.3e-20  Score=135.74  Aligned_cols=80  Identities=30%  Similarity=0.502  Sum_probs=76.8

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .++|||+|||+.+++++|+++|++||.|.++++.+++.+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.+++|
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            35799999999999999999999999999999999988999999999999999999999999999999999999999865

>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=99.80  E-value=7.3e-20  Score=137.53  Aligned_cols=82  Identities=33%  Similarity=0.613  Sum_probs=78.4

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .++|||+|||+++++++|+++|++||+|.++.++.|+.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++.+
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p   84 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKP   84 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            46899999999999999999999999999999999998999999999999999999999999999999999999999876


Q ss_pred             CC
Q psy2983         194 RN  195 (370)
Q Consensus       194 ~~  195 (370)
                      +.
T Consensus        85 ~~   86 (89)
T d2cqba1          85 MR   86 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.80  E-value=1.6e-19  Score=133.46  Aligned_cols=79  Identities=34%  Similarity=0.599  Sum_probs=76.3

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .+|||+|||+.+++++|+++|++||.|.+++++++..+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+++|
T Consensus         3 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           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            5799999999999999999999999999999999988999999999999999999999999999999999999999865

>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=99.80  E-value=5.9e-20  Score=137.72  Aligned_cols=84  Identities=20%  Similarity=0.352  Sum_probs=78.3

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEE
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIV   89 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v   89 (370)
                      +...+.++|||+|||.++|+++|+++|++||+|.++++++|+.+|+++|||||+|.+.++|..|++ ++|..+.|++|+|
T Consensus         2 ~~s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V   81 (88)
T d1rk8a_           2 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV   81 (88)
T ss_dssp             CCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            445577899999999999999999999999999999999999999999999999999999999996 9999999999999


Q ss_pred             ecccc
Q psy2983          90 QPTQA   94 (370)
Q Consensus        90 ~~~~~   94 (370)
                      .++..
T Consensus        82 ~~a~~   86 (88)
T d1rk8a_          82 DWCFV   86 (88)
T ss_dssp             EESEE
T ss_pred             EEecC
Confidence            98764

>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=99.80  E-value=2.3e-19  Score=137.55  Aligned_cols=88  Identities=27%  Similarity=0.526  Sum_probs=81.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ..++.+|||+|||+.+++++|+++|++||.|.+++++.|+.+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.+
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~   84 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34567899999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             eecCCCCc
Q psy2983         191 VTDRNESV  198 (370)
Q Consensus       191 ~~~~~~~~  198 (370)
                      +..+....
T Consensus        85 a~~~~~~~   92 (99)
T d1whwa_          85 STIKKEAS   92 (99)
T ss_dssp             CCCCSTTC
T ss_pred             CCCCCccC
Confidence            88765543

>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=99.80  E-value=1.1e-19  Score=137.57  Aligned_cols=84  Identities=30%  Similarity=0.563  Sum_probs=79.5

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ..++|||+|||..+++++|+++|++||.|.++++++++.+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.
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            34689999999999999999999999999999999999899999999999999999999999999999999999999987


Q ss_pred             cCCC
Q psy2983         193 DRNE  196 (370)
Q Consensus       193 ~~~~  196 (370)
                      ++..
T Consensus        88 ~~~~   91 (93)
T d1x5ua1          88 AHNK   91 (93)
T ss_dssp             TTSC
T ss_pred             CCCC
Confidence            7654

>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=99.79  E-value=1.6e-19  Score=132.79  Aligned_cols=77  Identities=35%  Similarity=0.570  Sum_probs=74.9

Q ss_pred             eEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       116 ~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      .|||+|||+.+|+++|+++|++||+|.++++++|+.+|.++|||||+|.++++|..|++.|||..+.|++|+|.+++
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            59999999999999999999999999999999999999999999999999999999999999999999999999974

>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=99.79  E-value=4.7e-20  Score=142.19  Aligned_cols=84  Identities=19%  Similarity=0.325  Sum_probs=78.4

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecc
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPT   92 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~   92 (370)
                      ....++|||+|||+++++++|+++|++||.|.++.|++|+.++.++|||||+|.+.++|.+|++++|..|.|+.|.|.++
T Consensus        17 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a   96 (103)
T d1x4ba1          17 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRA   96 (103)
T ss_dssp             HHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECC
T ss_pred             cCCCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEEC
Confidence            34458999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cccc
Q psy2983          93 QAEK   96 (370)
Q Consensus        93 ~~~~   96 (370)
                      .+..
T Consensus        97 ~~ke  100 (103)
T d1x4ba1          97 VARE  100 (103)
T ss_dssp             SSCC
T ss_pred             cccC
Confidence            7543

>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=99.79  E-value=7.3e-20  Score=138.66  Aligned_cols=83  Identities=24%  Similarity=0.373  Sum_probs=78.1

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      ....++|||+|||..+|+++|+++|++||+|.++++++++.++.++|||||+|.+.++|..|++ |+|..+.|++|+|++
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3456899999999999999999999999999999999999999999999999999999999995 999999999999999


Q ss_pred             cccc
Q psy2983          92 TQAE   95 (370)
Q Consensus        92 ~~~~   95 (370)
                      +.+.
T Consensus        86 A~~~   89 (93)
T d1x5ua1          86 ASAH   89 (93)
T ss_dssp             TTTT
T ss_pred             cCCC
Confidence            8754

>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=99.79  E-value=8.7e-20  Score=135.81  Aligned_cols=81  Identities=27%  Similarity=0.522  Sum_probs=77.6

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecC
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~  194 (370)
                      ++|||+|||+.+++++|+++|++||+|.++++++|+.+|.++|||||+|.++++|..|+..|||..+.|++|+|.++.+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999998764


Q ss_pred             C
Q psy2983         195 N  195 (370)
Q Consensus       195 ~  195 (370)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
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=99.79  E-value=4.5e-19  Score=134.21  Aligned_cols=83  Identities=27%  Similarity=0.417  Sum_probs=78.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ..+++|||+|||+.+++++|+++|++||.|.++.+++++.+|.++|||||+|.+.++|..|++.|||..+.|++|+|.++
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ecC
Q psy2983         192 TDR  194 (370)
Q Consensus       192 ~~~  194 (370)
                      ...
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

>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=99.79  E-value=7.6e-20  Score=137.73  Aligned_cols=84  Identities=26%  Similarity=0.372  Sum_probs=78.7

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      ...+.++|||+|||..+++++|+++|+.||+|.++.+++|+.++.++|||||+|.+.++|.+|++ ++|..+.|+.|+|+
T Consensus         4 ~~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~   83 (90)
T d2cq0a1           4 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   83 (90)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999996 99999999999999


Q ss_pred             ccccc
Q psy2983          91 PTQAE   95 (370)
Q Consensus        91 ~~~~~   95 (370)
                      ++++.
T Consensus        84 ~akp~   88 (90)
T d2cq0a1          84 WAKPS   88 (90)
T ss_dssp             ESSCC
T ss_pred             eeeCC
Confidence            98754

>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=99.79  E-value=7.5e-20  Score=135.32  Aligned_cols=79  Identities=22%  Similarity=0.346  Sum_probs=75.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecccc
Q psy2983          16 ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQA   94 (370)
Q Consensus        16 ~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~   94 (370)
                      .++|||+|||+++|+++|+++|++||+|.++++++++.+++++|||||+|.+.++|.+|++ |+|..+.|++|+|+++++
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            4689999999999999999999999999999999999999999999999999999999995 999999999999999864

>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=99.79  E-value=1.3e-19  Score=133.39  Aligned_cols=76  Identities=26%  Similarity=0.402  Sum_probs=73.6

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        18 ~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      +|||+|||+.+|+++|+++|++||+|.++++++|+.+++++|||||+|.++++|..|++ ++|..+.|++|+|.+++
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            59999999999999999999999999999999999999999999999999999999995 99999999999999875

>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=99.78  E-value=4.3e-19  Score=136.70  Aligned_cols=84  Identities=26%  Similarity=0.506  Sum_probs=79.5

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      +..+|||+|||+++++++|+++|++||.|.++.++.++.+|.++|||||+|.+.++|..|++.|||..|.|++|+|.++.
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            34689999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cCCC
Q psy2983         193 DRNE  196 (370)
Q Consensus       193 ~~~~  196 (370)
                      ++..
T Consensus        97 ~k~~  100 (102)
T d2cpza1          97 SKND  100 (102)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            7654

>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=99.78  E-value=3.9e-19  Score=131.67  Aligned_cols=77  Identities=36%  Similarity=0.638  Sum_probs=73.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV  188 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V  188 (370)
                      .+.++|||+|||+.+|+++|+++|++||.|.+++++.++.+|.++|||||+|.+.++|.+|+..|||..+.|++|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            34578999999999999999999999999999999999989999999999999999999999999999999999987

>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=99.78  E-value=1.2e-19  Score=135.08  Aligned_cols=79  Identities=24%  Similarity=0.374  Sum_probs=75.7

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccccc
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQAE   95 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~~   95 (370)
                      .+|||+|||..+|+++|+++|+.||+|.++++++|+.+|+++|||||+|.++++|..|++ ++|..+.|++|.|.++...
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            579999999999999999999999999999999999999999999999999999999996 9999999999999998654

>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=99.78  E-value=5.7e-20  Score=138.11  Aligned_cols=81  Identities=22%  Similarity=0.430  Sum_probs=77.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      ..++|||+|||.++|+++|+++|++||+|.++.+++|+.+++++|||||+|.+.++|..|++ ++|..+.|++|.|.++.
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            56899999999999999999999999999999999999999999999999999999999995 99999999999999986


Q ss_pred             cc
Q psy2983          94 AE   95 (370)
Q Consensus        94 ~~   95 (370)
                      +.
T Consensus        84 p~   85 (89)
T d2cqba1          84 PM   85 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.78  E-value=2.2e-19  Score=136.00  Aligned_cols=82  Identities=18%  Similarity=0.254  Sum_probs=77.8

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      .+.++||||+|||.++|+++|+++|++||+|.+|.+++++.++.++|||||+|.+.++|..|++ |+|..+.|++|+|.+
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            4578999999999999999999999999999999999999999999999999999999999996 999999999999998


Q ss_pred             ccc
Q psy2983          92 TQA   94 (370)
Q Consensus        92 ~~~   94 (370)
                      +..
T Consensus        84 a~~   86 (93)
T d1h2vz_          84 DAG   86 (93)
T ss_dssp             ESC
T ss_pred             cCC
Confidence            753

>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=99.78  E-value=7.9e-20  Score=133.29  Aligned_cols=76  Identities=21%  Similarity=0.343  Sum_probs=73.0

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecc
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPT   92 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~   92 (370)
                      .+|||+|||.++|+++|+++|++||+|.++++++|+.+++++|||||+|.+.++|.+|+++++..++|+.|.|+.+
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 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            4799999999999999999999999999999999999999999999999999999999999999999999998764

>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=99.78  E-value=3.1e-19  Score=134.12  Aligned_cols=83  Identities=20%  Similarity=0.297  Sum_probs=76.0

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEec
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQP   91 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~   91 (370)
                      ..+..++|||+|||+++|+++|+++|+.||+|.++.+++|+.+|+++|||||+|.+.++|.+|++ ++..++|+.|.|++
T Consensus         4 ~~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~-~~~~l~Gr~i~v~~   82 (90)
T d2cqga1           4 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDCKL   82 (90)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEEEC
T ss_pred             CCcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh-cCCccCCEEeEEEe
Confidence            34567899999999999999999999999999999999999999999999999999999999997 34478999999998


Q ss_pred             cccc
Q psy2983          92 TQAE   95 (370)
Q Consensus        92 ~~~~   95 (370)
                      +.+.
T Consensus        83 a~~k   86 (90)
T d2cqga1          83 PNSK   86 (90)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            8654

>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=99.78  E-value=5.4e-19  Score=131.13  Aligned_cols=79  Identities=30%  Similarity=0.630  Sum_probs=75.0

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ..++|||+|||+.+++++|+++|++||.|..+.++.|+.+|.++|||||+|.+.++|.+|++ +++..+.|+.|+|+.|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            34789999999999999999999999999999999999999999999999999999999998 69999999999998864

>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=99.78  E-value=1.1e-19  Score=131.91  Aligned_cols=75  Identities=32%  Similarity=0.420  Sum_probs=72.0

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecc
Q psy2983          18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPT   92 (370)
Q Consensus        18 ~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~   92 (370)
                      +|||+|||+++|+++|+++|++||+|.++.+++++.+++++|||||+|.+.++|++|+++++..+.|+.|.|+++
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 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeEC
Confidence            599999999999999999999999999999999999999999999999999999999999999999999998653

>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=99.77  E-value=2.9e-19  Score=132.10  Aligned_cols=78  Identities=22%  Similarity=0.429  Sum_probs=74.5

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecccc
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQA   94 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~   94 (370)
                      ++|||+|||.++++++|+++|++||+|.+++++++..+++++|||||+|.+.++|..|++ ++|..+.|++|+|.++++
T Consensus         3 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           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            569999999999999999999999999999999999999999999999999999999995 999999999999998753

>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=99.77  E-value=6.4e-20  Score=142.03  Aligned_cols=84  Identities=30%  Similarity=0.493  Sum_probs=78.7

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      .+++.|+|||+|||.++++++|+++|++||+|.++++++++.+++++|||||+|.+.++|..|++ |+|..|.|++|+|.
T Consensus         4 ~~~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~   83 (104)
T d1p1ta_           4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVD   83 (104)
T ss_dssp             SHHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999995 99999999999999


Q ss_pred             ccccc
Q psy2983          91 PTQAE   95 (370)
Q Consensus        91 ~~~~~   95 (370)
                      ++...
T Consensus        84 ~a~~~   88 (104)
T d1p1ta_          84 NAASE   88 (104)
T ss_dssp             ETTCT
T ss_pred             ECCCC
Confidence            87643

>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=99.77  E-value=3.5e-19  Score=137.23  Aligned_cols=83  Identities=20%  Similarity=0.363  Sum_probs=78.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      .+.++|||+|||.++++++|+++|+.||.|.++.++.+..++.++|||||+|.+.++|..|++ |+|..|.|++|+|+++
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            456789999999999999999999999999999999999999999999999999999999995 9999999999999998


Q ss_pred             cccc
Q psy2983          93 QAEK   96 (370)
Q Consensus        93 ~~~~   96 (370)
                      .+..
T Consensus        96 ~~k~   99 (102)
T d2cpza1          96 RSKN   99 (102)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            7654

>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=99.77  E-value=2.6e-19  Score=131.38  Aligned_cols=77  Identities=19%  Similarity=0.365  Sum_probs=74.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecc
Q psy2983          16 ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPT   92 (370)
Q Consensus        16 ~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~   92 (370)
                      .|+|||+|||+++|+++|+++|++||.|..+.+..++.++.++|||||+|.++++|.+|++++|..|.|++|.|+++
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999764

>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=99.77  E-value=7.7e-19  Score=130.65  Aligned_cols=78  Identities=31%  Similarity=0.546  Sum_probs=74.3

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCC--eeEEEEEe
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG--RPMKVGTV  191 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g--~~l~V~~~  191 (370)
                      .++|||+|||+.+++++|+++|++||.|.++++++++.+|.++|||||+|.+.++|.+|++.|||..+.|  ++|+|++|
T Consensus         6 ~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2           6 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            4679999999999999999999999999999999999999999999999999999999999999999976  88999885

>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=99.77  E-value=7.7e-19  Score=143.16  Aligned_cols=85  Identities=20%  Similarity=0.395  Sum_probs=79.1

