Psyllid ID: psy2141

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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---
Protein Sequence
MQHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHMPTAAAVAAAAATAKIQAMDGGATNAVGVLSKLSQVFFFFAFSHA
Secondary Structure (PSIPRED)
cccccccEEcccccccccccHHHHHHHHHcccccEEEEcccccccHHHHHHHHHccccEEEEEEcccccccccccEEEEEEccHHHHHHHHHHcccccccccEEEEEccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccEEccccccccccHHHHHHcccccccccEEEEEcccccccHHHHHHHHcccccccEEEEEEccccccccEEEEEEEccHHHHHHHHHHHcccEcccEEEEEcccccccccccccccccccccccccHHHHHHHccccccEEEEccccHHHHHHHHccccEEEcccccc
Coil and Loop (DISEMBL)
mqhfphvqvgrpsnmpqaQSVIDEITEEAKLYNRIYvasihpdlteeDIKSVFEafgpikycklqqgssphrhkgygfieyeTKQASNEAISSmnlfdlggqylrvgraitppnalhsskgpapstshmpTAAAVAAAAATAKIQAMDGGATNAVGVLSKLSQVFFFFAFSHA
Flexible Loop (DISEMBL)
mqhfphvqvgrpsnmpqAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYcklqqgssphrHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHMPTAAAVAAAAATAKIQAMDGGATNAVGVLSKLSQVFFFFAFSHA
Low Complexity Region (SEG)
MQHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHMPtaaavaaaaataKIQAMDGGATNAVGVLSKLSQVFFFFAFSHA
Disordered region (IsUnstruct)
*********************IDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQG****RHKGYGFIEYETKQA*NEAISSMNLFDLGGQYLRVGRAI**************************AAAATAKIQAMDGGATNAVGVLSKLSQVFFFFAF***
Disordered Region (DISOPRED)
****PHV**************************RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV******************************************GG***AV*V***LSQVFF**A****
Disordered Region (DISEMBL)
********VGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNA**************************AKIQAMDGGATNAVGVLSKLSQVFFFFAFSHA
Disordered Region (DISPRO)
***FPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI******************MPTAAAVAAAAATAKIQAMDGGATNAVGVLSKLSQVFFFFAFSH*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHMPTAAAVAAAAATAKIQAMDGGATNAVGVLSKLSQVFFFFAFSHA
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	173	2.2.26 [Sep-21-2011]
Q8T6B9	637	Poly(U)-binding-splicing	no	N/A	0.895	0.243	0.739	6e-55
Q2HJG2	530	Poly(U)-binding-splicing	yes	N/A	0.676	0.220	0.623	1e-40
Q9WV25	564	Poly(U)-binding-splicing	yes	N/A	0.682	0.209	0.618	1e-40
Q3UEB3	564	Poly(U)-binding-splicing	yes	N/A	0.682	0.209	0.618	1e-40
Q5R469	558	Poly(U)-binding-splicing	yes	N/A	0.676	0.209	0.623	1e-40
Q9UHX1	559	Poly(U)-binding-splicing	yes	N/A	0.676	0.209	0.623	2e-40
Q6IQE0	516	Poly(U)-binding-splicing	no	N/A	0.676	0.226	0.615	2e-39
O13845	603	RNA-binding protein rsd1	yes	N/A	0.427	0.122	0.413	3e-12
Q86U06	439	Probable RNA-binding prot	no	N/A	0.427	0.168	0.391	7e-11
Q5RC80	524	RNA-binding protein 39 OS	no	N/A	0.427	0.141	0.378	7e-11

>sp|Q8T6B9|PUF68_DROME Poly(U)-binding-splicing factor half pint OS=Drosophila melanogaster GN=pUf68 PE=1 SV=2

 Score =  213 bits (542), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 119/161 (73%), Positives = 134/161 (83%), Gaps = 6/161 (3%)

Query: 6   HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
           +++VGRPSNMPQAQ VIDE+ EEAK +NRIYVASIHPDL+EEDIKSVFEAFGPI YCKL 
Sbjct: 200 NIKVGRPSNMPQAQQVIDEVQEEAKSFNRIYVASIHPDLSEEDIKSVFEAFGPILYCKLA 259

Query: 66  QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
           QG+S H HKGYGFIEY  KQA +EAI+SMNLFDLGGQ LRVGR+ITPPNAL       P+
Sbjct: 260 QGTSLHTHKGYGFIEYANKQAMDEAIASMNLFDLGGQLLRVGRSITPPNALA-----CPT 314

Query: 126 T-SHMPTAAAVAAAAATAKIQAMDGGATNAVGVLSKLSQVF 165
           T S MPTAAAVAAAAATAKIQA+D  A+NAV  LS+ + V 
Sbjct: 315 TNSTMPTAAAVAAAAATAKIQALDAVASNAVLGLSQNTPVM 355

Splicing factor that regulates oogenesis and controls both mitosis and mRNA localization in the germline by regulating mRNA splicing of a subset of genes within the ovary. Probably acts by regulating the alternative splice site selection of the otu transcript. Also regulates the alternative splicing of eIF-4E and grk, while it is not involved in the splicing of par-1, sqd and psq.
Drosophila melanogaster (taxid: 7227)

>sp|Q2HJG2|PUF60_BOVIN Poly(U)-binding-splicing factor PUF60 OS=Bos taurus GN=PUF60 PE=2 SV=1

 Score =  165 bits (418), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 73/117 (62%), Positives = 95/117 (81%)

Query: 6   HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
           +++VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DIKSVFEAFG IK C L 
Sbjct: 170 NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLA 229

Query: 66  QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGP 122
           +  +  +HKGYGFIEYE  Q+S +A+SSMNLFDLGGQYLRVG+A+TPP  L +   P
Sbjct: 230 RDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPATP 286

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.

Bos taurus (taxid: 9913)

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

 Score =  165 bits (417), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 73/118 (61%), Positives = 95/118 (80%)

Query: 6   HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
           +++VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DIKSVFEAFG IK C L 
Sbjct: 204 NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLA 263

Query: 66  QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
           +  +  +HKGYGFIEYE  Q+S +A+SSMNLFDLGGQYLRVG+A+TPP  L +   P 
Sbjct: 264 RDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPATPG 321

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 =  165 bits (417), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 73/118 (61%), Positives = 95/118 (80%)

Query: 6   HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
           +++VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DIKSVFEAFG IK C L 
Sbjct: 204 NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLA 263

Query: 66  QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
           +  +  +HKGYGFIEYE  Q+S +A+SSMNLFDLGGQYLRVG+A+TPP  L +   P 
Sbjct: 264 RDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPATPG 321

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)

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

 Score =  165 bits (417), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 73/117 (62%), Positives = 95/117 (81%)

Query: 6   HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
           +++VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DIKSVFEAFG IK C L 
Sbjct: 198 NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLA 257

Query: 66  QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGP 122
           +  +  +HKGYGFIEYE  Q+S +A+SSMNLFDLGGQYLRVG+A+TPP  L +   P
Sbjct: 258 RDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPATP 314

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 =  165 bits (417), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 73/117 (62%), Positives = 95/117 (81%)

Query: 6   HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
           +++VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DIKSVFEAFG IK C L 
Sbjct: 199 NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLA 258

Query: 66  QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGP 122
           +  +  +HKGYGFIEYE  Q+S +A+SSMNLFDLGGQYLRVG+A+TPP  L +   P
Sbjct: 259 RDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPATP 315

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|Q6IQE0|PU60B_DANRE Poly(U)-binding-splicing factor PUF60-B OS=Danio rerio GN=puf60b PE=2 SV=2

 Score =  161 bits (408), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 72/117 (61%), Positives = 95/117 (81%)

Query: 6   HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
           +++VGRP ++ QAQ +I+++ EEA+ YNRIYVASIHPDL+++DIKSVFEAFG IK C L 
Sbjct: 156 NIKVGRPGSIGQAQPIIEQLAEEARAYNRIYVASIHPDLSDDDIKSVFEAFGKIKSCMLA 215

Query: 66  QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGP 122
           +  +  +HKG+GFIEYE  Q+S +A+SSMNLFDLGGQYLRVG+A+TPP  L +   P
Sbjct: 216 REPTTGKHKGFGFIEYEKPQSSLDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPTTP 272

DNA- and RNA-binding protein, involved in transcription repression and pre-mRNA splicing.

Danio rerio (taxid: 7955)

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

 Score = 71.2 bits (173), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 53/75 (70%), Gaps = 1/75 (1%)

Query: 32  YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
           ++R+ V++IH +LT+ED+K++FE FG I++  LQ+    +R KG+G+I+Y    ++  A+
Sbjct: 339 FHRLCVSNIHFNLTDEDVKAIFEPFGDIEFVHLQRDDQ-NRSKGFGYIQYRNPISARNAL 397

Query: 92  SSMNLFDLGGQYLRV 106
             MN FDL G+ +RV
Sbjct: 398 EKMNGFDLAGRNMRV 412

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

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

 Score = 66.6 bits (161), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 46/74 (62%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           R+YV S+H ++TE+ ++ +FE FG I    L + S   R KGYGFI +   + +  A+  
Sbjct: 264 RLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 323

Query: 94  MNLFDLGGQYLRVG 107
           +N F+L G+ +RVG
Sbjct: 324 LNGFELAGRPMRVG 337

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

Homo sapiens (taxid: 9606)

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

 Score = 66.6 bits (161), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 48/74 (64%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           R+YV S+H ++TE+ ++ +FE FG I+  +L   S   R KGYGFI +   + + +A+  
Sbjct: 251 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 310

Query: 94  MNLFDLGGQYLRVG 107
           +N F+L G+ ++VG
Sbjct: 311 LNGFELAGRPMKVG 324

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)

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	173
328696967	603	PREDICTED: poly(U)-binding-splicing fact	0.867	0.248	0.850	2e-61
307195017	561	Poly(U)-binding-splicing factor half pin	0.867	0.267	0.837	1e-59
322785180	545	hypothetical protein SINV_08068 [Solenop	0.867	0.275	0.831	2e-59
270001539	591	hypothetical protein TcasGA2_TC000381 [T	0.878	0.257	0.820	3e-59
380016392	592	PREDICTED: poly(U)-binding-splicing fact	0.867	0.253	0.831	3e-59
332022211	609	Poly(U)-binding-splicing factor half pin	0.867	0.246	0.831	3e-59
340725363	592	PREDICTED: poly(U)-binding-splicing fact	0.867	0.253	0.831	3e-59
328783360	592	PREDICTED: poly(U)-binding-splicing fact	0.867	0.253	0.831	3e-59
383861059	592	PREDICTED: poly(U)-binding-splicing fact	0.867	0.253	0.831	3e-59
307177474	510	Poly(U)-binding-splicing factor half pin	0.867	0.294	0.831	3e-59

>gi|328696967|ref|XP_001951881.2| PREDICTED: poly(U)-binding-splicing factor half pint-like [Acyrthosiphon pisum]

 Score =  239 bits (611), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 131/154 (85%), Positives = 140/154 (90%), Gaps = 4/154 (2%)

Query: 9   VGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS 68
           VGRPSNMPQAQSVIDEI EEAK YNRIYVASIHPDLTE+DIKSVFEAFGPI+ CKL QGS
Sbjct: 215 VGRPSNMPQAQSVIDEIQEEAKQYNRIYVASIHPDLTEDDIKSVFEAFGPIRTCKLAQGS 274

Query: 69  SPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSH 128
           +P+RH+GYGFIEYE +QA+ EAISSMNLFDLGGQYLRVGRAITPPNALH   GP+ S+SH
Sbjct: 275 TPNRHRGYGFIEYEGRQAAIEAISSMNLFDLGGQYLRVGRAITPPNALH---GPS-SSSH 330

Query: 129 MPTAAAVAAAAATAKIQAMDGGATNAVGVLSKLS 162
           MPTAAAVAAAAATAKIQAMD  ATNAV  LSKLS
Sbjct: 331 MPTAAAVAAAAATAKIQAMDAVATNAVLGLSKLS 364

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307195017|gb|EFN77085.1| Poly(U)-binding-splicing factor half pint [Harpegnathos saltator]

 Score =  234 bits (596), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 129/154 (83%), Positives = 136/154 (88%), Gaps = 4/154 (2%)

Query: 9   VGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS 68
           VGRPSNMPQAQSVIDEITEE+K YNRIY+ASIH DLTEEDIKSVFEAFGPI YCKL QGS
Sbjct: 164 VGRPSNMPQAQSVIDEITEESKHYNRIYIASIHQDLTEEDIKSVFEAFGPITYCKLAQGS 223

Query: 69  SPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSH 128
           SPHRHKGYGFIEYET QA+ EAI+SMNLFDLGGQYLRVGRAITPPNAL    GP   TS 
Sbjct: 224 SPHRHKGYGFIEYETMQAALEAIASMNLFDLGGQYLRVGRAITPPNALM---GPPSGTSM 280

Query: 129 MPTAAAVAAAAATAKIQAMDGGATNAVGV-LSKL 161
           MPTAAAVAAAAATAKIQAMD  A+NAV + L+KL
Sbjct: 281 MPTAAAVAAAAATAKIQAMDAVASNAVALGLTKL 314

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322785180|gb|EFZ11893.1| hypothetical protein SINV_08068 [Solenopsis invicta]

 Score =  233 bits (594), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 128/154 (83%), Positives = 136/154 (88%), Gaps = 4/154 (2%)

Query: 9   VGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS 68
           VGRPSNMPQAQSVIDEITEE+K YNRIY+ASIH DLTE+DIKSVFEAFGPI YCKL QGS
Sbjct: 147 VGRPSNMPQAQSVIDEITEESKHYNRIYIASIHQDLTEDDIKSVFEAFGPITYCKLAQGS 206

Query: 69  SPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSH 128
           SPHRHKGYGFIEYET QA+ EAI+SMNLFDLGGQYLRVGRAITPPNAL    GP   TS 
Sbjct: 207 SPHRHKGYGFIEYETMQAALEAIASMNLFDLGGQYLRVGRAITPPNALM---GPPSGTSM 263

Query: 129 MPTAAAVAAAAATAKIQAMDGGATNAVGV-LSKL 161
           MPTAAAVAAAAATAKIQAMD  A+NAV + L+KL
Sbjct: 264 MPTAAAVAAAAATAKIQAMDAVASNAVALGLTKL 297

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270001539|gb|EEZ97986.1| hypothetical protein TcasGA2_TC000381 [Tribolium castaneum]

 Score =  233 bits (593), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 128/156 (82%), Positives = 137/156 (87%), Gaps = 4/156 (2%)

Query: 9   VGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS 68
           VGRPSNMPQAQ+VIDEI EEAK YNRIYVASIHPDLTE+DIKSVFEAFGPI YCKL QGS
Sbjct: 215 VGRPSNMPQAQAVIDEIQEEAKQYNRIYVASIHPDLTEDDIKSVFEAFGPIIYCKLAQGS 274

Query: 69  SPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSH 128
           S H+HKGYGFIEYET QA+NEAI+SMNLFDLGGQYLRVGRAITPPNAL    GP+  +S 
Sbjct: 275 SGHKHKGYGFIEYETAQAANEAIASMNLFDLGGQYLRVGRAITPPNALL---GPSSGSSV 331

Query: 129 MPTAAAVAAAAATAKIQAMDGGATNAVGV-LSKLSQ 163
           MPTAAAVAAAAATAKIQAMD  A+NA  +  SKLSQ
Sbjct: 332 MPTAAAVAAAAATAKIQAMDAVASNAAALGFSKLSQ 367

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380016392|ref|XP_003692169.1| PREDICTED: poly(U)-binding-splicing factor half pint-like [Apis florea]

 Score =  233 bits (593), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 128/154 (83%), Positives = 136/154 (88%), Gaps = 4/154 (2%)

Query: 9   VGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS 68
           VGRPSNMPQAQSVIDEITEE+K YNRIY+ASIH DLTE+DIKSVFEAFGPI YCKL QGS
Sbjct: 194 VGRPSNMPQAQSVIDEITEESKHYNRIYIASIHQDLTEDDIKSVFEAFGPITYCKLAQGS 253

Query: 69  SPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSH 128
           SPHRHKGYGFIEYET QA+ EAI+SMNLFDLGGQYLRVGRAITPPNAL    GP   TS 
Sbjct: 254 SPHRHKGYGFIEYETMQAALEAIASMNLFDLGGQYLRVGRAITPPNALM---GPPSGTSM 310

Query: 129 MPTAAAVAAAAATAKIQAMDGGATNAVGV-LSKL 161
           MPTAAAVAAAAATAKIQAMD  A+NAV + L+KL
Sbjct: 311 MPTAAAVAAAAATAKIQAMDAVASNAVALGLTKL 344

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332022211|gb|EGI62526.1| Poly(U)-binding-splicing factor half pint [Acromyrmex echinatior]

 Score =  233 bits (593), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 128/154 (83%), Positives = 136/154 (88%), Gaps = 4/154 (2%)

Query: 9   VGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS 68
           VGRPSNMPQAQSVIDEITEE+K YNRIY+ASIH DLTE+DIKSVFEAFGPI YCKL QGS
Sbjct: 210 VGRPSNMPQAQSVIDEITEESKHYNRIYIASIHQDLTEDDIKSVFEAFGPITYCKLAQGS 269

Query: 69  SPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSH 128
           SPHRHKGYGFIEYET QA+ EAI+SMNLFDLGGQYLRVGRAITPPNAL    GP   TS 
Sbjct: 270 SPHRHKGYGFIEYETMQAALEAIASMNLFDLGGQYLRVGRAITPPNALM---GPPSGTSM 326

Query: 129 MPTAAAVAAAAATAKIQAMDGGATNAVGV-LSKL 161
           MPTAAAVAAAAATAKIQAMD  A+NAV + L+KL
Sbjct: 327 MPTAAAVAAAAATAKIQAMDAVASNAVALGLTKL 360

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340725363|ref|XP_003401040.1| PREDICTED: poly(U)-binding-splicing factor half pint-like [Bombus terrestris] gi|350403872|ref|XP_003486932.1| PREDICTED: poly(U)-binding-splicing factor half pint-like [Bombus impatiens]

 Score =  233 bits (593), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 128/154 (83%), Positives = 136/154 (88%), Gaps = 4/154 (2%)

Query: 9   VGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS 68
           VGRPSNMPQAQSVIDEITEE+K YNRIY+ASIH DLTE+DIKSVFEAFGPI YCKL QGS
Sbjct: 194 VGRPSNMPQAQSVIDEITEESKHYNRIYIASIHQDLTEDDIKSVFEAFGPITYCKLAQGS 253

Query: 69  SPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSH 128
           SPHRHKGYGFIEYET QA+ EAI+SMNLFDLGGQYLRVGRAITPPNAL    GP   TS 
Sbjct: 254 SPHRHKGYGFIEYETMQAALEAIASMNLFDLGGQYLRVGRAITPPNALM---GPPSGTSM 310

Query: 129 MPTAAAVAAAAATAKIQAMDGGATNAVGV-LSKL 161
           MPTAAAVAAAAATAKIQAMD  A+NAV + L+KL
Sbjct: 311 MPTAAAVAAAAATAKIQAMDAVASNAVALGLTKL 344

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328783360|ref|XP_001121000.2| PREDICTED: poly(U)-binding-splicing factor half pint-like [Apis mellifera]

 Score =  233 bits (593), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 128/154 (83%), Positives = 136/154 (88%), Gaps = 4/154 (2%)

Query: 9   VGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS 68
           VGRPSNMPQAQSVIDEITEE+K YNRIY+ASIH DLTE+DIKSVFEAFGPI YCKL QGS
Sbjct: 194 VGRPSNMPQAQSVIDEITEESKHYNRIYIASIHQDLTEDDIKSVFEAFGPITYCKLAQGS 253

Query: 69  SPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSH 128
           SPHRHKGYGFIEYET QA+ EAI+SMNLFDLGGQYLRVGRAITPPNAL    GP   TS 
Sbjct: 254 SPHRHKGYGFIEYETMQAALEAIASMNLFDLGGQYLRVGRAITPPNALM---GPPSGTSM 310

Query: 129 MPTAAAVAAAAATAKIQAMDGGATNAVGV-LSKL 161
           MPTAAAVAAAAATAKIQAMD  A+NAV + L+KL
Sbjct: 311 MPTAAAVAAAAATAKIQAMDAVASNAVALGLTKL 344

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383861059|ref|XP_003706004.1| PREDICTED: poly(U)-binding-splicing factor half pint-like [Megachile rotundata]

 Score =  233 bits (593), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 128/154 (83%), Positives = 136/154 (88%), Gaps = 4/154 (2%)

Query: 9   VGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS 68
           VGRPSNMPQAQSVIDEITEE+K YNRIY+ASIH DLTE+DIKSVFEAFGPI YCKL QGS
Sbjct: 194 VGRPSNMPQAQSVIDEITEESKHYNRIYIASIHQDLTEDDIKSVFEAFGPITYCKLAQGS 253

Query: 69  SPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSH 128
           SPHRHKGYGFIEYET QA+ EAI+SMNLFDLGGQYLRVGRAITPPNAL    GP   TS 
Sbjct: 254 SPHRHKGYGFIEYETMQAALEAIASMNLFDLGGQYLRVGRAITPPNALM---GPPSGTSM 310

Query: 129 MPTAAAVAAAAATAKIQAMDGGATNAVGV-LSKL 161
           MPTAAAVAAAAATAKIQAMD  A+NAV + L+KL
Sbjct: 311 MPTAAAVAAAAATAKIQAMDAVASNAVALGLTKL 344

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307177474|gb|EFN66601.1| Poly(U)-binding-splicing factor half pint [Camponotus floridanus]

 Score =  232 bits (592), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 128/154 (83%), Positives = 136/154 (88%), Gaps = 4/154 (2%)

Query: 9   VGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS 68
           VGRPSNMPQAQSVIDEITEE+K YNRIY+ASIH DLTE+DIKSVFEAFGPI YCKL QGS
Sbjct: 112 VGRPSNMPQAQSVIDEITEESKHYNRIYIASIHQDLTEDDIKSVFEAFGPITYCKLAQGS 171

Query: 69  SPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSH 128
           SPHRHKGYGFIEYET QA+ EAI+SMNLFDLGGQYLRVGRAITPPNAL    GP   TS 
Sbjct: 172 SPHRHKGYGFIEYETMQAALEAIASMNLFDLGGQYLRVGRAITPPNALM---GPPSGTSM 228

Query: 129 MPTAAAVAAAAATAKIQAMDGGATNAVGV-LSKL 161
           MPTAAAVAAAAATAKIQAMD  A+NAV + L+KL
Sbjct: 229 MPTAAAVAAAAATAKIQAMDAVASNAVALGLTKL 262

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

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	173
FB|FBgn0028577	637	pUf68 "poly U binding factor 6	0.890	0.241	0.668	7.4e-50
UNIPROTKB|J9P4I7	560	PUF60 "Uncharacterized protein	0.867	0.267	0.535	4.3e-38
UNIPROTKB|F1NA97	366	LOC426301 "Uncharacterized pro	0.867	0.409	0.535	4.3e-38
UNIPROTKB|F1P1V2	522	LOC426301 "Uncharacterized pro	0.867	0.287	0.535	4.3e-38
UNIPROTKB|F1N238	530	PUF60 "Poly(U)-binding-splicin	0.867	0.283	0.535	4.3e-38
UNIPROTKB|Q2HJG2	530	PUF60 "Poly(U)-binding-splicin	0.867	0.283	0.535	4.3e-38
MGI|MGI:1915209	564	Puf60 "poly-U binding splicing	0.867	0.265	0.535	4.3e-38
RGD|621674	564	Puf60 "poly-U binding splicing	0.867	0.265	0.535	4.3e-38
UNIPROTKB|E2RA48	543	PUF60 "Uncharacterized protein	0.867	0.276	0.535	4.3e-38
UNIPROTKB|Q9UHX1	559	PUF60 "Poly(U)-binding-splicin	0.861	0.266	0.538	5.5e-38

FB|FBgn0028577 pUf68 "poly U binding factor 68kD" [Drosophila melanogaster (taxid:7227)]

 Score = 519 (187.8 bits), Expect = 7.4e-50, P = 7.4e-50
 Identities = 107/160 (66%), Positives = 122/160 (76%)

Query:     6 HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
             +++VGRPSNMPQAQ VIDE+ EEAK +NRIYVASIHPDL+EEDIKSVFEAFGPI YCKL 
Sbjct:   200 NIKVGRPSNMPQAQQVIDEVQEEAKSFNRIYVASIHPDLSEEDIKSVFEAFGPILYCKLA 259

Query:    66 QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
             QG+S H HKGYGFIEY  KQA +EAI+SMNLFDLGGQ LRVGR+ITPPNAL       P+
Sbjct:   260 QGTSLHTHKGYGFIEYANKQAMDEAIASMNLFDLGGQLLRVGRSITPPNAL-----ACPT 314

Query:   126 T-SHMPXXXXXXXXXXXXKIQAMDGGATNAVGVLSKLSQV 164
             T S MP            KIQA+D  A+NAV  LS+ + V
Sbjct:   315 TNSTMPTAAAVAAAAATAKIQALDAVASNAVLGLSQNTPV 354

GO:0008266 "poly(U) RNA binding" evidence=ISS;NAS

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

GO:0003729 "mRNA binding" evidence=ISS

GO:0006376 "mRNA splice site selection" evidence=NAS;IMP

GO:0007282 "cystoblast division" evidence=IMP

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

GO:0005634 "nucleus" evidence=IC;IDA

GO:0051726 "regulation of cell cycle" evidence=IMP

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0043234 "protein complex" evidence=IPI

GO:0071011 "precatalytic spliceosome" evidence=IDA

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

GO:0001558 "regulation of cell growth" evidence=IMP

GO:0022008 "neurogenesis" evidence=IMP

UNIPROTKB|J9P4I7 PUF60 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 408 (148.7 bits), Expect = 4.3e-38, P = 4.3e-38
 Identities = 83/155 (53%), Positives = 109/155 (70%)

Query:     6 HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
             +++VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DIKSVFEAFG IK C L 
Sbjct:   200 NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLA 259

Query:    66 QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
             +  +  +HKGYGFIEYE  Q+S +A+SSMNLFDLGGQYLRVG+A+TPP  L +   PA +
Sbjct:   260 RDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLT---PA-T 315

Query:   126 TSHMPXXXXXXXXXXXXKIQAMDGGATNAV-GVLS 159
                +P            KI A +  A  AV G L+
Sbjct:   316 PGGLPPAAAVAAAAATAKITAQEAVAGAAVLGTLA 350

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1NA97 LOC426301 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 408 (148.7 bits), Expect = 4.3e-38, P = 4.3e-38
 Identities = 83/155 (53%), Positives = 109/155 (70%)

Query:     6 HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
             +++VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DIKSVFEAFG IK C L 
Sbjct:   156 NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLA 215

Query:    66 QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
             +  +  +HKGYGFIEYE  Q+S +A+SSMNLFDLGGQYLRVG+A+TPP  L +   PA +
Sbjct:   216 RDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLT---PA-T 271

Query:   126 TSHMPXXXXXXXXXXXXKIQAMDGGATNAV-GVLS 159
                +P            KI A +  A  AV G L+
Sbjct:   272 PGGLPPAAAVAAAAATAKITAQEAVAGAAVLGTLA 306

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1P1V2 LOC426301 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 408 (148.7 bits), Expect = 4.3e-38, P = 4.3e-38
 Identities = 83/155 (53%), Positives = 109/155 (70%)

Query:     6 HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
             +++VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DIKSVFEAFG IK C L 
Sbjct:   162 NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLA 221

Query:    66 QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
             +  +  +HKGYGFIEYE  Q+S +A+SSMNLFDLGGQYLRVG+A+TPP  L +   PA +
Sbjct:   222 RDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLT---PA-T 277

Query:   126 TSHMPXXXXXXXXXXXXKIQAMDGGATNAV-GVLS 159
                +P            KI A +  A  AV G L+
Sbjct:   278 PGGLPPAAAVAAAAATAKITAQEAVAGAAVLGTLA 312

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0019907 "cyclin-dependent protein kinase activating kinase holoenzyme complex" evidence=IEA

UNIPROTKB|F1N238 PUF60 "Poly(U)-binding-splicing factor PUF60" [Bos taurus (taxid:9913)]

 Score = 408 (148.7 bits), Expect = 4.3e-38, P = 4.3e-38
 Identities = 83/155 (53%), Positives = 109/155 (70%)

Query:     6 HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
             +++VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DIKSVFEAFG IK C L 
Sbjct:   170 NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLA 229

Query:    66 QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
             +  +  +HKGYGFIEYE  Q+S +A+SSMNLFDLGGQYLRVG+A+TPP  L +   PA +
Sbjct:   230 RDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLT---PA-T 285

Query:   126 TSHMPXXXXXXXXXXXXKIQAMDGGATNAV-GVLS 159
                +P            KI A +  A  AV G L+
Sbjct:   286 PGGLPPAAAVAAAAATAKITAQEAVAGAAVLGTLA 320

GO:0019907 "cyclin-dependent protein kinase activating kinase holoenzyme complex" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q2HJG2 PUF60 "Poly(U)-binding-splicing factor PUF60" [Bos taurus (taxid:9913)]

 Score = 408 (148.7 bits), Expect = 4.3e-38, P = 4.3e-38
 Identities = 83/155 (53%), Positives = 109/155 (70%)

Query:     6 HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
             +++VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DIKSVFEAFG IK C L 
Sbjct:   170 NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLA 229

Query:    66 QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
             +  +  +HKGYGFIEYE  Q+S +A+SSMNLFDLGGQYLRVG+A+TPP  L +   PA +
Sbjct:   230 RDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLT---PA-T 285

Query:   126 TSHMPXXXXXXXXXXXXKIQAMDGGATNAV-GVLS 159
                +P            KI A +  A  AV G L+
Sbjct:   286 PGGLPPAAAVAAAAATAKITAQEAVAGAAVLGTLA 320

GO:0005634 "nucleus" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

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

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

GO:0003723 "RNA binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:1915209 Puf60 "poly-U binding splicing factor 60" [Mus musculus (taxid:10090)]

 Score = 408 (148.7 bits), Expect = 4.3e-38, P = 4.3e-38
 Identities = 83/155 (53%), Positives = 109/155 (70%)

Query:     6 HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
             +++VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DIKSVFEAFG IK C L 
Sbjct:   204 NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLA 263

Query:    66 QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
             +  +  +HKGYGFIEYE  Q+S +A+SSMNLFDLGGQYLRVG+A+TPP  L +   PA +
Sbjct:   264 RDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLT---PA-T 319

Query:   126 TSHMPXXXXXXXXXXXXKIQAMDGGATNAV-GVLS 159
                +P            KI A +  A  AV G L+
Sbjct:   320 PGGLPPAAAVAAAAATAKITAQEAVAGAAVLGTLA 354

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" 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:0006915 "apoptotic process" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

RGD|621674 Puf60 "poly-U binding splicing factor 60" [Rattus norvegicus (taxid:10116)]

 Score = 408 (148.7 bits), Expect = 4.3e-38, P = 4.3e-38
 Identities = 83/155 (53%), Positives = 109/155 (70%)

Query:     6 HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
             +++VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DIKSVFEAFG IK C L 
Sbjct:   204 NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLA 263

Query:    66 QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
             +  +  +HKGYGFIEYE  Q+S +A+SSMNLFDLGGQYLRVG+A+TPP  L +   PA +
Sbjct:   264 RDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLT---PA-T 319

Query:   126 TSHMPXXXXXXXXXXXXKIQAMDGGATNAV-GVLS 159
                +P            KI A +  A  AV G L+
Sbjct:   320 PGGLPPAAAVAAAAATAKITAQEAVAGAAVLGTLA 354

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

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

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

GO:0006397 "mRNA processing" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0019907 "cyclin-dependent protein kinase activating kinase holoenzyme complex" evidence=IEA;ISO

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|E2RA48 PUF60 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 408 (148.7 bits), Expect = 4.3e-38, P = 4.3e-38
 Identities = 83/155 (53%), Positives = 109/155 (70%)

Query:     6 HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
             +++VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DIKSVFEAFG IK C L 
Sbjct:   183 NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLA 242

Query:    66 QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
             +  +  +HKGYGFIEYE  Q+S +A+SSMNLFDLGGQYLRVG+A+TPP  L +   PA +
Sbjct:   243 RDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLT---PA-T 298

Query:   126 TSHMPXXXXXXXXXXXXKIQAMDGGATNAV-GVLS 159
                +P            KI A +  A  AV G L+
Sbjct:   299 PGGLPPAAAVAAAAATAKITAQEAVAGAAVLGTLA 333

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q9UHX1 PUF60 "Poly(U)-binding-splicing factor PUF60" [Homo sapiens (taxid:9606)]

 Score = 407 (148.3 bits), Expect = 5.5e-38, P = 5.5e-38
 Identities = 83/154 (53%), Positives = 108/154 (70%)

Query:     6 HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
             +++VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DIKSVFEAFG IK C L 
Sbjct:   199 NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLA 258

Query:    66 QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
             +  +  +HKGYGFIEYE  Q+S +A+SSMNLFDLGGQYLRVG+A+TPP  L +   PA +
Sbjct:   259 RDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLT---PA-T 314

Query:   126 TSHMPXXXXXXXXXXXXKIQAMDGGATNAV-GVL 158
                +P            KI A +  A  AV G L
Sbjct:   315 PGGLPPAAAVAAAAATAKITAQEAVAGAAVLGTL 348

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003677 "DNA 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:0006915 "apoptotic process" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0019907 "cyclin-dependent protein kinase activating kinase holoenzyme complex" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5R469	PUF60_PONAB	No assigned EC number	0.6239	0.6763	0.2096	yes	N/A
Q9UHX1	PUF60_HUMAN	No assigned EC number	0.6239	0.6763	0.2093	yes	N/A
Q2HJG2	PUF60_BOVIN	No assigned EC number	0.6239	0.6763	0.2207	yes	N/A
Q3UEB3	PUF60_MOUSE	No assigned EC number	0.6186	0.6820	0.2092	yes	N/A
Q9WV25	PUF60_RAT	No assigned EC number	0.6186	0.6820	0.2092	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	173
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	1e-70
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	3e-49
smart00360	73	smart00360, RRM, RNA recognition motif	4e-21
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	9e-21
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	1e-19
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	9e-18
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-16
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	8e-16
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-14
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	4e-14
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	4e-14
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-13
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	3e-13
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	4e-13
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	4e-13
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	6e-13
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	1e-12
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-12
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-12
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-12
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	2e-12
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	3e-12
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	4e-12
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	5e-12
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	6e-12
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	6e-12
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	1e-11
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	1e-11
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	2e-11
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-11
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	4e-11
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	1e-10
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	2e-10
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	3e-10
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	3e-10
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	4e-10
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	4e-10
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	6e-10
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-09
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	1e-09
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-09
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	2e-09
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	3e-09
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	3e-09
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	7e-09
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	8e-09
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-08
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	2e-08
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-08
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	2e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-08
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	3e-08
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	3e-08
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	3e-08
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	3e-08
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	3e-08
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	4e-08
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	5e-08
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	6e-08
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	7e-08
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	7e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	8e-08
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	8e-08
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	8e-08
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	8e-08
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	9e-08
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	9e-08
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	1e-07
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	1e-07
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	2e-07
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	2e-07
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	2e-07
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	3e-07
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	3e-07
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	3e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-07
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	4e-07
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	5e-07
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	5e-07
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	6e-07
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	7e-07
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	8e-07
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	8e-07
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	1e-06
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	1e-06
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	1e-06
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	1e-06
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	1e-06
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	2e-06
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-06
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	2e-06
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	2e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-06
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	2e-06
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	2e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-06
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	3e-06
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	3e-06
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	3e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	3e-06
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-06
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	3e-06
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	3e-06
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	4e-06
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	4e-06
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	4e-06
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	5e-06
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	6e-06
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	6e-06
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	6e-06
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	8e-06
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	8e-06
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	9e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	9e-06
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	9e-06
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	1e-05
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	1e-05
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	1e-05
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	1e-05
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	1e-05
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	1e-05
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	1e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-05
cd12292	75	cd12292, RRM2_La_like, RNA recognition motif 2 in	2e-05
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	2e-05
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-05
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	2e-05
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	3e-05
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	4e-05
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	4e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	5e-05
cd12623	91	cd12623, RRM_PPARGC1A, RNA recognition motif in pe	5e-05
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	5e-05
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	5e-05
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	6e-05
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	6e-05
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	6e-05
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	6e-05
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	7e-05
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	7e-05
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	8e-05
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	8e-05
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	8e-05
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	9e-05
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	9e-05
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	9e-05
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	9e-05
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	1e-04
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	1e-04
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	1e-04
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	1e-04
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	2e-04
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	2e-04
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	2e-04
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	2e-04
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	2e-04
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-04
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	2e-04
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	3e-04
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	3e-04
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	3e-04
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	3e-04
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	3e-04
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	3e-04
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	3e-04
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	4e-04
cd12605	69	cd12605, RRM_RALYL, RNA recognition motif in verte	4e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	4e-04
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	4e-04
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	4e-04
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	5e-04
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	5e-04
cd12604	76	cd12604, RRM_RALY, RNA recognition motif in verteb	5e-04
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	5e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	6e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	6e-04
cd12667	92	cd12667, RRM3_RAVER1, RNA recognition motif 3 in v	6e-04
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	6e-04
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	7e-04
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	8e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	8e-04
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	8e-04
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	8e-04
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	8e-04
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	9e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	9e-04
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	9e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.001
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.001
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	0.001
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	0.001
cd12658	76	cd12658, RRM1_MYEF2, RNA recognition motif 1 in ve	0.001
pfam08777	102	pfam08777, RRM_3, RNA binding motif	0.001
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	0.001
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	0.002
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	0.002
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	0.002
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	0.002
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	0.002
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	0.002
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	0.002
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	0.002
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	0.003
cd12557	73	cd12557, RRM3_RBM15, RNA recognition motif 3 in ve	0.003
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	0.003
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	0.003
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	0.003
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	0.004
cd12426	79	cd12426, RRM4_PTBPH3, RNA recognition motif 4 in p	0.004
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	0.004
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	0.004
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	0.004
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	0.004

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

 Score =  223 bits (570), Expect = 1e-70
 Identities = 97/159 (61%), Positives = 117/159 (73%), Gaps = 4/159 (2%)

Query: 6   HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
           +++VGRPSNMPQAQ +ID + EEAK +NRIYVAS+HPDL+E DIKSVFEAFG I  C+L 
Sbjct: 178 NIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLA 237

Query: 66  QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
           +  +   HKGYGFIEY   Q+ +EAI+SMNLFDLGGQYLRVG+ +TPP+AL     PA +
Sbjct: 238 RAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDALLQ---PA-T 293

Query: 126 TSHMPTAAAVAAAAATAKIQAMDGGATNAVGVLSKLSQV 164
            S +P AAAVAAAAATAKI A +  A  AV      S  
Sbjct: 294 VSAIPAAAAVAAAAATAKIMAAEAVAGAAVLGPRAQSPA 332

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

 Score =  153 bits (389), Expect = 3e-49
 Identities = 54/77 (70%), Positives = 63/77 (81%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           NRIYVAS+HPDL+E+DIKSVFEAFG IK C L       +HKGYGFIEYE  Q++ +AI+
Sbjct: 1   NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 93  SMNLFDLGGQYLRVGRA 109
           SMNLFDLGGQ LRVG+A
Sbjct: 61  SMNLFDLGGQQLRVGKA 77

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|214636 smart00360, RRM, RNA recognition motif

 Score = 81.5 bits (202), Expect = 4e-21
 Identities = 21/73 (28%), Positives = 48/73 (65%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            ++V ++ PD TEE+++ +F  FG ++  +L +     + KG+ F+E+E+++ + +A+ +
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 94  MNLFDLGGQYLRV 106
           +N  +L G+ L+V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 80.8 bits (200), Expect = 9e-21
 Identities = 27/73 (36%), Positives = 51/73 (69%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV ++H ++TE+D++ +FE FG I++ +LQ+     R KGYGFI++   + + +A+  +
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 95  NLFDLGGQYLRVG 107
           N F+L G+ ++VG
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|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 77.9 bits (192), Expect = 1e-19
 Identities = 31/75 (41%), Positives = 45/75 (60%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           R+YV SI  +L E+ I+  F  FGPIK   +       +HKG+ F+EYE  +A+  A+  
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

Query: 94  MNLFDLGGQYLRVGR 108
           MN   LGG+ ++VGR
Sbjct: 62  MNGVMLGGRNIKVGR 76

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

 Score = 72.7 bits (179), Expect = 9e-18
 Identities = 22/72 (30%), Positives = 47/72 (65%), Gaps = 1/72 (1%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V ++ PD TEED++ +F  FG I+  ++ +     + KG+ F+E+E+ + + +A+ ++
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDG-KSKGFAFVEFESPEDAEKALEAL 59

Query: 95  NLFDLGGQYLRV 106
           N  +L G+ L+V
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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 74.5 bits (183), Expect = 4e-16
 Identities = 28/92 (30%), Positives = 54/92 (58%)

Query: 18  AQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYG 77
           A         +   + ++YV ++H ++TE++++ +FE FG I+  +L +     R KG+G
Sbjct: 172 AAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFG 231

Query: 78  FIEYETKQASNEAISSMNLFDLGGQYLRVGRA 109
           FI++   + + EA+  MN F+L G+ ++VG A
Sbjct: 232 FIQFHDAEEAKEALEVMNGFELAGRPIKVGYA 263

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 67.6 bits (166), Expect = 8e-16
 Identities = 26/71 (36%), Positives = 49/71 (69%), Gaps = 1/71 (1%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V ++ PD TEED+K +F  FGPI+  ++ +  +  R KG+ F+E+E ++ + +A+ ++
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDET-GRSKGFAFVEFEDEEDAEKALEAL 59

Query: 95  NLFDLGGQYLR 105
           N  +LGG+ LR
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|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 = 64.2 bits (157), Expect = 2e-14
 Identities = 25/75 (33%), Positives = 41/75 (54%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V +I  D TEE +  +F   GP+   +L       + KGYGF E+E  + +  AI ++
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 95  NLFDLGGQYLRVGRA 109
           N ++  G+ LRV  A
Sbjct: 61  NGYEFNGRALRVDFA 75

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

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

 Score = 63.5 bits (155), Expect = 4e-14
 Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 7/77 (9%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKL--QQGSSPHRHKGYGFIEYETKQASNEAIS 92
           +YV ++   +TE+ +  +F   GPIK CKL  + G+ P     Y F+EY   +++  A+ 
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP-----YAFVEYYDHRSAAAALQ 55

Query: 93  SMNLFDLGGQYLRVGRA 109
           +MN   + GQ ++V  A
Sbjct: 56  TMNGRLILGQEIKVNWA 72

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

 Score = 63.7 bits (156), Expect = 4e-14
 Identities = 25/81 (30%), Positives = 47/81 (58%), Gaps = 7/81 (8%)

Query: 32  YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQASN 88
           +  +YV ++  D+ +E +K +F  +G I   K+    +G S    KG+GF+ +E  +A+ 
Sbjct: 1   FTNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKS----KGFGFVNFENHEAAQ 56

Query: 89  EAISSMNLFDLGGQYLRVGRA 109
           +A+  +N  ++ G+ L VGRA
Sbjct: 57  KAVEELNGKEVNGKKLYVGRA 77

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|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 = 61.6 bits (150), Expect = 2e-13
 Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 6/71 (8%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V  + P +TE++++S+F  FG I Y K+  G      KG GF+++  + A+  AI  +
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPG------KGCGFVQFVHRAAAEAAIQQL 57

Query: 95  NLFDLGGQYLR 105
               +GG  +R
Sbjct: 58  QGTIIGGSRIR 68

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

 Score = 66.2 bits (161), Expect = 3e-13
 Identities = 33/82 (40%), Positives = 49/82 (59%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           R+YV SI  +L E+ I+  F+ FGPIK   +    +  +HKG+ F+EYE  +A+  A+  
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168

Query: 94  MNLFDLGGQYLRVGRAITPPNA 115
           MN   LGG+ ++VGR    P A
Sbjct: 169 MNGQMLGGRNIKVGRPSNMPQA 190

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

 Score = 65.7 bits (160), Expect = 4e-13
 Identities = 39/155 (25%), Positives = 64/155 (41%), Gaps = 13/155 (8%)

Query: 1   MQHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIK 60
            Q  P         +  + +V+D         +RIY+ ++   L E+ IK + E+FG +K
Sbjct: 271 SQKNPDDNAKNVEKLVNSTTVLDS-------KDRIYIGNLPLYLGEDQIKELLESFGDLK 323

Query: 61  YCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSK 120
              L +  +    KGY F EY+    ++ AI+++N  D G   L V RA         + 
Sbjct: 324 AFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACV------GAN 377

Query: 121 GPAPSTSHMPTAAAVAAAAATAKIQAMDGGATNAV 155
                TS+      + A A +  I  + G  T  V
Sbjct: 378 QATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVV 412

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

 Score = 61.1 bits (149), Expect = 4e-13
 Identities = 27/76 (35%), Positives = 44/76 (57%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            +YV ++  ++TEED+K +F  FG +   ++       R +G+GF+E ET + +N AI  
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 94  MNLFDLGGQYLRVGRA 109
           +N  D GG+ L V  A
Sbjct: 61  LNGTDFGGRTLTVNEA 76

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

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

 Score = 60.3 bits (147), Expect = 6e-13
 Identities = 20/71 (28%), Positives = 42/71 (59%), Gaps = 2/71 (2%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV ++ P +TEED++  F  +G ++  +L +  +  R +G+ F+E+ + + +  A+  +
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVR--NKDRPRGFAFVEFASPEDAEAALKKL 58

Query: 95  NLFDLGGQYLR 105
           N   L G+ LR
Sbjct: 59  NGLVLDGRTLR 69

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

>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 = 59.9 bits (146), Expect = 1e-12
 Identities = 26/77 (33%), Positives = 44/77 (57%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           N+I++  +   L+E+ +K + E+FG +K   L + S+    KGY F EY     +++AI+
Sbjct: 1   NKIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIA 60

Query: 93  SMNLFDLGGQYLRVGRA 109
            +N   LG + L V RA
Sbjct: 61  GLNGMQLGDKKLTVQRA 77

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|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 = 59.2 bits (144), Expect = 2e-12
 Identities = 21/73 (28%), Positives = 41/73 (56%), Gaps = 6/73 (8%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV ++   LTEE+++  F  FG I+  ++       + KGY F+ ++T +A+  AI ++
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRVF------KDKGYAFVRFDTHEAAATAIVAV 56

Query: 95  NLFDLGGQYLRVG 107
           N   + GQ ++  
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|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 59.6 bits (145), Expect = 2e-12
 Identities = 31/81 (38%), Positives = 48/81 (59%), Gaps = 8/81 (9%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQASNE 89
           NRI+V  I PD TEE+++  F  FG +K  K+   + G S    KGYGF+ +ET++ + +
Sbjct: 3   NRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVS----KGYGFVTFETQEDAEK 58

Query: 90  AISSMNLFDLGGQYLRVGRAI 110
            ++  NL    G+ L +G AI
Sbjct: 59  ILAMGNLN-FRGKKLNIGPAI 78

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

 Score = 59.2 bits (144), Expect = 2e-12
 Identities = 21/72 (29%), Positives = 41/72 (56%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV  +  ++ E+ + + F  FG IK  ++       +H+G+ F+E+E  + +  AI +M
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 95  NLFDLGGQYLRV 106
           N  +L G+ +RV
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|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 59.2 bits (144), Expect = 2e-12
 Identities = 28/72 (38%), Positives = 37/72 (51%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           I+V  +H +  EED+   F  FG IK   L         KGY  IEYETK+ +  AI  +
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 95  NLFDLGGQYLRV 106
           N  +L GQ + 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|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 58.9 bits (143), Expect = 3e-12
 Identities = 24/67 (35%), Positives = 46/67 (68%)

Query: 43  DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQ 102
           D+T+E+++S+FEA GPI+ CK+ +     +  GYGF++Y  +  + +AI+++N F++  +
Sbjct: 11  DMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNK 70

Query: 103 YLRVGRA 109
            L+V  A
Sbjct: 71  RLKVSYA 77

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

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

 Score = 58.2 bits (141), Expect = 4e-12
 Identities = 23/71 (32%), Positives = 40/71 (56%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           I+V  + P++  E +++ F  FG I   ++ +     + KGYGF+ +  K+ +  AI SM
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 95  NLFDLGGQYLR 105
           N   LGG+ +R
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|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 58.5 bits (142), Expect = 5e-12
 Identities = 19/64 (29%), Positives = 33/64 (51%)

Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
          +YV  +  + T E +K+VF  +G + Y  L +       KG+ FIE+ET + + +A   +
Sbjct: 2  VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 95 NLFD 98
          N   
Sbjct: 62 NNPP 65

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

 Score = 61.9 bits (149), Expect = 6e-12
 Identities = 26/102 (25%), Positives = 58/102 (56%)

Query: 8   QVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQG 67
                  + ++        +  +  N ++V ++  D+TEED++ +F+ FGP+K  +L + 
Sbjct: 91  TKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRD 150

Query: 68  SSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA 109
               + +G+ F+E+E+++++ +AI  +N  +L G+ LRV +A
Sbjct: 151 RETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKA 192

Length = 306

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

 Score = 58.1 bits (141), Expect = 6e-12
 Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 3/76 (3%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIK---YCKLQQGSSPHRHKGYGFIEYETKQASNEA 90
           R+++ ++   LTE  +  +F  +G IK   +   + G    + +GY F+ +ETK+ + +A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 91  ISSMNLFDLGGQYLRV 106
           + S+N     G+ L V
Sbjct: 61  LKSLNGKTALGKKLVV 76

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

 Score = 56.9 bits (138), Expect = 1e-11
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 6/74 (8%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            R++V ++  D+TEE+ K +F  +G +    L +       KG+GFI  +T+  + +A +
Sbjct: 2   CRLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKA 55

Query: 93  SMNLFDLGGQYLRV 106
            ++     G+ LRV
Sbjct: 56  ELDGIMRKGRQLRV 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|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 57.3 bits (139), Expect = 1e-11
 Identities = 19/59 (32%), Positives = 34/59 (57%)

Query: 32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEA 90
          +  ++VA ++ D TE  ++  FE +GPIK  +L +     + +GY FIE+E ++    A
Sbjct: 1  FKTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAA 59

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

 Score = 56.6 bits (137), Expect = 2e-11
 Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 3/73 (4%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           RIYV ++  D+ E DI+ +F  +GPIK   L+   +  R   + F+E+E  + + +A+  
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLK---NRRRGPPFAFVEFEDPRDAEDAVRG 57

Query: 94  MNLFDLGGQYLRV 106
            + +D  G  LRV
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|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 56.1 bits (136), Expect = 3e-11
 Identities = 20/80 (25%), Positives = 44/80 (55%), Gaps = 5/80 (6%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +++ ++  D TEE++K +F  FG +KY ++ +       KG  F++++TK+++ + + + 
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 95  NL-----FDLGGQYLRVGRA 109
           +        L G+ L V  A
Sbjct: 63  DNAEDSGLSLDGRRLIVTLA 82

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

>gnl|CDD|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 = 56.1 bits (136), Expect = 4e-11
 Identities = 19/79 (24%), Positives = 47/79 (59%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           N+++V+ +    TE++++++F  FG ++   L +       +G+GF+ +E+ + ++ AI 
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 93  SMNLFDLGGQYLRVGRAIT 111
            +N  +L G+ ++V +A  
Sbjct: 62  DLNGKELEGRVIKVEKAKR 80

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

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

 Score = 54.5 bits (132), Expect = 1e-10
 Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           I++ ++   +  + +   F AFG I  CK+    +    KGYGF+ +ET++A+  AI  +
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDEN-GGSKGYGFVHFETEEAAVRAIEKV 63

Query: 95  NLFDLGGQYLRVGR 108
           N   L  + + VG 
Sbjct: 64  NGMLLNDKKVFVGP 77

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

 Score = 54.6 bits (132), Expect = 2e-10
 Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 8/56 (14%)

Query: 32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQ----GSSPHRHKGYGFIEYET 83
          Y  ++V  +    TEE ++ VF  +G I+  +L +    G S    KGY F+EYE 
Sbjct: 3  YLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFS----KGYAFVEYEH 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|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 = 53.3 bits (128), Expect = 3e-10
 Identities = 25/75 (33%), Positives = 44/75 (58%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V +I  + TEE +K +F   GP+   +L       + KGYGF EY+ ++ +  A+ ++
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 95  NLFDLGGQYLRVGRA 109
           N ++L G+ LRV  A
Sbjct: 61  NGYELNGRQLRVDNA 75

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

 Score = 53.1 bits (128), Expect = 3e-10
 Identities = 26/76 (34%), Positives = 45/76 (59%), Gaps = 1/76 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           +I+V  + PD+TEE+ K  F  FG +   +L Q     R +G+GF+ ++++ A  E + S
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAV-ERVFS 59

Query: 94  MNLFDLGGQYLRVGRA 109
             + +LGG+ + V RA
Sbjct: 60  AGMLELGGKQVEVKRA 75

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

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

 Score = 53.4 bits (129), Expect = 4e-10
 Identities = 22/63 (34%), Positives = 36/63 (57%)

Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
          N ++V  ++P  T+ED++ +F  FG IK C++ +         Y FIE+ETK+   EA  
Sbjct: 4  NVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYF 63

Query: 93 SMN 95
           M+
Sbjct: 64 KMD 66

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|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 = 53.3 bits (129), Expect = 4e-10
 Identities = 14/62 (22%), Positives = 38/62 (61%)

Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
          +++V  +    TEED++++FE +G I+   + +     + KG  F+++ +++ + +AI +
Sbjct: 1  KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 94 MN 95
          ++
Sbjct: 61 LH 62

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

 Score = 52.8 bits (127), Expect = 6e-10
 Identities = 20/68 (29%), Positives = 41/68 (60%)

Query: 42  PDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG 101
            ++T+++I+S+F + G I+ CKL +     +  GYGF+ Y   + + +AI+++N   L  
Sbjct: 11  QNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQN 70

Query: 102 QYLRVGRA 109
           + ++V  A
Sbjct: 71  KTIKVSYA 78

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

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

 Score = 51.8 bits (125), Expect = 1e-09
 Identities = 18/77 (23%), Positives = 41/77 (53%), Gaps = 6/77 (7%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V  +  ++ ++ +K +F  +G +K   L      +  +GY ++E+E+ + + +AI  M
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 95  NLFDLGGQYLRVGRAIT 111
           +    GGQ    G+ +T
Sbjct: 61  D----GGQID--GQEVT 71

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

 Score = 51.8 bits (125), Expect = 1e-09
 Identities = 19/73 (26%), Positives = 39/73 (53%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            ++V +I   ++++ I+ + E  G +   K  +  S  + K +GF E+E  + +  A+  
Sbjct: 2   TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRL 61

Query: 94  MNLFDLGGQYLRV 106
           +N  +LGG+ L V
Sbjct: 62  LNGLELGGKKLLV 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|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 51.5 bits (124), Expect = 2e-09
 Identities = 21/67 (31%), Positives = 40/67 (59%)

Query: 45  TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYL 104
           TE D++ VF  +GPI+  ++       R +G+GF+ +E+ + + EA   +N  ++ G+ +
Sbjct: 12  TERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRI 71

Query: 105 RVGRAIT 111
           RV  +IT
Sbjct: 72  RVDYSIT 78

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

 Score = 51.3 bits (123), Expect = 2e-09
 Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 4/73 (5%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           RIYV ++ PD+  +DI+ +F  +G I+   L+    P     + F+E+E  + + +A+  
Sbjct: 1   RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGP----PFAFVEFEDPRDAEDAVYG 56

Query: 94  MNLFDLGGQYLRV 106
            + +D  G  LRV
Sbjct: 57  RDGYDYDGYRLRV 69

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

 Score = 51.1 bits (123), Expect = 3e-09
 Identities = 16/72 (22%), Positives = 37/72 (51%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V ++  D T+E ++  F   GPIK C + +     + +G+G++ +  ++ +  A+   
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 95  NLFDLGGQYLRV 106
                GG+ + 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|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 50.9 bits (122), Expect = 3e-09
 Identities = 15/72 (20%), Positives = 38/72 (52%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V ++  D+TE+++K  F+ FG +   ++       R   +GF+ ++  +A  + +++ 
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANK 65

Query: 95  NLFDLGGQYLRV 106
            ++  G   L V
Sbjct: 66  PIYFRGDHRLNV 77

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

 Score = 49.5 bits (118), Expect = 7e-09
 Identities = 22/73 (30%), Positives = 44/73 (60%), Gaps = 8/73 (10%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           +++V ++ P+ TE++I+S+FE +G +  C +         K YGF+  + K A++EAI +
Sbjct: 2   KLFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIRN 53

Query: 94  MNLFDLGGQYLRV 106
           ++ + L G  + V
Sbjct: 54  LHHYKLHGVAINV 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|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 50.0 bits (120), Expect = 8e-09
 Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 7/78 (8%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPI-KYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           +++ ++ P++ E+ +   F AFG I +  K+ +       KG+ FI Y++ +AS+ AI +
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 94  MNLFDLGGQYLRVGRAIT 111
           MN     GQYL   R IT
Sbjct: 64  MN-----GQYL-CNRPIT 75

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

 Score = 49.6 bits (119), Expect = 1e-08
 Identities = 23/72 (31%), Positives = 40/72 (55%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           IY+  +  +LTE DI  VF  +G I    L +     + KG+ F+ YE ++++  A+ ++
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 95  NLFDLGGQYLRV 106
           N   L G+ +RV
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|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 48.6 bits (116), Expect = 2e-08
 Identities = 16/53 (30%), Positives = 31/53 (58%)

Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQA 86
          +I+V  +  + TE+D+K  F  FG ++   L      +RH+G+GF+ +E++  
Sbjct: 1  KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDV 53

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

 Score = 48.7 bits (116), Expect = 2e-08
 Identities = 21/61 (34%), Positives = 38/61 (62%)

Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
          +YV ++   LTE++++ +FEA+G I  C L +  S    +G  F+ Y+ ++ +  AISS+
Sbjct: 3  LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 95 N 95
          N
Sbjct: 63 N 63

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|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 = 48.5 bits (116), Expect = 2e-08
 Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 3/78 (3%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           I+V  I   L+E+D+K  F   G +   +L           + F+E+   +++  A+ ++
Sbjct: 3   IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLC--GDRQHSARFAFVEFADAESALSAL-NL 59

Query: 95  NLFDLGGQYLRVGRAITP 112
           +   LGG  LRV  + TP
Sbjct: 60  SGTLLGGHPLRVSPSKTP 77

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

 Score = 51.7 bits (124), Expect = 3e-08
 Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 7/82 (8%)

Query: 31  LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQAS 87
               +YV ++   +T+E ++ +F   G I   K+   ++G S    +G+GF+ +   + +
Sbjct: 284 QGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVS----RGFGFVCFSNPEEA 339

Query: 88  NEAISSMNLFDLGGQYLRVGRA 109
           N A++ M+   LGG+ L V  A
Sbjct: 340 NRAVTEMHGRMLGGKPLYVALA 361

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

 Score = 48.4 bits (116), Expect = 3e-08
 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           R+ V+++H D+TEED++ +F   G +K  K+    S  R +G   + +E ++ +  AI  
Sbjct: 2   RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSG-RSEGTADVVFEKREDAERAIKQ 60

Query: 94  MNLFDLGGQYLRV 106
            N   L GQ ++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|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 48.0 bits (114), Expect = 3e-08
 Identities = 24/74 (32%), Positives = 44/74 (59%), Gaps = 6/74 (8%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           +R++V ++ PD+TEE+++ +FE +G      +      H+ KG+GFI  ET+  +  A +
Sbjct: 2   SRLFVGNLPPDITEEEMRKLFEKYGKAGEIFI------HKDKGFGFIRLETRTLAEIAKA 55

Query: 93  SMNLFDLGGQYLRV 106
            ++   L G+ LRV
Sbjct: 56  ELDNMPLRGKQLRV 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|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 48.2 bits (115), Expect = 3e-08
 Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 3/73 (4%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            +YV ++  D+ E +++ +F  +GPI    L+    P R  GY FIE+E  + + +AI  
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDLK---LPPRPPGYAFIEFEDARDAEDAIRG 57