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      .....++|||+|||.++|+++|+++|+.||.|.+|.+++++.+++++|||||+|.+.++|..|++ |+|..|.|++|+|.
T Consensus        38 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~  117 (139)
T d1u6fa1          38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34456899999999999999999999999999999999999999999999999999999999996 99999999999999


Q ss_pred             cccccc
Q psy2983          91 PTQAEK   96 (370)
Q Consensus        91 ~~~~~~   96 (370)
                      ++....
T Consensus       118 ~a~~~~  123 (139)
T d1u6fa1         118 LAASGH  123 (139)
T ss_dssp             ESSCCC
T ss_pred             EcCCCC
Confidence            987543

>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=99.77  E-value=2.4e-19  Score=132.82  Aligned_cols=76  Identities=30%  Similarity=0.413  Sum_probs=72.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEE
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIV   89 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v   89 (370)
                      .++++|||+|||..+|+++|+++|++||+|.++.+++++.+++++|||||+|.+.++|..|++ ++|..|.|++|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            356899999999999999999999999999999999999999999999999999999999995 9999999999986

>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=99.77  E-value=7.1e-19  Score=128.61  Aligned_cols=76  Identities=34%  Similarity=0.617  Sum_probs=73.3

Q ss_pred             eEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       116 ~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      +|||+|||+++++++|+++|++||.|.++++..++ +|+++|||||+|.+.++|.+|++.|||..+.|++|+|+++.
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 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            69999999999999999999999999999999986 89999999999999999999999999999999999999875

>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=99.77  E-value=8.2e-19  Score=130.48  Aligned_cols=78  Identities=33%  Similarity=0.573  Sum_probs=73.5

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCC--eeEEEEEe
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG--RPMKVGTV  191 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g--~~l~V~~~  191 (370)
                      ..+|||+|||+.+++++|+++|++||.|.+++++.|+.+|.++|||||+|.+.++|.+|++.|||..+.|  ++|+|.|+
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            3579999999999999999999999999999999998899999999999999999999999999999987  56888875

>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=99.77  E-value=9.3e-19  Score=142.68  Aligned_cols=86  Identities=29%  Similarity=0.580  Sum_probs=80.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||+++++++|+++|++||.|.+++++.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|+|.+
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34457899999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             eecCCC
Q psy2983         191 VTDRNE  196 (370)
Q Consensus       191 ~~~~~~  196 (370)
                      +.++..
T Consensus       119 a~~~~~  124 (139)
T d1u6fa1         119 AASGHQ  124 (139)
T ss_dssp             SSCCCC
T ss_pred             cCCCCC
Confidence            876544

>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=99.76  E-value=5.2e-19  Score=135.53  Aligned_cols=84  Identities=27%  Similarity=0.424  Sum_probs=78.5

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      ...+++|||+|||..+++++|+++|++||+|.++++++|+.+++++|||||+|.+.++|..|++ |+|..|.|++|+|.+
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~   84 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3457789999999999999999999999999999999999999999999999999999999995 999999999999999


Q ss_pred             ccccc
Q psy2983          92 TQAEK   96 (370)
Q Consensus        92 ~~~~~   96 (370)
                      +....
T Consensus        85 a~~~~   89 (99)
T d1whwa_          85 STIKK   89 (99)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            87654

>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=99.76  E-value=5.2e-19  Score=133.12  Aligned_cols=84  Identities=33%  Similarity=0.691  Sum_probs=79.0

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ...+|||+|||+.+++++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|..|+..|||..+.|++|+|.++.
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            34689999999999999999999999999999999988899999999999999999999999999999999999999987


Q ss_pred             cCCC
Q psy2983         193 DRNE  196 (370)
Q Consensus       193 ~~~~  196 (370)
                      ++..
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.76  E-value=1.7e-18  Score=129.99  Aligned_cols=82  Identities=26%  Similarity=0.406  Sum_probs=75.6

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ...+|||+|||+++|+++|+++|++||.|..++++.|+.+|.++|||||+|.+.++|.+|++  ++..++|+.|.|+++.
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 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECCC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh--cCCccCCEEeEEEeCC
Confidence            45689999999999999999999999999999999999999999999999999999999998  4558999999999987


Q ss_pred             cCCC
Q psy2983         193 DRNE  196 (370)
Q Consensus       193 ~~~~  196 (370)
                      ++..
T Consensus        85 ~k~~   88 (90)
T d2cqga1          85 SKQS   88 (90)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            7543

>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=99.76  E-value=2.6e-19  Score=134.78  Aligned_cols=82  Identities=26%  Similarity=0.432  Sum_probs=77.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      .++++|||+|||+++++++|+++|++||+|..+.++++..++.++|||||+|.+.++|..|++ ++|..|.|++|+|.++
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            467899999999999999999999999999999999999999999999999999999999995 9999999999999987


Q ss_pred             ccc
Q psy2983          93 QAE   95 (370)
Q Consensus        93 ~~~   95 (370)
                      ...
T Consensus        83 ~~~   85 (90)
T d1x5sa1          83 GKS   85 (90)
T ss_dssp             ECC
T ss_pred             CCC
Confidence            644

>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=99.76  E-value=1.2e-18  Score=132.14  Aligned_cols=83  Identities=25%  Similarity=0.508  Sum_probs=76.8

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCC-CCCcccEEEEEECCHHHHHHHHHHh-CCceeCCeeEEEEE
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPD-TGRSKGYGFITFHSADDAKKAQEQL-NGFELAGRPMKVGT  190 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~-~g~~~g~afV~f~~~~~a~~A~~~l-~g~~i~g~~l~V~~  190 (370)
                      ...+|||+|||+.+++++|+++|++||.|..++++.+.. +|.++|||||+|.+.++|.+|+..| ||..+.|++|+|.+
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            446899999999999999999999999999999988754 7999999999999999999999998 89999999999999


Q ss_pred             eecCC
Q psy2983         191 VTDRN  195 (370)
Q Consensus       191 ~~~~~  195 (370)
                      +....
T Consensus        87 A~~~~   91 (94)
T d2cpha1          87 ADSEV   91 (94)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            87654

>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=99.76  E-value=4e-18  Score=128.94  Aligned_cols=83  Identities=35%  Similarity=0.667  Sum_probs=76.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ..+++|||+|||+.+++++|+++|++||.|..++++.+.  +.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            446789999999999999999999999999999999884  447999999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy2983         192 TDRNE  196 (370)
Q Consensus       192 ~~~~~  196 (370)
                      .++..
T Consensus        87 ~~r~~   91 (93)
T d2cq3a1          87 TARVM   91 (93)
T ss_dssp             CSSCC
T ss_pred             CcCCC
Confidence            87643

>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=99.76  E-value=6.2e-19  Score=132.64  Aligned_cols=83  Identities=22%  Similarity=0.448  Sum_probs=75.8

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEE
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIV   89 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v   89 (370)
                      ++..+.|+|||+|||.++|+++|+++|+.||+|.++.+++++.++  +|||||+|.+.++|..|++ ++|..+.|++|+|
T Consensus         3 ~d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v   80 (90)
T d2cqia1           3 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKV   80 (90)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345678999999999999999999999999999999999987654  7899999999999999996 9999999999999


Q ss_pred             eccccc
Q psy2983          90 QPTQAE   95 (370)
Q Consensus        90 ~~~~~~   95 (370)
                      .++.+.
T Consensus        81 ~~a~~~   86 (90)
T d2cqia1          81 NWATTP   86 (90)
T ss_dssp             EECCCT
T ss_pred             EEcCCC
Confidence            998653

>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=99.76  E-value=6e-19  Score=131.27  Aligned_cols=80  Identities=20%  Similarity=0.385  Sum_probs=74.3

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCC--eeEEE
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLG--IPIIV   89 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g--~~l~v   89 (370)
                      ....++|||+|||.++++++|+++|++||+|.++++++++.+++++|||||+|.+.++|..|++ ++|..+.|  ++|+|
T Consensus         3 ~~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V   82 (85)
T d1b7fa2           3 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV   82 (85)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEE
Confidence            3456789999999999999999999999999999999999999999999999999999999996 99999976  88999


Q ss_pred             ecc
Q psy2983          90 QPT   92 (370)
Q Consensus        90 ~~~   92 (370)
                      +++
T Consensus        83 ~~A   85 (85)
T d1b7fa2          83 RLA   85 (85)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            874

>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=99.76  E-value=9.9e-19  Score=134.89  Aligned_cols=85  Identities=16%  Similarity=0.237  Sum_probs=76.1

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEe
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQ   90 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~   90 (370)
                      +.+...++|||+|||..+++++|+++|++||+|.++.+++++.+++++|||||+|.+.++|.+|++..+..+.|++|.|.
T Consensus         5 ~~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l~V~   84 (103)
T d2cqda1           5 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVN   84 (103)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEE
T ss_pred             CCCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEEEEE
Confidence            33445678999999999999999999999999999999999999999999999999999999999744457999999998


Q ss_pred             ccccc
Q psy2983          91 PTQAE   95 (370)
Q Consensus        91 ~~~~~   95 (370)
                      ++...
T Consensus        85 ~a~~~   89 (103)
T d2cqda1          85 LAYLG   89 (103)
T ss_dssp             ESTTT
T ss_pred             EcCCC
Confidence            87643

>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=99.76  E-value=2.8e-19  Score=129.55  Aligned_cols=74  Identities=26%  Similarity=0.361  Sum_probs=71.1

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEec
Q psy2983          18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQP   91 (370)
Q Consensus        18 ~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~   91 (370)
                      +|||+|||+++|+++|+++|++||+|.++.+++++.+++++|||||+|.+.++|.+|++.++..++|+.|.|+.
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKV   74 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEEC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEE
Confidence            59999999999999999999999999999999999999999999999999999999999888999999998865

>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=99.76  E-value=4.8e-19  Score=134.31  Aligned_cols=84  Identities=20%  Similarity=0.437  Sum_probs=76.9

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCC-CCCeecEEEEEecCCCChHHHhh-c-cCCccCCeeEE
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNK-TRRFKGIAYIEFKDPESVPLAMG-L-NGQKLLGIPII   88 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~-~~~~kg~afVeF~~~e~A~~Al~-l-~g~~i~g~~l~   88 (370)
                      ..+.+++|||+|||..+++++|+++|++||.|.+++++++.. +|+++|||||+|.+.++|.+|++ | +|..+.|++|.
T Consensus         4 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~   83 (94)
T d2cpha1           4 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   83 (94)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEE
Confidence            345778899999999999999999999999999999988754 78999999999999999999996 6 89999999999


Q ss_pred             Eeccccc
Q psy2983          89 VQPTQAE   95 (370)
Q Consensus        89 v~~~~~~   95 (370)
                      |.++..+
T Consensus        84 V~~A~~~   90 (94)
T d2cpha1          84 LEWADSE   90 (94)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCC
Confidence            9998754

>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=99.76  E-value=3.9e-19  Score=132.22  Aligned_cols=79  Identities=18%  Similarity=0.331  Sum_probs=73.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEeccc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~~   93 (370)
                      ...|+|||+|||.++|+++|+++|+.||+|.++.+.++. +++++|||||+|.+.++|.+|++++|..+.|+.|.|++..
T Consensus         4 ~~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           4 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HHTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEGG
T ss_pred             CCcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            457899999999999999999999999999999987765 7899999999999999999999999999999999998764

>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=99.75  E-value=9.2e-19  Score=129.64  Aligned_cols=79  Identities=42%  Similarity=0.693  Sum_probs=74.2

Q ss_pred             EEEecCCCCCCHHHHHhcccCCCceee-EEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecCC
Q psy2983         117 LYIGSLHFNITEDMLRGIFEPFGKIDN-IQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRN  195 (370)
Q Consensus       117 l~V~nlp~~~t~e~l~~~f~~~G~i~~-v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~~  195 (370)
                      |||+|||+++++++|+++|++||.|.. +.+++++.+|+++|||||+|.+.++|.+|++.|+|..+.|++|+|.++.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            799999999999999999999999866 4788898899999999999999999999999999999999999999987654

>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=99.75  E-value=8.4e-19  Score=129.25  Aligned_cols=79  Identities=16%  Similarity=0.301  Sum_probs=69.1

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .+|||+|||+++|+++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|.+|++.|||..+.|++|+|.++.|
T Consensus         2 ~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           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            5899999999999999999999999999988888878999999999999999999999999999999999999999865

>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=99.75  E-value=7.4e-19  Score=127.49  Aligned_cols=75  Identities=29%  Similarity=0.657  Sum_probs=71.6

Q ss_pred             eEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       116 ~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      +|||+|||+++++++|+++|++||.|.++.++.++.+|+++|||||+|.+.++|.+|++ +++..+.|+.|.|++|
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            58999999999999999999999999999999999999999999999999999999998 7999999999999753

>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=99.75  E-value=2.6e-18  Score=132.46  Aligned_cols=83  Identities=30%  Similarity=0.553  Sum_probs=76.6

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ..++|||+|||+.+++++|+++|++||.|.+++++.++.+|.++|||||+|.+.++|.+|++.+++ .+.|++|+|.++.
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            346899999999999999999999999999999999998999999999999999999999998876 7999999999987


Q ss_pred             cCCC
Q psy2983         193 DRNE  196 (370)
Q Consensus       193 ~~~~  196 (370)
                      ....
T Consensus        88 ~~~~   91 (103)
T d2cqda1          88 LGAK   91 (103)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            6544

>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=99.75  E-value=3.6e-19  Score=129.75  Aligned_cols=76  Identities=30%  Similarity=0.583  Sum_probs=72.9

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ++|||+|||+++++++|+++|++||.|.+++++.|+.+|+++|||||+|.+.++|.+|++ +++..++|+.|+|+.|
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            379999999999999999999999999999999999999999999999999999999998 7999999999999875

>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=99.75  E-value=8.4e-19  Score=130.41  Aligned_cols=78  Identities=27%  Similarity=0.470  Sum_probs=72.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCC--eeEEEec
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLG--IPIIVQP   91 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g--~~l~v~~   91 (370)
                      ..++|||+|||+.+|+++|+++|++||+|.++++++|+.+++++|||||+|.+.++|.+|++ |||..+.|  ++|.|.+
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            45789999999999999999999999999999999999999999999999999999999995 99999998  4588876


Q ss_pred             c
Q psy2983          92 T   92 (370)
Q Consensus        92 ~   92 (370)
                      +
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.75  E-value=2.6e-18  Score=129.13  Aligned_cols=82  Identities=27%  Similarity=0.516  Sum_probs=75.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ..+++|||+|||.++++++|+++|+.||.|..+++..+..+  .+|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            34579999999999999999999999999999999988644  4889999999999999999999999999999999998


Q ss_pred             ecCC
Q psy2983         192 TDRN  195 (370)
Q Consensus       192 ~~~~  195 (370)
                      .++.
T Consensus        84 ~~~~   87 (90)
T d2cqia1          84 TTPS   87 (90)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            7654

>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=99.75  E-value=1.4e-18  Score=129.22  Aligned_cols=78  Identities=29%  Similarity=0.603  Sum_probs=72.6

Q ss_pred             EEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCC---CcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTG---RSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       117 l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g---~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      |||+|||+++++++|+++|++||.|.++.++.++.++   .++|||||+|.+.++|.+|++.|||..+.|+.|+|.++..
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            7999999999999999999999999999999887655   4789999999999999999999999999999999999754