Query: 94  MNLFDLGGQYLRV 106
            + +D  GQ LRV
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|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 48.0 bits (115), Expect = 3e-08
 Identities = 22/74 (29%), Positives = 43/74 (58%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV ++   +TEE +  +F   GP+    + +      H+GYGF+E+ +++ ++ AI  M
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 95  NLFDLGGQYLRVGR 108
           N+  L G+ +RV +
Sbjct: 61  NMIKLYGKPIRVNK 74

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

 Score = 48.2 bits (115), Expect = 3e-08
 Identities = 24/77 (31%), Positives = 48/77 (62%), Gaps = 8/77 (10%)

Query: 34  RIYVASIHPDLTEEDIKSVF-EAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQASNE 89
           R+++++I  DL  +D+K +F E  G + Y +L   ++G S    +G G +E++ K++  +
Sbjct: 1   RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKS----RGCGVVEFKDKESVQK 56

Query: 90  AISSMNLFDLGGQYLRV 106
           A+ +MN ++L G+ L V
Sbjct: 57  ALETMNRYELKGRKLVV 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|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 48.2 bits (114), Expect = 4e-08
 Identities = 26/75 (34%), Positives = 41/75 (54%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V  + P++T EDIKS F  FG I   ++ +  +  + KGYGF+ +  K  +  AI  M
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 95  NLFDLGGQYLRVGRA 109
               LGG+ +R   A
Sbjct: 64  GGQWLGGRQIRTNWA 78

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

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

 Score = 47.4 bits (113), Expect = 5e-08
 Identities = 17/73 (23%), Positives = 43/73 (58%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            ++V ++   + +E +K+ FE FG +   ++       R +G+G++++E+ + + +AI +
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 94  MNLFDLGGQYLRV 106
           M+  +L G+ + 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|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 47.2 bits (113), Expect = 6e-08
 Identities = 18/77 (23%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQAS-NEAIS 92
           R++V  + P +TE D++  F  FG +   ++ +       +G+ +I+  T +A   +  S
Sbjct: 1   RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKS 60

Query: 93  SMNLFDLGGQYLRVGRA 109
           ++N     G  L++  A
Sbjct: 61  TLNGTKWKGSVLKIEEA 77

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

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

 Score = 47.1 bits (112), Expect = 7e-08
 Identities = 21/72 (29%), Positives = 37/72 (51%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           IY+  +     E+++K  F  FG +K  ++ +       K YGFI++   + +  A  SM
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 95  NLFDLGGQYLRV 106
           N + L G+ L+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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 47.3 bits (112), Expect = 7e-08
 Identities = 21/67 (31%), Positives = 34/67 (50%)

Query: 45  TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYL 104
           TE D++ VF  +GPI    +       R +G+ F+ +E    + EA    N  +L G+ +
Sbjct: 22  TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 81

Query: 105 RVGRAIT 111
           RV  +IT
Sbjct: 82  RVDFSIT 88

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

 Score = 50.6 bits (121), Expect = 8e-08
 Identities = 25/87 (28%), Positives = 47/87 (54%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV  + PD+TE  +  +F+ FGP+   ++ + S   R  GYG++ ++    +  A+ +M
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 95  NLFDLGGQYLRVGRAITPPNALHSSKG 121
           N   LGG+ +R+  +   P+   S  G
Sbjct: 63  NFKRLGGKPIRIMWSQRDPSLRRSGVG 89

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|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 47.0 bits (112), Expect = 8e-08
 Identities = 15/57 (26%), Positives = 31/57 (54%)

Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEA 90
          +I+V  + P+ TEE I+  F  FG I   +L      ++ +G+ FI +++++   + 
Sbjct: 1  KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKI 57

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

 Score = 46.9 bits (112), Expect = 8e-08
 Identities = 21/72 (29%), Positives = 41/72 (56%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           + V ++  + T+E  + +   FG ++ C L    S    KGYGF+EY +K ++ +A + +
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 95  NLFDLGGQYLRV 106
           +   +GG+ L+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|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 47.0 bits (111), Expect = 8e-08
 Identities = 24/75 (32%), Positives = 41/75 (54%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V  + P++T +DIK+ F  FG I   ++ +  +  + KGYGF+ +  K  +  AI  M
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 95  NLFDLGGQYLRVGRA 109
               LGG+ +R   A
Sbjct: 64  GGQWLGGRQIRTNWA 78

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

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

 Score = 47.0 bits (112), Expect = 9e-08
 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 12/73 (16%)

Query: 43  DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHK------GYGFIEYETKQASNEAISSMNL 96
            LT+E+ +S+F A GP+K CK+       R K      G+GF++Y++ + +  AI ++N 
Sbjct: 11  TLTDEEFRSLFLAVGPVKNCKIV------RDKRTGYSYGFGFVDYQSAEDAQRAIRTLNG 64

Query: 97  FDLGGQYLRVGRA 109
             L  + ++V  A
Sbjct: 65  LQLQNKRIKVAYA 77

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

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

 Score = 47.1 bits (112), Expect = 9e-08
 Identities = 11/62 (17%), Positives = 32/62 (51%)

Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           +++V  ++   ++  ++  F  +G +  C +    +  R +G+GFI + +   ++EA+ 
Sbjct: 3  CKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAME 62

Query: 93 SM 94
          + 
Sbjct: 63 AQ 64

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

 Score = 46.3 bits (110), Expect = 1e-07
 Identities = 20/72 (27%), Positives = 38/72 (52%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           I+V  + P++T+  + + F AF      ++       R +GYGF+ + ++Q +  AI+ M
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 95  NLFDLGGQYLRV 106
           N   LG + +R 
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|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 46.5 bits (111), Expect = 1e-07
 Identities = 16/76 (21%), Positives = 42/76 (55%), Gaps = 5/76 (6%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++YV ++ P  T+ +++  FE +GP++   + +        G+ F+E+E  + + +A+ +
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWVAR-----NPPGFAFVEFEDPRDAEDAVRA 55

Query: 94  MNLFDLGGQYLRVGRA 109
           ++   + G  +RV  +
Sbjct: 56  LDGRRICGNRVRVELS 71

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

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

 Score = 45.9 bits (109), Expect = 2e-07
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 8/73 (10%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           R+YV    PD +E  I+ +F  +G +K  K+           + F+E+E+ +++  A  S
Sbjct: 1   RLYVRPFPPDTSESAIREIFSPYGAVKEVKMI--------SNFAFVEFESLESAIRAKDS 52

Query: 94  MNLFDLGGQYLRV 106
           ++   L    L 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|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 46.1 bits (109), Expect = 2e-07
 Identities = 21/67 (31%), Positives = 35/67 (52%)

Query: 45  TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYL 104
           TE D++ VF  +GP+    +       R +G+ F+ +E    S EA+   N  +L G+ +
Sbjct: 12  TERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRI 71

Query: 105 RVGRAIT 111
           RV  +IT
Sbjct: 72  RVDYSIT 78

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|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 = 46.0 bits (109), Expect = 2e-07
 Identities = 18/76 (23%), Positives = 41/76 (53%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++++  +  D  E+ ++ VF  +G I    + +     R +G+GF+ +E    + +A+ +
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 94  MNLFDLGGQYLRVGRA 109
           MN   + G+ +RV +A
Sbjct: 62  MNGKSVDGRQIRVDQA 77

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

 Score = 45.7 bits (109), Expect = 3e-07
 Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV ++   + +E ++  F  FG I   K+       R KG+GF+ + + + + +A++ M
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKG-RSKGFGFVCFSSPEEATKAVTEM 62

Query: 95  NLFDLGGQYLRVGRA 109
           N   +GG+ L V  A
Sbjct: 63  NGRIIGGKPLYVALA 77

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

 Score = 45.7 bits (108), Expect = 3e-07
 Identities = 17/82 (20%), Positives = 43/82 (52%), Gaps = 8/82 (9%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +++  ++ + T++ ++  F  FG +  C + + S+  R +G+GF+ ++  ++ NE +   
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 95  NLFDLGGQYLRVGRAITPPNAL 116
           ++ D        G+ I P  A+
Sbjct: 61  HILD--------GKIIDPKRAI 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 = 76

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

 Score = 45.3 bits (108), Expect = 3e-07
 Identities = 13/58 (22%), Positives = 30/58 (51%)

Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
          +I+V  +    T++ ++  F  FG I+   +       + +GYGF+ ++ K+++  A 
Sbjct: 2  KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERAC 59

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

 Score = 48.6 bits (116), Expect = 4e-07
 Identities = 27/93 (29%), Positives = 45/93 (48%), Gaps = 12/93 (12%)

Query: 24  EITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPI---KYCKLQQGSSPHRHKGYGFIE 80
           E     K  N +YV ++ P + E+ ++ +F  FG I      K   G    R +G+ F+ 
Sbjct: 171 EAAPLKKFTN-LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSG----RSRGFAFVN 225

Query: 81  YETKQASNEAISSMNLFDLG----GQYLRVGRA 109
           +E  + + +A+  MN   +G    G+ L VGRA
Sbjct: 226 FEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRA 258

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

 Score = 45.1 bits (107), Expect = 4e-07
 Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 3/72 (4%)

Query: 36  YVASIHPDLTEEDIKSVFEAFGPIKYCKLQ-QGSSPHRHKGYGFIEYETKQASNEAISSM 94
           Y+ ++  D+TEEDIK  F     +   +L  +   P R +G+G+ E+E + +  +A+ S+
Sbjct: 5   YLGNLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQAL-SL 62

Query: 95  NLFDLGGQYLRV 106
           N   L  + +RV
Sbjct: 63  NDESLKNRRIRV 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|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 45.2 bits (108), Expect = 5e-07
 Identities = 17/71 (23%), Positives = 37/71 (52%)

Query: 36  YVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMN 95
           YV  +HPD+TE  +  +F   GP+   ++ +     R  GY ++ ++    +  A+ ++N
Sbjct: 3   YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

Query: 96  LFDLGGQYLRV 106
              + G+ +R+
Sbjct: 63  FDVIKGKPIRI 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|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 44.8 bits (106), Expect = 5e-07
 Identities = 18/72 (25%), Positives = 37/72 (51%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V ++   +T+ED+   F    PIK+  +         +GYGF+ +   + + EA++ +
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 95  NLFDLGGQYLRV 106
               L G+ LR+
Sbjct: 62  KNKKLHGRILRL 73

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|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 45.0 bits (107), Expect = 6e-07
 Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 7/63 (11%)

Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKG--YGFIEYETKQASNEAIS 92
          IYV  I  D T  +++  F+ FG I+   L       R  G  YGF+ Y     +  AI 
Sbjct: 5  IYVGKIPIDTTRSELRQRFQPFGEIEEITLH-----FRDDGDNYGFVTYRYACDAFRAIE 59

Query: 93 SMN 95
            N
Sbjct: 60 HGN 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|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 44.5 bits (106), Expect = 7e-07
 Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKL-----QQGSSPHRHKGYGFIEYETKQASNE 89
           ++V +++   TEE +K  FE  G ++   +      +G       GYGF+E+++K+A+ +
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 90  AISSMNLFDLGG 101
           A+  +    L G
Sbjct: 63  ALKRLQGTVLDG 74

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

 Score = 44.1 bits (105), Expect = 8e-07
 Identities = 20/72 (27%), Positives = 43/72 (59%), Gaps = 9/72 (12%)

Query: 34  RIYVASIHPD-LTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           R++V +++ D +++ED++ +F  +G I    L        HKGYGF++++ ++ +  A++
Sbjct: 2   RVFVGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVA 53

Query: 93  SMNLFDLGGQYL 104
             N  ++ GQ L
Sbjct: 54  GENGREIAGQKL 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|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 44.2 bits (105), Expect = 8e-07
 Identities = 18/75 (24%), Positives = 40/75 (53%), Gaps = 4/75 (5%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQASNEAI 91
           IYV ++   L E+D++ +F  FG ++  ++   Q       + G+ F+ ++   ++  A+
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 92  SSMNLFDLGGQYLRV 106
             +N  +LGG+ + 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|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 44.2 bits (105), Expect = 1e-06
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 2/72 (2%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           I+V  + PD+T+E++   F   G I    L + ++      + FI++E +QA+  A+ S 
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTN--AFAFIKFEREQAAARAVESE 63

Query: 95  NLFDLGGQYLRV 106
           N   L  + + 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|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 44.3 bits (104), Expect = 1e-06
 Identities = 21/66 (31%), Positives = 40/66 (60%)

Query: 44  LTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQY 103
           +T+E++KS+F + G I+ CKL +     +  GYGF+ Y   + + +AI+++N   L  + 
Sbjct: 16  MTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKT 75

Query: 104 LRVGRA 109
           ++V  A
Sbjct: 76  IKVSYA 81

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|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 44.0 bits (104), Expect = 1e-06
 Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 7/75 (9%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ--QGSSPHRHKGYGFIEYETKQASNEAI 91
           RIYV ++  D+ E+D++ +F  +G I+  +L+  +G  P     + F+ +E  + + +A+
Sbjct: 1   RIYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVP-----FAFVRFEDPRDAEDAV 55

Query: 92  SSMNLFDLGGQYLRV 106
              N +D G   LRV
Sbjct: 56  FGRNGYDFGQCRLRV 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|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 43.8 bits (104), Expect = 1e-06
 Identities = 17/73 (23%), Positives = 40/73 (54%), Gaps = 8/73 (10%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           +++V ++    T E+++++FE +G +  C           K YGF+  E ++ + +AI +
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVTECD--------VVKNYGFVHMEEEEDAEDAIKA 52

Query: 94  MNLFDLGGQYLRV 106
           +N ++  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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 44.0 bits (103), Expect = 1e-06
 Identities = 21/67 (31%), Positives = 40/67 (59%)

Query: 43  DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQ 102
           ++T+E+ KS+F + G I+ CKL +     +  GYGF+ Y     +++AI+++N   L  +
Sbjct: 14  NMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQTK 73

Query: 103 YLRVGRA 109
            ++V  A
Sbjct: 74  TIKVSYA 80

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|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 43.6 bits (103), Expect = 2e-06
 Identities = 19/83 (22%), Positives = 49/83 (59%), Gaps = 7/83 (8%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL--QQGSSPHRHKGYGFIEYETKQASNEA 90
           ++++V+ +   +T+E+++ +F+  G +K  +L   +   P   KG  ++EYE + ++++A
Sbjct: 3   HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKP---KGLAYVEYENESSASQA 59

Query: 91  ISSMNLFDLGGQYLRVGRAITPP 113
           +  M+  ++  + + V  AI+ P
Sbjct: 60  VLKMDGTEIKEKTISV--AISNP 80

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|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 = 43.4 bits (103), Expect = 2e-06
 Identities = 19/72 (26%), Positives = 42/72 (58%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +++  +  + T++D+  +F  FG +   K+    +  + K +GF+ Y+  +++  AI +M
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 95  NLFDLGGQYLRV 106
           N F +GG+ L+V
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|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 45.0 bits (106), Expect = 2e-06
 Identities = 21/94 (22%), Positives = 45/94 (47%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++++  +     +  ++  F  FG +   K+       R +G+GF+ +  + A+  AIS 
Sbjct: 36  KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95

Query: 94  MNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTS 127
           M+  +L G+++RV  A   P+A  +  G    + 
Sbjct: 96  MDGKELNGRHIRVNPANDRPSAPRAYGGGGGYSG 129

Length = 144

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

 Score = 43.4 bits (102), Expect = 2e-06
 Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 6/73 (8%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           R++V ++  D+TEED K +FE +G      +      +R +G+GFI  E++  +  A + 
Sbjct: 3   RLFVGNLPTDITEEDFKKLFEKYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 56

Query: 94  MNLFDLGGQYLRV 106
           ++   L  + LR+
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|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 43.4 bits (103), Expect = 2e-06
 Identities = 17/66 (25%), Positives = 36/66 (54%), Gaps = 4/66 (6%)

Query: 43  DLTEEDIKSVFEAFGPIK--YCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLG 100
             T +D++ VFE +G +   Y    + +     +G+ F+ +  K+ + +A+ +M+  +L 
Sbjct: 9   RTTPDDLRRVFEKYGEVGDVYIPRDRYT--RESRGFAFVRFYDKRDAEDAMDAMDGKELD 66

Query: 101 GQYLRV 106
           G+ LRV
Sbjct: 67  GRELRV 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|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 43.1 bits (101), Expect = 2e-06
 Identities = 17/51 (33%), Positives = 31/51 (60%)

Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETK 84
          +I+V  +  + T ED+K  FE FG +    L    + +RH+G+GF+ +E++
Sbjct: 1  KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE 51

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

 Score = 43.2 bits (102), Expect = 2e-06
 Identities = 14/71 (19%), Positives = 37/71 (52%), Gaps = 6/71 (8%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V ++   +TEE+++  FE +G ++   +++     +   Y F+++     ++ A  +M
Sbjct: 5   LFVGNLEITITEEELRRAFERYGVVEDVDIKR-PPRGQGNAYAFVKFLNLDMAHRAKVAM 63

Query: 95  NLFDLGGQYLR 105
           +     GQY+ 
Sbjct: 64  S-----GQYIG 69

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

 Score = 45.6 bits (108), Expect = 3e-06
 Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 7/79 (8%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQ---GSSPHRHKGYGFIEYETKQASNEAI 91
           I+V ++   +  + +   F  FG I  CK+     G S    +GYGF+ +E ++++  AI
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKS----RGYGFVHFEKEESAKAAI 146

Query: 92  SSMNLFDLGGQYLRVGRAI 110
             +N   L  + + VGR I
Sbjct: 147 QKVNGMLLNDKEVYVGRFI 165

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

 Score = 42.9 bits (102), Expect = 3e-06
 Identities = 16/72 (22%), Positives = 35/72 (48%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +Y+  +     E +++  F  FG +   +L +     + KGY F+E+E+ + +     +M
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 95  NLFDLGGQYLRV 106
           N + L  + L+ 
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|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 42.7 bits (101), Expect = 3e-06
 Identities = 19/76 (25%), Positives = 40/76 (52%), Gaps = 8/76 (10%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           R+Y+  +     E D++  F+ +G I+   L+ G        +GF+E+E  + +++A+  
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRIREINLKNG--------FGFVEFEDPRDADDAVYE 52

Query: 94  MNLFDLGGQYLRVGRA 109
           +N  +L G+ + V  A
Sbjct: 53  LNGKELCGERVIVEHA 68

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

>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 42.6 bits (101), Expect = 3e-06
 Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 7/73 (9%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           R+ V+++HP +TE+DI  +F A G +K  +L          G   + Y  K  +  AI  
Sbjct: 2   RLVVSNLHPSVTEDDIVELFSAIGALKRARLV-------RPGVAEVVYVRKDDALTAIDK 54

Query: 94  MNLFDLGGQYLRV 106
            N  +L GQ ++ 
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|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 42.6 bits (101), Expect = 3e-06
 Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 8/72 (11%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV ++    TEE ++ +F  +G ++  K          K Y F+ +E +  + +A+  M
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKI--------KDYAFVHFEERDDAVKAMEEM 55

Query: 95  NLFDLGGQYLRV 106
           N  +L G  + 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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 45.7 bits (108), Expect = 3e-06
 Identities = 21/66 (31%), Positives = 40/66 (60%)

Query: 44  LTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQY 103
           +T+E+I+S+F + G I+ CKL +     +  GYGF+ Y   + + +A++S+N   L  + 
Sbjct: 15  MTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKT 74

Query: 104 LRVGRA 109
           ++V  A
Sbjct: 75  IKVSYA 80

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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 42.9 bits (101), Expect = 3e-06
 Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 7/81 (8%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQASNE 89
           NRI+V  I     E D++  F  +G +K  K+   + G S    KGYGF+ +ET++ + +
Sbjct: 3   NRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVS----KGYGFVTFETQEDAQK 58

Query: 90  AISSMNLFDLGGQYLRVGRAI 110
            +   N      + L +G+AI
Sbjct: 59  ILQEANRLCFRDKKLNIGQAI 79

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

 Score = 42.4 bits (100), Expect = 3e-06
 Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 4/75 (5%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            +Y           D+K +FE  GP++  K+   S     + + FI +E  +A+  AI +
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVR--KVTMLSR--TVQPHAFITFENLEAAQLAIET 56

Query: 94  MNLFDLGGQYLRVGR 108
           +N   + G  ++V R
Sbjct: 57  LNGASVDGNCIKVQR 71

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|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 42.8 bits (101), Expect = 4e-06
 Identities = 17/63 (26%), Positives = 39/63 (61%), Gaps = 1/63 (1%)

Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL-QQGSSPHRHKGYGFIEYETKQASNEAI 91
          ++I V +I  + T ++++ +F  FG +K  +L ++ +    H+G+GF+++ TKQ +  A 
Sbjct: 1  SKILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAF 60

Query: 92 SSM 94
           ++
Sbjct: 61 KAL 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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 42.4 bits (100), Expect = 4e-06
 Identities = 15/50 (30%), Positives = 29/50 (58%), Gaps = 1/50 (2%)

Query: 32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY 81
            R++V  I    TEED++  F+ FG I+Y  + +  +    KG+G++++
Sbjct: 1  LTRLFVV-IPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKF 49

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

 Score = 42.6 bits (100), Expect = 4e-06
 Identities = 21/70 (30%), Positives = 36/70 (51%)

Query: 37  VASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNL 96
           +A++ P  T++  + +   FG ++ C L    +    KGYGF+EY  K ++  A S +  
Sbjct: 4   IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLG 63

Query: 97  FDLGGQYLRV 106
             LG + L V
Sbjct: 64  KQLGSRTLYV 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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 42.4 bits (99), Expect = 5e-06
 Identities = 20/67 (29%), Positives = 40/67 (59%)

Query: 43  DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQ 102
           ++T+E+ +S+F + G I+ CKL +     +  GYGF+ Y   + + +AI+++N   L  +
Sbjct: 13  NMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTK 72

Query: 103 YLRVGRA 109
            ++V  A
Sbjct: 73  TIKVSYA 79

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|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 42.3 bits (99), Expect = 6e-06
 Identities = 22/73 (30%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V  I  DL E+++  +FE  GPI   +L       +++GY FI +  K+A+ EA+   
Sbjct: 4   VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKLC 63

Query: 95  NLFDL-GGQYLRV 106
           + +++  G++L V
Sbjct: 64  DNYEIRPGKHLGV 76

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|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 = 41.9 bits (99), Expect = 6e-06
 Identities = 21/73 (28%), Positives = 38/73 (52%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           R++V ++    TEE+++ +FEAFG I    L       R KG+ F+ +   + + +A S 
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 94  MNLFDLGGQYLRV 106
           ++     G+ L V
Sbjct: 61  LDGSIFQGRLLHV 73

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

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

 Score = 42.1 bits (100), Expect = 6e-06
 Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 8/76 (10%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHK----GYGFIEYETKQASNEA 90
           +YV ++    TEE I  +F   G IK  ++  G    R      G+ F+EY T++ +  A
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIK--RIIMGL--DRFTKTPCGFCFVEYYTREDAENA 56

Query: 91  ISSMNLFDLGGQYLRV 106
           +  +N   L  + +RV
Sbjct: 57  VKYLNGTKLDDRIIRV 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|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 41.7 bits (98), Expect = 8e-06
 Identities = 17/65 (26%), Positives = 34/65 (52%), Gaps = 7/65 (10%)

Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQASNEA 90
          +++V  +     E D++ +F  FG I+ C +   Q G S    +G  F+ + ++Q +  A
Sbjct: 3  KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQS----RGCAFVTFASRQCALNA 58

Query: 91 ISSMN 95
          I +M+
Sbjct: 59 IKAMH 63

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

 Score = 41.6 bits (98), Expect = 8e-06
 Identities = 20/78 (25%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 32  YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
             +I+V  + P++TE D++  F  FG +    +       R +G+GFI +E++ +  + +
Sbjct: 2   TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSV-DQV 60

Query: 92  SSMNLFDLGGQYLRVGRA 109
            + +  D+ G+ + V RA
Sbjct: 61  VNEHFHDINGKKVEVKRA 78

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|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 = 41.3 bits (97), Expect = 9e-06
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 9/73 (12%)

Query: 35  IYVASIHPDLT-EEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++V    P  T EEDI+ +FE FGP+  C ++        K + F+E+E  + + +A+ +
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFGPLVRCDIR--------KTFAFVEFEDSEDATKALEA 53

Query: 94  MNLFDLGGQYLRV 106
           ++   + G  L V
Sbjct: 54  LHGSRIDGSVLTV 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|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 41.8 bits (99), Expect = 9e-06
 Identities = 21/76 (27%), Positives = 37/76 (48%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            I V ++  D  E+D++ +F  FGPI    L +     + +G+ F+ + T++ +  AI  
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 94  MNLFDLGGQYLRVGRA 109
           +N F      L V  A
Sbjct: 61  LNGFGYDNLILSVEWA 76

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|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 41.6 bits (98), Expect = 9e-06
 Identities = 12/72 (16%), Positives = 36/72 (50%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV ++      +D++ +F  +GPI    +       R +G+ ++++E  + + +A+  +
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 95  NLFDLGGQYLRV 106
           +     G+ + +
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|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 = 41.6 bits (98), Expect = 1e-05
 Identities = 20/78 (25%), Positives = 41/78 (52%), Gaps = 6/78 (7%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +++  +   +TEED+K++FE +G I+   +     P R  G  ++  ET+Q ++ A+  +
Sbjct: 5   LWIGHLSKKVTEEDLKNLFEEYGEIQSIDM----IPPR--GCAYVCMETRQDAHRALQKL 58

Query: 95  NLFDLGGQYLRVGRAITP 112
               L G+ ++V  A   
Sbjct: 59  RNVKLAGKKIKVAWAPNK 76

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|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 41.6 bits (97), Expect = 1e-05
 Identities = 18/76 (23%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           +I+V  +  +   ED+K  FE FG ++   L    + +RH+G+GF+ +E +    E +  
Sbjct: 5   KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVV-EKVCE 63

Query: 94  MNLFDLGGQYLRVGRA 109
           ++  ++  + +   +A
Sbjct: 64  IHFHEINNKMVECKKA 79

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|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 41.5 bits (97), Expect = 1e-05
 Identities = 21/61 (34%), Positives = 34/61 (55%)

Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
          I+V  I  DL E+++  +FE  GPI   +L        ++GY F+ + TK+A+ EA+   
Sbjct: 4  IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKLY 63

Query: 95 N 95
          N
Sbjct: 64 N 64

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

 Score = 41.5 bits (98), Expect = 1e-05
 Identities = 19/76 (25%), Positives = 40/76 (52%), Gaps = 3/76 (3%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPH---RHKGYGFIEYETKQASNEAI 91
           +YV +++P +TEE +   F  FGP+   K+    +     R++  GF+ +  +  +  A+
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 92  SSMNLFDLGGQYLRVG 107
             ++  D+ G  L++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|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 41.6 bits (97), Expect = 1e-05
 Identities = 21/72 (29%), Positives = 40/72 (55%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           I+V ++ PD  E  +  +F  FG +   K+ +  + ++ KG+GF+       +  AI+S+
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 95  NLFDLGGQYLRV 106
           N + LG + L+V
Sbjct: 66  NGYRLGDRVLQV 77

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

 Score = 41.5 bits (98), Expect = 1e-05
 Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 4/74 (5%)

Query: 35  IYVASIHPDLTEEDI-KSVFEAFGPIKYCKLQQG-SSPHRHKGYGFIEYETKQASNEAIS 92
           ++V  +     +  I + +F   G   +C+L    +   R  G+ F+EY T + + EA  
Sbjct: 5   LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPR--GFAFVEYATAEDAEEAQQ 62

Query: 93  SMNLFDLGGQYLRV 106
           ++N   L G  +RV
Sbjct: 63  ALNGHSLQGSPIRV 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|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 41.3 bits (96), Expect = 1e-05
 Identities = 24/81 (29%), Positives = 42/81 (51%), Gaps = 8/81 (9%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQASNEAI 91
           +YV ++  D+TE  I  +F   GP K CK+      + P     Y F+E+   + +  A+
Sbjct: 2   LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-----YCFVEFYEHRDAAAAL 56

Query: 92  SSMNLFDLGGQYLRVGRAITP 112
           ++MN   + G+ ++V  A TP
Sbjct: 57  AAMNGRKILGKEVKVNWATTP 77

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 40.2 bits (95), Expect = 1e-05
 Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 5/58 (8%)

Query: 49  IKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV 106
           +  +F  FG ++  KL       +  G+ F+E+ T++A+ +A+  +N    GG+ LRV
Sbjct: 1   LYKLFSPFGNVEKIKLL-----KKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRV 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|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 or PIP7S) and similar proteins

 Score = 40.8 bits (96), Expect = 2e-05
 Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 6/65 (9%)

Query: 37  VASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNL 96
           + SI P +T EDIK+VF  FG +KY    +G+        G+I ++T +A+ +A  +   
Sbjct: 6   ITSIGPGVTREDIKAVFAQFGEVKYVDFTEGAD------TGYIRFKTPEAAQKAREAFVE 59

Query: 97  FDLGG 101
              G 
Sbjct: 60  KGEGL 64

This subfamily corresponds to the RRM2 of La and LARP7. La is 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. LARP7 is an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP), 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. LARP7 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. Both La and LARP7 contain an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 75

>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 40.7 bits (95), Expect = 2e-05
 Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 8/76 (10%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           R+Y+  +   + E+DI+  F  +G +    L+ G        YGF+E+E  + +++A+  
Sbjct: 1   RVYIGRLSYHVREKDIQRFFGGYGKLLEIDLKNG--------YGFVEFEDSRDADDAVYE 52

Query: 94  MNLFDLGGQYLRVGRA 109
           +N  DL G+ + V  A
Sbjct: 53  LNGKDLCGERVIVEHA 68

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|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 = 40.7 bits (96), Expect = 2e-05
 Identities = 18/65 (27%), Positives = 38/65 (58%), Gaps = 1/65 (1%)

Query: 45  TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYL 104
           T+++++ +F  FG +K  +L +      H+G+ F+E+ TKQ +  A+ ++    L G++L
Sbjct: 13  TKKELRELFSPFGQVKSVRLPKKFD-GSHRGFAFVEFVTKQEAQNAMEALKSTHLYGRHL 71

Query: 105 RVGRA 109
            +  A
Sbjct: 72  VLEYA 76

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

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

 Score = 41.2 bits (96), Expect = 2e-05
 Identities = 21/72 (29%), Positives = 40/72 (55%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           I+V ++ PD  E  +  +F  FG +   K+ +  + ++ KG+GF+       +  AI+S+
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 95  NLFDLGGQYLRV 106
           N + LG + L+V
Sbjct: 66  NGYRLGDRVLQV 77