Q ss_pred             C
Q psy2983         194 R  194 (370)
Q Consensus       194 ~  194 (370)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
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=99.75  E-value=3.2e-18  Score=125.39  Aligned_cols=76  Identities=28%  Similarity=0.583  Sum_probs=73.1

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ++|||+|||+++|+++|+++|++||.|..+.+..++.++.++|||||+|.+.+++.+|+. ++|..|+|+.|+|+.|
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            689999999999999999999999999999999999999999999999999999999997 8999999999999875

>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=99.75  E-value=1.1e-18  Score=134.34  Aligned_cols=82  Identities=34%  Similarity=0.635  Sum_probs=77.1

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .++|||+|||+++++++|+++|++||.|..+.+..|+.++.++|||||+|.+.++|.+|+. ++|..|.|+.|.|.++.+
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            3689999999999999999999999999999999999899999999999999999999997 799999999999999877


Q ss_pred             CCC
Q psy2983         194 RNE  196 (370)
Q Consensus       194 ~~~  196 (370)
                      +..
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            643

>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=99.75  E-value=8.7e-19  Score=134.53  Aligned_cols=80  Identities=24%  Similarity=0.418  Sum_probs=75.7

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .++|||+|||+.+++++|+++|+.||.|.+++++++..+|.++|||||+|.+.++|.+|+. |||..+.|+.|+|.++.+
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            3689999999999999999999999999999999999899999999999999999999996 999999999999998754


Q ss_pred             C
Q psy2983         194 R  194 (370)
Q Consensus       194 ~  194 (370)
                      +
T Consensus        97 ~   97 (101)
T d2cq4a1          97 E   97 (101)
T ss_dssp             H
T ss_pred             C
Confidence            3

>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=99.74  E-value=1.6e-18  Score=132.57  Aligned_cols=86  Identities=23%  Similarity=0.356  Sum_probs=78.0

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-c------cCCcc
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-L------NGQKL   82 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l------~g~~i   82 (370)
                      |....+.++|||+|||.++|+++|+++|++||+|.++.++.+..++.++|||||+|.+.++|..|++ +      +|..+
T Consensus         2 P~~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~   81 (98)
T d1x4ha1           2 PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKL   81 (98)
T ss_dssp             CCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEES
T ss_pred             ccCCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEE
Confidence            4456678999999999999999999999999999999999999999999999999999999999996 4      46788


Q ss_pred             CCeeEEEeccccc
Q psy2983          83 LGIPIIVQPTQAE   95 (370)
Q Consensus        83 ~g~~l~v~~~~~~   95 (370)
                      .|++|.|.++.+.
T Consensus        82 ~gr~l~v~~a~~k   94 (98)
T d1x4ha1          82 DGRQLKVDLAVTR   94 (98)
T ss_dssp             SSCEEEEECCCCC
T ss_pred             CCEEEEEEECCCC
Confidence            9999999998654

>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=99.74  E-value=1.1e-18  Score=134.91  Aligned_cols=80  Identities=31%  Similarity=0.681  Sum_probs=76.4

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecC
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~  194 (370)
                      ++|||+|||+++++++|+++|++||.|.+++++.++.+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.+.
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            57999999999999999999999999999999999989999999999999999999999999999999999999997553

>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=99.74  E-value=7e-19  Score=131.17  Aligned_cols=81  Identities=20%  Similarity=0.253  Sum_probs=71.3

Q ss_pred             CCCCeEEEcCCCCCCc-HHHHHHHhhcCCCeeEEEEeee-CCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEec
Q psy2983          14 RDARTIFCMQLSQRIR-TRDLEEFFSSVGKVRDVRLITC-NKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQP   91 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~t-e~~L~~~f~~~G~v~~v~i~~d-~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~   91 (370)
                      .+.|+|||+|||.+++ +++|+++|++||.|.++++..+ ..+++++|||||+|.+.++|.+|++++|..+.|++|.|.+
T Consensus         2 ~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           2 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSL   81 (86)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEE
Confidence            4679999999999986 5679999999999999998764 5678999999999999999999999999999999999998


Q ss_pred             ccc
Q psy2983          92 TQA   94 (370)
Q Consensus        92 ~~~   94 (370)
                      +.+
T Consensus        82 a~~   84 (86)
T d2ghpa3          82 ADK   84 (86)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            864

>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=99.74  E-value=7.5e-19  Score=129.50  Aligned_cols=78  Identities=15%  Similarity=0.308  Sum_probs=67.7

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecccc
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQA   94 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~   94 (370)
                      +||||+|||+++|+++|+++|++||+|..+.++.+..+++++|||||+|.+.++|.+|++ ++|..+.|++|.|+++++
T Consensus         2 ~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           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            689999999999999999999999999988888888889999999999999999999996 999999999999998764

>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=99.73  E-value=1.4e-18  Score=127.04  Aligned_cols=75  Identities=23%  Similarity=0.350  Sum_probs=70.8

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        18 ~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      +|||+|||+++++++|+++|++||+|.++++.+++ +++++|||||+|.+.++|..|++ +||..+.|++|+|+.+.
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 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            59999999999999999999999999999999886 68899999999999999999996 99999999999998764

>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=99.73  E-value=9e-19  Score=127.08  Aligned_cols=75  Identities=21%  Similarity=0.371  Sum_probs=72.2

Q ss_pred             eEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecc
Q psy2983          18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPT   92 (370)
Q Consensus        18 ~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~   92 (370)
                      +|||+|||+++|+++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|.+|++++|..+.|++|.|+++
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEEC
Confidence            599999999999999999999999999999999999999999999999999999999999999999999999764

>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=99.73  E-value=3.1e-18  Score=128.46  Aligned_cols=80  Identities=33%  Similarity=0.578  Sum_probs=74.2

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      ..+|||+|||+++++++|+++|++||.|..++++.+.  +.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.+
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            3579999999999999999999999999999999884  45789999999999999999999999999999999999876


Q ss_pred             CC
Q psy2983         194 RN  195 (370)
Q Consensus       194 ~~  195 (370)
                      +.
T Consensus        86 ~~   87 (89)
T d1cvja2          86 RK   87 (89)
T ss_dssp             TT
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=99.73  E-value=9.1e-19  Score=126.81  Aligned_cols=75  Identities=25%  Similarity=0.521  Sum_probs=71.1

Q ss_pred             eEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       116 ~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      +|||+|||+++|+++|+++|++||.|..++++.++.+|+++|||||+|.+.++|.+|++ .++..+.|+.|.|+.|
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            59999999999999999999999999999999999999999999999999999999998 5888999999999764

>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=99.73  E-value=5e-18  Score=128.36  Aligned_cols=84  Identities=25%  Similarity=0.430  Sum_probs=76.1

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPII   88 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~   88 (370)
                      .+.....++|||+|||..+++++|+++|+.||+|.++.++++..+  ++|||||+|.+.++|.+|++ ++|..+.|+.|+
T Consensus         5 ~~~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~--~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~   82 (93)
T d2cq3a1           5 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHGTVVEGRKIE   82 (93)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT--TCCEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC--CcceeEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            445567789999999999999999999999999999999988743  68999999999999999995 999999999999


Q ss_pred             Eeccccc
Q psy2983          89 VQPTQAE   95 (370)
Q Consensus        89 v~~~~~~   95 (370)
                      |.++.+.
T Consensus        83 V~~A~~r   89 (93)
T d2cq3a1          83 VNNATAR   89 (93)
T ss_dssp             EEECCSS
T ss_pred             EEecCcC
Confidence            9998754

>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=99.73  E-value=9.6e-18  Score=128.83  Aligned_cols=85  Identities=25%  Similarity=0.448  Sum_probs=77.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCcee--------eEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCC
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKID--------NIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG  183 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~--------~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g  183 (370)
                      ....+|||+|||..+++++|+++|+.||.|.        .+.+..+..+|.++|||||+|.+.++|.+|++.|||..+.|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            3457999999999999999999999999874        56777888889999999999999999999999999999999


Q ss_pred             eeEEEEEeecCCC
Q psy2983         184 RPMKVGTVTDRNE  196 (370)
Q Consensus       184 ~~l~V~~~~~~~~  196 (370)
                      +.|+|.++.++..
T Consensus        86 r~i~V~~a~~~~p   98 (101)
T d2cpea1          86 SKLKVSLARKKPP   98 (101)
T ss_dssp             EECEEECSSCCCC
T ss_pred             EEEEEEEcCCCCC
Confidence            9999999877543

>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=99.73  E-value=3.5e-18  Score=127.05  Aligned_cols=76  Identities=22%  Similarity=0.410  Sum_probs=70.9

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCC---CeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecccc
Q psy2983          19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTR---RFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQA   94 (370)
Q Consensus        19 v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~---~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~   94 (370)
                      |||+|||.++|+++|+++|++||+|.++.+++++.++   .++|||||+|.+.++|..|++ ++|..+.|++|.|+++..
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            7999999999999999999999999999999987765   579999999999999999995 999999999999998753

>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=99.73  E-value=9.7e-18  Score=128.04  Aligned_cols=85  Identities=29%  Similarity=0.583  Sum_probs=77.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhC------CceeCCee
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN------GFELAGRP  185 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~------g~~i~g~~  185 (370)
                      ...++|||+|||+.+++++|+++|++||.|..+.+..+..++.++|||||+|.+.++|.+|++.|+      |..+.|+.
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~   85 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   85 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEE
Confidence            345789999999999999999999999999999999998899999999999999999999999886      67789999


Q ss_pred             EEEEEeecCCC
Q psy2983         186 MKVGTVTDRNE  196 (370)
Q Consensus       186 l~V~~~~~~~~  196 (370)
                      |+|.++.++..
T Consensus        86 l~v~~a~~k~~   96 (98)
T d1x4ha1          86 LKVDLAVTRDE   96 (98)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEECCCCCc
Confidence            99999877543

>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=99.72  E-value=1.7e-18  Score=128.22  Aligned_cols=77  Identities=29%  Similarity=0.386  Sum_probs=71.8

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCCeeE-EEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccccc
Q psy2983          19 IFCMQLSQRIRTRDLEEFFSSVGKVRD-VRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQAE   95 (370)
Q Consensus        19 v~V~nLp~~~te~~L~~~f~~~G~v~~-v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~~   95 (370)
                      |||+|||.++|+++|+++|++||.|.+ +.+++++.+++++|||||+|.+.++|..|++ ++|..+.|++|+|.++.+.
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            799999999999999999999999865 4788999999999999999999999999995 9999999999999998654

>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=99.72  E-value=4.3e-18  Score=126.77  Aligned_cols=80  Identities=25%  Similarity=0.440  Sum_probs=70.1

Q ss_pred             CceEEEecCCCCCC-HHHHHhcccCCCceeeEEEeec-CCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         114 PMRLYIGSLHFNIT-EDMLRGIFEPFGKIDNIQLMVD-PDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       114 ~~~l~V~nlp~~~t-~e~l~~~f~~~G~i~~v~~~~~-~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      .++|||+|||++++ +++|+++|++||.|.++++..+ ..+|.++|||||+|.+.++|.+|++ |||..+.|+.|+|.++
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEEC
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEc
Confidence            47899999999986 5569999999999999998764 4689999999999999999999996 9999999999999998


Q ss_pred             ecC
Q psy2983         192 TDR  194 (370)
Q Consensus       192 ~~~  194 (370)
                      .++
T Consensus        83 ~~k   85 (86)
T d2ghpa3          83 DKK   85 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>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=99.72  E-value=3.7e-18  Score=123.74  Aligned_cols=75  Identities=33%  Similarity=0.636  Sum_probs=72.1

Q ss_pred             eEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       116 ~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      +|||+|||+++|+++|+++|++||.+..+.+..++.+|.++|||||+|.+.++|.+|++ +||..+.|++|+|++|
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            59999999999999999999999999999999998899999999999999999999997 9999999999999875

>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=99.72  E-value=1e-17  Score=128.65  Aligned_cols=80  Identities=25%  Similarity=0.516  Sum_probs=74.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ..+++|||+|||+++++++|+++|++||.|..+.+..+. ++.++|||||+|.+.++|.+|++.|||..|.|+++.|.++
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            345789999999999999999999999999999998884 8999999999999999999999999999999999988665


Q ss_pred             e
Q psy2983         192 T  192 (370)
Q Consensus       192 ~  192 (370)
                      .
T Consensus        95 ~   95 (101)
T d1x5oa1          95 E   95 (101)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.72  E-value=3.7e-18  Score=131.20  Aligned_cols=84  Identities=24%  Similarity=0.459  Sum_probs=76.3

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCee--------EEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCcc
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVR--------DVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL   82 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~--------~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i   82 (370)
                      ++.+.++|||+|||..+|+++|+++|+.||+|.        .+.+.+++.+++++|||||+|.+.++|..|++ ++|..|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            445778999999999999999999999999874        56677888889999999999999999999996 999999


Q ss_pred             CCeeEEEeccccc
Q psy2983          83 LGIPIIVQPTQAE   95 (370)
Q Consensus        83 ~g~~l~v~~~~~~   95 (370)
                      .|++|+|.++...
T Consensus        84 ~gr~i~V~~a~~~   96 (101)
T d2cpea1          84 QGSKLKVSLARKK   96 (101)
T ss_dssp             TTEECEEECSSCC
T ss_pred             CCEEEEEEEcCCC
Confidence            9999999998754

>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=99.71  E-value=2.9e-18  Score=128.62  Aligned_cols=80  Identities=23%  Similarity=0.394  Sum_probs=73.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      ...+|||+|||.++|+++|+++|+.||.|.+++++.+..  .++|||||+|.+.++|.+|++ |+|..+.|++|.|.++.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~   84 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   84 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT--BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            456899999999999999999999999999999998864  468999999999999999995 99999999999999987


Q ss_pred             ccc
Q psy2983          94 AEK   96 (370)
Q Consensus        94 ~~~   96 (370)
                      +..
T Consensus        85 ~~~   87 (89)
T d1cvja2          85 SRK   87 (89)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>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=99.70  E-value=2.6e-17  Score=122.13  Aligned_cols=77  Identities=25%  Similarity=0.245  Sum_probs=72.4

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      .++|||+|||.++|+++|+++|+.||+|..+.+..+. +|.++|||||+|.+.++|.+|++ ++|..+.|+.|.|.+..
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 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            3689999999999999999999999999999998885 89999999999999999999997 79999999999998854

>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=99.70  E-value=6.7e-18  Score=129.69  Aligned_cols=82  Identities=20%  Similarity=0.453  Sum_probs=74.5

Q ss_pred             cccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEE
Q psy2983          11 PEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIV   89 (370)
Q Consensus        11 ~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v   89 (370)
                      +.+++.++|||+|||.++++++|+++|++||+|..+.+..+. ++.++|||||+|.+.++|.+|++ |||..|.|+++.+
T Consensus        13 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v   91 (101)
T d1x5oa1          13 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVS   91 (101)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSC
T ss_pred             cccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCcc
Confidence            445667899999999999999999999999999999988874 68899999999999999999995 9999999999888


Q ss_pred             eccc
Q psy2983          90 QPTQ   93 (370)
Q Consensus        90 ~~~~   93 (370)
                      .++.
T Consensus        92 ~~~~   95 (101)
T d1x5oa1          92 APTE   95 (101)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            6654

>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=99.70  E-value=3.2e-17  Score=128.74  Aligned_cols=78  Identities=28%  Similarity=0.457  Sum_probs=72.3

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      .+++|||+|||..+++++|+++|++||.|.+|++..   ++.++|||||+|.+.++|..|+..|||..|.|+.|+|.++.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~---~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC---STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc---cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            357899999999999999999999999999999874   46779999999999999999999999999999999999975


Q ss_pred             c
Q psy2983         193 D  193 (370)
Q Consensus       193 ~  193 (370)
                      .
T Consensus        83 ~   83 (114)
T d2f9da1          83 A   83 (114)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=99.70  E-value=2.9e-18  Score=129.07  Aligned_cols=82  Identities=27%  Similarity=0.489  Sum_probs=75.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      +..+.+|||+|||+++++++|+++|+.||.|..+.++.+ .+|+++|||||+|.+.++|.+|++ |||..+.|+.|+|.+
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~   87 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEe
Confidence            345679999999999999999999999999999988765 589999999999999999999997 999999999999998


Q ss_pred             eecC
Q psy2983         191 VTDR  194 (370)
Q Consensus       191 ~~~~  194 (370)
                      ++.+
T Consensus        88 ak~k   91 (91)
T d1fjeb1          88 PKGR   91 (91)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            7653

>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=99.70  E-value=8.3e-18  Score=120.87  Aligned_cols=71  Identities=34%  Similarity=0.563  Sum_probs=68.6

Q ss_pred             EEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEE
Q psy2983         117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMK  187 (370)
Q Consensus       117 l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~  187 (370)
                      |||+|||+++++++|+++|++||.|..+++..++.++.++|||||+|.+.++|.+|++.|||..+.|+.|+
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            79999999999999999999999999999999998999999999999999999999999999999999874

>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=99.70  E-value=2.8e-18  Score=132.16  Aligned_cols=83  Identities=25%  Similarity=0.400  Sum_probs=77.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      .++++|||+|||.++++++|+++|+.||.|..+.++.+..+++++|||||+|.+.++|..|++ ++|..|.|++|.|.++
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            467999999999999999999999999999999999988889999999999999999999995 9999999999999998


Q ss_pred             cccc
Q psy2983          93 QAEK   96 (370)
Q Consensus        93 ~~~~   96 (370)
                      +...
T Consensus        96 k~k~   99 (102)
T d2cpxa1          96 KNKK   99 (102)
T ss_dssp             CCCS
T ss_pred             CCcc
Confidence            7643

>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=99.70  E-value=2.6e-17  Score=123.29  Aligned_cols=76  Identities=20%  Similarity=0.363  Sum_probs=69.8

Q ss_pred             CceEEEecCCCCCCHHHH---HhcccCCCceeeEEEeecCCCCCc---ccEEEEEECCHHHHHHHHHHhCCceeCCeeEE
Q psy2983         114 PMRLYIGSLHFNITEDML---RGIFEPFGKIDNIQLMVDPDTGRS---KGYGFITFHSADDAKKAQEQLNGFELAGRPMK  187 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l---~~~f~~~G~i~~v~~~~~~~~g~~---~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~  187 (370)
                      .++|||+|||+.+++++|   +++|++||.|..+.+++++.++.+   +|||||+|.+.++|.+|++.|||..+.|+.|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            467999999999999999   789999999999999998766554   48999999999999999999999999999999


Q ss_pred             EE
Q psy2983         188 VG  189 (370)
Q Consensus       188 V~  189 (370)
                      |+
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            84

>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=99.70  E-value=2.3e-17  Score=127.37  Aligned_cols=89  Identities=16%  Similarity=0.186  Sum_probs=79.1

Q ss_pred             CCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeE
Q psy2983           8 DLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPI   87 (370)
Q Consensus         8 ~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l   87 (370)
                      ...+...+..+|||+|||+++|+++|+++|..+|.+....++.+..+++++|||||+|.++++|.+|+++++..|.|+.|
T Consensus         7 ~~~~~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i   86 (104)
T d1wg5a_           7 GNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYI   86 (104)
T ss_dssp             CCCSSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCC
T ss_pred             CCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEE
Confidence            33444556778999999999999999999999999988777777788999999999999999999999999999999999


Q ss_pred             EEecccccc
Q psy2983          88 IVQPTQAEK   96 (370)
Q Consensus        88 ~v~~~~~~~   96 (370)
                      .|.++....
T Consensus        87 ~V~~~~~~~   95 (104)
T d1wg5a_          87 EIFKSSRAE   95 (104)
T ss_dssp             EEEEECTTT
T ss_pred             EEEECCHHH
Confidence            998887553

>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=99.70  E-value=2.5e-17  Score=125.08  Aligned_cols=76  Identities=28%  Similarity=0.554  Sum_probs=71.3

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .++|||+|||..+++++|+++|++||.|.++++.++      +|||||+|.+.++|.+|+..|||..+.|+.|+|.|+++
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~   91 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   91 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            468999999999999999999999999999999865      78999999999999999999999999999999999876


Q ss_pred             CC
Q psy2983         194 RN  195 (370)
Q Consensus       194 ~~  195 (370)
                      +.
T Consensus        92 ~p   93 (96)
T d1x4ga1          92 SP   93 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.69  E-value=3.3e-17  Score=121.82  Aligned_cols=77  Identities=31%  Similarity=0.584  Sum_probs=71.3

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      +..+|||+|||.++++++|+++|++||.|.++++.++      +|||||+|.+.++|.+|+..|||..+.|+.|+|.++.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            3468999999999999999999999999999999855      6899999999999999999999999999999999987


Q ss_pred             cCC
Q psy2983         193 DRN  195 (370)
Q Consensus       193 ~~~  195 (370)
                      ...
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            643

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=6.9e-17  Score=122.47  Aligned_cols=80  Identities=23%  Similarity=0.447  Sum_probs=72.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      .++++|||+|||+.+++++|+++|++||.|..+.+..   ++.++|||||+|.+.++|..|++.|||..+.|++|+|.++
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~---~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a   88 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecc---cccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            4456899999999999999999999999999988754   4567899999999999999999999999999999999998


Q ss_pred             ecC
Q psy2983         192 TDR  194 (370)
Q Consensus       192 ~~~  194 (370)
                      ++.
T Consensus        89 ~~~   91 (95)
T d1x4aa1          89 RSG   91 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            654

>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=99.69  E-value=1.1e-18  Score=131.46  Aligned_cols=81  Identities=19%  Similarity=0.319  Sum_probs=74.1

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecc
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPT   92 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~   92 (370)
                      ....++|||+|||.++|+++|+++|+.||.|.++.++. ..+|+++|||||+|.+.++|.+|++++|..+.|++|.|.++
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~-~~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVD-VRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCE-EEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeee-cCCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEec
Confidence            44667999999999999999999999999999888765 45789999999999999999999999999999999999987


Q ss_pred             cc
Q psy2983          93 QA   94 (370)
Q Consensus        93 ~~   94 (370)
                      +.
T Consensus        89 k~   90 (91)
T d1fjeb1          89 KG   90 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=1.8e-17  Score=130.12  Aligned_cols=79  Identities=20%  Similarity=0.348  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      ..+|+|||+|||..+|+++|+++|+.||+|.+|++..+   +.++|||||+|.+.++|..|++ |+|..|.|++|.|.++
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            35789999999999999999999999999999998764   5668999999999999999995 9999999999999987


Q ss_pred             ccc
Q psy2983          93 QAE   95 (370)
Q Consensus        93 ~~~   95 (370)
                      ...
T Consensus        82 ~~~   84 (114)
T d2f9da1          82 NAN   84 (114)
T ss_dssp             CHH
T ss_pred             CCC
Confidence            643

>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=99.69  E-value=2.9e-17  Score=126.82  Aligned_cols=83  Identities=28%  Similarity=0.412  Sum_probs=73.5

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeC-CCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCN-KTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~-~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~   91 (370)
                      ..+.++|||+|||.++|+++|+++|+.|| +.++.++.+. .+++++|||||+|.+.++|++|+++++..|.|+.|+|.+
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34679999999999999999999999999 6677777655 468899999999999999999999999999999999998


Q ss_pred             ccccc
Q psy2983          92 TQAEK   96 (370)
Q Consensus        92 ~~~~~   96 (370)
                      +....
T Consensus        91 a~~~~   95 (104)
T d1wi8a_          91 ADQAQ   95 (104)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76543

>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=99.69  E-value=6e-18  Score=130.25  Aligned_cols=84  Identities=26%  Similarity=0.387  Sum_probs=78.7

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ++++|||+|||..+++++|+++|++||.|..+.+..+..+|.++|||||+|.+.++|.+|+..|||..+.|++|+|.+++
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            45789999999999999999999999999999988887789999999999999999999999999999999999999998


Q ss_pred             cCCC
Q psy2983         193 DRNE  196 (370)
Q Consensus       193 ~~~~  196 (370)
                      ++..
T Consensus        97 ~k~~  100 (102)
T d2cpxa1          97 NKKQ  100 (102)
T ss_dssp             CCSC
T ss_pred             Cccc
Confidence            7644

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.68  E-value=2e-17  Score=119.73  Aligned_cols=74  Identities=19%  Similarity=0.217  Sum_probs=68.4

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecc
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPT   92 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~   92 (370)
                      .+|||+|||+++++++|+++|+.||+|.++++.+++.++  ++||||+|.+.++|.+|+++++..|.|++|.|...
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--FRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS--SEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc--ceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            479999999999999999999999999999999987543  57999999999999999999999999999999764

>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=99.68  E-value=5.5e-17  Score=120.73  Aligned_cols=79  Identities=23%  Similarity=0.373  Sum_probs=71.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceee-EEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDN-IQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~-v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      +.+..|||+|||+++++++|+++|+.||.+.. +.+..+ .+|.++|+|||+|.+.++|.+|++.||+..+.|++|+|..
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~-~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeC-CCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34578999999999999999999999999876 455555 5899999999999999999999999999999999999986


Q ss_pred             e
Q psy2983         191 V  191 (370)
Q Consensus       191 ~  191 (370)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=7.6e-17  Score=119.08  Aligned_cols=75  Identities=23%  Similarity=0.411  Sum_probs=68.8

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeC-CeeEEEEEe
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELA-GRPMKVGTV  191 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~-g~~l~V~~~  191 (370)
                      ++++|||+|||..+++++|+++|++||.|..+++.++.     +|||||+|.+.++|..|+..|||..+. |++|+|.|+
T Consensus         7 P~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~a   81 (83)
T d2b0ga1           7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFA   81 (83)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEe
Confidence            45799999999999999999999999999999997553     789999999999999999999999985 689999997


Q ss_pred             e
Q psy2983         192 T  192 (370)
Q Consensus       192 ~  192 (370)
                      +
T Consensus        82 k   82 (83)
T d2b0ga1          82 K   82 (83)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.68  E-value=2.9e-16  Score=133.44  Aligned_cols=134  Identities=23%  Similarity=0.446  Sum_probs=115.4

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .++|||+|||+.+|+++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|.+|+. +++..+.++.+.+.....
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhh
Confidence            3789999999999999999999999999999999999999999999999999999999998 678888999988887644


Q ss_pred             CCC-------------CcCCCCCCCCHHHHHHhcccCCceeeeeeeeccc----cCCC---CCChHHHHHHHhhh
Q psy2983         194 RNE-------------SVGGGPSNLDTDEMERAGVDLGATGRLQLMFKLA----EGTG---LELPPAAASALNLA  248 (370)
Q Consensus       194 ~~~-------------~~~~~~~~~~~~~l~~~~~~~g~~~~~~l~~~~~----~~~~---~~~~~~a~~a~~~~  248 (370)
                      ...             .+++++..+++++|+..|..+|.+..+.++.+..    +|++   |..+.+|..|+.+.
T Consensus        85 ~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~~~  159 (183)
T d1u1qa_          85 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK  159 (183)
T ss_dssp             TTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHTSS
T ss_pred             cccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHHhC
Confidence            332             2678999999999999999999999998887533    2334   67888888887643

>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=99.68  E-value=6.7e-17  Score=122.82  Aligned_cols=81  Identities=33%  Similarity=0.498  Sum_probs=73.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||+++++++|+++|++||.|..+..     +|.++|||||+|.+.++|.+|+..|||..+.|++|+|.+
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            344689999999999999999999999998876642     688999999999999999999999999999999999999


Q ss_pred             eecCCC
Q psy2983         191 VTDRNE  196 (370)
Q Consensus       191 ~~~~~~  196 (370)
                      +.++..
T Consensus        88 a~~k~~   93 (96)
T d1fjca_          88 TGEKGG   93 (96)
T ss_dssp             CSSSCC
T ss_pred             eCCCCC
Confidence            887654

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=2.2e-16  Score=121.79  Aligned_cols=84  Identities=24%  Similarity=0.539  Sum_probs=73.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecC-CCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDP-DTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~-~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      .++++|||+|||+++++++|+++|+.|| +..+.++.+. .+|.++|||||+|.+.++|.+|+. ||+..|.|+.|+|.+
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            3568999999999999999999999999 6677777654 478899999999999999987775 999999999999999


Q ss_pred             eecCCCC
Q psy2983         191 VTDRNES  197 (370)
Q Consensus       191 ~~~~~~~  197 (370)
                      +.++...
T Consensus        91 a~~~~~~   97 (104)
T d1wi8a_          91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            8776554

>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=99.67  E-value=5.7e-17  Score=124.59  Aligned_cols=84  Identities=19%  Similarity=0.199  Sum_probs=74.2

Q ss_pred             CcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEE
Q psy2983          10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIV   89 (370)
Q Consensus        10 ~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v   89 (370)
                      .......++|||+|||+++|+++|+++|..||. ..+.++.+. ++..+|||||+|.+.++|++|+++++..|.||.|.|
T Consensus         9 ~~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V   86 (102)
T d1weza_           9 SFQSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVEL   86 (102)
T ss_dssp             SCCCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEE
T ss_pred             CCcCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec-CCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEE
Confidence            445567789999999999999999999999985 467777775 478999999999999999999999999999999999


Q ss_pred             eccccc
Q psy2983          90 QPTQAE   95 (370)
Q Consensus        90 ~~~~~~   95 (370)
                      .++...
T Consensus        87 ~~s~~~   92 (102)
T d1weza_          87 FLNSTA   92 (102)
T ss_dssp             EEECCC
T ss_pred             EEcCCC
Confidence            987654

>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=99.67  E-value=3.3e-17  Score=124.42  Aligned_cols=78  Identities=19%  Similarity=0.391  Sum_probs=71.2

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      .....++|||+|||..+++++|+++|++||+|.+|+++++      +|||||+|.+.++|..|+. ++|..+.|++|+|.
T Consensus        14 ~~~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~   87 (96)
T d1x4ga1          14 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY   87 (96)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3455689999999999999999999999999999999865      6899999999999999995 99999999999999


Q ss_pred             ccccc
Q psy2983          91 PTQAE   95 (370)
Q Consensus        91 ~~~~~   95 (370)
                      |++..
T Consensus        88 ~ak~~   92 (96)
T d1x4ga1          88 WGKES   92 (96)
T ss_dssp             CCCCC
T ss_pred             EcCCC
Confidence            98643

>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=99.67  E-value=1.1e-16  Score=119.65  Aligned_cols=78  Identities=15%  Similarity=0.252  Sum_probs=69.6

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeC-CeeEEEEEe
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELA-GRPMKVGTV  191 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~-g~~l~V~~~  191 (370)
                      ++++|||+|||+++++++|+++|++||.|..+.+..    ++++|||||+|.+.++|.+|+..|||..+. |+.|+|.++
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            457899999999999999999999999998877653    445889999999999999999999999984 899999997