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

 Score = 39.9 bits (94), Expect = 3e-05
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 8/75 (10%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V  + P  +  +++  F+ FG I+             + Y +IEYE+ +A+  A  ++
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYD------PGRNYAYIEYESIEAAQAAKEAL 54

Query: 95  NLFDLG--GQYLRVG 107
             F LG  G+ LRV 
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|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 39.6 bits (92), Expect = 4e-05
 Identities = 18/60 (30%), Positives = 33/60 (55%)

Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
          +++V  + PD TEE IK  F AFG I+  +L   +  +  +G+ F+ Y  ++   + + S
Sbjct: 1  KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60

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

 Score = 39.6 bits (93), Expect = 4e-05
 Identities = 16/73 (21%), Positives = 35/73 (47%), Gaps = 7/73 (9%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS-S 93
           +YV  +   +TE+D++  F  FG I+   +         +   F+ + T++A+ +A    
Sbjct: 4   LYVGGLGERVTEKDLRDHFYQFGEIRSITV------VPRQQCAFVTFTTREAAEKAAERL 57

Query: 94  MNLFDLGGQYLRV 106
            N   + G+ L++
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|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 39.6 bits (93), Expect = 5e-05
 Identities = 13/58 (22%), Positives = 35/58 (60%), Gaps = 1/58 (1%)

Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
          ++V+++   + E++++ +F   G I   +L + +   + KGY ++E+E +++  EA+ 
Sbjct: 2  VFVSNLDYSVPEDELRKLFSKCGEITDVRLVK-NYKGKSKGYAYVEFENEESVQEALK 58

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|241067 cd12623, RRM_PPARGC1A, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1alpha, or PPARGC-1-alpha) and similar proteins

 Score = 39.9 bits (93), Expect = 5e-05
 Identities = 20/49 (40%), Positives = 25/49 (51%), Gaps = 7/49 (14%)

Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKG--YGFIEY 81
          IYV  I PD T  +++  FE FG I+ C +       R  G  YGFI Y
Sbjct: 5  IYVGKIRPDTTRTELRDRFEVFGEIEECTVNL-----RDDGDSYGFITY 48

This subgroup corresponds to the RRM of PGC-1alpha, also termed PPARGC-1-alpha, or ligand effect modulator 6, a member of a family of transcription coactivators that plays a central role in the regulation of cellular energy metabolism. As an inducible transcription coactivator, PGC-1alpha can interact with a broad range of transcription factors involved in a wide variety of biological responses, such as adaptive thermogenesis, skeletal muscle fiber type switching, glucose/fatty acid metabolism, and heart development. PGC-1alpha stimulates mitochondrial biogenesis and promotes oxidative metabolism. It participates in the regulation of both carbohydrate and lipid metabolism and plays a role in disorders such as obesity, diabetes, and cardiomyopathy. PGC-1alpha is a multi-domain protein containing an N-terminal activation domain region, a central region involved in the interaction with at least a nuclear receptor, and a C-terminal domain region. The N-terminal domain region consists of three leucine-rich motifs (L1, NR box 2 and 3), among which the two last are required for interaction with nuclear receptors, potential nuclear localization signals (NLS), and a proline-rich region overlapping a putative repression domain. The C-terminus of PGC-1alpha is composed of two arginine/serine-rich regions (SR domains), a putative dimerization domain, and an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). PGC-1alpha could interact favorably with single-stranded RNA. . Length = 91

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

 Score = 39.5 bits (92), Expect = 5e-05
 Identities = 20/73 (27%), Positives = 41/73 (56%), Gaps = 6/73 (8%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           R++V ++  D+TE++ K +F  +G      + +G      KG+GFI+ E++  +  A + 
Sbjct: 3   RLFVGNLPADITEDEFKKLFAKYGEPGEVFINKG------KGFGFIKLESRALAEIAKAE 56

Query: 94  MNLFDLGGQYLRV 106
           ++   + G+ LRV
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|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 39.5 bits (93), Expect = 5e-05
 Identities = 11/59 (18%), Positives = 31/59 (52%)

Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
          +++  +  D TEE ++  F  +G +  C + +     R +G+GF+ +    + ++ +++
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|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 39.6 bits (92), Expect = 6e-05
 Identities = 15/53 (28%), Positives = 30/53 (56%)

Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQA 86
          +I+V  ++P+ TEE I+  F  FG I+  +L      ++ +G+ FI ++ +  
Sbjct: 6  KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDP 58

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

 Score = 39.6 bits (93), Expect = 6e-05
 Identities = 13/61 (21%), Positives = 35/61 (57%)

Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
          +YV+ +   +T+++++++F  +G I   ++   +     +G GFI ++ +  +  AI ++
Sbjct: 3  LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 95 N 95
          N
Sbjct: 63 N 63

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

 Score = 39.7 bits (92), Expect = 6e-05
 Identities = 17/67 (25%), Positives = 38/67 (56%)

Query: 43  DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQ 102
           ++T+++++S+F + G ++  KL +        GYGF+ Y   + +  AI+++N   L  +
Sbjct: 12  NMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLNGLRLQSK 71

Query: 103 YLRVGRA 109
            ++V  A
Sbjct: 72  TIKVSYA 78

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|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 = 39.3 bits (92), Expect = 6e-05
 Identities = 17/65 (26%), Positives = 37/65 (56%), Gaps = 7/65 (10%)

Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQASNEA 90
          +++V  +    TE+D++ +FE FG I+ C +     G+S    KG  F+++ +   +  A
Sbjct: 3  KLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNS----KGCAFVKFSSHAEAQAA 58

Query: 91 ISSMN 95
          I++++
Sbjct: 59 INALH 63

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|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 39.4 bits (91), Expect = 7e-05
 Identities = 15/60 (25%), Positives = 38/60 (63%)

Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
          +Y+  +HP  T++D+  + + +G I   K     + ++ KGYGF+++++  A+ +A++++
Sbjct: 4  LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 63

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

 Score = 39.1 bits (92), Expect = 7e-05
 Identities = 18/72 (25%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V ++  D+ EE+++  FE  G ++  ++ +       KG+G++ ++TK +   A+  +
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KL 60

Query: 95  NLFDLGGQYLRV 106
           N   L G+ +RV
Sbjct: 61  NGIKLKGRKIRV 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|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 38.9 bits (91), Expect = 8e-05
 Identities = 13/48 (27%), Positives = 26/48 (54%)

Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY 81
          R+++ ++    TEED++ +F  +GP+    L       + KG+ F+ Y
Sbjct: 4  RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTY 51

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

 Score = 38.8 bits (91), Expect = 8e-05
 Identities = 10/49 (20%), Positives = 28/49 (57%)

Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYE 82
          +++V  +  D+TEED++  F  +G ++  ++       + +G+ F+ ++
Sbjct: 1  KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFD 49

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|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 39.9 bits (93), Expect = 8e-05
 Identities = 16/57 (28%), Positives = 28/57 (49%)

Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
          ++V ++  D TEE +   F  FG ++Y       S  R KG GF+ ++ +   N  +
Sbjct: 4  LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

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|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 38.8 bits (90), Expect = 9e-05
 Identities = 16/71 (22%), Positives = 41/71 (57%), Gaps = 13/71 (18%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           R+++  ++P   E+D++  F+ +G I+   L+        +G+GF+E++  + +++A+  
Sbjct: 1   RVFIGRLNPAAREKDVERFFKGYGRIRDIDLK--------RGFGFVEFDDPRDADDAV-- 50

Query: 94  MNLFDLGGQYL 104
              ++L G+ L
Sbjct: 51  ---YELDGKEL 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|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 38.6 bits (90), Expect = 9e-05
 Identities = 15/72 (20%), Positives = 43/72 (59%), Gaps = 5/72 (6%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           + V ++ P ++ +D+  +F A+G IK  +     +P++ + + FIE+   +++  A+ ++
Sbjct: 4   LVVFNLDPSVSNDDLHQIFGAYGEIKEIR----ETPNK-RHHKFIEFYDVRSAEAALKAL 58

Query: 95  NLFDLGGQYLRV 106
           N  ++ G+ +++
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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 39.3 bits (91), Expect = 9e-05
 Identities = 20/72 (27%), Positives = 40/72 (55%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           I+V ++ P+  E  +  +F  FG +   K+ +  + ++ KG+GF+       +  AI+S+
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 95  NLFDLGGQYLRV 106
           N + LG + L+V
Sbjct: 64  NGYRLGDRVLQV 75

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

 Score = 38.7 bits (90), Expect = 9e-05
 Identities = 18/66 (27%), Positives = 36/66 (54%), Gaps = 11/66 (16%)

Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKL-----QQGSSPHRHKGYGFIEYETKQASNE 89
          +YV ++ P +TE+ +K +F+  GP++  K+      +G +      YGF+EY     +  
Sbjct: 1  LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVN------YGFVEYHQSHDAEI 54

Query: 90 AISSMN 95
          A+ ++N
Sbjct: 55 ALQTLN 60

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|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 38.7 bits (90), Expect = 1e-04
 Identities = 19/62 (30%), Positives = 37/62 (59%), Gaps = 5/62 (8%)

Query: 45  TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYL 104
           +E+ ++ VFE    I+  +   G    R KGY F+E+E+ + + EA++S N  ++ G+ +
Sbjct: 14  SEDSLQEVFEKATSIRIPQ-NNG----RPKGYAFVEFESAEDAKEALNSCNNTEIEGRSI 68

Query: 105 RV 106
           R+
Sbjct: 69  RL 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|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 38.8 bits (90), Expect = 1e-04
 Identities = 21/89 (23%), Positives = 43/89 (48%), Gaps = 18/89 (20%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           R+Y+  +     E D++  F+ +G I    L+ G        YGF+E++  + +++A+  
Sbjct: 1   RVYIGRLSYQARERDVERFFKGYGKILEVDLKNG--------YGFVEFDDLRDADDAV-- 50

Query: 94  MNLFDLGGQYLRVGRAITPPNALHSSKGP 122
              ++L G+ L   R I     +  ++GP
Sbjct: 51  ---YELNGKDLCGERVI-----VEHARGP 71

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

 Score = 38.6 bits (90), Expect = 1e-04
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 6/73 (8%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV +I P  T+ D+  +F+ FG I   + Q        +G+ F++ +T + +  AI  +
Sbjct: 3   VYVGNIPPYTTQADLIPLFQNFGYILEFRHQPD------RGFAFVKLDTHEQAAMAIVQL 56

Query: 95  NLFDLGGQYLRVG 107
             F + G+ LR G
Sbjct: 57  QGFPVHGRPLRCG 69

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

 Score = 38.5 bits (90), Expect = 1e-04
 Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 3/44 (6%)

Query: 43 DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFI---EYET 83
            TE+D+K  F  FG +   ++++     + KG+GF+   +YE 
Sbjct: 10 KTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYED 53

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

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 17/65 (26%), Positives = 38/65 (58%), Gaps = 4/65 (6%)

Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
          R+ V ++   + E+ ++ +FEAFG I   +L+  +   + + +GF+ Y+T++   EA  +
Sbjct: 2  RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKY-TKDGKFRKFGFVGYKTEE---EAQKA 57

Query: 94 MNLFD 98
          +  F+
Sbjct: 58 LKHFN 62

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|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 = 38.2 bits (89), Expect = 2e-04
 Identities = 17/61 (27%), Positives = 35/61 (57%)

Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
          +++V  I  +L E+D++ +FE FG I    + +      HKG  F+ Y  ++++ +A S+
Sbjct: 7  KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSA 66

Query: 94 M 94
          +
Sbjct: 67 L 67

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

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 11/60 (18%), Positives = 34/60 (56%)

Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
          ++++  +  + T++ +K+ F  +G I  C + +  +  R +G+GF+ + +    + A+++
Sbjct: 1  KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

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|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 17/75 (22%), Positives = 39/75 (52%), Gaps = 5/75 (6%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYG-FIEYETKQASNEAI 91
            +I +++I P +  ED+ S+   +G +K C+      P + +     + YE+ + + +A+
Sbjct: 1   RKIQISNIPPHVRWEDLDSLLSTYGTVKNCE----QVPTKSETATVNVTYESPEQAQQAV 56

Query: 92  SSMNLFDLGGQYLRV 106
           + +N  +  G  L+V
Sbjct: 57  NKLNGHEYEGSKLKV 71

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|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 37.7 bits (87), Expect = 2e-04
 Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 8/78 (10%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQASNEAI 91
           +YV ++  D+TE  I  +F   GP K CK+     G+ P     Y F+E+   + +  ++
Sbjct: 2   LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDP-----YCFVEFFEHRHAAASL 56

Query: 92  SSMNLFDLGGQYLRVGRA 109
           ++MN   + G+ ++V  A
Sbjct: 57  AAMNGRKIMGKEVKVNWA 74

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

 Score = 37.6 bits (88), Expect = 2e-04
 Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGP-IKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           I+V  + PD+T+  ++  F A  P ++  K+       R KGYGF+ +  +   + A++ 
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 94  MNLFDLGGQYLRVGRAI 110
           MN      + +RV  A 
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|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 37.9 bits (89), Expect = 2e-04
 Identities = 18/78 (23%), Positives = 38/78 (48%), Gaps = 12/78 (15%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAF--------GPIKYCKLQQGSSPHRHKGYGFIEYETK 84
            R+YV ++   +TEED+  +F  F               + +G    R KG  F+ + ++
Sbjct: 2   KRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEG----RMKGQAFVTFPSE 57

Query: 85  QASNEAISSMNLFDLGGQ 102
           + + +A++ +N + L G+
Sbjct: 58  EIATKALNLVNGYVLKGK 75

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|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 37.7 bits (87), Expect = 3e-04
 Identities = 18/72 (25%), Positives = 37/72 (51%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +++  +  + T+ D+   F  FG +   K+      +  K +GF+ Y+   ++  AI +M
Sbjct: 7   LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66

Query: 95  NLFDLGGQYLRV 106
           N F +G + L+V
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|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 37.7 bits (87), Expect = 3e-04
 Identities = 15/52 (28%), Positives = 31/52 (59%)

Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQ 85
          +I+V  + PD  EE I+  F AFG ++  +L   +  ++ +G+ FI ++ ++
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEE 52

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

 Score = 37.7 bits (88), Expect = 3e-04
 Identities = 16/73 (21%), Positives = 40/73 (54%), Gaps = 2/73 (2%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            ++V ++     ++D++  F+  G +   ++ Q     R KG+G +E+ T++ + +A+  
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKAL-E 58

Query: 94  MNLFDLGGQYLRV 106
            +  +L G+ +RV
Sbjct: 59  KSGEELLGREIRV 71

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|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 37.1 bits (86), Expect = 3e-04
 Identities = 17/73 (23%), Positives = 37/73 (50%), Gaps = 8/73 (10%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           +I+V ++    T ++++ +FE FG +  C           K Y F+  E ++ +  AI +
Sbjct: 2   KIFVGNVSATCTSDELRGLFEEFGRVVECDKV--------KDYAFVHMEREEEALAAIEA 53

Query: 94  MNLFDLGGQYLRV 106
           +N  ++ G+ + 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|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 37.9 bits (87), Expect = 3e-04
 Identities = 15/60 (25%), Positives = 38/60 (63%)

Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
          +Y+  + P+ T++D+  + + +G I   K     + ++ KGYGF+++++  A+ +A+S++
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|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 37.2 bits (87), Expect = 3e-04
 Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 2/73 (2%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V  I  DL E+++  +FE  GPI   +L    S   ++GY F+ Y  K+A+  A+  +
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGL-NRGYAFVTYTNKEAAQRAVKQL 62

Query: 95  NLFDL-GGQYLRV 106
           + +++  G+ L 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|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 37.3 bits (86), Expect = 3e-04
 Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V  I  D+ E+++  VFE+ G I   +L       +++GY F+ Y  K  +  A+  +
Sbjct: 4   VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFD-GKNRGYAFVMYTQKHEAKRAVREL 62

Query: 95  NLFDLGGQYLRVGR 108
           N ++     +R GR
Sbjct: 63  NNYE-----IRPGR 71

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|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 36.9 bits (86), Expect = 4e-04
 Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV  I    TE++I+S F   G I+   L       R +G  FI ++T++A+  A  ++
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRA-LAL 59

Query: 95  NLFDLGGQYLRV 106
           +  D+GG++L+V
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|241049 cd12605, RRM_RALYL, RNA recognition motif in vertebrate RNA-binding Raly-like protein (RALYL)

 Score = 36.9 bits (85), Expect = 4e-04
 Identities = 18/75 (24%), Positives = 43/75 (57%), Gaps = 9/75 (12%)

Query: 33  NRIYVASIHPDLTEE-DIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
           +R+++ +++  + ++ DI+++F  +G I  C +        HKGY F++Y +++ +  A+
Sbjct: 2   SRVFIGNLNTAIVKKADIEAIFAKYGKIVGCSV--------HKGYAFVQYISERHARAAV 53

Query: 92  SSMNLFDLGGQYLRV 106
           +  N   + GQ L +
Sbjct: 54  AGENARIIAGQPLDI 68

This subgroup corresponds to the RRM of RALYL, also termed heterogeneous nuclear ribonucleoprotein C-like 3, or hnRNP core protein C-like 3, a putative RNA-binding protein that shows high sequence homology with Raly, an RNA-binding protein playing a critical role in embryonic development. The biological role of RALYL remains unclear. Like Raly, RALYL contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. . Length = 69

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

 Score = 37.0 bits (86), Expect = 4e-04
 Identities = 11/58 (18%), Positives = 32/58 (55%)

Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
          ++V ++  + TE+++++ F   G I+  ++       + KG+ F+++E  + +  A+ 
Sbjct: 1  LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALK 58

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

 Score = 36.9 bits (86), Expect = 4e-04
 Identities = 14/67 (20%), Positives = 33/67 (49%), Gaps = 1/67 (1%)

Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           R++V      +T+E +  +F+    ++YC L++     + KG+ ++ Y    ++  A  
Sbjct: 1  QRLFVVV-SKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKE 59

Query: 93 SMNLFDL 99
           +N F+ 
Sbjct: 60 KLNGFEY 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|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 37.4 bits (86), Expect = 4e-04
 Identities = 19/72 (26%), Positives = 40/72 (55%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           I++ ++  D  E  +  +F  FG +   K+ +  + ++ KG+GF+     + +  AI+S+
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 95  NLFDLGGQYLRV 106
           N + LG + L+V
Sbjct: 64  NGYRLGDKILQV 75

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

 Score = 36.9 bits (86), Expect = 5e-04
 Identities = 23/72 (31%), Positives = 42/72 (58%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           I+V ++ PD  E  +  +F  FG +   K+ +  + ++ KGYGF+     + +  AI+S+
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 95  NLFDLGGQYLRV 106
           N + LGG+ L+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|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 37.0 bits (85), Expect = 5e-04
 Identities = 15/62 (24%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
          ++++  +     E DI+ +F  FG I+ C++ +G      +G  F+ + T+  +  AI +
Sbjct: 3  KLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKA 61

Query: 94 MN 95
          M+
Sbjct: 62 MH 63

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|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding protein Raly

 Score = 37.0 bits (85), Expect = 5e-04
 Identities = 19/81 (23%), Positives = 43/81 (53%), Gaps = 9/81 (11%)

Query: 33  NRIYVASIHPDLTEE-DIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
           +R+++ +++  + ++ D++++F  +G +  C +        HKGY F++Y  ++ +  A+
Sbjct: 2   SRVFIGNLNTAVVKKSDVETIFSKYGRVVGCSV--------HKGYAFVQYSNERHARGAV 53

Query: 92  SSMNLFDLGGQYLRVGRAITP 112
              N   L GQ L +  A  P
Sbjct: 54  IGENGRVLAGQTLDINMAGEP 74

This subgroup corresponds to the RRM of Raly, also termed autoantigen p542, or heterogeneous nuclear ribonucleoprotein C-like 2, or hnRNP core protein C-like 2, or hnRNP associated with lethal yellow protein homolog, an RNA-binding protein that may play a critical role in embryonic development. It is encoded by Raly, a ubiquitously expressed gene of unknown function. Raly shows a high degree of identity with the 5' sequences of p542 gene encoding autoantigen, which can cross-react with EBNA-1 of the Epstein Barr virus. Raly contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes a unique glycine/serine-rich stretch. . Length = 76

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

 Score = 36.9 bits (86), Expect = 5e-04
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 8/77 (10%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           N +YV      LTEE +K  F  FG I    ++      + K  GF+ +E  ++++ AI+
Sbjct: 5   NTLYVHGY--GLTEEILKKAFSPFGNIINISME------KEKNCGFVTFEKMESADRAIA 56

Query: 93  SMNLFDLGGQYLRVGRA 109
            +N   + G  L+V  A
Sbjct: 57  ELNGTTVQGVQLKVSLA 73

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

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

 Score = 36.5 bits (85), Expect = 6e-04
 Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 7/77 (9%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           I+V ++    T E+++  F++ G I    +       + KG+ +IE+  K +   A+   
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL--- 58

Query: 95  NLFDLGGQYLRVGRAIT 111
               L     R GR I 
Sbjct: 59  ---LLNESEFR-GRQIK 71

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

 Score = 38.8 bits (90), Expect = 6e-04
 Identities = 17/67 (25%), Positives = 36/67 (53%)

Query: 43  DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQ 102
           D+T+ ++ ++F   GPI  C++ +        GY F+++ ++  S  AI ++N   +  +
Sbjct: 118 DMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNK 177

Query: 103 YLRVGRA 109
            L+V  A
Sbjct: 178 RLKVSYA 184

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|241111 cd12667, RRM3_RAVER1, RNA recognition motif 3 in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 37.1 bits (86), Expect = 6e-04
 Identities = 14/66 (21%), Positives = 27/66 (40%), Gaps = 1/66 (1%)

Query: 41  HPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLG 100
                  D++  F       +C+L  G    + KG+  +EYE+ + +       +   L 
Sbjct: 12  PSLCDVGDLREAFSKIHAPTFCQLACGQD-GQLKGFAVLEYESAEMAEMVQQQADGLSLA 70

Query: 101 GQYLRV 106
           G ++RV
Sbjct: 71  GSHIRV 76

This subgroup corresponds to the RRM3 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 = 92

>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 = 6e-04
 Identities = 13/58 (22%), Positives = 32/58 (55%)

Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
          +++  +  D T++D+K  F  FG +  C L+      R +G+GF+ ++  ++ ++ + 
Sbjct: 1  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD 58

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

 Score = 36.6 bits (85), Expect = 7e-04
 Identities = 19/80 (23%), Positives = 41/80 (51%), Gaps = 8/80 (10%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQASNE 89
            R++V++I     + D++ +F  FGPI   ++   ++GS     KG+GF+ +     ++ 
Sbjct: 1   KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGS-----KGFGFVTFANSADADR 55

Query: 90  AISSMNLFDLGGQYLRVGRA 109
           A   ++   + G+ + V  A
Sbjct: 56  AREKLHGTVVEGRKIEVNNA 75

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

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 36.5 bits (84), Expect = 8e-04
 Identities = 18/82 (21%), Positives = 39/82 (47%), Gaps = 7/82 (8%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           +++V  +  D +++D+K  F  FG +  C ++   +  R +G+GFI ++   +  + +  
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

Query: 94  MNLFDLGGQYLRVGRAITPPNA 115
                   ++   GR I P  A
Sbjct: 61  K-------EHRLDGRLIDPKKA 75

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|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 36.4 bits (84), Expect = 8e-04
 Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 7/81 (8%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V  +  D T++D+K  F  FG +  C ++      R +G+GF+ ++      +A S  
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFK------DAASVE 54

Query: 95  NLFDLGGQYLRVGRAITPPNA 115
            + D     L  GR I P  A
Sbjct: 55  KVLDQKEHKLD-GRVIDPKRA 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|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 36.2 bits (83), Expect = 8e-04
 Identities = 17/73 (23%), Positives = 37/73 (50%), Gaps = 8/73 (10%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           +++V +I    T +++++ FE +GP+  C +         K Y F+  E  + + EAI  
Sbjct: 2   KLHVGNISSSCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRG 53

Query: 94  MNLFDLGGQYLRV 106
           ++  +  G+ + V
Sbjct: 54  LDNTEFQGKRMHV 66

This subgroup corresponds to the RRM2 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|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 36.3 bits (83), Expect = 8e-04
 Identities = 15/60 (25%), Positives = 37/60 (61%)

Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
          +Y+  + P  T++D+  + + +G I   K     + ++ KGYGF+++++  A+ +A++S+
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|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 36.2 bits (84), Expect = 8e-04
 Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 8/77 (10%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            +Y+ ++  D+TE+D++  F     I   +L         KG+G +++  +++ + A+  
Sbjct: 1   TVYIGNLAWDITEDDVREFF-KGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALK- 58

Query: 94  MNLFDLGGQYLRVGRAI 110
                L G  L  GR I
Sbjct: 59  -----LDGTVLC-GRPI 69

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|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 36.0 bits (83), Expect = 9e-04
 Identities = 17/54 (31%), Positives = 29/54 (53%)

Query: 37 VASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEA 90
          V ++    T E+ + +  A+G I+ C L         KGYGF+EY  K ++++A
Sbjct: 4  VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKA 57

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

 Score = 36.1 bits (84), Expect = 9e-04
 Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 7/75 (9%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPI---KYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
           ++V ++   +TEE +  +F   GP+   K  K   G    + K + F+ ++ + +   AI
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNG----KPKSFAFVTFKHEVSVPYAI 59

Query: 92  SSMNLFDLGGQYLRV 106
             +N   L G+ LR+
Sbjct: 60  QLLNGIRLFGRELRI 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|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 36.1 bits (84), Expect = 9e-04
 Identities = 18/61 (29%), Positives = 38/61 (62%)

Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
          +Y+  + P+ T+ED++ + + FG I   K       ++ KGYGF+++++ +A+ +AI  +
Sbjct: 3  VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGL 62

Query: 95 N 95
          N
Sbjct: 63 N 63

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

 Score = 38.4 bits (89), Expect = 0.001
 Identities = 26/119 (21%), Positives = 50/119 (42%), Gaps = 10/119 (8%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV+ +   +T+ +++S+F  FG I   ++   +     KG GFI ++ +  ++ AI ++
Sbjct: 92  LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTL 151

Query: 95  NLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSH--MPTAAAVAAAAATAKIQAMDGGA 151
           N     G         T P  +  +  P+ S S   +    AV     T    +    A
Sbjct: 152 N-----GT---TPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTA 202

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

 Score = 38.0 bits (88), Expect = 0.001
 Identities = 22/72 (30%), Positives = 40/72 (55%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           I+V ++ PD  E  +  +F  FG ++  K+ +  + ++ KGYGF+       +  AI S+
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 95  NLFDLGGQYLRV 106
           N + LG + L+V
Sbjct: 332 NGYTLGNRVLQV 343

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

 Score = 36.2 bits (84), Expect = 0.001
 Identities = 13/64 (20%), Positives = 31/64 (48%), Gaps = 1/64 (1%)

Query: 32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
           +R+++      +TE+D++  F  FG I+   + +       KG  ++++    ++  A+
Sbjct: 3  NSRLFIV-CGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAM 61

Query: 92 SSMN 95
            MN
Sbjct: 62 EEMN 65

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

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 45  TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG 101
           TE D+K +F  FG +    + +     + KG+ F+++ +K  + +AI  +N   + G
Sbjct: 12  TEADLKKLFSPFGFVWEVTIPRKPDG-KKKGFAFVQFTSKADAEKAIKGVNGKKIKG 67

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|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 35.8 bits (82), Expect = 0.001
 Identities = 19/74 (25%), Positives = 43/74 (58%), Gaps = 2/74 (2%)

Query: 34  RIYVASIHPDLTEEDIKSVF-EAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           R+++++I  D+  + IK +  E  G + Y +L +  +  + +G G +E++ ++   +A+ 
Sbjct: 1   RVFISNIPYDMKWQAIKDLMREKVGEVTYVELFK-DAEGKSRGCGVVEFKDEEFVKKALE 59

Query: 93  SMNLFDLGGQYLRV 106
            MN +DL G+ L +
Sbjct: 60  VMNKYDLNGRPLNI 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|220013 pfam08777, RRM_3, RNA binding motif

 Score = 36.2 bits (84), Expect = 0.001
 Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 6/58 (10%)

Query: 42 PDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDL 99
             + EDIK  F   G +KY    +G         G++ ++T +A+ +A+       L
Sbjct: 11 KPTSREDIKEAFSQHGEVKYVDFLEGDKE------GYVRFKTPEAAKKALEKATEAKL 62

This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif. Length = 102

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

 Score = 35.8 bits (82), Expect = 0.001
 Identities = 13/60 (21%), Positives = 36/60 (60%)

Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
          ++++  +  + T+E ++S FE +G +  C + +  +  R +G+GF+ Y + +  + A+++
Sbjct: 4  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 63

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

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 17/72 (23%), Positives = 38/72 (52%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +++  +  +  ++D+  +F  FG +   K+      +  K +GF+ Y+   ++  AI +M
Sbjct: 10  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69

Query: 95  NLFDLGGQYLRV 106
           N F +G + L+V
Sbjct: 70  NGFQIGMKRLKV 81

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

 Score = 35.4 bits (82), Expect = 0.002
 Identities = 18/64 (28%), Positives = 35/64 (54%)

Query: 43  DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQ 102
           D  E+ I   F  +G I   +L       R KG+G++E+ +++A+  A+ ++   DL G+
Sbjct: 9   DADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDALGGTDLLGR 68

Query: 103 YLRV 106
            +R+
Sbjct: 69  PVRL 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|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 35.3 bits (81), Expect = 0.002
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYC--KLQQGSSPHRHKGYGFIEYETKQASNEAI 91
           +I+V ++  D T + +K  F   G + Y   K++ G S    KG G + +E+ + +  A 
Sbjct: 1   QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKS----KGCGVVRFESPEVAERAC 56

Query: 92  SSMNLFDLGGQYLRV 106
             MN + L G+ + V
Sbjct: 57  RMMNGYKLNGREIDV 71

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|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 35.3 bits (81), Expect = 0.002
 Identities = 14/61 (22%), Positives = 34/61 (55%)

Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
          +YV+ +   +T+++++ +F  +G I   ++ +       +G GFI ++ +  + EAI  +
Sbjct: 3  LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 95 N 95
          N
Sbjct: 63 N 63