Q ss_pred             ecC
Q psy2983         192 TDR  194 (370)
Q Consensus       192 ~~~  194 (370)
                      +.+
T Consensus        85 k~~   87 (88)
T d2adca2          85 KST   87 (88)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            653

>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=99.67  E-value=4.4e-18  Score=127.90  Aligned_cols=80  Identities=16%  Similarity=0.344  Sum_probs=70.5

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEE-----eeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEe
Q psy2983          16 ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRL-----ITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQ   90 (370)
Q Consensus        16 ~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i-----~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~   90 (370)
                      .|+|||+|||.++|+++|+++|+.||.+..+.+     ..+..+++++|||||+|.+.++|..|++|+|..+.|++|+|+
T Consensus         1 aRrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIR   80 (90)
T ss_dssp             CCEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCCB
T ss_pred             CCEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEEC
Confidence            489999999999999999999999998776554     345566788999999999999999999999999999999998


Q ss_pred             ccccc
Q psy2983          91 PTQAE   95 (370)
Q Consensus        91 ~~~~~   95 (370)
                      +++..
T Consensus        81 r~k~~   85 (90)
T d1u2fa_          81 RPHDY   85 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            76543

>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=99.66  E-value=2.6e-16  Score=116.98  Aligned_cols=77  Identities=25%  Similarity=0.403  Sum_probs=69.9

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .++|||+|||+.+++++|+++|++||.+..+.+.+      ++|||||+|.+.++|..|+..|||..+.|+.|+|.+++|
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP   81 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   81 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccC
Confidence            46899999999999999999999999988777643      488999999999999999999999999999999999876


Q ss_pred             CCC
Q psy2983         194 RNE  196 (370)
Q Consensus       194 ~~~  196 (370)
                      +..
T Consensus        82 ~~~   84 (86)
T d2cpda1          82 VDK   84 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.66  E-value=3.7e-16  Score=120.44  Aligned_cols=85  Identities=18%  Similarity=0.191  Sum_probs=75.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ....+|||+|||+++|+++|+++|+.+|.+....++.+..++.++|||||+|.++++|.+|++ +|+..|.||.|+|.++
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEEC
Confidence            345689999999999999999999999998886666666789999999999999999999997 9999999999999998


Q ss_pred             ecCCCC
Q psy2983         192 TDRNES  197 (370)
Q Consensus       192 ~~~~~~  197 (370)
                      .+....
T Consensus        92 ~~~~~~   97 (104)
T d1wg5a_          92 SRAEVR   97 (104)
T ss_dssp             CTTTSC
T ss_pred             CHHHhc
Confidence            776543

>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=99.66  E-value=5.9e-17  Score=122.89  Aligned_cols=81  Identities=27%  Similarity=0.418  Sum_probs=72.4

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      ..+++++|||+|||+++|+++|+++|+.||.|..+.+..+   +.++|||||+|.+.++|..|++ |+|..|.|++|+|+
T Consensus        10 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~   86 (95)
T d1x4aa1          10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   86 (95)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3466789999999999999999999999999999887654   4568999999999999999996 99999999999999


Q ss_pred             ccccc
Q psy2983          91 PTQAE   95 (370)
Q Consensus        91 ~~~~~   95 (370)
                      +++..
T Consensus        87 ~a~~~   91 (95)
T d1x4aa1          87 FPRSG   91 (95)
T ss_dssp             CCCCC
T ss_pred             eccCC
Confidence            98643

>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=99.66  E-value=4.9e-17  Score=119.22  Aligned_cols=76  Identities=32%  Similarity=0.444  Sum_probs=68.6

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCc-eeCCeeEEEEEeec
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF-ELAGRPMKVGTVTD  193 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~-~i~g~~l~V~~~~~  193 (370)
                      ++|||+|||.++++++|+++|++||.|..+.+...      +|||||+|.+.++|.+|++.|||. .+.|++|+|.++.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            36999999999999999999999999887766543      789999999999999999999995 79999999999887


Q ss_pred             CCC
Q psy2983         194 RNE  196 (370)
Q Consensus       194 ~~~  196 (370)
                      +..
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            654

>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=99.66  E-value=8.9e-18  Score=120.71  Aligned_cols=70  Identities=19%  Similarity=0.337  Sum_probs=67.0

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEE
Q psy2983          19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPII   88 (370)
Q Consensus        19 v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~   88 (370)
                      |||+|||.++|+++|+++|++||+|..+++.+++.++.++|||||+|.+.++|.+|++ |||..++|+.++
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            7999999999999999999999999999999999999999999999999999999995 999999998763

>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=99.66  E-value=1.1e-16  Score=121.64  Aligned_cols=83  Identities=17%  Similarity=0.304  Sum_probs=74.0

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCc-eeeEEEeecC-CCCCcccEEEEEECCHHHHHHHHHHhCC--ceeCCeeEEEEE
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGK-IDNIQLMVDP-DTGRSKGYGFITFHSADDAKKAQEQLNG--FELAGRPMKVGT  190 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~-i~~v~~~~~~-~~g~~~g~afV~f~~~~~a~~A~~~l~g--~~i~g~~l~V~~  190 (370)
                      ++|||+|||..+++++|+++|++||+ |..+.++++. .+|.++|||||+|.+.++|..|++.|++  ..++|++|+|.|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            57999999999999999999999996 9999999875 3689999999999999999999999965  456799999999


Q ss_pred             eecCCCC
Q psy2983         191 VTDRNES  197 (370)
Q Consensus       191 ~~~~~~~  197 (370)
                      +.++..+
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9876554

>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=99.66  E-value=1.5e-16  Score=114.95  Aligned_cols=74  Identities=14%  Similarity=0.149  Sum_probs=67.8

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      .+|||+|||+++++++|+++|++||.|..+++..++.  ..+|||||+|.+.++|.+|+. +|+..|+|++|.|..+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            3799999999999999999999999999999998853  345799999999999999996 8999999999999874

>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=99.66  E-value=3.9e-17  Score=124.11  Aligned_cols=83  Identities=30%  Similarity=0.403  Sum_probs=73.3

Q ss_pred             CCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeE
Q psy2983           9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPI   87 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l   87 (370)
                      .....+++++|||+|||.++|+++|+++|++||.|..+.     .+++++|||||+|.+.++|..|++ |+|..+.|++|
T Consensus         9 ~~~~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i   83 (96)
T d1fjca_           9 TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV   83 (96)
T ss_dssp             TTSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEE
T ss_pred             ccCcCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEE
Confidence            345567789999999999999999999999999887653     257889999999999999999995 99999999999


Q ss_pred             EEecccccc
Q psy2983          88 IVQPTQAEK   96 (370)
Q Consensus        88 ~v~~~~~~~   96 (370)
                      +|.++.+..
T Consensus        84 ~V~~a~~k~   92 (96)
T d1fjca_          84 SLYYTGEKG   92 (96)
T ss_dssp             EEEECSSSC
T ss_pred             EEEEeCCCC
Confidence            999987653

>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=99.65  E-value=4.9e-16  Score=118.29  Aligned_cols=76  Identities=22%  Similarity=0.478  Sum_probs=68.4

Q ss_pred             CCceEEEecCC-CCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         113 GPMRLYIGSLH-FNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       113 ~~~~l~V~nlp-~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ...+|||+||| ..+++++|+++|++||.|..+++.        +|||||+|.+.++|.+|+..|||..+.|++|+|.++
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   85 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA   85 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEET
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34679999997 578899999999999999999883        789999999999999999999999999999999998


Q ss_pred             ecCCC
Q psy2983         192 TDRNE  196 (370)
Q Consensus       192 ~~~~~  196 (370)
                      .++..
T Consensus        86 ~~~~~   90 (98)
T d1wf2a_          86 AEPKV   90 (98)
T ss_dssp             TSCCC
T ss_pred             CCCCC
Confidence            76443

>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=99.65  E-value=2.5e-17  Score=123.36  Aligned_cols=76  Identities=21%  Similarity=0.354  Sum_probs=68.8

Q ss_pred             CCCeEEEcCCCCCCcHHHH---HHHhhcCCCeeEEEEeeeCCCCCe---ecEEEEEecCCCChHHHhh-ccCCccCCeeE
Q psy2983          15 DARTIFCMQLSQRIRTRDL---EEFFSSVGKVRDVRLITCNKTRRF---KGIAYIEFKDPESVPLAMG-LNGQKLLGIPI   87 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L---~~~f~~~G~v~~v~i~~d~~~~~~---kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l   87 (370)
                      ..++|||+|||+++++++|   .++|++||+|.++.+++++.++.+   +|||||+|.+.++|.+|++ |||..+.|++|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            4578999999999999999   678999999999999998876654   4899999999999999995 99999999999


Q ss_pred             EEe
Q psy2983          88 IVQ   90 (370)
Q Consensus        88 ~v~   90 (370)
                      ++.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            873

>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=99.65  E-value=7.3e-17  Score=119.18  Aligned_cols=75  Identities=20%  Similarity=0.308  Sum_probs=67.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCcc-CCeeEEEec
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL-LGIPIIVQP   91 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i-~g~~l~v~~   91 (370)
                      .++++|||+|||.++|+++|+++|+.||+|.+++++++.     +|||||+|.+.++|..|++ |+|..+ .|++|+|.+
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~   80 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITF   80 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEE
Confidence            457899999999999999999999999999999997643     6899999999999999996 999988 468999998


Q ss_pred             cc
Q psy2983          92 TQ   93 (370)
Q Consensus        92 ~~   93 (370)
                      ++
T Consensus        81 ak   82 (83)
T d2b0ga1          81 AK   82 (83)
T ss_dssp             CC
T ss_pred             ec
Confidence            75

>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=99.65  E-value=6.5e-17  Score=126.45  Aligned_cols=82  Identities=17%  Similarity=0.264  Sum_probs=74.8

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecc
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPT   92 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~   92 (370)
                      ....++|||+|||+++|+++|+++|+.||.+..+.++.+..+|.++|||||+|.+.++|.+|++++|..|+|+.|.|.++
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEc
Confidence            44667999999999999999999999999998766777778899999999999999999999999999999999999876


Q ss_pred             cc
Q psy2983          93 QA   94 (370)
Q Consensus        93 ~~   94 (370)
                      ..
T Consensus        95 ~~   96 (112)
T d1wela1          95 TK   96 (112)
T ss_dssp             CH
T ss_pred             Ch
Confidence            54

>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=99.65  E-value=8.9e-17  Score=120.84  Aligned_cols=80  Identities=26%  Similarity=0.520  Sum_probs=71.5

Q ss_pred             CceEEEecCCCCCCHHHHHh----cccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEE
Q psy2983         114 PMRLYIGSLHFNITEDMLRG----IFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG  189 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~----~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~  189 (370)
                      +++|||+|||+.+++++|++    +|++||.|.+|++..   ++.++|||||+|.+.++|.+|+..|||..+.|+.|+|.
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~   79 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   79 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            47899999999999998864    589999999988753   57789999999999999999999999999999999999


Q ss_pred             EeecCCC
Q psy2983         190 TVTDRNE  196 (370)
Q Consensus       190 ~~~~~~~  196 (370)
                      +++++..
T Consensus        80 ~ak~~~~   86 (91)
T d1nu4a_          80 YAKTDSD   86 (91)
T ss_dssp             ECSSCCT
T ss_pred             EeCCCch
Confidence            9876543

>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=99.64  E-value=2.5e-16  Score=115.12  Aligned_cols=74  Identities=27%  Similarity=0.511  Sum_probs=68.0

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ..++|||+|+|  +|+++|+++|++||.|.++.+.++      +|||||+|.+.++|..|+..|||..+.|++|+|.+++
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   75 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   75 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            34689999986  899999999999999999998754      6899999999999999999999999999999999987


Q ss_pred             cC
Q psy2983         193 DR  194 (370)
Q Consensus       193 ~~  194 (370)
                      ++
T Consensus        76 ~~   77 (79)
T d2bz2a1          76 KQ   77 (79)
T ss_dssp             SS
T ss_pred             CC
Confidence            64

>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=99.64  E-value=4.3e-17  Score=125.61  Aligned_cols=82  Identities=16%  Similarity=0.196  Sum_probs=73.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEeccc
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~~   93 (370)
                      ....+|||+|||+++|+++|+++|..||.|....++.+..+|+++|||||+|.+.++|.+|++++|..|+|+.|.|.+..
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEEC
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEECC
Confidence            34578999999999999999999999999987556666678999999999999999999999999999999999998865


Q ss_pred             cc
Q psy2983          94 AE   95 (370)
Q Consensus        94 ~~   95 (370)
                      ..
T Consensus        86 ~~   87 (103)
T d2cpya1          86 LE   87 (103)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=99.64  E-value=3.9e-17  Score=122.85  Aligned_cols=80  Identities=24%  Similarity=0.498  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHH----HhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEE
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEE----FFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPII   88 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~----~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~   88 (370)
                      |+++||||+|||..+++++|++    +|++||+|.+|.+.+   +++++|||||+|.+.++|..|++ ++|..+.|++|.
T Consensus         1 ~P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~   77 (91)
T d1nu4a_           1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   77 (91)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            5689999999999999999864    689999999988754   36678999999999999999995 999999999999


Q ss_pred             Eecccccc
Q psy2983          89 VQPTQAEK   96 (370)
Q Consensus        89 v~~~~~~~   96 (370)
                      |.+++...
T Consensus        78 v~~ak~~~   85 (91)
T d1nu4a_          78 IQYAKTDS   85 (91)
T ss_dssp             EEECSSCC
T ss_pred             EEEeCCCc
Confidence            99987553

>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=99.64  E-value=4.7e-16  Score=119.36  Aligned_cols=84  Identities=18%  Similarity=0.278  Sum_probs=74.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       111 ~~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      ....++|||+|||+++|+++|+++|+.||. ..+.++.+. +|.++|||||+|.+.++|.+|++ +|+..|.||.|+|.+
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~   88 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            345579999999999999999999999984 578888885 78999999999999999999987 899999999999999


Q ss_pred             eecCCCC
Q psy2983         191 VTDRNES  197 (370)
Q Consensus       191 ~~~~~~~  197 (370)
                      +......
T Consensus        89 s~~~~~~   95 (102)
T d1weza_          89 NSTAGTS   95 (102)
T ss_dssp             ECCCCCC
T ss_pred             cCCCCCC
Confidence            8776543

>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=99.64  E-value=4.6e-16  Score=116.03  Aligned_cols=77  Identities=13%  Similarity=0.287  Sum_probs=66.8

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ++++|||+|||+++++++|+++|++|| +..+.+      +.++|||||+|.+.++|.+|+..|||..+.|++|+|+++.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            457899999999999999999999999 333333      4468999999999999999999999999999999999986


Q ss_pred             cCCC
Q psy2983         193 DRNE  196 (370)
Q Consensus       193 ~~~~  196 (370)
                      .+..
T Consensus        77 ~~~~   80 (88)
T d1wg1a_          77 TDAL   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            5443

>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=99.64  E-value=1.3e-16  Score=118.61  Aligned_cols=75  Identities=23%  Similarity=0.341  Sum_probs=68.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      ..++|||+|||.++++++|+++|+.||.|..+.+.      +++|||||+|.+.++|..|+. |+|..+.|+.|.|++++
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            45899999999999999999999999999887763      347899999999999999996 99999999999999986


Q ss_pred             cc
Q psy2983          94 AE   95 (370)
Q Consensus        94 ~~   95 (370)
                      +.
T Consensus        81 P~   82 (86)
T d2cpda1          81 PV   82 (86)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=1.7e-16  Score=123.52  Aligned_cols=77  Identities=21%  Similarity=0.454  Sum_probs=70.5

Q ss_pred             CceEEEecCCC-CCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         114 PMRLYIGSLHF-NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       114 ~~~l~V~nlp~-~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      +.+|||+|||+ .+++++|+++|+.||.|..+.+++++     +|||||+|.+.++|.+|++.|||..+.|+.|+|.++.
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~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            46899999965 59999999999999999999998774     7899999999999999999999999999999999986


Q ss_pred             cCC
Q psy2983         193 DRN  195 (370)
Q Consensus       193 ~~~  195 (370)
                      ...
T Consensus        77 ~~~   79 (109)
T d2adca1          77 HQN   79 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.64  E-value=1.3e-16  Score=119.13  Aligned_cols=77  Identities=19%  Similarity=0.205  Sum_probs=68.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCcc-CCeeEEEec
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL-LGIPIIVQP   91 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i-~g~~l~v~~   91 (370)
                      .++++|||+|||.++++++|+++|++||.|..+.+..    ++++|||||+|.+.++|.+|+. |+|..+ .|++|+|.+
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            3579999999999999999999999999998877654    3457899999999999999995 999988 589999998


Q ss_pred             ccc
Q psy2983          92 TQA   94 (370)
Q Consensus        92 ~~~   94 (370)
                      ++.
T Consensus        84 sk~   86 (88)
T d2adca2          84 SKS   86 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            864

>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=99.63  E-value=9.3e-17  Score=119.43  Aligned_cols=77  Identities=13%  Similarity=0.164  Sum_probs=68.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      ...+|||+|||.++++++|+++|+.||.+....++.+..+++++|+|||+|.+.++|.+|++ +++..+.|++|+|..
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            45679999999999999999999999998764445555679999999999999999999995 999999999999875

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=2e-16  Score=117.54  Aligned_cols=75  Identities=20%  Similarity=0.316  Sum_probs=68.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      ..++|||+|||.++++++|+++|++||+|.++.+.++      +|||||+|.+.++|..|++ ++|..+.|++|+|+++.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            3467999999999999999999999999999998754      6899999999999999996 99999999999999986


Q ss_pred             cc
Q psy2983          94 AE   95 (370)
Q Consensus        94 ~~   95 (370)
                      ..
T Consensus        81 ~~   82 (86)
T d2cpja1          81 HS   82 (86)
T ss_dssp             CC
T ss_pred             Cc
Confidence            43

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=9.3e-17  Score=119.95  Aligned_cols=78  Identities=22%  Similarity=0.424  Sum_probs=69.1

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCeeEEEecc
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPT   92 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~l~v~~~   92 (370)
                      +..+++|||+|||.++|+++|+++|++||+|.++++..     .++|||||+|.+.++|++|+. ++..|.|++|.|.++
T Consensus         2 s~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG-EDLIIKGISVHISNA   75 (88)
T ss_dssp             CSCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT-CEEEETTEEEEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh-CCCEECCEEeEEEeC
Confidence            34689999999999999999999999999999987643     457999999999999999996 778999999999998


Q ss_pred             cccc
Q psy2983          93 QAEK   96 (370)
Q Consensus        93 ~~~~   96 (370)
                      .+..
T Consensus        76 ~~k~   79 (88)
T d1wf0a_          76 EPKH   79 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>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=99.63  E-value=8.7e-17  Score=125.54  Aligned_cols=78  Identities=22%  Similarity=0.257  Sum_probs=70.0

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      ..|..++|||+|||+.+++++|+++|+.||+|..|.|.      +++|||||+|.+.++|.+|++ |+|..|.|++|.|.
T Consensus         6 ~~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~   79 (111)
T d1whxa_           6 SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLE   79 (111)
T ss_dssp             TSEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEE
Confidence            34567899999999999999999999999999999873      357999999999999999995 99999999999998


Q ss_pred             ccccc
Q psy2983          91 PTQAE   95 (370)
Q Consensus        91 ~~~~~   95 (370)
                      ++...
T Consensus        80 ~a~~~   84 (111)
T d1whxa_          80 WAPIG   84 (111)
T ss_dssp             EEETT
T ss_pred             ECCCC
Confidence            87543

>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=99.63  E-value=2.1e-16  Score=117.98  Aligned_cols=78  Identities=17%  Similarity=0.268  Sum_probs=70.6

Q ss_pred             ccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh---ccCCccCCeeEE
Q psy2983          12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG---LNGQKLLGIPII   88 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~---l~g~~i~g~~l~   88 (370)
                      +..++++|||+|||.++++++|+++|++||.|.++++.++      +|||||+|.+.++|..|++   +++..+.|++|+
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            4568999999999999999999999999999999988754      5899999999999999995   578899999999


Q ss_pred             Eeccccc
Q psy2983          89 VQPTQAE   95 (370)
Q Consensus        89 v~~~~~~   95 (370)
                      |.+++.+
T Consensus        78 v~~sk~~   84 (88)
T d2cq1a1          78 IQYSNHK   84 (88)
T ss_dssp             EEECSCS
T ss_pred             EEECCCC
Confidence            9998654

>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=99.63  E-value=3.6e-16  Score=121.97  Aligned_cols=76  Identities=14%  Similarity=0.139  Sum_probs=69.7

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeec
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD  193 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~  193 (370)
                      .++|||+|||+.+++++|+++|++||.|..|.+.      .++|||||+|.+.++|.+|++.|||..|.|++|+|.++..
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~   83 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCC
Confidence            3689999999999999999999999999999874      2478999999999999999999999999999999999866


Q ss_pred             CC
Q psy2983         194 RN  195 (370)
Q Consensus       194 ~~  195 (370)
                      ..
T Consensus        84 ~~   85 (111)
T d1whxa_          84 GV   85 (111)
T ss_dssp             TT
T ss_pred             Cc
Confidence            43

>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=99.63  E-value=3.6e-16  Score=120.30  Aligned_cols=80  Identities=25%  Similarity=0.319  Sum_probs=71.2

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ...+|||+|||+++++++|+++|+.||.+....++.+..+|.++|||||+|.+.++|.+|+. |||..|.|+.|.|.++.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            34689999999999999999999999998875444454699999999999999999999997 99999999999998864


Q ss_pred             c
Q psy2983         193 D  193 (370)
Q Consensus       193 ~  193 (370)
                      .
T Consensus        86 ~   86 (103)
T d2cpya1          86 L   86 (103)
T ss_dssp             H
T ss_pred             H
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=99.62  E-value=2e-16  Score=120.44  Aligned_cols=82  Identities=16%  Similarity=0.196  Sum_probs=73.1

Q ss_pred             CCCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCee
Q psy2983           8 DLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIP   86 (370)
Q Consensus         8 ~~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~   86 (370)
                      .-++..+..++|||+|||.++++++|+++|++||+|..+.+.+       +|||||+|.+.++|.+|++ |||..|.|+.
T Consensus         7 ~gp~~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~   79 (98)
T d1wg4a_           7 GGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHE   79 (98)
T ss_dssp             SCCCCCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTT
T ss_pred             CCCCCCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeE
Confidence            3455667888999999999999999999999999999998854       5899999999999999995 9999999999


Q ss_pred             EEEecccccc
Q psy2983          87 IIVQPTQAEK   96 (370)
Q Consensus        87 l~v~~~~~~~   96 (370)
                      |+|.+.+...
T Consensus        80 i~v~~~~~~~   89 (98)
T d1wg4a_          80 GETSYIRVYP   89 (98)
T ss_dssp             SCEEEEEEEC
T ss_pred             EEEEEEecCC
Confidence            9998876544

>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=99.62  E-value=2.7e-16  Score=117.34  Aligned_cols=79  Identities=19%  Similarity=0.418  Sum_probs=70.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ..+++|||+|||+.+++++|+++|++||.|..+++.     +.++|||||+|.+.++|.+|+.  +++.+.|+.|+|.++
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC
Confidence            346799999999999999999999999999998764     3458999999999999999985  889999999999998


Q ss_pred             ecCCCC
Q psy2983         192 TDRNES  197 (370)
Q Consensus       192 ~~~~~~  197 (370)
                      .++...
T Consensus        76 ~~k~~~   81 (88)
T d1wf0a_          76 EPKHNS   81 (88)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            776554

>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=99.62  E-value=2.5e-16  Score=122.48  Aligned_cols=75  Identities=28%  Similarity=0.469  Sum_probs=68.6

Q ss_pred             CCeEEEcCCCC-CCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          16 ARTIFCMQLSQ-RIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        16 ~r~v~V~nLp~-~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      +++|||+|||+ .+|+++|+++|+.||+|.++.+++++     +|||||+|.+.++|.+|++ ++|..|.|+.|+|.++.
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~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            58999999965 59999999999999999999998864     6899999999999999996 99999999999999986


Q ss_pred             cc
Q psy2983          94 AE   95 (370)
Q Consensus        94 ~~   95 (370)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.62  E-value=1.8e-15  Score=112.85  Aligned_cols=78  Identities=21%  Similarity=0.273  Sum_probs=70.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHh--CCceeCCeeEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL--NGFELAGRPMKVG  189 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l--~g~~i~g~~l~V~  189 (370)
                      .++++|||+|||.++++++|+++|++||.|.++++.++      +|||||+|.+.++|.+|+..+  ++..+.|++|+|.
T Consensus         6 ~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~   79 (88)
T d2cq1a1           6 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   79 (88)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEE
Confidence            45689999999999999999999999999999998755      689999999999999999865  6789999999999


Q ss_pred             EeecCC
Q psy2983         190 TVTDRN  195 (370)
Q Consensus       190 ~~~~~~  195 (370)
                      +++.+.
T Consensus        80 ~sk~~~   85 (88)
T d2cq1a1          80 YSNHKE   85 (88)
T ss_dssp             ECSCSS
T ss_pred             ECCCCC
Confidence            986553

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=8.1e-17  Score=118.02  Aligned_cols=74  Identities=20%  Similarity=0.328  Sum_probs=66.3

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCC-ccCCeeEEEecccc
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQ-KLLGIPIIVQPTQA   94 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~-~i~g~~l~v~~~~~   94 (370)
                      ++|||+|||.++|+++|+++|++||.|.++.+.+      ++|||||+|.+.++|..|++ ++|. .++|++|.|+++.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            4799999999999999999999999998777655      37899999999999999995 9986 69999999999876


Q ss_pred             cc
Q psy2983          95 EK   96 (370)
Q Consensus        95 ~~   96 (370)
                      ..
T Consensus        76 k~   77 (80)
T d2cqha1          76 KK   77 (80)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>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=99.62  E-value=1.4e-15  Score=115.78  Aligned_cols=79  Identities=13%  Similarity=0.184  Sum_probs=71.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ....+|||+|||+.+++++|+++|++||.|..+++..       +|||||+|.+.++|.+|++.|||..+.|+.|+|.+.
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~   85 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEE
Confidence            3457899999999999999999999999999998863       589999999999999999999999999999999998


Q ss_pred             ecCCCC
Q psy2983         192 TDRNES  197 (370)
Q Consensus       192 ~~~~~~  197 (370)
                      ..+...
T Consensus        86 ~~~~~~   91 (98)
T d1wg4a_          86 RVYPER   91 (98)
T ss_dssp             EEECCC
T ss_pred             ecCCCC
Confidence            765544

>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=99.62  E-value=1.7e-16  Score=116.00  Aligned_cols=75  Identities=20%  Similarity=0.360  Sum_probs=68.0

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEec
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP   91 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~   91 (370)
                      .+..++|||+|+|  +|+++|+++|++||.|.++.+.++      +|||||+|.+.++|..|++ ++|..+.|++|+|.+
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   73 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   73 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4678999999996  899999999999999999998643      6899999999999999995 999999999999999


Q ss_pred             cccc
Q psy2983          92 TQAE   95 (370)
Q Consensus        92 ~~~~   95 (370)
                      ++.+
T Consensus        74 a~~~   77 (79)
T d2bz2a1          74 ARKQ   77 (79)
T ss_dssp             CCSS
T ss_pred             ecCC
Confidence            8643

>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=99.62  E-value=3e-16  Score=119.13  Aligned_cols=80  Identities=20%  Similarity=0.288  Sum_probs=70.8

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCC-eeEEEEeeeCC-CCCeecEEEEEecCCCChHHHhh-cc--CCccCCeeEEEec
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGK-VRDVRLITCNK-TRRFKGIAYIEFKDPESVPLAMG-LN--GQKLLGIPIIVQP   91 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~-v~~v~i~~d~~-~~~~kg~afVeF~~~e~A~~Al~-l~--g~~i~g~~l~v~~   91 (370)
                      .+|||+|||..+++++|+++|+.||+ |.++.++++.. +++++|||||+|.+.++|..|++ |+  +..+.|++|.|.+
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            57999999999999999999999996 99999998754 68899999999999999999996 64  4566899999999


Q ss_pred             ccccc
Q psy2983          92 TQAEK   96 (370)
Q Consensus        92 ~~~~~   96 (370)
                      +.+..
T Consensus        82 A~p~~   86 (96)
T d2disa1          82 AEPEI   86 (96)
T ss_dssp             SCSSC
T ss_pred             cCCCC
Confidence            87543

>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=1.3e-16  Score=118.90  Aligned_cols=73  Identities=15%  Similarity=0.204  Sum_probs=66.9

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecC
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~  194 (370)
                      ++|||+|||+.+++++|+++|++||.|..+++.++       |||||+|.+.++|.+|+..|||..|.|+.|+|.++..+
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            36999999999999999999999999999988643       79999999999999999999999999999998876543

>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=99.61  E-value=1.3e-15  Score=110.03  Aligned_cols=71  Identities=17%  Similarity=0.298  Sum_probs=63.5

Q ss_pred             EEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEeecC
Q psy2983         117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR  194 (370)
Q Consensus       117 l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~~~  194 (370)
                      |||+|||+++++++|+++|++|| +..+.+      ++++|||||+|.+.++|.+|+..|||..+.|++|+|+++...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 444433      456899999999999999999999999999999999998553

>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=99.61  E-value=1.7e-15  Score=115.05  Aligned_cols=78  Identities=28%  Similarity=0.507  Sum_probs=70.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCC--eeEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG--RPMKVG  189 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g--~~l~V~  189 (370)
                      .+.++|||+|||+++++++|+++|++||.|..+++.++      ++||||+|.+.++|.+|++.|||..+.|  ++|+|.
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~   88 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEE
Confidence            34579999999999999999999999999999998754      6799999999999999999999999986  589999


Q ss_pred             EeecCC
Q psy2983         190 TVTDRN  195 (370)
Q Consensus       190 ~~~~~~  195 (370)
                      ++++.+
T Consensus        89 ~ak~~~   94 (97)
T d1whya_          89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             eCCCCC
Confidence            987643

>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=99.61  E-value=5.3e-16  Score=118.09  Aligned_cols=75  Identities=19%  Similarity=0.377  Sum_probs=66.9

Q ss_pred             cCCCCeEEEcCCC-CCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEe
Q psy2983          13 ERDARTIFCMQLS-QRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQ   90 (370)
Q Consensus        13 ~~~~r~v~V~nLp-~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~   90 (370)
                      ....++|||+||| ..+++++|+++|++||+|.++.+        ++|||||+|.+.++|.+|++ |+|..+.|++|+|.
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~   83 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDIN   83 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            4455779999997 56889999999999999999988        36899999999999999995 99999999999999