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

 Score = 35.5 bits (81), Expect = 0.002
 Identities = 11/62 (17%), Positives = 35/62 (56%)

Query: 32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
          + ++++  +  + TEE +++ +E +G +  C + +  +  R +G+GF+ +      + A+
Sbjct: 2  FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAM 61

Query: 92 SS 93
          ++
Sbjct: 62 AA 63

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

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 8/65 (12%)

Query: 35 IYVASIHPDLTEEDIKSVFEAFG---PIKYCKLQQ-GSSPHRHKGYGFIEYETKQASNEA 90
          +++  + P + E  I S F   G    +K  + +Q G S     GYGF+E+ T +A+ +A
Sbjct: 2  LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSA----GYGFVEFATHEAAEQA 57

Query: 91 ISSMN 95
          + S+N
Sbjct: 58 LQSLN 62

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|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 34.9 bits (80), Expect = 0.002
 Identities = 18/73 (24%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           I++  +  DL E+++  + E  G I   ++    + + ++GY F+ +  KQ +  AI  +
Sbjct: 4   IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGN-NRGYAFVTFSNKQEAKNAIKQL 62

Query: 95  NLFDL-GGQYLRV 106
           N +++  G+ L 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|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 35.0 bits (80), Expect = 0.002
 Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 8/72 (11%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V ++   +TEE ++  F  FG ++  K        + K Y F+ +E + A+  A+  M
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVK--------KLKDYAFVHFEERDAAVRAMDEM 55

Query: 95  NLFDLGGQYLRV 106
           N  ++ 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|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 = 34.8 bits (80), Expect = 0.003
 Identities = 15/72 (20%), Positives = 39/72 (54%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +++  +  +  + ++  +F  FG +   K+    + ++ K +GF+ ++   ++  AI +M
Sbjct: 7   LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66

Query: 95  NLFDLGGQYLRV 106
           N F +G + L+V
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|241001 cd12557, RRM3_RBM15, RNA recognition motif 3 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 34.5 bits (79), Expect = 0.003
 Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 6/73 (8%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           R++V  + P +    +   F+ FG I+    ++G S      + +I+YE+  A+  A + 
Sbjct: 1   RLWVGGLGPWVPLAALAREFDRFGTIRTIDYRKGDS------WAYIQYESLDAAQAACTH 54

Query: 94  MNLFDLGGQYLRV 106
           M  F LGG   R+
Sbjct: 55  MRGFPLGGPDRRL 67

This subgroup corresponds to the RRM3 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor 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 contains three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralogue 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 = 73

>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 34.6 bits (80), Expect = 0.003
 Identities = 10/51 (19%), Positives = 27/51 (52%), Gaps = 5/51 (9%)

Query: 43 DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
          D +E++++ +F  +G +    +       + KG   +E+ +K+A+  A+ +
Sbjct: 15 DYSEDELRKIFSKYGDVSDVVVSS-----KKKGSAIVEFASKKAAEAAVEN 60

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

 Score = 34.5 bits (80), Expect = 0.003
 Identities = 16/69 (23%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++ V+++   ++++DIK +F  FG +K   +    S  R  G   + +E +  + +A+  
Sbjct: 2   KLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRS-GRSLGTADVVFERRADALKAMKQ 60

Query: 94  MNLFDLGGQ 102
            N   L G+
Sbjct: 61  YNGVPLDGR 69

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|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 34.9 bits (80), Expect = 0.003
 Identities = 19/65 (29%), Positives = 36/65 (55%), Gaps = 1/65 (1%)

Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
          ++V  I  D+ E+++  +FE  G I   +L    S   ++GY F+ Y TK+ +  AI  +
Sbjct: 4  VFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFS-GENRGYAFVMYTTKEEAQLAIRIL 62

Query: 95 NLFDL 99
          N +++
Sbjct: 63 NNYEI 67

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

 Score = 34.5 bits (80), Expect = 0.004
 Identities = 19/76 (25%), Positives = 41/76 (53%), Gaps = 4/76 (5%)

Query: 33  NRI-YVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
           NRI YV ++   ++ E++  +F  +G I+  +++ G++    +G  F+ YE    +  A 
Sbjct: 2   NRILYVRNLPFKISSEELYDLFGKYGAIR--QIRIGNTKET-RGTAFVVYEDIYDAKNAC 58

Query: 92  SSMNLFDLGGQYLRVG 107
             ++ F++  +YL V 
Sbjct: 59  DHLSGFNVANRYLVVL 74

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|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3)

 Score = 34.4 bits (79), Expect = 0.004
 Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           I+V+++  D+TEED+ +     G I   K+ +       K    +E+ T++ + EA++  
Sbjct: 10  IHVSNLPSDVTEEDVINHLAEHGVIVNVKVFES----NGKKQALVEFATEEQATEALACK 65

Query: 95  NLFDLGGQYLRV 106
           +   L G  +R+
Sbjct: 66  HASSLNGSTIRL 77

This subfamily corresponds to the RRM4 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

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

 Score = 34.5 bits (79), Expect = 0.004
 Identities = 15/78 (19%), Positives = 40/78 (51%), Gaps = 1/78 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           +++V  +  D+ E D+   F  FGP++  ++       + +G+GF+ ++   ++++A   
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAA-V 59

Query: 94  MNLFDLGGQYLRVGRAIT 111
           +    + G  + V +A+ 
Sbjct: 60  VKFHPINGHRVEVKKAVP 77

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|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 34.3 bits (79), Expect = 0.004
 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 5/76 (6%)

Query: 35  IYVASIHPDLTEEDIK-SVFEAFGP---IKYCKLQQGSSPHRHKGYGFIEYETKQASNEA 90
           I+V      L E+DI+ S+ E F     I    +         KG+ +IE+++     +A
Sbjct: 2   IFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61

Query: 91  ISSMNLFDLGGQYLRV 106
           +  ++  DLGG  L V
Sbjct: 62  L-ELDGSDLGGGNLVV 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|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 = 34.4 bits (80), Expect = 0.004
 Identities = 22/89 (24%), Positives = 40/89 (44%), Gaps = 24/89 (26%)

Query: 34  RIYVASIHPDLTEEDIKSVF----EAFG-------PIKYCKLQQGSSPHRHKGYGFIEYE 82
           R+YV ++ P +TEE++   F     A G       P+   ++         K + F+E+ 
Sbjct: 3   RLYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPE------KNFAFVEFR 56

Query: 83  TKQASNEAISSMNLFD---LGGQYLRVGR 108
           T +   EA +++   D     GQ L++ R
Sbjct: 57  TVE---EATAALA-LDGIIFKGQPLKIRR 81

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

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

 Score = 34.1 bits (79), Expect = 0.004
 Identities = 16/65 (24%), Positives = 36/65 (55%), Gaps = 7/65 (10%)

Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQASNEA 90
          RI V ++   +TE+ ++  FE+ G +   K+   + G S  R   +GF+ +++++ + +A
Sbjct: 2  RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKS--RR--FGFVGFKSEEDAQQA 57

Query: 91 ISSMN 95
          +   N
Sbjct: 58 VKYFN 62

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	173
KOG0124|consensus	544		99.93
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.93
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.85
KOG0148|consensus	321		99.82
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.79
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.78
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.76
KOG0121|consensus	153		99.76
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.76
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.74
KOG0122|consensus	270		99.74
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.72
KOG0149|consensus	247		99.7
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.7
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.7
KOG0125|consensus	376		99.69
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.69
KOG0113|consensus	335		99.68
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.67
PLN03120	260	nucleic acid binding protein; Provisional	99.65
KOG0107|consensus	195		99.64
KOG0148|consensus	321		99.64
PLN03213	759	repressor of silencing 3; Provisional	99.64
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.63
KOG0126|consensus	219		99.63
KOG4207|consensus	256		99.63
KOG0111|consensus	298		99.62
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.62
KOG0145|consensus	360		99.62
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.61
KOG0108|consensus	435		99.61
KOG0131|consensus	203		99.61
KOG0144|consensus	510		99.6
smart00362	72	RRM_2 RNA recognition motif.	99.6
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.58
KOG0130|consensus	170		99.57
KOG0114|consensus	124		99.57
KOG0117|consensus	506		99.56
smart00360	71	RRM RNA recognition motif.	99.56
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.56
KOG0144|consensus	510		99.55
KOG0131|consensus	203		99.55
PLN03121	243	nucleic acid binding protein; Provisional	99.55
KOG0146|consensus	371		99.54
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.54
KOG0117|consensus	506		99.54
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.53
KOG0124|consensus	544		99.51
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.51
KOG0127|consensus	678		99.5
KOG0145|consensus	360		99.48
KOG0105|consensus	241		99.47
KOG0147|consensus	549		99.47
KOG0123|consensus	369		99.44
smart00361	70	RRM_1 RNA recognition motif.	99.43
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.42
KOG0109|consensus	346		99.42
KOG4206|consensus	221		99.38
KOG0127|consensus	678		99.38
KOG0109|consensus	346		99.36
KOG0146|consensus	371		99.35
KOG0415|consensus	479		99.32
KOG4212|consensus	608		99.32
KOG4208|consensus	214		99.3
KOG0110|consensus	725		99.26
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.26
KOG4205|consensus	311		99.21
KOG0132|consensus	894		99.2
KOG4205|consensus	311		99.19
KOG4661|consensus	940		99.18
KOG0153|consensus	377		99.16
KOG4212|consensus	608		99.09
KOG0110|consensus	725		99.08
KOG0123|consensus	369		99.03
KOG0533|consensus	243		99.03
KOG0151|consensus	877		98.97
KOG0226|consensus	290		98.94
KOG0120|consensus	500		98.92
KOG0116|consensus	419		98.91
KOG4209|consensus	231		98.9
KOG1457|consensus	284		98.89
KOG1548|consensus	382		98.86
KOG4660|consensus	549		98.85
KOG0106|consensus	216		98.82
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.77
KOG4454|consensus	267		98.71
KOG0147|consensus	549		98.59
KOG1190|consensus	492		98.56
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.43
KOG4211|consensus	510		98.42
KOG4211|consensus	510		98.41
KOG1456|consensus	494		98.34
KOG1457|consensus	284		98.28
KOG4849|consensus	498		98.23
KOG4206|consensus	221		98.16
KOG4210|consensus	285		98.07
KOG1995|consensus	351		98.05
KOG0106|consensus	216		97.9
KOG3152|consensus	278		97.81
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.81
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.77
KOG1855|consensus	484		97.73
KOG2314|consensus	698		97.67
KOG0120|consensus	500		97.65
KOG4307|consensus	944		97.58
KOG1190|consensus	492		97.56
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.51
KOG0129|consensus	520		97.4
KOG1548|consensus	382		97.34
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.19
KOG0105|consensus	241		97.17
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.12
KOG1456|consensus	494		97.11
KOG0112|consensus	975		97.01
KOG1365|consensus	508		96.95
KOG0128|consensus	881		96.93
KOG0129|consensus	520		96.91
KOG1996|consensus	378		96.91
KOG0128|consensus	881		96.84
KOG2193|consensus	584		96.6
KOG0112|consensus	975		96.59
KOG2416|consensus	718		96.48
KOG2202|consensus	260		96.45
KOG1365|consensus	508		96.4
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	96.15
KOG4307|consensus	944		96.04
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.98
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.93
KOG2068|consensus	327		95.92
KOG0115|consensus	275		95.87
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.72
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.54
KOG4676|consensus	479		95.52
KOG2253|consensus	668		94.58
KOG4660|consensus	549		94.57
KOG4285|consensus	350		94.18
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	94.16
KOG2591|consensus	684		93.78
KOG4574|consensus	1007		93.63
KOG2135|consensus	526		93.23
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	92.91
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	92.14
KOG4210|consensus	285		91.19
KOG0804|consensus	493		90.26
COG0724	306	RNA-binding proteins (RRM domain) [General functio	89.85
KOG4454|consensus	267		86.7
KOG4410|consensus	396		85.78
smart00596	69	PRE_C2HC PRE_C2HC domain.	82.2
PF07530	68	PRE_C2HC: Associated with zinc fingers; InterPro:	81.4
KOG4676|consensus	479		81.32

>KOG0124|consensus

Probab=99.93  E-value=4.2e-26  Score=179.35  Aligned_cols=155  Identities=61%  Similarity=0.933  Sum_probs=145.3

Q ss_pred             CCCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEE
Q psy2141           1 MQHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIE   80 (173)
Q Consensus         1 ~l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~   80 (173)
                      ||+||.|+|+||++.|++++++|+++++.+...+|||..+.++.+|+||+..|+.||+|..|++.++...+.+|||+|++
T Consensus       179 mlGGRNiKVgrPsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiE  258 (544)
T KOG0124|consen  179 MLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIE  258 (544)
T ss_pred             cccCccccccCCCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEE
Confidence            79999999999999999999999999999999999999999999999999999999999999999999889999999999


Q ss_pred             EcCHHHHHHHHHhcCCceeCCeEEEEEEeeCCCCCCCCCCCCCCCCCCCChHHHHHHHHHHHhhhhhcccc-hhhhhhhh
Q psy2141          81 YETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHMPTAAAVAAAAATAKIQAMDGGA-TNAVGVLS  159 (173)
Q Consensus        81 f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~aa~a~~~~~~a~~~~~-~~~~~~~~  159 (173)
                      |.+..+-..|+..||-+.++|+-|+|..+..++.....    |..++.+|++++++++++++++++.++.+ +.++++.+
T Consensus       259 y~n~qs~~eAiasMNlFDLGGQyLRVGk~vTPP~aLl~----Pat~s~~P~aaaVAaAAaTAKi~A~eAvAg~avlg~~G  334 (544)
T KOG0124|consen  259 YNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDALLQ----PATVSAIPAAAAVAAAAATAKIMAAEAVAGSAVLGTVG  334 (544)
T ss_pred             eccccchHHHhhhcchhhcccceEecccccCCCchhcC----CCCcccCchHHHHHHHHHHHHHHHHHHhccCCcccccC
Confidence            99999999999999999999999999999988888765    88899999999999999999999998877 44455544

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

Probab=99.93  E-value=2e-25  Score=189.50  Aligned_cols=147  Identities=63%  Similarity=0.945  Sum_probs=130.1

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY   81 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f   81 (173)
                      |+||.|+|+++.+.+...+..+....+....++|||+|||.++++++|+++|+.||.|..+++.+++.+++++|||||+|
T Consensus       174 i~GR~IkV~rp~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeF  253 (612)
T TIGR01645       174 LGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEY  253 (612)
T ss_pred             EecceeeecccccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEE
Confidence            68999999999887776666565555566778999999999999999999999999999999999998999999999999


Q ss_pred             cCHHHHHHHHHhcCCceeCCeEEEEEEeeCCCCCCCCCCCCCCCCCCCChHHHHHHHHHHHhhhhhcccch
Q psy2141          82 ETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHMPTAAAVAAAAATAKIQAMDGGAT  152 (173)
Q Consensus        82 ~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~aa~a~~~~~~a~~~~~~  152 (173)
                      .+.++|.+|++.||+..|+|+.|+|.++.+++.....    +.....+|++++++++++++++++.+++++
T Consensus       254 e~~e~A~kAI~amNg~elgGr~LrV~kAi~pP~~~~~----pa~~~~~p~aaa~Aaaaa~a~~~a~~~~~~  320 (612)
T TIGR01645       254 NNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDALLQ----PATVSAIPAAAAVAAAAATAKIMAAEAVAG  320 (612)
T ss_pred             CCHHHHHHHHHHhCCCeeCCeEEEEEecCCCccccCC----CCCCCCCchHHHHHHHHhhhhhhhhhhhhc
Confidence            9999999999999999999999999999987666543    455677899999999999999999987753

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=99.85  E-value=3.4e-20  Score=132.68  Aligned_cols=87  Identities=23%  Similarity=0.479  Sum_probs=81.7

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ....++|||+|||++++|++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..|+|++|+|++
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            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeCCCCC
Q psy2141         109 AITPPNA  115 (173)
Q Consensus       109 a~~~~~~  115 (173)
                      +..++..
T Consensus       111 a~~~~~~  117 (144)
T PLN03134        111 ANDRPSA  117 (144)
T ss_pred             CCcCCCC
Confidence            9866543

>KOG0148|consensus

Probab=99.82  E-value=1.3e-19  Score=137.75  Aligned_cols=110  Identities=26%  Similarity=0.489  Sum_probs=95.0

Q ss_pred             CCCCcccccCCCCCCCC----Ccchhhhhhhh-hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcce
Q psy2141           1 MQHFPHVQVGRPSNMPQ----AQSVIDEITEE-AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKG   75 (173)
Q Consensus         1 ~l~gr~i~v~~~~~~~~----~~~~~~~~~~~-~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g   75 (173)
                      ||++|.||.+|+..+|.    .....+++-.. ....++|||||++..++|++|++.|+.||+|.+|++..+      +|
T Consensus       128 WlG~R~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qG  201 (321)
T KOG0148|consen  128 WLGRRTIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QG  201 (321)
T ss_pred             eeccceeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cc
Confidence            79999999999887652    22334444433 455889999999999999999999999999999999998      69


Q ss_pred             EEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCCCCCC
Q psy2141          76 YGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNAL  116 (173)
Q Consensus        76 ~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~~~~~  116 (173)
                      |+||.|.+.|.|.+||..+|+.+|+|+.++|.|.+......
T Consensus       202 YaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~~~  242 (321)
T KOG0148|consen  202 YAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDDGI  242 (321)
T ss_pred             eEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCCCCC
Confidence            99999999999999999999999999999999998765544

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.79  E-value=8.2e-19  Score=142.09  Aligned_cols=82  Identities=27%  Similarity=0.457  Sum_probs=78.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeC
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAIT  111 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~  111 (173)
                      ..+|||+|||+++++++|+++|++||.|..+++++|+.+|.++|||||+|.+.++|.+|+..|||..++|+.|+|.|...
T Consensus       269 ~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~  348 (352)
T TIGR01661       269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTN  348 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccC
Confidence            34799999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             CC
Q psy2141         112 PP  113 (173)
Q Consensus       112 ~~  113 (173)
                      +.
T Consensus       349 ~~  350 (352)
T TIGR01661       349 KA  350 (352)
T ss_pred             CC
Confidence            54

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.78  E-value=2e-18  Score=139.77  Aligned_cols=84  Identities=26%  Similarity=0.506  Sum_probs=79.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      +..+|||+|||.+++|++|+++|+.||+|.+|+|++++.+|+++|||||+|.+.++|++|++.|||..+.|++|+|.+++
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            46899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCCC
Q psy2141         111 TPPN  114 (173)
Q Consensus       111 ~~~~  114 (173)
                      +...
T Consensus        82 ~~~~   85 (352)
T TIGR01661        82 PSSD   85 (352)
T ss_pred             cccc
Confidence            6543

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.76  E-value=6.8e-18  Score=136.42  Aligned_cols=101  Identities=20%  Similarity=0.322  Sum_probs=87.6

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY   81 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f   81 (173)
                      |.+++|+|.++..  ..         +....++|||+|||..++|++|+++|++||.|..++|++++.+++++|||||+|
T Consensus       174 l~gr~i~V~~a~p--~~---------~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F  242 (346)
T TIGR01659       174 VRNKRLKVSYARP--GG---------ESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRF  242 (346)
T ss_pred             cCCceeeeecccc--cc---------cccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEE
Confidence            6788888887642  11         112457899999999999999999999999999999999999999999999999


Q ss_pred             cCHHHHHHHHHhcCCceeCC--eEEEEEEeeCCC
Q psy2141          82 ETKQASNEAISSMNLFDLGG--QYLRVGRAITPP  113 (173)
Q Consensus        82 ~~~~~a~~a~~~l~g~~i~g--~~l~v~~a~~~~  113 (173)
                      .+.++|++|++.||+..+.+  ++|+|.++....
T Consensus       243 ~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~  276 (346)
T TIGR01659       243 NKREEAQEAISALNNVIPEGGSQPLTVRLAEEHG  276 (346)
T ss_pred             CCHHHHHHHHHHhCCCccCCCceeEEEEECCccc
Confidence            99999999999999998876  789999987543

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

>KOG0121|consensus

Probab=99.76  E-value=2.8e-18  Score=117.28  Aligned_cols=87  Identities=20%  Similarity=0.288  Sum_probs=81.5

Q ss_pred             hhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEE
Q psy2141          25 ITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYL  104 (173)
Q Consensus        25 ~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l  104 (173)
                      ..+....+++||||||++.++|++|.++|++.|+|..+.+-.|+.+..++|||||+|.+.++|+.|++.++|..++.++|
T Consensus        29 ~~~a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~i  108 (153)
T KOG0121|consen   29 QLEALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPI  108 (153)
T ss_pred             HHHHHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccce
Confidence            34455779999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeeC
Q psy2141         105 RVGRAIT  111 (173)
Q Consensus       105 ~v~~a~~  111 (173)
                      +++|...
T Consensus       109 r~D~D~G  115 (153)
T KOG0121|consen  109 RIDWDAG  115 (153)
T ss_pred             eeecccc
Confidence            9999754

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.76  E-value=5e-18  Score=137.18  Aligned_cols=85  Identities=21%  Similarity=0.436  Sum_probs=80.3

Q ss_pred             hhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q psy2141          28 EAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG  107 (173)
Q Consensus        28 ~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~  107 (173)
                      +....++|||+|||++++|++|+++|+.||+|++|+|++|+.+++++|||||+|.+.++|++|++.|++..+.+++|+|.
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            34468899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeeCC
Q psy2141         108 RAITP  112 (173)
Q Consensus       108 ~a~~~  112 (173)
                      ++++.
T Consensus       183 ~a~p~  187 (346)
T TIGR01659       183 YARPG  187 (346)
T ss_pred             ccccc
Confidence            98754

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.74  E-value=1.4e-17  Score=104.17  Aligned_cols=70  Identities=33%  Similarity=0.719  Sum_probs=67.2

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q psy2141          35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLR  105 (173)
Q Consensus        35 l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~  105 (173)
                      |||+|||.++++++|+++|++||.|..+.+..+ .++..+++|||+|.+.++|++|++.|+|..++|++|+
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            799999999999999999999999999999997 6889999999999999999999999999999999885

(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 ....

>KOG0122|consensus

Probab=99.74  E-value=1.6e-17  Score=124.81  Aligned_cols=85  Identities=25%  Similarity=0.483  Sum_probs=81.0

Q ss_pred             hhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q psy2141          28 EAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG  107 (173)
Q Consensus        28 ~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~  107 (173)
                      ...+.++|-|.||+.+++|++|+++|.+||.|..+.+.+|+.||.+||||||.|.+.++|.+||+.|||.-++.-.|+|.
T Consensus       185 ~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvE  264 (270)
T KOG0122|consen  185 ERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVE  264 (270)
T ss_pred             cCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEE
Confidence            34568899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeeCC
Q psy2141         108 RAITP  112 (173)
Q Consensus       108 ~a~~~  112 (173)
                      |++++
T Consensus       265 wskP~  269 (270)
T KOG0122|consen  265 WSKPS  269 (270)
T ss_pred             ecCCC
Confidence            99875

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

Probab=99.72  E-value=5.2e-17  Score=137.53  Aligned_cols=83  Identities=33%  Similarity=0.498  Sum_probs=78.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|..|++.|+|..++|+.|.|.++
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            34679999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             eCC
Q psy2141         110 ITP  112 (173)
Q Consensus       110 ~~~  112 (173)
                      ...
T Consensus       373 ~~~  375 (509)
T TIGR01642       373 CVG  375 (509)
T ss_pred             ccC
Confidence            754

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

>KOG0149|consensus

Probab=99.70  E-value=4.6e-17  Score=121.78  Aligned_cols=80  Identities=23%  Similarity=0.397  Sum_probs=74.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      ..++||||+|+|++..+.|+++|++||.|.+..++.|+.+|++||||||+|.+.+.|++||+. ..-.|+||+..|+.+.
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLAS   89 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhh
Confidence            357899999999999999999999999999999999999999999999999999999999976 4578999999998875


Q ss_pred             C
Q psy2141         111 T  111 (173)
Q Consensus       111 ~  111 (173)
                      -
T Consensus        90 l   90 (247)
T KOG0149|consen   90 L   90 (247)
T ss_pred             h
Confidence            4

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

Probab=99.70  E-value=1e-16  Score=136.65  Aligned_cols=82  Identities=38%  Similarity=0.692  Sum_probs=77.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||||||+++++++|+++|++||.|.+|++++|+.+|+++|||||+|.+.++|++|++.|||..++|+.|+|++.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             eC
Q psy2141         110 IT  111 (173)
Q Consensus       110 ~~  111 (173)
                      ..
T Consensus       185 ~~  186 (612)
T TIGR01645       185 SN  186 (612)
T ss_pred             cc
Confidence            43

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

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

Probab=99.70  E-value=1.7e-16  Score=132.78  Aligned_cols=110  Identities=25%  Similarity=0.488  Sum_probs=88.1

Q ss_pred             CCCcccccCCCCCCCCCcch-hhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSV-IDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIE   80 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~-~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~   80 (173)
                      +.|++|.|..+......... ...........++|||+|||..+++++|+++|+.||.|..|.+++++.+|+++|||||+
T Consensus       155 ~~g~~i~v~~~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~  234 (457)
T TIGR01622       155 LLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQ  234 (457)
T ss_pred             ECCeeeEEeecchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEE
Confidence            56778887654321111000 01111112336899999999999999999999999999999999998889999999999


Q ss_pred             EcCHHHHHHHHHhcCCceeCCeEEEEEEeeC
Q psy2141          81 YETKQASNEAISSMNLFDLGGQYLRVGRAIT  111 (173)
Q Consensus        81 f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~  111 (173)
                      |.+.++|.+|++.|+|..|.|++|+|.++..
T Consensus       235 f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       235 FHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             ECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            9999999999999999999999999999763

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.

>KOG0125|consensus

Probab=99.69  E-value=1.3e-16  Score=124.29  Aligned_cols=81  Identities=21%  Similarity=0.387  Sum_probs=74.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||.|||+...|.||+.+|.+||+|.+|.|+.+.  .-+||||||+|++.++|++|-+.|||..+.||+|.|+.+
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~A  171 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNA  171 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEecc
Confidence            447899999999999999999999999999999999872  347999999999999999999999999999999999998


Q ss_pred             eCC
Q psy2141         110 ITP  112 (173)
Q Consensus       110 ~~~  112 (173)
                      ..+
T Consensus       172 Tar  174 (376)
T KOG0125|consen  172 TAR  174 (376)
T ss_pred             chh
Confidence            644

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.69  E-value=3.6e-16  Score=98.23  Aligned_cols=70  Identities=27%  Similarity=0.693  Sum_probs=65.1

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q psy2141          35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLR  105 (173)
Q Consensus        35 l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~  105 (173)
                      |||+|||+.+++++|+++|+.||.|..+.+..++. +..+|+|||+|.+.++|.+|++.+++..++|+.|+
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 89999999999999999999999999999999875

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0113|consensus

Probab=99.68  E-value=1.8e-16  Score=122.09  Aligned_cols=83  Identities=28%  Similarity=0.514  Sum_probs=79.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ++.+||||+.|+.+++|.+|+..|+.||+|+.+.|++|+.||+++|||||+|....+...|.+..+|..|+|+.|.|++-
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999886


Q ss_pred             eCC
Q psy2141         110 ITP  112 (173)
Q Consensus       110 ~~~  112 (173)
                      ...
T Consensus       179 RgR  181 (335)
T KOG0113|consen  179 RGR  181 (335)
T ss_pred             ccc
Confidence            643

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

Probab=99.67  E-value=3.2e-16  Score=134.41  Aligned_cols=108  Identities=22%  Similarity=0.378  Sum_probs=88.4

Q ss_pred             CcccccCCCCCCCCCcchhh----hhh---hhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceE
Q psy2141           4 FPHVQVGRPSNMPQAQSVID----EIT---EEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGY   76 (173)
Q Consensus         4 gr~i~v~~~~~~~~~~~~~~----~~~---~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~   76 (173)
                      |+.|.|++.....+......    +..   .......+|||+||+..+++++|+++|+.||.|.+++++.+ .+|.++||
T Consensus       250 g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~  328 (562)
T TIGR01628       250 GKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGF  328 (562)
T ss_pred             ceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCe
Confidence            77777877654332211111    111   11335678999999999999999999999999999999999 68999999


Q ss_pred             EEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCC
Q psy2141          77 GFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITP  112 (173)
Q Consensus        77 afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~  112 (173)
                      |||+|.+.++|.+|++.|||..++|++|.|.++..+
T Consensus       329 gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k  364 (562)
T TIGR01628       329 GFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRK  364 (562)
T ss_pred             EEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCc
Confidence            999999999999999999999999999999998753

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

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.65  E-value=1.2e-15  Score=117.17  Aligned_cols=77  Identities=19%  Similarity=0.306  Sum_probs=71.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeC
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAIT  111 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~  111 (173)
                      .++|||+|||+.++|++|+++|+.||.|.++.|.+++.   .+|||||+|.+.++|+.|+ .|+|..|.|+.|+|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETAL-LLSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHH-HhcCCeeCCceEEEEeccC
Confidence            57999999999999999999999999999999998853   5799999999999999999 5999999999999999874


Q ss_pred             C
Q psy2141         112 P  112 (173)
Q Consensus       112 ~  112 (173)
                      .
T Consensus        80 ~   80 (260)
T PLN03120         80 Y   80 (260)
T ss_pred             C
Confidence            3

>KOG0107|consensus

Probab=99.64  E-value=6.9e-16  Score=110.81  Aligned_cols=80  Identities=20%  Similarity=0.493  Sum_probs=74.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      -.++||||||+..+++.+|+..|..||++..+-|-+.     ..|||||+|++..+|+.|+..|+|..|.|..|+|+...
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            4789999999999999999999999999999988775     48999999999999999999999999999999999988


Q ss_pred             CCCCC
Q psy2141         111 TPPNA  115 (173)
Q Consensus       111 ~~~~~  115 (173)
                      ..+..
T Consensus        84 G~~r~   88 (195)
T KOG0107|consen   84 GRPRG   88 (195)
T ss_pred             CCccc
Confidence            66553