Q ss_pred             ccccc
Q psy2983          91 PTQAE   95 (370)
Q Consensus        91 ~~~~~   95 (370)
                      ++...
T Consensus        84 ~a~~~   88 (98)
T d1wf2a_          84 LAAEP   88 (98)
T ss_dssp             ETTSC
T ss_pred             ECCCC
Confidence            98643

>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=99.60  E-value=2.9e-16  Score=119.85  Aligned_cols=82  Identities=16%  Similarity=0.210  Sum_probs=72.2

Q ss_pred             CCCcccCCCCeEEEcCCCCC-CcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh---ccCCccC
Q psy2983           8 DLSPEERDARTIFCMQLSQR-IRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG---LNGQKLL   83 (370)
Q Consensus         8 ~~~~~~~~~r~v~V~nLp~~-~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~---l~g~~i~   83 (370)
                      ...+....+++|||+|||.+ +|+++|.++|+.||.|.++.++++      +|||||+|.+.++|..|++   +++..++
T Consensus        10 ~~~~~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~   83 (99)
T d1x4fa1          10 KFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQ   83 (99)
T ss_dssp             CCCCSSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSS
T ss_pred             ccccCCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceEC
Confidence            34455678899999999975 899999999999999999998754      6899999999999999995   8899999


Q ss_pred             CeeEEEeccccc
Q psy2983          84 GIPIIVQPTQAE   95 (370)
Q Consensus        84 g~~l~v~~~~~~   95 (370)
                      |++|+|.+++..
T Consensus        84 gr~l~V~~s~~~   95 (99)
T d1x4fa1          84 GRCVKVDLSEKY   95 (99)
T ss_dssp             SSCCEEEEECSC
T ss_pred             CEEEEEEEcCCc
Confidence            999999988654

>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=99.60  E-value=1.3e-15  Score=118.05  Aligned_cols=81  Identities=17%  Similarity=0.303  Sum_probs=71.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeC--CeeEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELA--GRPMKVG  189 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~--g~~l~V~  189 (370)
                      .+..+|||+|||+.+|+++|+++|++||.|.++.+..++    ++|||||+|.+.++|.+|+..|||..+.  ++.|+|.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            345789999999999999999999999999999998764    4899999999999999999999999984  7889988


Q ss_pred             EeecCCC
Q psy2983         190 TVTDRNE  196 (370)
Q Consensus       190 ~~~~~~~  196 (370)
                      ++++...
T Consensus        81 ~s~~~~~   87 (108)
T d2adba1          81 FSKLTSL   87 (108)
T ss_dssp             ECSSCSC
T ss_pred             ecCCccc
Confidence            8766443

>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=99.60  E-value=1.5e-15  Score=116.88  Aligned_cols=82  Identities=15%  Similarity=0.175  Sum_probs=71.9

Q ss_pred             CCcccCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-c--cCCccCCe
Q psy2983           9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-L--NGQKLLGI   85 (370)
Q Consensus         9 ~~~~~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l--~g~~i~g~   85 (370)
                      ......++++|||+|||..+|+++|+++|++||.|..+++.++      ||+|||+|.+.++|..|++ +  ++..+.|+
T Consensus         8 ~~~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~   81 (104)
T d1wexa_           8 SHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQ   81 (104)
T ss_dssp             SCCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSS
T ss_pred             CCCcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeE
Confidence            3445668999999999999999999999999999999998653      6899999999999999995 4  67788999


Q ss_pred             eEEEecccccc
Q psy2983          86 PIIVQPTQAEK   96 (370)
Q Consensus        86 ~l~v~~~~~~~   96 (370)
                      +|+|++++...
T Consensus        82 ~l~v~~s~~~~   92 (104)
T d1wexa_          82 QAFFNYSTSKR   92 (104)
T ss_dssp             BCEEEECSSSS
T ss_pred             EEEEEEcCCCc
Confidence            99999987543

>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=99.59  E-value=1.7e-16  Score=118.25  Aligned_cols=72  Identities=17%  Similarity=0.203  Sum_probs=65.7

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccccc
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQAE   95 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~~   95 (370)
                      ++|||+|||+++++++|+++|++||+|.++.+.+       +|||||+|.+.++|.+|++ |+|..|.|+.|.|.+....
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-------TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc-------cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            4699999999999999999999999999999865       3899999999999999995 9999999999998876544

>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=99.59  E-value=2.8e-15  Score=114.28  Aligned_cols=78  Identities=23%  Similarity=0.304  Sum_probs=69.7

Q ss_pred             CCCceEEEecCCCC-CCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHH--HhCCceeCCeeEEE
Q psy2983         112 GGPMRLYIGSLHFN-ITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE--QLNGFELAGRPMKV  188 (370)
Q Consensus       112 ~~~~~l~V~nlp~~-~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~--~l~g~~i~g~~l~V  188 (370)
                      ..+++|||+|||.+ +|+++|.++|++||.|.++.+.++      +|+|||+|.+.++|.+|++  .+++..+.|++|+|
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V   89 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   89 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEE
Confidence            44578999999985 899999999999999999999755      6899999999999999997  47888999999999


Q ss_pred             EEeecCC
Q psy2983         189 GTVTDRN  195 (370)
Q Consensus       189 ~~~~~~~  195 (370)
                      .+++.+.
T Consensus        90 ~~s~~~~   96 (99)
T d1x4fa1          90 DLSEKYK   96 (99)
T ss_dssp             EEECSCS
T ss_pred             EEcCCcc
Confidence            9987654

>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=99.59  E-value=5e-16  Score=115.85  Aligned_cols=74  Identities=16%  Similarity=0.275  Sum_probs=64.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      .+++|||+|||.+++++||+++|++|| +..+.+      ++.+|||||+|.+.++|.+|++ |++..+.|++|.|+++.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            468899999999999999999999999 333333      3458999999999999999995 99999999999999986


Q ss_pred             cc
Q psy2983          94 AE   95 (370)
Q Consensus        94 ~~   95 (370)
                      ..
T Consensus        77 ~~   78 (88)
T d1wg1a_          77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.59  E-value=8.3e-16  Score=120.04  Aligned_cols=80  Identities=19%  Similarity=0.343  Sum_probs=72.1

Q ss_pred             CCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       113 ~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      ...+|||+|||+.+|+++|+++|+.||.+..+.++.+..+|.++|||||+|.+.++|.+|+. |||..|+|+.|.|..+.
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            45689999999999999999999999998776566565799999999999999999999997 99999999999998764


Q ss_pred             c
Q psy2983         193 D  193 (370)
Q Consensus       193 ~  193 (370)
                      .
T Consensus        96 ~   96 (112)
T d1wela1          96 K   96 (112)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=99.58  E-value=9.2e-16  Score=116.60  Aligned_cols=77  Identities=17%  Similarity=0.292  Sum_probs=69.1

Q ss_pred             cCCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCC--eeEEE
Q psy2983          13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLG--IPIIV   89 (370)
Q Consensus        13 ~~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g--~~l~v   89 (370)
                      ..++++|||+|||+++++++|+++|++||+|..+++.++      ++||||+|.+.++|..|++ |++..|.|  ++|+|
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v   87 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEE
Confidence            456899999999999999999999999999999998654      6899999999999999995 99999986  47999


Q ss_pred             eccccc
Q psy2983          90 QPTQAE   95 (370)
Q Consensus        90 ~~~~~~   95 (370)
                      .+++..
T Consensus        88 ~~ak~~   93 (97)
T d1whya_          88 DFAKSG   93 (97)
T ss_dssp             EECCCC
T ss_pred             EeCCCC
Confidence            988754

>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=99.58  E-value=1e-14  Score=112.14  Aligned_cols=79  Identities=20%  Similarity=0.187  Sum_probs=70.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHh--CCceeCCeeEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL--NGFELAGRPMKVG  189 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l--~g~~i~g~~l~V~  189 (370)
                      .++++|||+|||..+++++|+++|++||.|.++.+.++      +|+|||+|.+.++|..|+..|  ++..+.|++|+|.
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~   86 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEE
Confidence            45679999999999999999999999999999998754      789999999999999999987  4567889999999


Q ss_pred             EeecCCC
Q psy2983         190 TVTDRNE  196 (370)
Q Consensus       190 ~~~~~~~  196 (370)
                      +++.+..
T Consensus        87 ~s~~~~~   93 (104)
T d1wexa_          87 YSTSKRI   93 (104)
T ss_dssp             ECSSSSC
T ss_pred             EcCCCcc
Confidence            9866543

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=1.2e-15  Score=118.31  Aligned_cols=78  Identities=22%  Similarity=0.231  Sum_probs=69.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCcc--CCeeEEEe
Q psy2983          14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL--LGIPIIVQ   90 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i--~g~~l~v~   90 (370)
                      .+..+|||+|||..+|+++|+++|++||.|.++.+.+++    ++|||||+|.+.++|..|++ ++|..+  .|+.|.|.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            456789999999999999999999999999999998864    47999999999999999995 999988  57788888


Q ss_pred             ccccc
Q psy2983          91 PTQAE   95 (370)
Q Consensus        91 ~~~~~   95 (370)
                      +++..
T Consensus        81 ~s~~~   85 (108)
T d2adba1          81 FSKLT   85 (108)
T ss_dssp             ECSSC
T ss_pred             ecCCc
Confidence            87654

>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=99.58  E-value=9.5e-16  Score=110.69  Aligned_cols=70  Identities=16%  Similarity=0.331  Sum_probs=62.1

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccccc
Q psy2983          19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQAE   95 (370)
Q Consensus        19 v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~~~   95 (370)
                      |||+|||+++++++|+++|++|| +..+.+      ++++|||||+|.+.++|.+|++ +||..+.|++|+|+++..+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 444443      3468999999999999999995 9999999999999998643

>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=99.57  E-value=6e-15  Score=110.05  Aligned_cols=78  Identities=21%  Similarity=0.252  Sum_probs=69.5

Q ss_pred             CCCceEEEecCCCC-CCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHh--CCceeCCeeEEE
Q psy2983         112 GGPMRLYIGSLHFN-ITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL--NGFELAGRPMKV  188 (370)
Q Consensus       112 ~~~~~l~V~nlp~~-~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l--~g~~i~g~~l~V  188 (370)
                      .++++|||+|||.. +|+++|.++|++||.|.++.+.++      +++|||+|.+.++|..|+..|  ++..+.|++|+|
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V   79 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   79 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEE
Confidence            45688999999986 789999999999999999999765      569999999999999999966  678899999999


Q ss_pred             EEeecCC
Q psy2983         189 GTVTDRN  195 (370)
Q Consensus       189 ~~~~~~~  195 (370)
                      .+++...
T Consensus        80 ~~s~~~~   86 (89)
T d1x4da1          80 HLSQKYK   86 (89)
T ss_dssp             EEECCCT
T ss_pred             EECCCcc
Confidence            9987543

>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=99.55  E-value=1.5e-15  Score=113.34  Aligned_cols=78  Identities=17%  Similarity=0.240  Sum_probs=69.7

Q ss_pred             ccCCCCeEEEcCCCCC-CcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh---ccCCccCCeeE
Q psy2983          12 EERDARTIFCMQLSQR-IRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG---LNGQKLLGIPI   87 (370)
Q Consensus        12 ~~~~~r~v~V~nLp~~-~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~---l~g~~i~g~~l   87 (370)
                      ....+|+|||+|||.. +|++||.++|++||.|.++.++++      +++|||+|.+.++|..|++   .++..+.|++|
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l   77 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   77 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceE
Confidence            4568899999999986 899999999999999999999764      5789999999999999995   57889999999


Q ss_pred             EEeccccc
Q psy2983          88 IVQPTQAE   95 (370)
Q Consensus        88 ~v~~~~~~   95 (370)
                      +|.+++..
T Consensus        78 ~V~~s~~~   85 (89)
T d1x4da1          78 RVHLSQKY   85 (89)
T ss_dssp             EEEEECCC
T ss_pred             EEEECCCc
Confidence            99998643

>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=99.52  E-value=1.1e-16  Score=120.00  Aligned_cols=78  Identities=24%  Similarity=0.554  Sum_probs=68.4

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEe-----ecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEE
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLM-----VDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG  189 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~-----~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~  189 (370)
                      ++|||+|||+++++++|+++|+.||.+..+.+.     .+..++.++|||||+|.+.++|.+|++ |||..+.|+.|+|+
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            589999999999999999999999987765543     344578899999999999999999996 99999999999997


Q ss_pred             Eeec
Q psy2983         190 TVTD  193 (370)
Q Consensus       190 ~~~~  193 (370)
                      ++++
T Consensus        81 r~k~   84 (90)
T d1u2fa_          81 RPHD   84 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            6544

>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=99.50  E-value=9.3e-15  Score=112.19  Aligned_cols=79  Identities=18%  Similarity=0.187  Sum_probs=69.5

Q ss_pred             CCCceEEEecCCCCC-C----HHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeE
Q psy2983         112 GGPMRLYIGSLHFNI-T----EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM  186 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~-t----~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l  186 (370)
                      .+..+|||+||+.++ +    +++|+++|++||.|..+++++.      +|||||+|.+.++|.+|+..|||..|.|++|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            456789999999886 3    3569999999999999998743      7899999999999999999999999999999


Q ss_pred             EEEEeecCCC
Q psy2983         187 KVGTVTDRNE  196 (370)
Q Consensus       187 ~V~~~~~~~~  196 (370)
                      +|.++.++..
T Consensus        77 ~v~~a~~~~~   86 (104)
T d1weya_          77 KLYFAQTLHI   86 (104)
T ss_dssp             EEECCCCSSC
T ss_pred             EEeecccCCC
Confidence            9999876544

>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=99.49  E-value=3.4e-14  Score=108.98  Aligned_cols=78  Identities=15%  Similarity=0.156  Sum_probs=68.2

Q ss_pred             CCCCeEEEcCCCCCC-cH----HHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeE
Q psy2983          14 RDARTIFCMQLSQRI-RT----RDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPI   87 (370)
Q Consensus        14 ~~~r~v~V~nLp~~~-te----~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l   87 (370)
                      ..+.+|||+||+.++ ++    ++|+++|+.||.|.++.+++      +++||||+|.+.++|.+|++ |+|..|.|++|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            467889999999886 33    56899999999999999874      46899999999999999995 99999999999


Q ss_pred             EEeccccccc
Q psy2983          88 IVQPTQAEKN   97 (370)
Q Consensus        88 ~v~~~~~~~~   97 (370)
                      +|.+++....
T Consensus        77 ~v~~a~~~~~   86 (104)
T d1weya_          77 KLYFAQTLHI   86 (104)
T ss_dssp             EEECCCCSSC
T ss_pred             EEeecccCCC
Confidence            9999875543

>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=99.43  E-value=8.2e-15  Score=112.49  Aligned_cols=76  Identities=17%  Similarity=0.285  Sum_probs=71.0

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      ..++|.+++..+++++|+++|++||.|.++.++++ .+|.++|+|||+|.+.++|.+|+..|||..+.|++|+|.+.
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            35888899999999999999999999999999877 48999999999999999999999999999999999999874

>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=99.37  E-value=1.8e-14  Score=110.52  Aligned_cols=75  Identities=17%  Similarity=0.236  Sum_probs=69.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEecc
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPT   92 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~   92 (370)
                      ..++|++++.+++|++|+++|++||+|.+|.|+++ .+++++|||||+|.+.++|.+|++ |+|..++|++|.|.++
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            45888999999999999999999999999999876 578999999999999999999995 9999999999999875

>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=99.36  E-value=6e-13  Score=103.56  Aligned_cols=76  Identities=21%  Similarity=0.194  Sum_probs=66.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCH-HHHHHHHHHhCCceeCCeeEEEEE
Q psy2983         112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA-DDAKKAQEQLNGFELAGRPMKVGT  190 (370)
Q Consensus       112 ~~~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~-~~a~~A~~~l~g~~i~g~~l~V~~  190 (370)
                      .+...+||+|||+.+|+++|+++|++||+|.+|.++++      +|||||+|.++ ++|..|+..|++..+.++.+.|.+
T Consensus         9 ~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~   82 (113)
T d1owxa_           9 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTW   82 (113)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEE
T ss_pred             CCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEE
Confidence            44567899999999999999999999999999999854      78999999985 789999999999999888877777


Q ss_pred             eec
Q psy2983         191 VTD  193 (370)
Q Consensus       191 ~~~  193 (370)
                      ...
T Consensus        83 ~~~   85 (113)
T d1owxa_          83 EVL   85 (113)
T ss_dssp             EEC
T ss_pred             eec
Confidence            543

>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=99.35  E-value=3.6e-13  Score=98.09  Aligned_cols=73  Identities=14%  Similarity=0.108  Sum_probs=61.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCee-EEEeccc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIP-IIVQPTQ   93 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~~-l~v~~~~   93 (370)
                      +.+.|+|+|+|++.+++ +.++|++||+|.++++.      +.+|||||+|.++++|.+||++||..++|+. |.|.+..
T Consensus         3 ~~~wV~V~G~p~~~~~~-il~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           3 DDTWVTVFGFPQASASY-ILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGGEEEEECCCGGGHHH-HHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECC
T ss_pred             cccEEEEECCChHHHHH-HHHHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCC
Confidence            45679999999999865 45689999999999873      4479999999999999999999999999985 5677654


Q ss_pred             c
Q psy2983          94 A   94 (370)
Q Consensus        94 ~   94 (370)
                      .
T Consensus        76 ~   76 (81)
T d1wwha1          76 D   76 (81)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=8.6e-13  Score=100.44  Aligned_cols=64  Identities=23%  Similarity=0.445  Sum_probs=57.2

Q ss_pred             CCceEEEe--cCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeC
Q psy2983         113 GPMRLYIG--SLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELA  182 (370)
Q Consensus       113 ~~~~l~V~--nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~  182 (370)
                      +..+|+|.  |||.++|+++|+++|++||.|..+.+.++      +|||||+|.+.++|.+|+..|||..+.
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            34678885  59999999999999999999999988754      679999999999999999999998873

>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=99.32  E-value=4.7e-13  Score=101.95  Aligned_cols=66  Identities=15%  Similarity=0.263  Sum_probs=58.6

Q ss_pred             cccCCCCeEEEcC--CCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCcc
Q psy2983          11 PEERDARTIFCMQ--LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL   82 (370)
Q Consensus        11 ~~~~~~r~v~V~n--Lp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i   82 (370)
                      ....+.++++|+|  ||.++|+++|+++|++||.|.++.+.++      ++||||+|.+.++|.+|+. |+|..+
T Consensus        13 ~~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CCSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             cCCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            3456788999955  9999999999999999999999988653      6899999999999999995 999877

>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=99.31  E-value=3.9e-12  Score=96.38  Aligned_cols=80  Identities=18%  Similarity=0.304  Sum_probs=68.2

Q ss_pred             CCCceEEEecC--CCCCC---------HHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCce
Q psy2983         112 GGPMRLYIGSL--HFNIT---------EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFE  180 (370)
Q Consensus       112 ~~~~~l~V~nl--p~~~t---------~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~  180 (370)
                      ...++|+|.|+  |.++.         +++|++.|++||.|..+.+..+    ..+|+|||+|.+.++|.+|+..|||..
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            34578999999  54431         3689999999999999988644    468999999999999999999999999


Q ss_pred             eCCeeEEEEEeecCC
Q psy2983         181 LAGRPMKVGTVTDRN  195 (370)
Q Consensus       181 i~g~~l~V~~~~~~~  195 (370)
                      +.||+|+|.+..++.
T Consensus        82 ~~gr~i~v~~~~g~~   96 (99)
T d2dita1          82 FGGRQITAQAWDGTT   96 (99)
T ss_dssp             ETTEECEEEECCSCC
T ss_pred             ECCEEEEEEEeCCcC
Confidence            999999999976654

>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=99.29  E-value=1.6e-12  Score=98.57  Aligned_cols=80  Identities=24%  Similarity=0.388  Sum_probs=68.3

Q ss_pred             cccCCCCeEEEcCC--CCCCc---------HHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-cc
Q psy2983          11 PEERDARTIFCMQL--SQRIR---------TRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LN   78 (370)
Q Consensus        11 ~~~~~~r~v~V~nL--p~~~t---------e~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~   78 (370)
                      ...+.+|+|+|+||  |.++.         +++|++.|++||.|..+.+..+    ..+|+|||+|.++++|.+|+. |+
T Consensus         3 ~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~ln   78 (99)
T d2dita1           3 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLD   78 (99)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHST
T ss_pred             CCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhC
Confidence            45689999999999  65432         3688999999999999988664    347999999999999999995 99


Q ss_pred             CCccCCeeEEEecccc
Q psy2983          79 GQKLLGIPIIVQPTQA   94 (370)
Q Consensus        79 g~~i~g~~l~v~~~~~   94 (370)
                      |..+.|++|.|.+...
T Consensus        79 g~~~~gr~i~v~~~~g   94 (99)
T d2dita1          79 GRWFGGRQITAQAWDG   94 (99)
T ss_dssp             TCEETTEECEEEECCS
T ss_pred             CcEECCEEEEEEEeCC
Confidence            9999999999998653

>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=99.24  E-value=4.7e-12  Score=92.02  Aligned_cols=72  Identities=17%  Similarity=0.179  Sum_probs=61.1

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCee-EEEEEeec
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRP-MKVGTVTD  193 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~-l~V~~~~~  193 (370)
                      ..|+|+|+|++.+++.| ++|++||.|.++++.      .++|||||+|.++++|.+|++ +||..++|+. |.|..+.+
T Consensus         5 ~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           5 TWVTVFGFPQASASYIL-LQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             cEEEEECCChHHHHHHH-HHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            56999999999987655 579999999998764      347899999999999999997 9999999985 56877655


Q ss_pred             C
Q psy2983         194 R  194 (370)
Q Consensus       194 ~  194 (370)
                      +
T Consensus        77 k   77 (81)
T d1wwha1          77 K   77 (81)
T ss_dssp             H
T ss_pred             h
Confidence            3

>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=99.24  E-value=2.3e-12  Score=100.18  Aligned_cols=72  Identities=18%  Similarity=0.133  Sum_probs=60.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCC-CChHHHh-hccCCccCCeeEEEecc
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDP-ESVPLAM-GLNGQKLLGIPIIVQPT   92 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~-e~A~~Al-~l~g~~i~g~~l~v~~~   92 (370)
                      -...+||+|||..+|+++|+++|++||+|.+|.++++      +|||||.|.++ ++|..|+ .+++..+.++.+.|.+.
T Consensus        10 g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_          10 GCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             CCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            3566799999999999999999999999999999753      78999999997 5787787 48988877665555443

>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=99.20  E-value=8e-12  Score=95.55  Aligned_cols=81  Identities=20%  Similarity=0.212  Sum_probs=68.8

Q ss_pred             CCceEEEecC--CCCCC--------HHHHHhcccCCCceeeEEEeecCCC--CCcccEEEEEECCHHHHHHHHHHhCCce
Q psy2983         113 GPMRLYIGSL--HFNIT--------EDMLRGIFEPFGKIDNIQLMVDPDT--GRSKGYGFITFHSADDAKKAQEQLNGFE  180 (370)
Q Consensus       113 ~~~~l~V~nl--p~~~t--------~e~l~~~f~~~G~i~~v~~~~~~~~--g~~~g~afV~f~~~~~a~~A~~~l~g~~  180 (370)
                      +++.|+|.|+  |..+.        .++|++.|++||.|.++.+.++..+  ....|++||+|.+.++|.+|+..|||..
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            4578999999  55443        3679999999999999999877644  3456899999999999999999999999


Q ss_pred             eCCeeEEEEEeec
Q psy2983         181 LAGRPMKVGTVTD  193 (370)
Q Consensus       181 i~g~~l~V~~~~~  193 (370)
                      ++||.|.+.+..+
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            9999999999643

>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=99.11  E-value=1.4e-11  Score=94.21  Aligned_cols=81  Identities=16%  Similarity=0.231  Sum_probs=68.2

Q ss_pred             CCCCeEEEcCC--CCCC--------cHHHHHHHhhcCCCeeEEEEeeeCCC--CCeecEEEEEecCCCChHHHhh-ccCC
Q psy2983          14 RDARTIFCMQL--SQRI--------RTRDLEEFFSSVGKVRDVRLITCNKT--RRFKGIAYIEFKDPESVPLAMG-LNGQ   80 (370)
Q Consensus        14 ~~~r~v~V~nL--p~~~--------te~~L~~~f~~~G~v~~v~i~~d~~~--~~~kg~afVeF~~~e~A~~Al~-l~g~   80 (370)
                      .+++.|.|+||  |..+        ..+||++.|++||.|.+|.|.++..+  ....|++||+|.+.++|.+|+. |+|.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            36899999999  4443        24678999999999999999876544  3356899999999999999995 9999


Q ss_pred             ccCCeeEEEecccc
Q psy2983          81 KLLGIPIIVQPTQA   94 (370)
Q Consensus        81 ~i~g~~l~v~~~~~   94 (370)
                      .+.||+|.+.+...
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999988764

>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=97.32  E-value=0.00049  Score=49.35  Aligned_cols=69  Identities=14%  Similarity=0.338  Sum_probs=58.7

Q ss_pred             ceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcc--cEEEEEECCHHHHHHHHHHhCCceeCC
Q psy2983         115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSK--GYGFITFHSADDAKKAQEQLNGFELAG  183 (370)
Q Consensus       115 ~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~--g~afV~f~~~~~a~~A~~~l~g~~i~g  183 (370)
                      .+|.|+.||+.+|++++.+.+.+.|.+........+.+.+..  .-|+|.|.+.++.....+..+|+.+.+
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            479999999999999999999999999888887765543322  349999999999999999999998853

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.22  E-value=0.00024  Score=50.30  Aligned_cols=71  Identities=18%  Similarity=0.242  Sum_probs=56.9

Q ss_pred             CCCeEEEcCCCCCCcH---------HHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhhccCCccCCe
Q psy2983          15 DARTIFCMQLSQRIRT---------RDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGI   85 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te---------~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~l~g~~i~g~   85 (370)
                      +.-||.|.=..++..+         .+|.+-|..||+|.=|+++.+        -..|.|.+-+.|-+|+.++|..+.|+
T Consensus        14 pDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~l~g~~v~G~   85 (95)
T d1ufwa_          14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLDVDGMKVKGR   85 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHHGGGSEETTE
T ss_pred             CCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhccCCeEEcce
Confidence            4456777555433333         577888999999999998765        48999999999999999999999999


Q ss_pred             eEEEeccc
Q psy2983          86 PIIVQPTQ   93 (370)
Q Consensus        86 ~l~v~~~~   93 (370)
                      .|.|....
T Consensus        86 ~l~It~~~   93 (95)
T d1ufwa_          86 AVKISGPS   93 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEecCC
Confidence            99997653

>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=97.07  E-value=0.00049  Score=49.38  Aligned_cols=68  Identities=18%  Similarity=0.314  Sum_probs=54.6

Q ss_pred             CeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCC--eecEEEEEecCCCChHHHhh-ccCCccCC
Q psy2983          17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRR--FKGIAYIEFKDPESVPLAMG-LNGQKLLG   84 (370)
Q Consensus        17 r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~--~kg~afVeF~~~e~A~~Al~-l~g~~i~g   84 (370)
                      .+|-|+.||+++||+++.+.+...|++.-......+.+.+  .-.-|||.|.+.++.....+ .+|..+.+
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            4799999999999999999999999888776665443322  22469999999999988885 88888743

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.02  E-value=0.00029  Score=49.82  Aligned_cols=54  Identities=19%  Similarity=0.362  Sum_probs=48.7

Q ss_pred             HHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEe
Q psy2983         129 DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTV  191 (370)
Q Consensus       129 e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~  191 (370)
                      .+|.+.|..||+|.-+++..+        ...|+|.+-++|.+|+. ++|.++.|+.|+|+..
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEEcceEEEEecC
Confidence            578888999999999999855        58999999999999999 9999999999999753

>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=96.90  E-value=0.0018  Score=43.44  Aligned_cols=61  Identities=18%  Similarity=0.336  Sum_probs=51.9

Q ss_pred             HHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhCCceeCCeeEEEEEee
Q psy2983         129 DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVT  192 (370)
Q Consensus       129 e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~i~g~~l~V~~~~  192 (370)
                      +.|...|.++|.|.++.+.... .|..  .|-|...+..+|.-|+..||...|++++|.|.++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~-dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT-DYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-STTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEecc-CCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            4566778899999999987663 3333  69999999999999999999999999999998864

>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=95.05  E-value=0.066  Score=38.06  Aligned_cols=56  Identities=16%  Similarity=0.261  Sum_probs=46.6

Q ss_pred             CceEEEecCCCCCCHHHHHhcccCCCceeeEEEeecCCCCCcccEEEEEECCHHHHHHHHHHhC
Q psy2983         114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN  177 (370)
Q Consensus       114 ~~~l~V~nlp~~~t~e~l~~~f~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~  177 (370)
                      ..-+|.-.+|..+...+|.++|++||.|. |..+-|.       -|||...+.++|..++..+.
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-------eEEEEecCHHHHHHHHHHhc
Confidence            45689999999999999999999999874 4555442       69999999999999988654

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.30  E-value=0.025  Score=37.71  Aligned_cols=64  Identities=23%  Similarity=0.349  Sum_probs=50.6

Q ss_pred             CCcHHHHH----HHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh-ccCCccCCeeEEEeccc
Q psy2983          27 RIRTRDLE----EFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQPTQ   93 (370)
Q Consensus        27 ~~te~~L~----~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~i~g~~l~v~~~~   93 (370)
                      .+++++|+    +.|.++|+|.++.+..-..   ..-.|-|...+..+|..|+. |+...+++++|.|.++.
T Consensus         3 ~L~~kelqq~L~~~f~~h~~V~sv~l~~~~d---g~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1           3 RLSRKELQQLLQEAFARHGKVKSVELSPHTD---YQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             TSCHHHHHHHHHHHHHHHSCEEEEEECSCCS---TTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             cCCHHHHHHHHHHHHHhheeEEEEEEEeccC---CcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            44555554    5688899999998865322   23479999999999999996 99999999999998764

>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=93.59  E-value=0.035  Score=39.55  Aligned_cols=54  Identities=20%  Similarity=0.444  Sum_probs=45.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHhhcCCCeeEEEEeeeCCCCCeecEEEEEecCCCChHHHhh
Q psy2983          15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG   76 (370)
Q Consensus        15 ~~r~v~V~nLp~~~te~~L~~~f~~~G~v~~v~i~~d~~~~~~kg~afVeF~~~e~A~~Al~   76 (370)
                      ....||.-.+|..+...||.++|++||.|.--+| -|.       -|||...+.++|..++.
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-ddT-------Sa~V~L~~~e~~~~v~~   67 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DDT-------SAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ETT-------EEEEECSCHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cCc-------eEEEEecCHHHHHHHHH
Confidence            3445999999999999999999999999874444 332       49999999999999986