>KOG0148|consensus

Probab=99.64  E-value=4.4e-16  Score=118.68  Aligned_cols=86  Identities=26%  Similarity=0.532  Sum_probs=81.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      ....+|||-|..+++.++|++.|.+||.|.++++++|..|+++|||+||.|.+.++|++||..|||.-|++|.|+.+|+.
T Consensus        61 ~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWAT  140 (321)
T KOG0148|consen   61 QHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWAT  140 (321)
T ss_pred             cceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccc
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCCC
Q psy2141         111 TPPNAL  116 (173)
Q Consensus       111 ~~~~~~  116 (173)
                      .++...
T Consensus       141 RKp~e~  146 (321)
T KOG0148|consen  141 RKPSEM  146 (321)
T ss_pred             cCcccc
Confidence            877443

>PLN03213 repressor of silencing 3; Provisional

Probab=99.64  E-value=7e-16  Score=126.05  Aligned_cols=80  Identities=15%  Similarity=0.302  Sum_probs=73.0

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCH--HHHHHHHHhcCCceeCCeEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETK--QASNEAISSMNLFDLGGQYLRV  106 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~--~~a~~a~~~l~g~~i~g~~l~v  106 (173)
                      .....+||||||++.+++++|+..|+.||.|..+.|++  .+|  ||||||+|.+.  .+..+||..|||..|.|+.|+|
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKV   82 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRL   82 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEE
Confidence            34568999999999999999999999999999999995  466  99999999987  6899999999999999999999


Q ss_pred             EEeeCC
Q psy2141         107 GRAITP  112 (173)
Q Consensus       107 ~~a~~~  112 (173)
                      ..|++.
T Consensus        83 NKAKP~   88 (759)
T PLN03213         83 EKAKEH   88 (759)
T ss_pred             eeccHH
Confidence            998754

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

Probab=99.63  E-value=1.7e-15  Score=129.97  Aligned_cols=79  Identities=28%  Similarity=0.633  Sum_probs=75.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCC
Q psy2141          34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITP  112 (173)
Q Consensus        34 ~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~  112 (173)
                      +|||||||.+++|++|+++|++||.|.+|++.+|+.+++++|||||+|.+.++|++|++.|++..+.|++|+|.|+...
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~~~   80 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRD   80 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccccc
Confidence            6999999999999999999999999999999999989999999999999999999999999999999999999997643

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

>KOG0126|consensus

Probab=99.63  E-value=5.2e-17  Score=117.25  Aligned_cols=82  Identities=28%  Similarity=0.462  Sum_probs=77.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+..-|||||||+++||.+|...|++||.|..+.+++|+.||+++||||+.|++..+.--|+..|||..|.||.|+|+..
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            45778999999999999999999999999999999999999999999999999999999999999999999999999775


Q ss_pred             eC
Q psy2141         110 IT  111 (173)
Q Consensus       110 ~~  111 (173)
                      ..
T Consensus       113 ~~  114 (219)
T KOG0126|consen  113 SN  114 (219)
T ss_pred             cc
Confidence            43

>KOG4207|consensus

Probab=99.63  E-value=5.4e-16  Score=114.14  Aligned_cols=82  Identities=21%  Similarity=0.413  Sum_probs=78.6

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      .....+|-|.||.+.++.++|+.+|++||.|-+|.|.+|+.|++++|||||.|....+|+.|++.|+|..|+|+.|+|+.
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            34578899999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             ee
Q psy2141         109 AI  110 (173)
Q Consensus       109 a~  110 (173)
                      |+
T Consensus        90 ar   91 (256)
T KOG4207|consen   90 AR   91 (256)
T ss_pred             hh
Confidence            86

>KOG0111|consensus

Probab=99.62  E-value=2.8e-16  Score=116.66  Aligned_cols=84  Identities=29%  Similarity=0.518  Sum_probs=80.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++||||+|..+++|..|...|-+||.|..+++..|-.++++|||+||+|...++|.+||..||+.++.||.|+|+++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCCC
Q psy2141         110 ITPP  113 (173)
Q Consensus       110 ~~~~  113 (173)
                      +|.+
T Consensus        88 kP~k   91 (298)
T KOG0111|consen   88 KPEK   91 (298)
T ss_pred             CCcc
Confidence            8754

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

Probab=99.62  E-value=3.3e-15  Score=127.11  Aligned_cols=99  Identities=20%  Similarity=0.292  Sum_probs=82.1

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhcc--CceeEEEEccCCCCCCcceEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAF--GPIKYCKLQQGSSPHRHKGYGFI   79 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~--G~v~~~~i~~~~~~g~~~g~afv   79 (173)
                      +.|+.|+|.|........      .+.....++|||+||+.++++++|+++|++|  |.|+.|+++        ++||||
T Consensus       209 l~Gr~I~VdwA~p~~~~d------~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFV  274 (578)
T TIGR01648       209 LWGHVIAVDWAEPEEEVD------EDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFV  274 (578)
T ss_pred             ecCceEEEEeeccccccc------ccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEE
Confidence            568889998875321111      1112346789999999999999999999999  999999775        459999


Q ss_pred             EEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCCCC
Q psy2141          80 EYETKQASNEAISSMNLFDLGGQYLRVGRAITPPN  114 (173)
Q Consensus        80 ~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~~~  114 (173)
                      +|.+.++|++|++.||+.+|+|+.|+|+|+++...
T Consensus       275 eF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       275 HFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDK  309 (578)
T ss_pred             EeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCCc
Confidence            99999999999999999999999999999987543

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=99.62  E-value=1.9e-15  Score=114.80  Aligned_cols=89  Identities=22%  Similarity=0.496  Sum_probs=83.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      +..+.|.|.-||.++++++|+.+|...|.|++|++++|+-+|++.||+||.|.+.++|++|+..|||..+..+.|+|+|+
T Consensus        39 ~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyA  118 (360)
T KOG0145|consen   39 ESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYA  118 (360)
T ss_pred             cccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEec
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCCCCCCCC
Q psy2141         110 ITPPNALHS  118 (173)
Q Consensus       110 ~~~~~~~~~  118 (173)
                      ++.......
T Consensus       119 RPSs~~Ik~  127 (360)
T KOG0145|consen  119 RPSSDSIKD  127 (360)
T ss_pred             cCChhhhcc
Confidence            988776554

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

Probab=99.61  E-value=4.1e-15  Score=124.48  Aligned_cols=84  Identities=15%  Similarity=0.259  Sum_probs=78.0

Q ss_pred             hhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q psy2141          28 EAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG  107 (173)
Q Consensus        28 ~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~  107 (173)
                      ...+.++|||+|||..+++++|+++|++||.|..|+++.++.+++++|||||+|.+.++|++|+. |+|..+.|++|.|.
T Consensus        85 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~  163 (457)
T TIGR01622        85 AERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQ  163 (457)
T ss_pred             cccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEe
Confidence            44568899999999999999999999999999999999999999999999999999999999995 89999999999998


Q ss_pred             EeeCC
Q psy2141         108 RAITP  112 (173)
Q Consensus       108 ~a~~~  112 (173)
                      ++...
T Consensus       164 ~~~~~  168 (457)
T TIGR01622       164 SSQAE  168 (457)
T ss_pred             ecchh
Confidence            86543

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.

>KOG0108|consensus

Probab=99.61  E-value=2e-15  Score=124.25  Aligned_cols=82  Identities=28%  Similarity=0.512  Sum_probs=79.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCC
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITP  112 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~  112 (173)
                      +.+||||+|++++|++|..+|+..|.|..++++.|+.+|+.+||||++|.+.++++.|++.|||.++.|++|+|.|+...
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            89999999999999999999999999999999999999999999999999999999999999999999999999998765


Q ss_pred             CC
Q psy2141         113 PN  114 (173)
Q Consensus       113 ~~  114 (173)
                      +.
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            44

>KOG0131|consensus

Probab=99.61  E-value=1e-15  Score=110.57  Aligned_cols=81  Identities=27%  Similarity=0.534  Sum_probs=78.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ....|||||||+..++++.|.++|-+.|+|..+.+.+|+.++.++||||++|.+.++|+-|++.||...+.|++|+|+.+
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            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             e
Q psy2141         110 I  110 (173)
Q Consensus       110 ~  110 (173)
                      .
T Consensus        87 s   87 (203)
T KOG0131|consen   87 S   87 (203)
T ss_pred             c
Confidence            7

>KOG0144|consensus

Probab=99.60  E-value=1e-15  Score=123.01  Aligned_cols=85  Identities=25%  Similarity=0.417  Sum_probs=77.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCC-ceeCC--eEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNL-FDLGG--QYLRV  106 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g-~~i~g--~~l~v  106 (173)
                      ...++||||.|+..++|.+++++|++||.|++|.|++| ..+.+||||||.|.+.+.|..||+.||| ..+.|  .+|.|
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 VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRD-PDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVV  200 (510)
T ss_pred             ccchhhhhhhccccccHHHHHHHHHhhCccchhhheec-ccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEE
Confidence            44789999999999999999999999999999999999 5899999999999999999999999999 44555  79999


Q ss_pred             EEeeCCCCC
Q psy2141         107 GRAITPPNA  115 (173)
Q Consensus       107 ~~a~~~~~~  115 (173)
                      +|+.++++.
T Consensus       201 kFADtqkdk  209 (510)
T KOG0144|consen  201 KFADTQKDK  209 (510)
T ss_pred             EecccCCCc
Confidence            999876554

>smart00362 RRM_2 RNA recognition motif

Probab=99.60  E-value=1.2e-14  Score=90.20  Aligned_cols=72  Identities=39%  Similarity=0.797  Sum_probs=67.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q psy2141          34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG  107 (173)
Q Consensus        34 ~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~  107 (173)
                      +|||+|||..+++++|+++|.+||.+..+.+..++  +.++|+|||+|.+.++|++|++.+++..+.|++|.|+
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            58999999999999999999999999999998875  7789999999999999999999999999999998873

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

Probab=99.58  E-value=8.2e-15  Score=124.76  Aligned_cols=79  Identities=27%  Similarity=0.504  Sum_probs=73.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeC-CeEEEEEEe
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLG-GQYLRVGRA  109 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~-g~~l~v~~a  109 (173)
                      ..++|||+|||.+++|++|+++|++||.|.+++|++| .+|+++|||||+|.+.++|++|++.||+..+. |+.|.|+++
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            4689999999999999999999999999999999999 79999999999999999999999999998885 777777655


Q ss_pred             e
Q psy2141         110 I  110 (173)
Q Consensus       110 ~  110 (173)
                      .
T Consensus       136 ~  136 (578)
T TIGR01648       136 V  136 (578)
T ss_pred             c
Confidence            3

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.

>KOG0130|consensus

Probab=99.57  E-value=1.3e-14  Score=100.31  Aligned_cols=81  Identities=33%  Similarity=0.502  Sum_probs=77.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCCC
Q psy2141          34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPP  113 (173)
Q Consensus        34 ~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~~  113 (173)
                      .|||.++..+.+|+++.+.|..||.|+.+.+..|+.||..+||++|+|.+.++|++|+..|||..+.|++|.|+|+..+.
T Consensus        74 Ii~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~g  153 (170)
T KOG0130|consen   74 IIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVKG  153 (170)
T ss_pred             EEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEecC
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999997654


Q ss_pred             C
Q psy2141         114 N  114 (173)
Q Consensus       114 ~  114 (173)
                      .
T Consensus       154 p  154 (170)
T KOG0130|consen  154 P  154 (170)
T ss_pred             C
Confidence            3

>KOG0114|consensus

Probab=99.57  E-value=2.4e-14  Score=94.69  Aligned_cols=78  Identities=18%  Similarity=0.392  Sum_probs=71.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      -++.|||.|||+.++.++..++|.+||.|..+++-..+.   .+|-|||.|++..+|.+|++.|+|..+.++.|.|-+-.
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            468899999999999999999999999999999987654   48999999999999999999999999999999998865


Q ss_pred             C
Q psy2141         111 T  111 (173)
Q Consensus       111 ~  111 (173)
                      +
T Consensus        94 ~   94 (124)
T KOG0114|consen   94 P   94 (124)
T ss_pred             H
Confidence            3

>KOG0117|consensus

Probab=99.56  E-value=2.2e-14  Score=115.91  Aligned_cols=83  Identities=25%  Similarity=0.469  Sum_probs=77.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeC-CeEEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLG-GQYLRVGR  108 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~-g~~l~v~~  108 (173)
                      ...+.||||.||.++.|++|.-+|++.|+|-+++|++|+.+|.+||||||.|.+.+.|++|++.||+++|. |+.|.|+.
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            45789999999999999999999999999999999999999999999999999999999999999999985 89999987


Q ss_pred             eeCC
Q psy2141         109 AITP  112 (173)
Q Consensus       109 a~~~  112 (173)
                      +...
T Consensus       161 Svan  164 (506)
T KOG0117|consen  161 SVAN  164 (506)
T ss_pred             eeec
Confidence            6543

>smart00360 RRM RNA recognition motif

Probab=99.56  E-value=2.7e-14  Score=88.17  Aligned_cols=71  Identities=31%  Similarity=0.674  Sum_probs=66.9

Q ss_pred             EcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q psy2141          37 VASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG  107 (173)
Q Consensus        37 V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~  107 (173)
                      |+|||..+++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|.+|++.|++..+.|+.|+|+
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            57999999999999999999999999999987788999999999999999999999999999999998873

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

Probab=99.56  E-value=2.5e-14  Score=110.05  Aligned_cols=79  Identities=33%  Similarity=0.677  Sum_probs=76.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      .++|||+|||..+++++|+++|..||.+..+.+..++.+++++|+|||+|.+.+++..|++.+++..+.|++|.|.+..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            5999999999999999999999999999999999998899999999999999999999999999999999999999965

>KOG0144|consensus

Probab=99.55  E-value=1.4e-14  Score=116.63  Aligned_cols=86  Identities=24%  Similarity=0.402  Sum_probs=77.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCce-eCC--eEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFD-LGG--QYLRV  106 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~-i~g--~~l~v  106 (173)
                      .+.-++|||.||..++|.+|+++|++||.|.+|.|++||.++.++|||||.|.+.++|.+|+.+||+.. +-|  ++|.|
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            345689999999999999999999999999999999999999999999999999999999999999844 444  78999


Q ss_pred             EEeeCCCCC
Q psy2141         107 GRAITPPNA  115 (173)
Q Consensus       107 ~~a~~~~~~  115 (173)
                      +++....++
T Consensus       112 k~Ad~E~er  120 (510)
T KOG0144|consen  112 KYADGERER  120 (510)
T ss_pred             cccchhhhc
Confidence            999866555

>KOG0131|consensus

Probab=99.55  E-value=9.4e-15  Score=105.61  Aligned_cols=102  Identities=25%  Similarity=0.379  Sum_probs=89.2

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeE-EEEccCCCCCCcceEEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKY-CKLQQGSSPHRHKGYGFIE   80 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~-~~i~~~~~~g~~~g~afv~   80 (173)
                      |.||+|+|.+.+..          +...+...+|||+||.++++|..|.+.|+.||.+.. -+++++..||.++||||+.
T Consensus        76 LYgrpIrv~kas~~----------~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~  145 (203)
T KOG0131|consen   76 LYGRPIRVNKASAH----------QKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFIN  145 (203)
T ss_pred             hcCceeEEEecccc----------cccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEe
Confidence            67999999987621          112234689999999999999999999999998866 4899999999999999999


Q ss_pred             EcCHHHHHHHHHhcCCceeCCeEEEEEEeeCCC
Q psy2141          81 YETKQASNEAISSMNLFDLGGQYLRVGRAITPP  113 (173)
Q Consensus        81 f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~~  113 (173)
                      |.+.+.+.+|++.|||..+..++|+|.++..+.
T Consensus       146 ~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~  178 (203)
T KOG0131|consen  146 YASFEASDAAIGSMNGQYLCNRPITVSYAFKKD  178 (203)
T ss_pred             chhHHHHHHHHHHhccchhcCCceEEEEEEecC
Confidence            999999999999999999999999999997653

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.55  E-value=5e-14  Score=106.85  Aligned_cols=76  Identities=16%  Similarity=0.183  Sum_probs=69.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      ...+|||+||++.++|++|+++|+.||.|..|+|+++.   ..+++|||+|.+.++++.|+ .|+|..|.+++|.|....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCc
Confidence            45799999999999999999999999999999999984   44689999999999999999 889999999999997754

>KOG0146|consensus

Probab=99.54  E-value=8.5e-15  Score=111.70  Aligned_cols=98  Identities=17%  Similarity=0.357  Sum_probs=88.7

Q ss_pred             CcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCc
Q psy2141          18 AQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLF   97 (173)
Q Consensus        18 ~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~   97 (173)
                      -.+.....+.+....|+|||..||.+..+.+|.++|-.||.|.+.++..|+.|.++|+|+||.|.+..+++.||..|||.
T Consensus       271 ~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGF  350 (371)
T KOG0146|consen  271 PPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGF  350 (371)
T ss_pred             CcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcch
Confidence            34445555667778999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeCCeEEEEEEeeCCCCC
Q psy2141          98 DLGGQYLRVGRAITPPNA  115 (173)
Q Consensus        98 ~i~g~~l~v~~a~~~~~~  115 (173)
                      .|+-++|+|...+++...
T Consensus       351 QIGMKRLKVQLKRPkdan  368 (371)
T KOG0146|consen  351 QIGMKRLKVQLKRPKDAN  368 (371)
T ss_pred             hhhhhhhhhhhcCccccC
Confidence            999999999998876543

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

Probab=99.54  E-value=4.4e-14  Score=119.25  Aligned_cols=78  Identities=19%  Similarity=0.273  Sum_probs=72.4

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          30 KLYNRIYVASIHP-DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        30 ~~~~~l~V~nLp~-~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      .+.++|||+|||+ .+++++|+++|+.||.|..|++++++     +|+|||+|.+.++|+.|++.|||..|.|++|+|.+
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~  347 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCP  347 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            3578999999998 69999999999999999999999874     79999999999999999999999999999999999


Q ss_pred             eeCC
Q psy2141         109 AITP  112 (173)
Q Consensus       109 a~~~  112 (173)
                      ++..
T Consensus       348 s~~~  351 (481)
T TIGR01649       348 SKQQ  351 (481)
T ss_pred             cccc
Confidence            8654

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).

>KOG0117|consensus

Probab=99.54  E-value=2.4e-14  Score=115.68  Aligned_cols=101  Identities=20%  Similarity=0.328  Sum_probs=83.7

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY   81 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f   81 (173)
                      |.|-.|.|.|+.  |...+.    .+....-+.|||.||+.++||+.|+++|+.||.|+.|+.++|        ||||.|
T Consensus       235 lwgn~~tVdWAe--p~~e~d----ed~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf  300 (506)
T KOG0117|consen  235 LWGNAITVDWAE--PEEEPD----EDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHF  300 (506)
T ss_pred             ecCCcceeeccC--cccCCC----hhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEee
Confidence            446677788876  333322    222345678999999999999999999999999999988765        999999


Q ss_pred             cCHHHHHHHHHhcCCceeCCeEEEEEEeeCCCCCC
Q psy2141          82 ETKQASNEAISSMNLFDLGGQYLRVGRAITPPNAL  116 (173)
Q Consensus        82 ~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~~~~~  116 (173)
                      .+.++|-+|++.|||++|+|..|.|..|++..+..
T Consensus       301 ~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~k  335 (506)
T KOG0117|consen  301 AEREDAVKAMKETNGKELDGSPIEVTLAKPVDKKK  335 (506)
T ss_pred             cchHHHHHHHHHhcCceecCceEEEEecCChhhhc
Confidence            99999999999999999999999999999764443

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

Probab=99.53  E-value=5.3e-14  Score=118.73  Aligned_cols=107  Identities=11%  Similarity=0.077  Sum_probs=81.1

Q ss_pred             CCCcccccCCCCCCCCCcchhhh-hhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDE-ITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIE   80 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~-~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~   80 (173)
                      |+|++|+|.++....-....... .........+|||+||++.+++++|+++|+.||.|.++.+.+++    .+++|||+
T Consensus        65 l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~----~~~~afVe  140 (481)
T TIGR01649        65 IRGQPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKN----NVFQALVE  140 (481)
T ss_pred             EcCeEEEEEecCCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecC----CceEEEEE
Confidence            78999999886521100000000 00111223479999999999999999999999999999998764    24789999


Q ss_pred             EcCHHHHHHHHHhcCCceeCC--eEEEEEEeeCC
Q psy2141          81 YETKQASNEAISSMNLFDLGG--QYLRVGRAITP  112 (173)
Q Consensus        81 f~~~~~a~~a~~~l~g~~i~g--~~l~v~~a~~~  112 (173)
                      |.+.++|.+|++.|||..|.+  ..|+|.|++..
T Consensus       141 f~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~  174 (481)
T TIGR01649       141 FESVNSAQHAKAALNGADIYNGCCTLKIEYAKPT  174 (481)
T ss_pred             ECCHHHHHHHHHHhcCCcccCCceEEEEEEecCC
Confidence            999999999999999999965  58999998753

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

>KOG0124|consensus

Probab=99.51  E-value=1.1e-14  Score=115.38  Aligned_cols=79  Identities=39%  Similarity=0.706  Sum_probs=76.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      .|+||||.|.+++.|+.|+..|..||+|+++.+-||+.|+++|||+||+|+-.+.|+-|++.|||..++||.|+|.+..
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCC
Confidence            7899999999999999999999999999999999999999999999999999999999999999999999999998543

>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=99.51  E-value=2.8e-13  Score=84.33  Aligned_cols=74  Identities=31%  Similarity=0.706  Sum_probs=68.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        34 ~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      +|+|+|||..+++++|+++|+.+|.|..+.+..++.+ ..+|+|||+|.+.++|..|++.+++..+.|+.+.|.+
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            4899999999999999999999999999999987544 7789999999999999999999999999999998864

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).

>KOG0127|consensus

Probab=99.50  E-value=1.6e-13  Score=113.31  Aligned_cols=82  Identities=18%  Similarity=0.353  Sum_probs=76.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeC
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAIT  111 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~  111 (173)
                      .-+|.|.|||+.+.+.+|+.+|+.||.|.++.|++.+ .|+.+|||||.|....+|..|++.+|+.+|+||+|.|+||.+
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~-dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~  195 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-DGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVD  195 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-CCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecc
Confidence            5689999999999999999999999999999999775 677779999999999999999999999999999999999987


Q ss_pred             CCC
Q psy2141         112 PPN  114 (173)
Q Consensus       112 ~~~  114 (173)
                      +..
T Consensus       196 Kd~  198 (678)
T KOG0127|consen  196 KDT  198 (678)
T ss_pred             ccc
Confidence            643

>KOG0145|consensus

Probab=99.48  E-value=2.7e-13  Score=103.25  Aligned_cols=81  Identities=26%  Similarity=0.441  Sum_probs=76.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeC
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAIT  111 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~  111 (173)
                      .-.|||.||.++..|..|+++|.+||.|..+++++|..+.+.|||+||.+.+.++|..||..|||..++++.|-|.+...
T Consensus       278 g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtn  357 (360)
T KOG0145|consen  278 GWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTN  357 (360)
T ss_pred             eeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecC
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999998754


Q ss_pred             C
Q psy2141         112 P  112 (173)
Q Consensus       112 ~  112 (173)
                      +
T Consensus       358 k  358 (360)
T KOG0145|consen  358 K  358 (360)
T ss_pred             C
Confidence            3

>KOG0105|consensus

Probab=99.47  E-value=1.2e-13  Score=100.23  Aligned_cols=80  Identities=26%  Similarity=0.461  Sum_probs=72.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||||||.++.|.+|+++|.+||.|.++.+...   .....||||+|++..+|+.||..-+|..++|..|+|.++
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            46799999999999999999999999999999988544   234689999999999999999999999999999999998


Q ss_pred             eCC
Q psy2141         110 ITP  112 (173)
Q Consensus       110 ~~~  112 (173)
                      ...
T Consensus        81 rgg   83 (241)
T KOG0105|consen   81 RGG   83 (241)
T ss_pred             cCC
Confidence            754

>KOG0147|consensus

Probab=99.47  E-value=6.5e-14  Score=115.60  Aligned_cols=81  Identities=32%  Similarity=0.668  Sum_probs=76.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+...||||||.++++|++|+.+|++||.|+.+.+.+|..+|+++||+|++|.+.++|.+|++.|||.+|.|+.|+|..-
T Consensus       276 ~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v  355 (549)
T KOG0147|consen  276 GPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVV  355 (549)
T ss_pred             cchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEe
Confidence            45556999999999999999999999999999999999889999999999999999999999999999999999998765


Q ss_pred             e
Q psy2141         110 I  110 (173)
Q Consensus       110 ~  110 (173)
                      .
T Consensus       356 ~  356 (549)
T KOG0147|consen  356 T  356 (549)
T ss_pred             e
Confidence            4

>KOG0123|consensus

Probab=99.44  E-value=5.1e-13  Score=108.84  Aligned_cols=97  Identities=19%  Similarity=0.372  Sum_probs=85.3

Q ss_pred             CCCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEE
Q psy2141           1 MQHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIE   80 (173)
Q Consensus         1 ~l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~   80 (173)
                      .+.|++|++-|...                +...|||.||+.+++..+|.++|+.||.|.+|++..+. .| ++|| ||+
T Consensus        61 ~~~~~~~rim~s~r----------------d~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~  121 (369)
T KOG0123|consen   61 VLKGKPIRIMWSQR----------------DPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQ  121 (369)
T ss_pred             ccCCcEEEeehhcc----------------CCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEE
Confidence            47899999988763                22229999999999999999999999999999999995 55 9999 999


Q ss_pred             EcCHHHHHHHHHhcCCceeCCeEEEEEEeeCCCCCC
Q psy2141          81 YETKQASNEAISSMNLFDLGGQYLRVGRAITPPNAL  116 (173)
Q Consensus        81 f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~~~~~  116 (173)
                      |.+.+.|.+|++.|||..+.|++|.|.....+....
T Consensus       122 f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~  157 (369)
T KOG0123|consen  122 FESEESAKKAIEKLNGMLLNGKKIYVGLFERKEERE  157 (369)
T ss_pred             eCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhhc
Confidence            999999999999999999999999998877655443

>smart00361 RRM_1 RNA recognition motif

Probab=99.43  E-value=8.9e-13  Score=82.97  Aligned_cols=61  Identities=20%  Similarity=0.376  Sum_probs=55.4

Q ss_pred             HHHHHHHhh----ccCceeEEE-EccCCCC--CCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q psy2141          46 EEDIKSVFE----AFGPIKYCK-LQQGSSP--HRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV  106 (173)
Q Consensus        46 e~~L~~~F~----~~G~v~~~~-i~~~~~~--g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v  106 (173)
                      +++|+++|+    +||.|.++. +..++.+  +.++|++||+|.+.++|.+|++.|||..+.|+.|++
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            578888888    999999995 7777666  899999999999999999999999999999999976

>PF13893 RRM_5: RNA recognition motif

Probab=99.42  E-value=1.5e-12  Score=78.27  Aligned_cols=56  Identities=27%  Similarity=0.552  Sum_probs=51.1

Q ss_pred             HHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          49 IKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        49 L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      |+++|++||.|..+.+..++     +++|||+|.+.++|..|++.|||..+.|++|+|+|+
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            67899999999999997763     689999999999999999999999999999999986

(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 ....

>KOG0109|consensus

Probab=99.42  E-value=5.4e-13  Score=102.83  Aligned_cols=76  Identities=25%  Similarity=0.583  Sum_probs=70.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCC
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITP  112 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~  112 (173)
                      .+|||||||.++++.+|+.+|++||+|.+|.|+++        ||||..++...++.+|+.|||..|+|..|.|+-++.+
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            47999999999999999999999999999999854        9999999999999999999999999999999999877


Q ss_pred             CCCC
Q psy2141         113 PNAL  116 (173)
Q Consensus       113 ~~~~  116 (173)
                      ....
T Consensus        75 sk~s   78 (346)
T KOG0109|consen   75 SKAS   78 (346)
T ss_pred             CCCc
Confidence            4443

>KOG4206|consensus

Probab=99.38  E-value=1.6e-12  Score=97.04  Aligned_cols=86  Identities=16%  Similarity=0.408  Sum_probs=76.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHH----HhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKS----VFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLR  105 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~----~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~  105 (173)
                      .+..||||.||+..+..++|+.    +|++||.|..|....   +.+.+|-|||.|.+.+.|..|++.|+|..+.|++++
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mr   83 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMR   83 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhh
Confidence            4556999999999999999888    999999999987754   578899999999999999999999999999999999


Q ss_pred             EEEeeCCCCCCCC
Q psy2141         106 VGRAITPPNALHS  118 (173)
Q Consensus       106 v~~a~~~~~~~~~  118 (173)
                      +.||+.+.+....
T Consensus        84 iqyA~s~sdii~~   96 (221)
T KOG4206|consen   84 IQYAKSDSDIIAQ   96 (221)
T ss_pred             eecccCccchhhc
Confidence            9999977665444

>KOG0127|consensus

Probab=99.38  E-value=1.7e-12  Score=107.36  Aligned_cols=82  Identities=28%  Similarity=0.485  Sum_probs=75.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhc-----CC-ceeCCeEEE
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM-----NL-FDLGGQYLR  105 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l-----~g-~~i~g~~l~  105 (173)
                      ..+|||.|||++++|++|.+.|++||.|..+.|+.++.|+.++|.|||.|.+...+..||..-     .| ..++||.|+
T Consensus       292 ~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lk  371 (678)
T KOG0127|consen  292 GKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLK  371 (678)
T ss_pred             cceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEe
Confidence            579999999999999999999999999999999999999999999999999999999999876     23 678999999


Q ss_pred             EEEeeCCC
Q psy2141         106 VGRAITPP  113 (173)
Q Consensus       106 v~~a~~~~  113 (173)
                      |..+.++.
T Consensus       372 v~~Av~Rk  379 (678)
T KOG0127|consen  372 VTLAVTRK  379 (678)
T ss_pred             eeeccchH
Confidence            99987653

>KOG0109|consensus

Probab=99.36  E-value=1.3e-12  Score=100.83  Aligned_cols=90  Identities=21%  Similarity=0.484  Sum_probs=80.0

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY   81 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f   81 (173)
                      |+|..|.|..+.+.             .+...+|+||||.+.++.++|+..|++||+|.+|+|++|        |+||.|
T Consensus        61 Lhg~nInVeaSksK-------------sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~  119 (346)
T KOG0109|consen   61 LHGVNINVEASKSK-------------SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHF  119 (346)
T ss_pred             ecceEEEEEecccc-------------CCCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEE
Confidence            67788888776542             246789999999999999999999999999999999865        999999


Q ss_pred             cCHHHHHHHHHhcCCceeCCeEEEEEEeeCC
Q psy2141          82 ETKQASNEAISSMNLFDLGGQYLRVGRAITP  112 (173)
Q Consensus        82 ~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~  112 (173)
                      .-.++|..|++.|++.++.|++++|..+..+
T Consensus       120 d~~eda~~air~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen  120 DRAEDAVEAIRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             eeccchHHHHhcccccccccceeeeeeeccc
Confidence            9999999999999999999999999887644

>KOG0146|consensus

Probab=99.35  E-value=1.8e-12  Score=99.04  Aligned_cols=84  Identities=23%  Similarity=0.458  Sum_probs=75.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCce-eCC--eEEEEE
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFD-LGG--QYLRVG  107 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~-i~g--~~l~v~  107 (173)
                      .+++||||.|...-.|+|++.+|..||.+.+|.+++.. .|.+|||+||.|.+..+|+.||..|||.. +-|  ..|.|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            57899999999999999999999999999999999984 89999999999999999999999999933 434  688999


Q ss_pred             EeeCCCCC
Q psy2141         108 RAITPPNA  115 (173)
Q Consensus       108 ~a~~~~~~  115 (173)
                      ++...+++
T Consensus        97 ~ADTdkER  104 (371)
T KOG0146|consen   97 FADTDKER  104 (371)
T ss_pred             eccchHHH
Confidence            99876554

>KOG0415|consensus

Probab=99.32  E-value=2.5e-12  Score=101.62  Aligned_cols=82  Identities=24%  Similarity=0.448  Sum_probs=78.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      +|...|||..|.+-+++++|.-+|+.||+|..|.+++|+.||.+..||||+|.+.+++++|.-.|++..|++++|.|.++
T Consensus       237 PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFS  316 (479)
T KOG0415|consen  237 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFS  316 (479)
T ss_pred             CCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehh
Confidence            67889999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             eC
Q psy2141         110 IT  111 (173)
Q Consensus       110 ~~  111 (173)
                      ..
T Consensus       317 QS  318 (479)
T KOG0415|consen  317 QS  318 (479)
T ss_pred             hh
Confidence            64

>KOG4212|consensus

Probab=99.32  E-value=5.4e-12  Score=102.13  Aligned_cols=81  Identities=17%  Similarity=0.390  Sum_probs=75.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhh-ccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFE-AFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~-~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ..++.+||.|||+++.+.+|+++|. +.|.|+.|.++.| .+|++||||.|+|+++|.+++|++.||.+++.||+|+|+-
T Consensus        42 ~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKE  120 (608)
T KOG4212|consen   42 ARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKE  120 (608)
T ss_pred             cccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEec
Confidence            4567899999999999999999995 6799999999999 5999999999999999999999999999999999999987


Q ss_pred             eeC
Q psy2141         109 AIT  111 (173)
Q Consensus       109 a~~  111 (173)
                      ...
T Consensus       121 d~d  123 (608)
T KOG4212|consen  121 DHD  123 (608)
T ss_pred             cCc
Confidence            544

>KOG4208|consensus

Probab=99.30  E-value=9.7e-12  Score=91.71  Aligned_cols=83  Identities=24%  Similarity=0.419  Sum_probs=76.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhcc-CceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAF-GPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~-G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ....-+|++.+|..+.+.++..+|.++ |.+..+++-+++.||.++|||||+|.+.+.|.-|.+.||++.+.++.|.|.+
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~v  126 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHV  126 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEE
Confidence            345679999999999999999999998 7888899999999999999999999999999999999999999999999988


Q ss_pred             eeCC
Q psy2141         109 AITP  112 (173)
Q Consensus       109 a~~~  112 (173)
                      -.+.
T Consensus       127 mppe  130 (214)
T KOG4208|consen  127 MPPE  130 (214)
T ss_pred             eCch
Confidence            6554

>KOG0110|consensus

Probab=99.26  E-value=4.2e-12  Score=107.67  Aligned_cols=109  Identities=21%  Similarity=0.363  Sum_probs=89.8

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY   81 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f   81 (173)
                      |+|+.|.+..+.+.|...-. .... .....++|+|.|||+..+-.+++.+|..||.+..|+|+.-...+.++|||||+|
T Consensus       585 ldGH~l~lk~S~~k~~~~~g-K~~~-~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f  662 (725)
T KOG0110|consen  585 LDGHKLELKISENKPASTVG-KKKS-KKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDF  662 (725)
T ss_pred             ecCceEEEEeccCccccccc-cccc-cccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeec
Confidence            67888888766543333222 1111 112367999999999999999999999999999999988766778899999999


Q ss_pred             cCHHHHHHHHHhcCCceeCCeEEEEEEeeCC
Q psy2141          82 ETKQASNEAISSMNLFDLGGQYLRVGRAITP  112 (173)
Q Consensus        82 ~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~  112 (173)
                      -+..+|.+|++.|.+..+.||+|.+.|++..
T Consensus       663 ~t~~ea~nA~~al~STHlyGRrLVLEwA~~d  693 (725)
T KOG0110|consen  663 LTPREAKNAFDALGSTHLYGRRLVLEWAKSD  693 (725)
T ss_pred             cCcHHHHHHHHhhcccceechhhheehhccc
Confidence            9999999999999999999999999999753

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

Probab=99.26  E-value=3.6e-11  Score=102.03  Aligned_cols=81  Identities=19%  Similarity=0.276  Sum_probs=68.5

Q ss_pred             CCCCeEEEcCCCCC--C--------CHHHHHHHhhccCceeEEEEccC---CCCCCcceEEEEEEcCHHHHHHHHHhcCC
Q psy2141          30 KLYNRIYVASIHPD--L--------TEEDIKSVFEAFGPIKYCKLQQG---SSPHRHKGYGFIEYETKQASNEAISSMNL   96 (173)
Q Consensus        30 ~~~~~l~V~nLp~~--~--------~e~~L~~~F~~~G~v~~~~i~~~---~~~g~~~g~afv~f~~~~~a~~a~~~l~g   96 (173)
                      .+.++|+|.||...  +        ..++|+++|++||.|..|.|+++   ..++.++|++||+|.+.++|++|+..|||
T Consensus       407 ~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnG  486 (509)
T TIGR01642       407 KPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNG  486 (509)
T ss_pred             CCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCC
Confidence            46788999999642  1        12578999999999999999875   23456789999999999999999999999


Q ss_pred             ceeCCeEEEEEEee
Q psy2141          97 FDLGGQYLRVGRAI  110 (173)
Q Consensus        97 ~~i~g~~l~v~~a~  110 (173)
                      ..++|+.|.|.|..
T Consensus       487 r~~~gr~v~~~~~~  500 (509)
T TIGR01642       487 RKFNDRVVVAAFYG  500 (509)
T ss_pred             CEECCeEEEEEEeC
Confidence            99999999999864

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

>KOG4205|consensus

Probab=99.21  E-value=3.3e-11  Score=95.71  Aligned_cols=109  Identities=24%  Similarity=0.408  Sum_probs=88.4

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY   81 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f   81 (173)
                      |+||.|.+.++...-......     ......++|||+||.++++++|+++|.+||.|..+.++.|+.+.+++||+||.|
T Consensus        72 ~dgr~ve~k~av~r~~~~~~~-----~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~  146 (311)
T KOG4205|consen   72 LDGRSVEPKRAVSREDQTKVG-----RHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTF  146 (311)
T ss_pred             cCCccccceeccCcccccccc-----cccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEe
Confidence            678888877765321111100     011467999999999999999999999999999999999999999999999999


Q ss_pred             cCHHHHHHHHHhcCCceeCCeEEEEEEeeCCCCCC
Q psy2141          82 ETKQASNEAISSMNLFDLGGQYLRVGRAITPPNAL  116 (173)
Q Consensus        82 ~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~~~~~  116 (173)
                      .+.+.+++++ ...-+.+.|+.+.|+.|.++....
T Consensus       147 ~~e~sVdkv~-~~~f~~~~gk~vevkrA~pk~~~~  180 (311)
T KOG4205|consen  147 DSEDSVDKVT-LQKFHDFNGKKVEVKRAIPKEVMQ  180 (311)
T ss_pred             ccccccceec-ccceeeecCceeeEeeccchhhcc
Confidence            9999999988 447789999999999998765443

>KOG0132|consensus

Probab=99.20  E-value=4.5e-11  Score=102.38  Aligned_cols=76  Identities=22%  Similarity=0.456  Sum_probs=71.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeC
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAIT  111 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~  111 (173)
                      .+|||||.|+..++|.+|..+|+.||.|.+|.++..      +|||||.+....+|++|+..|+...+.++.|+|.|+..
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            679999999999999999999999999999998765      79999999999999999999999999999999999986


Q ss_pred             CC
Q psy2141         112 PP  113 (173)
Q Consensus       112 ~~  113 (173)
                      +.
T Consensus       495 ~G  496 (894)
T KOG0132|consen  495 KG  496 (894)
T ss_pred             CC
Confidence            53

>KOG4205|consensus

Probab=99.19  E-value=2.4e-11  Score=96.48  Aligned_cols=86  Identities=20%  Similarity=0.503  Sum_probs=77.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      ..++||||+|+++++++.|++.|.+||.|.+|.+++|+.+++++||+||+|.+.+...+++.. .-+.|+|+.|.+..+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceecc
Confidence            678999999999999999999999999999999999999999999999999999998888743 5578999999999988


Q ss_pred             CCCCCCC
Q psy2141         111 TPPNALH  117 (173)
Q Consensus       111 ~~~~~~~  117 (173)
                      ++.....
T Consensus        84 ~r~~~~~   90 (311)
T KOG4205|consen   84 SREDQTK   90 (311)
T ss_pred             Ccccccc
Confidence            7655443

>KOG4661|consensus

Probab=99.18  E-value=1.1e-10  Score=97.49  Aligned_cols=86  Identities=20%  Similarity=0.426  Sum_probs=79.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||.+|...+..-+|+.+|++||+|...+++.+..+.-.++|+||++.+..+|.+||..||..+|.|+.|.|..+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            44789999999999999999999999999999999998777778999999999999999999999999999999999998


Q ss_pred             eCCCCC
Q psy2141         110 ITPPNA  115 (173)
Q Consensus       110 ~~~~~~  115 (173)
                      +..+..
T Consensus       483 KNEp~G  488 (940)
T KOG4661|consen  483 KNEPGG  488 (940)
T ss_pred             ccCccc
Confidence            866544

>KOG0153|consensus

Probab=99.16  E-value=1.2e-10  Score=91.88  Aligned_cols=76  Identities=21%  Similarity=0.462  Sum_probs=68.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhc-CCceeCCeEEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM-NLFDLGGQYLRVGR  108 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l-~g~~i~g~~l~v~~  108 (173)
                      ....+||||+|...++|.+|++.|.+||.|+.+.+...      +++|||+|.+.+.|+.|.+.+ +...|+|++|+|.|
T Consensus       226 ~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~W  299 (377)
T KOG0153|consen  226 TSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKW  299 (377)
T ss_pred             cceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEEEe
Confidence            45789999999999999999999999999999998776      579999999999999987754 55778999999999


Q ss_pred             eeC
Q psy2141         109 AIT  111 (173)
Q Consensus       109 a~~  111 (173)
                      ..+
T Consensus       300 g~~  302 (377)
T KOG0153|consen  300 GRP  302 (377)
T ss_pred             CCC
Confidence            987

>KOG4212|consensus

Probab=99.09  E-value=2.5e-10  Score=92.59  Aligned_cols=76  Identities=20%  Similarity=0.331  Sum_probs=69.4

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      .++.|+|+|.|||+++|+..|++-|..||.|....|+.   .|+++|  .|.|.+.++|++||..|+|..++|+.|+|.|
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y  607 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTY  607 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeee
Confidence            35788999999999999999999999999999998843   577777  9999999999999999999999999999987


Q ss_pred             e
Q psy2141         109 A  109 (173)
Q Consensus       109 a  109 (173)
                      .
T Consensus       608 ~  608 (608)
T KOG4212|consen  608 F  608 (608)
T ss_pred             C
Confidence            3

>KOG0110|consensus

Probab=99.08  E-value=6e-10  Score=94.80  Aligned_cols=81  Identities=20%  Similarity=0.409  Sum_probs=70.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCC---CcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPH---RHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG  107 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g---~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~  107 (173)
                      ..++|||.||+++++.++|...|..+|.|..+.|...+...   .+.|||||+|.+.++|++|++.|+|+.|+|+.|.|+
T Consensus       514 ~~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk  593 (725)
T KOG0110|consen  514 TETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELK  593 (725)
T ss_pred             cchhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEE
Confidence            34449999999999999999999999999999887664221   134999999999999999999999999999999999


Q ss_pred             EeeC
Q psy2141         108 RAIT  111 (173)
Q Consensus       108 ~a~~  111 (173)
                      ++..
T Consensus       594 ~S~~  597 (725)
T KOG0110|consen  594 ISEN  597 (725)
T ss_pred             eccC
Confidence            9873

>KOG0123|consensus

Probab=99.03  E-value=9.8e-10  Score=89.74  Aligned_cols=77  Identities=23%  Similarity=0.479  Sum_probs=70.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCC
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITP  112 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~  112 (173)
                      ..||||   ++++|..|.+.|+++|++.++++-+|. |  +-|||||.|.+.++|++|++.||...+.|++|++-|+...
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC
Confidence            468999   889999999999999999999999996 5  9999999999999999999999999999999999998765


Q ss_pred             CCC
Q psy2141         113 PNA  115 (173)
Q Consensus       113 ~~~  115 (173)
                      +..
T Consensus        76 ~~~   78 (369)
T KOG0123|consen   76 PSL   78 (369)
T ss_pred             Cce
Confidence            443

>KOG0533|consensus

Probab=99.03  E-value=1.5e-09  Score=83.30  Aligned_cols=84  Identities=17%  Similarity=0.360  Sum_probs=76.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ....+|+|.|||..+.+++|+++|..||.++.+.+.+++ .|.+.|.|-|.|...++|.++++.+||..++|+.|++...
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i  159 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEII  159 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEe
Confidence            345789999999999999999999999999999999995 9999999999999999999999999999999999988876


Q ss_pred             eCCCC
Q psy2141         110 ITPPN  114 (173)
Q Consensus       110 ~~~~~  114 (173)
                      .+...
T Consensus       160 ~~~~~  164 (243)
T KOG0533|consen  160 SSPSQ  164 (243)
T ss_pred             cCccc
Confidence            65433

>KOG0151|consensus

Probab=98.97  E-value=2.5e-09  Score=91.17  Aligned_cols=82  Identities=17%  Similarity=0.381  Sum_probs=74.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCC---CCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSS---PHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG  107 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~---~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~  107 (173)
                      .+++|||+||++.++|+.|...|..||+|..++|++.+.   ..+.+.|+||.|-+..++++|++.|+|..+.++.+++.
T Consensus       173 ~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~g  252 (877)
T KOG0151|consen  173 QTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLG  252 (877)
T ss_pred             cccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeec
Confidence            467899999999999999999999999999999999752   24456799999999999999999999999999999999


Q ss_pred             EeeCC
Q psy2141         108 RAITP  112 (173)
Q Consensus       108 ~a~~~  112 (173)
                      |++.-
T Consensus       253 Wgk~V  257 (877)
T KOG0151|consen  253 WGKAV  257 (877)
T ss_pred             ccccc
Confidence            99654

>KOG0226|consensus

Probab=98.94  E-value=1.1e-09  Score=83.21  Aligned_cols=83  Identities=18%  Similarity=0.366  Sum_probs=76.1

Q ss_pred             hhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q psy2141          27 EEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV  106 (173)
Q Consensus        27 ~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v  106 (173)
                      +....+.+||+|-|.-+++++.|-..|.+|-.-...++++|+.+|+++||+||.|.+..++.+|++.|+|.-++.++|++
T Consensus       185 ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpikl  264 (290)
T KOG0226|consen  185 EWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKL  264 (290)
T ss_pred             cCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHh
Confidence            33456889999999999999999999999988888999999999999999999999999999999999999999999987


Q ss_pred             EEe
Q psy2141         107 GRA  109 (173)
Q Consensus       107 ~~a  109 (173)
                      ...
T Consensus       265 RkS  267 (290)
T KOG0226|consen  265 RKS  267 (290)
T ss_pred             hhh
Confidence            554

>KOG0120|consensus

Probab=98.92  E-value=1.4e-09  Score=90.76  Aligned_cols=112  Identities=28%  Similarity=0.460  Sum_probs=95.3

Q ss_pred             CCCcccccCCCCCCCCCcchhhhh------------hhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCC
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEI------------TEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSS   69 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~------------~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~   69 (173)
                      +.|+.+++.++..+.....+....            .......+++||++||...++..++++...||++....++.+..
T Consensus       247 f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~  326 (500)
T KOG0120|consen  247 FEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSA  326 (500)
T ss_pred             hCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccc
Confidence            578999999888775444333222            22234467899999999999999999999999999999999999


Q ss_pred             CCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCCC
Q psy2141          70 PHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPP  113 (173)
Q Consensus        70 ~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~~  113 (173)
                      +|.++||||.+|.+......|+..|||+.+++++|.|..+....
T Consensus       327 ~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~  370 (500)
T KOG0120|consen  327 TGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGA  370 (500)
T ss_pred             cccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccc
Confidence            99999999999999999999999999999999999999987543

>KOG0116|consensus

Probab=98.91  E-value=3.6e-09  Score=87.16  Aligned_cols=86  Identities=29%  Similarity=0.478  Sum_probs=71.4

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      .....+|||+|||.++++++|++.|..||.|+...|..-.-.++..+||||+|.+.++++.+|++ +-..+++++|.|+-
T Consensus       285 ~~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Vee  363 (419)
T KOG0116|consen  285 RADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEE  363 (419)
T ss_pred             eecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEe
Confidence            34456799999999999999999999999999887766432344559999999999999999987 57889999999988


Q ss_pred             eeCCCCC
Q psy2141         109 AITPPNA  115 (173)
Q Consensus       109 a~~~~~~  115 (173)
                      .++....
T Consensus       364 k~~~~~g  370 (419)
T KOG0116|consen  364 KRPGFRG  370 (419)
T ss_pred             ccccccc
Confidence            7764333

>KOG4209|consensus

Probab=98.90  E-value=6.5e-09  Score=79.71  Aligned_cols=85  Identities=18%  Similarity=0.264  Sum_probs=78.3

Q ss_pred             hhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q psy2141          27 EEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV  106 (173)
Q Consensus        27 ~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v  106 (173)
                      ....+.+.+||+|+.+.++.+++...|+.||.+..+.+..|+..++++||+||+|.+.+..+.++. |++..+.|+.+.|
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~v  174 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEV  174 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccccccccee
Confidence            344567899999999999998999999999999999999999999999999999999999999997 9999999999999


Q ss_pred             EEeeCC
Q psy2141         107 GRAITP  112 (173)
Q Consensus       107 ~~a~~~  112 (173)
                      .+.+..
T Consensus       175 t~~r~~  180 (231)
T KOG4209|consen  175 TLKRTN  180 (231)
T ss_pred             eeeeee
Confidence            887755

>KOG1457|consensus

Probab=98.89  E-value=2.1e-08  Score=75.18  Aligned_cols=88  Identities=17%  Similarity=0.260  Sum_probs=70.1

Q ss_pred             hhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccC-CCCCCcceEEEEEEcCHHHHHHHHHhcCCceeC---CeE
Q psy2141          28 EAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQG-SSPHRHKGYGFIEYETKQASNEAISSMNLFDLG---GQY  103 (173)
Q Consensus        28 ~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~-~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~---g~~  103 (173)
                      +...-+||||.+||.++...+|..+|..|.--+.+.+... +..+-.+-+||++|.+..+|.+|+..|||..++   +..
T Consensus        30 ~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~st  109 (284)
T KOG1457|consen   30 EPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGST  109 (284)
T ss_pred             cccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCce
Confidence            3445899999999999999999999999866666655442 222223579999999999999999999998876   688


Q ss_pred             EEEEEeeCCCCC
Q psy2141         104 LRVGRAITPPNA  115 (173)
Q Consensus       104 l~v~~a~~~~~~  115 (173)
                      |+++.++.....
T Consensus       110 LhiElAKSNtK~  121 (284)
T KOG1457|consen  110 LHIELAKSNTKR  121 (284)
T ss_pred             eEeeehhcCccc
Confidence            999998854433

>KOG1548|consensus

Probab=98.86  E-value=8.7e-09  Score=81.46  Aligned_cols=82  Identities=27%  Similarity=0.370  Sum_probs=74.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeE--------EEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKY--------CKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG  101 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~--------~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g  101 (173)
                      .....|||.|||.++|.+++.++|+++|-|..        |++-++. .|+.+|=|.+.|...++++-|++.|++..+.|
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            34667999999999999999999999997754        7888884 69999999999999999999999999999999


Q ss_pred             eEEEEEEeeCC
Q psy2141         102 QYLRVGRAITP  112 (173)
Q Consensus       102 ~~l~v~~a~~~  112 (173)
                      +.|+|..|+-.
T Consensus       211 ~~~rVerAkfq  221 (382)
T KOG1548|consen  211 KKLRVERAKFQ  221 (382)
T ss_pred             cEEEEehhhhh
Confidence            99999998743

>KOG4660|consensus

Probab=98.85  E-value=1.9e-09  Score=89.73  Aligned_cols=72  Identities=15%  Similarity=0.378  Sum_probs=66.1

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLR  105 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~  105 (173)
                      ..+.++|+|-|||..+++++|+++|+.||.|+.++....     .+|..||+|.+..+|++|++.|++.++.|+.|+
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~-----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN-----KRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc-----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            346889999999999999999999999999999776444     589999999999999999999999999999888

>KOG0106|consensus

Probab=98.82  E-value=6.3e-09  Score=78.36  Aligned_cols=72  Identities=25%  Similarity=0.554  Sum_probs=66.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCC
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITP  112 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~  112 (173)
                      ..+|||+||+.+.+.+|+.+|..||.+..+.+.        .||+||+|.+..+|..|+..||+.++.|-.+.|.++...
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            469999999999999999999999999999874        468999999999999999999999999988999998853

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

Probab=98.77  E-value=7.5e-08  Score=64.03  Aligned_cols=79  Identities=15%  Similarity=0.235  Sum_probs=68.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhcc--CceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeC----CeEEEE
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAF--GPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLG----GQYLRV  106 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~--G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~----g~~l~v  106 (173)
                      +||.|.|||-..+.++|.+++...  |....+.++.|..++.+.|||||.|.+.+.+.+-.+.++|..|.    .+...|
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            689999999999999999988653  66677888889889999999999999999999999999998886    355577


Q ss_pred             EEeeC
Q psy2141         107 GRAIT  111 (173)
Q Consensus       107 ~~a~~  111 (173)
                      .||+-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            77653

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

>KOG4454|consensus

Probab=98.71  E-value=5.3e-09  Score=78.11  Aligned_cols=78  Identities=15%  Similarity=0.210  Sum_probs=70.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      ..+||||+|+...++|+.|.++|-+-|+|.++.|..++ .++.| ||||.|.++....-|++.|||..+.++.+.+..-.
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~   85 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            46899999999999999999999999999999998885 66666 99999999999999999999999999888876644

>KOG0147|consensus

Probab=98.59  E-value=1.8e-08  Score=83.84  Aligned_cols=88  Identities=16%  Similarity=0.251  Sum_probs=81.2

Q ss_pred             hhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2141          22 IDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG  101 (173)
Q Consensus        22 ~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g  101 (173)
                      ...+..+++..+++|+.-|+...++.+|.++|+.+|+|..|+++.|+.++.++|.+||+|.+.+....|| .|.|..+.|
T Consensus       169 ~~~l~~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg  247 (549)
T KOG0147|consen  169 SRILSPEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLG  247 (549)
T ss_pred             cccCCchHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccC
Confidence            4455667788999999999999999999999999999999999999999999999999999999999999 889999999


Q ss_pred             eEEEEEEee
Q psy2141         102 QYLRVGRAI  110 (173)
Q Consensus       102 ~~l~v~~a~  110 (173)
                      .+|.|....
T Consensus       248 ~pv~vq~sE  256 (549)
T KOG0147|consen  248 VPVIVQLSE  256 (549)
T ss_pred             ceeEecccH
Confidence            999997754

>KOG1190|consensus

Probab=98.56  E-value=5.1e-07  Score=73.08  Aligned_cols=76  Identities=18%  Similarity=0.296  Sum_probs=69.7

Q ss_pred             CCeEEEcCCCCC-CCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          32 YNRIYVASIHPD-LTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        32 ~~~l~V~nLp~~-~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      ...|.|.||..+ +|.+.|.-+|.-||.|.+++|++.+     +--|.|.|.+...|+-|++.|+|..|.|++|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk-----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK-----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC-----CcceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            578889999865 9999999999999999999999986     4679999999999999999999999999999999988


Q ss_pred             CC
Q psy2141         111 TP  112 (173)
Q Consensus       111 ~~  112 (173)
                      ..
T Consensus       372 H~  373 (492)
T KOG1190|consen  372 HT  373 (492)
T ss_pred             Cc
Confidence            44

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.43  E-value=1.2e-06  Score=56.10  Aligned_cols=69  Identities=13%  Similarity=0.246  Sum_probs=47.5

Q ss_pred             CeEEEcCCCCCCCHHH----HHHHhhccC-ceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q psy2141          33 NRIYVASIHPDLTEED----IKSVFEAFG-PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG  107 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~----L~~~F~~~G-~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~  107 (173)
                      ..|||.|||.+.....    |++++..+| +|..+.          .+.|++.|.+.+.|.+|.+.|+|..+.|++|.|+
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            3589999999887755    566666665 676652          4689999999999999999999999999999999


Q ss_pred             EeeC
Q psy2141         108 RAIT  111 (173)
Q Consensus       108 ~a~~  111 (173)
                      +...
T Consensus        73 ~~~~   76 (90)
T PF11608_consen   73 FSPK   76 (90)
T ss_dssp             SS--
T ss_pred             EcCC
Confidence            9743

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

>KOG4211|consensus

Probab=98.42  E-value=1.5e-06  Score=71.74  Aligned_cols=80  Identities=16%  Similarity=0.257  Sum_probs=67.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ....-|-+.+|||++|+++|.++|+.+ .|+.+.+.+.  +|+..|-|||+|.+.+++++|++. +...+..+-|.|--+
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPRR--NGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVFTA   83 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcC-ceeEEEEecc--CCCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEEcc
Confidence            445667889999999999999999999 5888777664  799999999999999999999965 778888899988666


Q ss_pred             eCCC
Q psy2141         110 ITPP  113 (173)
Q Consensus       110 ~~~~  113 (173)
                      ...+
T Consensus        84 ~~~e   87 (510)
T KOG4211|consen   84 GGAE   87 (510)
T ss_pred             CCcc
Confidence            4443

>KOG4211|consensus

Probab=98.41  E-value=9.5e-07  Score=72.95  Aligned_cols=107  Identities=18%  Similarity=0.224  Sum_probs=79.5

Q ss_pred             CCCCcccccCCCCCCCCCcchhhhhhhhh-CCCCeEEEcCCCCCCCHHHHHHHhhccCceeE-EEEccCCCCCCcceEEE
Q psy2141           1 MQHFPHVQVGRPSNMPQAQSVIDEITEEA-KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKY-CKLQQGSSPHRHKGYGF   78 (173)
Q Consensus         1 ~l~gr~i~v~~~~~~~~~~~~~~~~~~~~-~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~-~~i~~~~~~g~~~g~af   78 (173)
                      +|+.|.|.|..... .+++..++...... .+...|-+.+||+.|++++|.++|+..--|.. +.++.+ ..+++.|-||
T Consensus        72 ~mg~RYIEVf~~~~-~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d-~rgR~tGEAf  149 (510)
T KOG4211|consen   72 SMGHRYIEVFTAGG-AEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMD-QRGRPTGEAF  149 (510)
T ss_pred             HhCCceEEEEccCC-ccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeecc-CCCCcccceE
Confidence            36788999877643 22333333333222 35678899999999999999999998754444 556666 4788999999


Q ss_pred             EEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          79 IEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        79 v~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      |.|.+.+.|++|+.. |...|+.+-|.|-.+.
T Consensus       150 VqF~sqe~ae~Al~r-hre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  150 VQFESQESAEIALGR-HRENIGHRYIEVFRSS  180 (510)
T ss_pred             EEecCHHHHHHHHHH-HHHhhccceEEeehhH
Confidence            999999999999976 6778888888885543

>KOG1456|consensus

Probab=98.34  E-value=1.2e-06  Score=70.32  Aligned_cols=128  Identities=13%  Similarity=0.120  Sum_probs=89.1

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          30 KLYNRIYVASIHPD-LTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        30 ~~~~~l~V~nLp~~-~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      .+.+.+.|.+|... ++.+.|..+|-.||.|+++++++.+     .|-|.|++.+....++|+..||+..+-|.+|.|+.
T Consensus       285 ~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~  359 (494)
T KOG1456|consen  285 APGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCV  359 (494)
T ss_pred             CCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEEee
Confidence            45788999999875 8889999999999999999999875     78999999999999999999999999999999988


Q ss_pred             eeCCCCCCCCCCCCCCCCCCCChHHHHHHHHHHHhhhhhcccchhhhhhhhhhHHHHH
Q psy2141         109 AITPPNALHSSKGPAPSTSHMPTAAAVAAAAATAKIQAMDGGATNAVGVLSKLSQVFF  166 (173)
Q Consensus       109 a~~~~~~~~~~~~~~~~~~~~~~~~~~aa~a~~~~~~a~~~~~~~~~~~~~~~~~~~~  166 (173)
                      ++...-....+=.-+...+..    -.-+.+-..+-.+..-++.|+++.++++.++||
T Consensus       360 SkQ~~v~~~~pflLpDgSpSf----Kdys~SkNnRFssp~qAsKNrIq~Ps~vLHffN  413 (494)
T KOG1456|consen  360 SKQNFVSPVQPFLLPDGSPSF----KDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFN  413 (494)
T ss_pred             ccccccccCCceecCCCCcch----hhcccccccccCChhHhhcccccCCcceeEEec
Confidence            764311110100001111110    001122223333334445677888888777776

>KOG1457|consensus

Probab=98.28  E-value=7.8e-07  Score=66.90  Aligned_cols=66  Identities=15%  Similarity=0.358  Sum_probs=54.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCcee
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDL   99 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i   99 (173)
                      +...||||.||..+++|++|+.+|+.|..-..++|...  .  .-..||++|++.+.|..|+..|+|..|
T Consensus       208 ~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~--g~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  208 RACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--G--GMPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             hhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--C--CcceEeecHHHHHHHHHHHHHhhccee
Confidence            44679999999999999999999999976566665322  2  245899999999999999999998665

>KOG4849|consensus

Probab=98.23  E-value=1.1e-06  Score=70.07  Aligned_cols=73  Identities=16%  Similarity=0.240  Sum_probs=65.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccC--ceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEE
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFG--PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYL  104 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G--~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l  104 (173)
                      .-.+|||||-|.+|+++|.+.+...|  .+.++++..++.+|++||||+|...+.....+-++.|..++|+|+.=
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P  154 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSP  154 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCC
Confidence            44799999999999999999998877  67788899999999999999999999999999999999999999643

>KOG4206|consensus

Probab=98.16  E-value=9.5e-06  Score=61.05  Aligned_cols=77  Identities=19%  Similarity=0.334  Sum_probs=69.0

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeC-CeEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLG-GQYLRVG  107 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~-g~~l~v~  107 (173)
                      ..+...+|+.|||.+++.+.|..+|.+|..-++++++..+     ++.|||+|.+...+..|...|++..|- .+.+.|.
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~  217 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQIT  217 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEec
Confidence            5678899999999999999999999999988999988764     789999999999999999999998887 7888887


Q ss_pred             Eee
Q psy2141         108 RAI  110 (173)
Q Consensus       108 ~a~  110 (173)
                      +++
T Consensus       218 ~a~  220 (221)
T KOG4206|consen  218 FAK  220 (221)
T ss_pred             ccC
Confidence            764

>KOG4210|consensus

Probab=98.07  E-value=2.9e-06  Score=67.19  Aligned_cols=88  Identities=20%  Similarity=0.399  Sum_probs=78.7

Q ss_pred             CCCCeEE-EcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          30 KLYNRIY-VASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        30 ~~~~~l~-V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ....++| |+++++.+++++|+..|..+|.|..+++..++.++..+||++++|.+......++.. +...+.++++.+.+
T Consensus       182 ~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~  260 (285)
T KOG4210|consen  182 GPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEE  260 (285)
T ss_pred             CccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCccccccc
Confidence            3455666 999999999999999999999999999999999999999999999999999999877 88999999999999


Q ss_pred             eeCCCCCCCC
Q psy2141         109 AITPPNALHS  118 (173)
Q Consensus       109 a~~~~~~~~~  118 (173)
                      ..+.+.....
T Consensus       261 ~~~~~~~~~~  270 (285)
T KOG4210|consen  261 DEPRPKSDGG  270 (285)
T ss_pred             CCCCcccccc
Confidence            9887666444

>KOG1995|consensus

Probab=98.05  E-value=4.1e-06  Score=66.85  Aligned_cols=84  Identities=24%  Similarity=0.242  Sum_probs=75.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeE--------EEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKY--------CKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG  101 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~--------~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g  101 (173)
                      ....+|||-+||..+++++|.++|.++|.|..        +.|-++++|+..||-|.|.|.+...|+.|+.-+++..+.+
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            44678999999999999999999999997743        6677889999999999999999999999999999999999


Q ss_pred             eEEEEEEeeCCC
Q psy2141         102 QYLRVGRAITPP  113 (173)
Q Consensus       102 ~~l~v~~a~~~~  113 (173)
                      ..|+|..+..+.
T Consensus       144 n~ikvs~a~~r~  155 (351)
T KOG1995|consen  144 NTIKVSLAERRT  155 (351)
T ss_pred             CCchhhhhhhcc
Confidence            999998887554

>KOG0106|consensus

Probab=97.90  E-value=1.3e-05  Score=60.51  Aligned_cols=73  Identities=18%  Similarity=0.432  Sum_probs=63.7

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ....+.+.|.|++..+.+.+|.+.|..+|.+....+        ..+++||+|...+++.+|+..|++..+.++.|++..
T Consensus        96 ~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen   96 SRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             ccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeeecc
Confidence            455778999999999999999999999999854433        367999999999999999999999999999999944


Q ss_pred             e
Q psy2141         109 A  109 (173)
Q Consensus       109 a  109 (173)
                      .
T Consensus       168 ~  168 (216)
T KOG0106|consen  168 N  168 (216)
T ss_pred             c
Confidence            3

>KOG3152|consensus

Probab=97.81  E-value=1.8e-05  Score=60.71  Aligned_cols=73  Identities=16%  Similarity=0.358  Sum_probs=62.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCC--------CCcceE----EEEEEcCHHHHHHHHHhcCCce
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSP--------HRHKGY----GFIEYETKQASNEAISSMNLFD   98 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~--------g~~~g~----afv~f~~~~~a~~a~~~l~g~~   98 (173)
                      ..-.||+++||+.++...|+++|+.||.|-.|.+.....+        |.+++.    |-|+|.+...|.++...||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            4568999999999999999999999999999988776544        333332    5699999999999999999999


Q ss_pred             eCCeE
Q psy2141          99 LGGQY  103 (173)
Q Consensus        99 i~g~~  103 (173)
                      |+|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99964

>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=97.81  E-value=5.6e-05  Score=51.15  Aligned_cols=58  Identities=22%  Similarity=0.516  Sum_probs=38.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCC
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNL   96 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g   96 (173)
                      +.|+|.+++..++-++|++.|+.||.|..|.+...      ..-|+|.|.+.+.|+.|+..+..
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~   59 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKE   59 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHH
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHh
Confidence            46888899999999999999999999999998665      34799999999999999987643

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.77  E-value=7.2e-05  Score=59.61  Aligned_cols=79  Identities=25%  Similarity=0.403  Sum_probs=60.4

Q ss_pred             CeEEEcCCCCCCCHHH------HHHHhhccCceeEEEEccCCCCCC-cce-E-EEEEEcCHHHHHHHHHhcCCceeCCeE
Q psy2141          33 NRIYVASIHPDLTEED------IKSVFEAFGPIKYCKLQQGSSPHR-HKG-Y-GFIEYETKQASNEAISSMNLFDLGGQY  103 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~------L~~~F~~~G~v~~~~i~~~~~~g~-~~g-~-afv~f~~~~~a~~a~~~l~g~~i~g~~  103 (173)
                      .-+||-+||+.+..++      -.++|.+||.|..+.+.+...+-. ..+ + .||+|.+.++|.+||...+|..++|+.
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            3589999998765554      356899999999987755321111 122 2 399999999999999999999999999


Q ss_pred             EEEEEeeC
Q psy2141         104 LRVGRAIT  111 (173)
Q Consensus       104 l~v~~a~~  111 (173)
                      |+..|...
T Consensus       195 lkatYGTT  202 (480)
T COG5175         195 LKATYGTT  202 (480)
T ss_pred             EeeecCch
Confidence            99988653

>KOG1855|consensus

Probab=97.73  E-value=2.9e-05  Score=63.42  Aligned_cols=72  Identities=22%  Similarity=0.298  Sum_probs=58.7

Q ss_pred             hhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccC---CCCC--C--------cceEEEEEEcCHHHHHHHH
Q psy2141          25 ITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQG---SSPH--R--------HKGYGFIEYETKQASNEAI   91 (173)
Q Consensus        25 ~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~---~~~g--~--------~~g~afv~f~~~~~a~~a~   91 (173)
                      ...++.+.++|.+.|||.+-.-+.|.++|+.+|.|..|+|...   ..+.  .        .+-+|+|+|...+.|.+|.
T Consensus       224 ~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~  303 (484)
T KOG1855|consen  224 FDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAR  303 (484)
T ss_pred             ccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHH
Confidence            3344568999999999999777999999999999999998765   2221  1        2458999999999999999


Q ss_pred             HhcCC
Q psy2141          92 SSMNL   96 (173)
Q Consensus        92 ~~l~g   96 (173)
                      +.|+.
T Consensus       304 e~~~~  308 (484)
T KOG1855|consen  304 ELLNP  308 (484)
T ss_pred             Hhhch
Confidence            98865

>KOG2314|consensus

Probab=97.67  E-value=0.00027  Score=59.74  Aligned_cols=77  Identities=21%  Similarity=0.201  Sum_probs=62.4

Q ss_pred             CCeEEEcCCCCCCC------HHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeC-CeEE
Q psy2141          32 YNRIYVASIHPDLT------EEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLG-GQYL  104 (173)
Q Consensus        32 ~~~l~V~nLp~~~~------e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~-g~~l  104 (173)
                      ...|+|.|+|.--.      ..-|..+|+++|++..+.+.-+..+| .+||.|++|.+..+|+.|++.|||+.++ .++.
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            56789999996321      13467789999999999999885444 8999999999999999999999998887 4667


Q ss_pred             EEEEe
Q psy2141         105 RVGRA  109 (173)
Q Consensus       105 ~v~~a  109 (173)
                      .|..-
T Consensus       137 ~v~~f  141 (698)
T KOG2314|consen  137 FVRLF  141 (698)
T ss_pred             Eeehh
Confidence            77543

>KOG0120|consensus

Probab=97.65  E-value=0.00022  Score=60.17  Aligned_cols=64  Identities=14%  Similarity=0.283  Sum_probs=52.3

Q ss_pred             HHHHHhhccCceeEEEEccCC---CCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeC
Q psy2141          48 DIKSVFEAFGPIKYCKLQQGS---SPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAIT  111 (173)
Q Consensus        48 ~L~~~F~~~G~v~~~~i~~~~---~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~  111 (173)
                      +++.-+++||.|..|.+.++-   ...-..|.-||+|.+.+++++|++.|+|.++.|+.|...|-..
T Consensus       425 dvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  425 DVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             HHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence            355556689999999998872   2233466789999999999999999999999999999988643

>KOG4307|consensus

Probab=97.58  E-value=0.00029  Score=60.99  Aligned_cols=76  Identities=13%  Similarity=0.222  Sum_probs=66.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCce-eEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPI-KYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v-~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      .+.|-+.|+|++++-+||.++|..|-.+ .+|.+.+. ..|...|-|.|.|++.++|.+|...|+++.|..++|++..
T Consensus       867 p~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  867 PRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CeEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            3478899999999999999999999654 34555555 6899999999999999999999999999999999998764

>KOG1190|consensus

Probab=97.56  E-value=0.00026  Score=57.71  Aligned_cols=78  Identities=19%  Similarity=0.261  Sum_probs=64.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCe-EEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQ-YLRVGR  108 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~-~l~v~~  108 (173)
                      .++.+|...|+|.+++|++|+..|..-|-..+.....    ++.+.++++.+.+.++|-.|+..++.+.+++. .|+|++
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff----~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSF  487 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF----QKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSF  487 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCceEEeeeec----CCCcceeecccCChhHhhhhccccccccCCCCceEEEEe
Confidence            4567999999999999999999999988665443322    23467999999999999999999999988864 889999


Q ss_pred             eeC
Q psy2141         109 AIT  111 (173)
Q Consensus       109 a~~  111 (173)
                      ++.
T Consensus       488 Sks  490 (492)
T KOG1190|consen  488 SKS  490 (492)
T ss_pred             ecc
Confidence            864

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.51  E-value=0.00076  Score=45.13  Aligned_cols=78  Identities=17%  Similarity=0.194  Sum_probs=52.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEE-EccCC------CCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeE
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCK-LQQGS------SPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQY  103 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~-i~~~~------~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~  103 (173)
                      ..+.|.|-+.|.. ....+.+.|++||.|.+.. +.++.      .......+-.|.|.+..+|.+|+.. ||..+.|..
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEETTCE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEEcCcE
Confidence            4567888899988 4567778999999998764 11110      0112356899999999999999966 999999865


Q ss_pred             E-EEEEee
Q psy2141         104 L-RVGRAI  110 (173)
Q Consensus       104 l-~v~~a~  110 (173)
                      | -|.+.+
T Consensus        83 mvGV~~~~   90 (100)
T PF05172_consen   83 MVGVKPCD   90 (100)
T ss_dssp             EEEEEE-H
T ss_pred             EEEEEEcH
Confidence            5 466654

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.

>KOG0129|consensus

Probab=97.40  E-value=0.00055  Score=57.30  Aligned_cols=69  Identities=23%  Similarity=0.391  Sum_probs=61.9

Q ss_pred             hhhhhCCCCeEEEcCCCCCCCHHHHHHHhh-ccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHh
Q psy2141          25 ITEEAKLYNRIYVASIHPDLTEEDIKSVFE-AFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS   93 (173)
Q Consensus        25 ~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~-~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~   93 (173)
                      .....++.+|||||+||.-++.++|-.+|. -||.|.-+-|=.|.+-+-.+|-|-|+|.+...--+||..
T Consensus       363 ~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  363 HNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            344557899999999999999999999998 799999999999977888999999999999999999864

>KOG1548|consensus

Probab=97.34  E-value=0.00099  Score=53.33  Aligned_cols=77  Identities=13%  Similarity=0.231  Sum_probs=60.9

Q ss_pred             CCCCeEEEcCCC----CCCC-------HHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCce
Q psy2141          30 KLYNRIYVASIH----PDLT-------EEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFD   98 (173)
Q Consensus        30 ~~~~~l~V~nLp----~~~~-------e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~   98 (173)
                      +..++|.+.|+=    +..+       .++|++-.++||.|..+.+.-    ..+.|.+-|.|.+.++|..||+.|+|.-
T Consensus       263 r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d----~hPdGvvtV~f~n~eeA~~ciq~m~GR~  338 (382)
T KOG1548|consen  263 RADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYD----RHPDGVVTVSFRNNEEADQCIQTMDGRW  338 (382)
T ss_pred             cCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEec----cCCCceeEEEeCChHHHHHHHHHhcCee
Confidence            347789999883    2333       245666678999999997642    3468999999999999999999999999


Q ss_pred             eCCeEEEEEEee
Q psy2141          99 LGGQYLRVGRAI  110 (173)
Q Consensus        99 i~g~~l~v~~a~  110 (173)
                      ++||.|.-..-.
T Consensus       339 fdgRql~A~i~D  350 (382)
T KOG1548|consen  339 FDGRQLTASIWD  350 (382)
T ss_pred             ecceEEEEEEeC
Confidence            999999776543

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.19  E-value=0.0014  Score=38.67  Aligned_cols=52  Identities=23%  Similarity=0.525  Sum_probs=41.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHH
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI   91 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~   91 (173)
                      +.|-|.+.+.+.. +.+...|..||.|..+.+..      ...+.++.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~~------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVPE------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcCC------CCcEEEEEECCHHHHHhhC
Confidence            4677888887755 44555889999999988752      3568999999999999884

>KOG0105|consensus

Probab=97.17  E-value=0.0056  Score=45.21  Aligned_cols=63  Identities=21%  Similarity=0.377  Sum_probs=56.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCcee
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDL   99 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i   99 (173)
                      .....|.|.+||..-++++|++...+-|.|....+.+|       |++.|+|...++.+-|++.|+...+
T Consensus       113 rSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~  175 (241)
T KOG0105|consen  113 RSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKF  175 (241)
T ss_pred             ccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhccccc
Confidence            44678999999999999999999999999999998877       5899999999999999999988554

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.12  E-value=0.0045  Score=44.04  Aligned_cols=77  Identities=10%  Similarity=0.268  Sum_probs=53.4

Q ss_pred             hhhhCCCCeEEEcCCC-----C-CCCH---HHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCC
Q psy2141          26 TEEAKLYNRIYVASIH-----P-DLTE---EDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNL   96 (173)
Q Consensus        26 ~~~~~~~~~l~V~nLp-----~-~~~e---~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g   96 (173)
                      ....++..||.|.-+.     . ...+   .+|.+.|..||.+.-++++.+        .-.|+|.+-++|.+|+ .++|
T Consensus        21 ~~~GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaal-s~dg   91 (146)
T PF08952_consen   21 SSQGPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAAL-SLDG   91 (146)
T ss_dssp             -----TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHH-HGCC
T ss_pred             HhcCCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHH-ccCC
Confidence            4455678888887665     1 2222   267888899999988888654        4689999999999999 6799


Q ss_pred             ceeCCeEEEEEEeeC
Q psy2141          97 FDLGGQYLRVGRAIT  111 (173)
Q Consensus        97 ~~i~g~~l~v~~a~~  111 (173)
                      .++.|+.|+|+...+
T Consensus        92 ~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   92 IQVNGRTLKIRLKTP  106 (146)
T ss_dssp             SEETTEEEEEEE---
T ss_pred             cEECCEEEEEEeCCc
Confidence            999999999987654

; PDB: 1UFW_A 2DNR_A.

>KOG1456|consensus

Probab=97.11  E-value=0.0027  Score=51.46  Aligned_cols=77  Identities=10%  Similarity=0.128  Sum_probs=61.5

Q ss_pred             CCCeEEEcCCC--CCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC--eEEEE
Q psy2141          31 LYNRIYVASIH--PDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG--QYLRV  106 (173)
Q Consensus        31 ~~~~l~V~nLp--~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g--~~l~v  106 (173)
                      +...|.+.=|.  +-++.+-|..+....|+|.++.|++.  +|   --|.|+|.+.+.|++|...|||..|.-  .+|+|
T Consensus       119 pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ng---VQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKI  193 (494)
T KOG1456|consen  119 PNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NG---VQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKI  193 (494)
T ss_pred             CCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cc---eeeEEeechhHHHHHHHhhcccccccccceeEEE
Confidence            34444444443  45888999999999999999988764  33   358999999999999999999988763  68899


Q ss_pred             EEeeCC
Q psy2141         107 GRAITP  112 (173)
Q Consensus       107 ~~a~~~  112 (173)
                      +|+++.
T Consensus       194 eyAkP~  199 (494)
T KOG1456|consen  194 EYAKPT  199 (494)
T ss_pred             EecCcc
Confidence            999865

>KOG0112|consensus

Probab=97.01  E-value=0.00079  Score=59.72  Aligned_cols=78  Identities=28%  Similarity=0.477  Sum_probs=68.8

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC--eEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG--QYLRV  106 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g--~~l~v  106 (173)
                      ....+.+|+++|...+....|...|..||.|..+.+-.      ..-|+++.|.+...++.|++.|-|..+++  ++++|
T Consensus       452 st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h------gq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rv  525 (975)
T KOG0112|consen  452 STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH------GQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRV  525 (975)
T ss_pred             cccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc------CCcceeeecccCccchhhHHHHhcCcCCCCCccccc
Confidence            35678899999999999999999999999999987633      25699999999999999999999999987  78999


Q ss_pred             EEeeCC
Q psy2141         107 GRAITP  112 (173)
Q Consensus       107 ~~a~~~  112 (173)
                      .++...
T Consensus       526 dla~~~  531 (975)
T KOG0112|consen  526 DLASPP  531 (975)
T ss_pred             ccccCC
Confidence            998754

>KOG1365|consensus

Probab=96.95  E-value=0.00098  Score=54.12  Aligned_cols=80  Identities=16%  Similarity=0.260  Sum_probs=65.8

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCc-eeE--EEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGP-IKY--CKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLR  105 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~-v~~--~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~  105 (173)
                      .++...|-+.+||++.+.++|..+|..|.. |..  +.++.+ ..|+..|-|||+|.+.+.|..|...-+.+....|-|.
T Consensus       277 ~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N-~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiE  355 (508)
T KOG1365|consen  277 TRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN-GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIE  355 (508)
T ss_pred             CCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc-CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEE
Confidence            344678889999999999999999999863 333  677777 5789999999999999999999988777777788888


Q ss_pred             EEEe
Q psy2141         106 VGRA  109 (173)
Q Consensus       106 v~~a  109 (173)
                      |-.+
T Consensus       356 vfp~  359 (508)
T KOG1365|consen  356 VFPC  359 (508)
T ss_pred             Eeec
Confidence            7544

>KOG0128|consensus

Probab=96.93  E-value=0.00063  Score=59.98  Aligned_cols=79  Identities=15%  Similarity=0.159  Sum_probs=69.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeC
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAIT  111 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~  111 (173)
                      ...|+|.|.|+..|.++|+.++.++|.+++++++..+ .|+.+|.++|.|.+..++.++....+...+.-+.+.|....+
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            5679999999999999999999999999999988885 899999999999999999999888887777777777766444

>KOG0129|consensus

Probab=96.91  E-value=0.0027  Score=53.26  Aligned_cols=62  Identities=24%  Similarity=0.485  Sum_probs=46.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEcc-C--CCCCCcce---EEEEEEcCHHHHHHHHHh
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQ-G--SSPHRHKG---YGFIEYETKQASNEAISS   93 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~-~--~~~g~~~g---~afv~f~~~~~a~~a~~~   93 (173)
                      -.++||||+||++++|+.|...|..||.+.- .... .  +.--.++|   |.|+.|+++.....-+..
T Consensus       258 ~S~KVFvGGlp~dise~~i~~~F~~FGs~~V-dWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~a  325 (520)
T KOG0129|consen  258 YSRKVFVGGLPWDITEAQINASFGQFGSVKV-DWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSA  325 (520)
T ss_pred             cccceeecCCCccccHHHHHhhcccccceEe-ecCCCccccccCCCCCcccEEEEEecchHHHHHHHHH
Confidence            3679999999999999999999999997532 2221 0  11122466   999999999988776544

>KOG1996|consensus

Probab=96.91  E-value=0.0038  Score=49.14  Aligned_cols=65  Identities=18%  Similarity=0.251  Sum_probs=53.9

Q ss_pred             HHHHHHHhhccCceeEEEEccCCCCCCcceE-EEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          46 EEDIKSVFEAFGPIKYCKLQQGSSPHRHKGY-GFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        46 e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~-afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      ++++++...+||+|..|.|...+........ -||+|...++|.+|+-.|||..++|+.++-++-.
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            3567888899999999988887644444444 5999999999999999999999999998877654

>KOG0128|consensus

Probab=96.84  E-value=5.1e-05  Score=66.60  Aligned_cols=72  Identities=19%  Similarity=0.396  Sum_probs=62.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCe
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQ  102 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~  102 (173)
                      ...++||.||+..+.+.+|...|..+|.+..+++.-.+..++.+|.|+++|...+.+.+|+....++.++..
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK~  737 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGKI  737 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhhhh
Confidence            356899999999999999999999999988887776667899999999999999999999977666555533

>KOG2193|consensus

Probab=96.60  E-value=0.0017  Score=53.45  Aligned_cols=77  Identities=23%  Similarity=0.445  Sum_probs=59.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCC-ceeCCeEEEEEEeeC
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNL-FDLGGQYLRVGRAIT  111 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g-~~i~g~~l~v~~a~~  111 (173)
                      .++|+|||.+..+..+|+.+|...---..-.++.      .-||+||.+.+..-+.+|++.++| .++.|.++.+....+
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            4799999999999999999997641111111111      147999999999999999999999 568899999988876


Q ss_pred             CCCC
Q psy2141         112 PPNA  115 (173)
Q Consensus       112 ~~~~  115 (173)
                      +...
T Consensus        76 kkqr   79 (584)
T KOG2193|consen   76 KKQR   79 (584)
T ss_pred             HHHH
Confidence            6544

>KOG0112|consensus

Probab=96.59  E-value=0.00055  Score=60.67  Aligned_cols=82  Identities=15%  Similarity=0.302  Sum_probs=68.7

Q ss_pred             hhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q psy2141          27 EEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV  106 (173)
Q Consensus        27 ~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v  106 (173)
                      ++...+++||+|||+..+++.+|+..|..+|.|.+|.|-+.+ -+..--|+||.|.+...+..++..+.+..|....+++
T Consensus       367 DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~  445 (975)
T KOG0112|consen  367 DDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRI  445 (975)
T ss_pred             cchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCcccc
Confidence            344568999999999999999999999999999999987764 2334458999999999999999999998887666666


Q ss_pred             EEe
Q psy2141         107 GRA  109 (173)
Q Consensus       107 ~~a  109 (173)
                      .+.
T Consensus       446 glG  448 (975)
T KOG0112|consen  446 GLG  448 (975)
T ss_pred             ccc
Confidence            555

>KOG2416|consensus

Probab=96.48  E-value=0.003  Score=53.95  Aligned_cols=75  Identities=9%  Similarity=0.112  Sum_probs=61.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhc-cCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCcee---CCeEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEA-FGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDL---GGQYLR  105 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~-~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i---~g~~l~  105 (173)
                      ...+.|||.||-.-+|.-+|+.++.. .|.|....|  |+    -+..|||.|.+.++|.+...+|||..|   +.+.|.
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--Dk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~  515 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--DK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLI  515 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHHHH--HH----hhcceeEecccHHHHHHHHHHHhccccCCCCCceeE
Confidence            45789999999988999999999994 556666522  22    467899999999999999999999776   457888


Q ss_pred             EEEee
Q psy2141         106 VGRAI  110 (173)
Q Consensus       106 v~~a~  110 (173)
                      +.|..
T Consensus       516 adf~~  520 (718)
T KOG2416|consen  516 ADFVR  520 (718)
T ss_pred             eeecc
Confidence            88865

>KOG2202|consensus

Probab=96.45  E-value=0.0016  Score=50.21  Aligned_cols=63  Identities=13%  Similarity=0.240  Sum_probs=50.0

Q ss_pred             HHHHHhh-ccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeC
Q psy2141          48 DIKSVFE-AFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAIT  111 (173)
Q Consensus        48 ~L~~~F~-~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~  111 (173)
                      ++...|+ +||.|+.+.+-.+ ..-...|-.+|.|...++|++|++.||+.-+.|++|...+...
T Consensus        84 d~f~E~~~kygEiee~~Vc~N-l~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDN-LGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhcc-cchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            3444444 8999998855443 3344588899999999999999999999999999999888653

>KOG1365|consensus

Probab=96.40  E-value=0.021  Score=46.64  Aligned_cols=73  Identities=15%  Similarity=0.233  Sum_probs=54.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcc----CceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAF----GPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV  106 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~----G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v  106 (173)
                      .-.|-+.+||+++++.++.++|..-    |..+.+.+++. .+|+..|=|||.|...++|+.|+.. |...++.|-|.+
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIEl  237 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIEL  237 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHH
Confidence            3457778999999999999999732    23455555554 4788999999999999999999976 544555554433

>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=96.15  E-value=0.056  Score=36.81  Aligned_cols=69  Identities=9%  Similarity=0.028  Sum_probs=50.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccC-ceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFG-PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG  101 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G-~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g  101 (173)
                      ....+.+...|..++.++|..+.+.+- .|..++|++|.  ..++-.+.+.|.+.+.|..-.+.+||+.+.-
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            344455555555566667766655553 67788999873  3367789999999999999999999988754

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG4307|consensus

Probab=96.04  E-value=0.0084  Score=52.29  Aligned_cols=78  Identities=15%  Similarity=0.099  Sum_probs=64.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeE-EEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKY-CKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~-~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ....|||..||..+++.++..+|..--.|++ |.|.+.. +++.++.|||.|...+.+..|...-+.+-++.+.|+|+-.
T Consensus       433 ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si  511 (944)
T KOG4307|consen  433 AGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSI  511 (944)
T ss_pred             ccceEEeccCCccccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEeech
Confidence            3668999999999999999999998777777 6666664 7888999999999988888887665666677788888654

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=95.98  E-value=0.063  Score=32.62  Aligned_cols=55  Identities=11%  Similarity=0.241  Sum_probs=43.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcc---CceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhc
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAF---GPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM   94 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~---G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l   94 (173)
                      ..+|+|.++.. ++.++++.+|..|   .....+..+-|.       -|-|.|.+.+.|.+|+..|
T Consensus         5 peavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            46799999865 7889999999998   134577777663       5789999999999999764

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.93  E-value=0.04  Score=39.09  Aligned_cols=73  Identities=15%  Similarity=0.275  Sum_probs=55.5

Q ss_pred             hCCCCeEEEcCCCCCCCH-H---HHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEE
Q psy2141          29 AKLYNRIYVASIHPDLTE-E---DIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYL  104 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e-~---~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l  104 (173)
                      +.+..||.|.=|..++.. +   .+.+.++.||+|.++.+.       ++.-|.|+|.+..+|-+|+.+.+. ...|..+
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-------GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~  154 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-------GRQSAVVVFKDITSACKAVSAFQS-RAPGTMF  154 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-------CCceEEEEehhhHHHHHHHHhhcC-CCCCceE
Confidence            357788999877665432 3   355566789999998652       356899999999999999999876 5567788


Q ss_pred             EEEEe
Q psy2141         105 RVGRA  109 (173)
Q Consensus       105 ~v~~a  109 (173)
                      .|.|-
T Consensus       155 qCsWq  159 (166)
T PF15023_consen  155 QCSWQ  159 (166)
T ss_pred             Eeecc
Confidence            88874

>KOG2068|consensus

Probab=95.92  E-value=0.0031  Score=50.35  Aligned_cols=79  Identities=23%  Similarity=0.376  Sum_probs=60.0

Q ss_pred             CeEEEcCCCCCCCHHH-HH--HHhhccCceeEEEEccCCC----CCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q psy2141          33 NRIYVASIHPDLTEED-IK--SVFEAFGPIKYCKLQQGSS----PHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLR  105 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~-L~--~~F~~~G~v~~~~i~~~~~----~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~  105 (173)
                      .-+||-+|+.....+. |+  +.|.+||.|..+.+..+..    .+... -++|+|...++|..||...+|...+|+.|+
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~-s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTC-SVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCC-cccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            4578888887755444 33  4788999999998887652    12122 379999999999999999999999999887


Q ss_pred             EEEeeCC
Q psy2141         106 VGRAITP  112 (173)
Q Consensus       106 v~~a~~~  112 (173)
                      ..+..++
T Consensus       157 a~~gttk  163 (327)
T KOG2068|consen  157 ASLGTTK  163 (327)
T ss_pred             HhhCCCc
Confidence            7776544

>KOG0115|consensus

Probab=95.87  E-value=0.01  Score=45.82  Aligned_cols=62  Identities=18%  Similarity=0.385  Sum_probs=54.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcC
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMN   95 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~   95 (173)
                      ..|||.||+..++.+.|.+-|+.||+|....+.-| ..++..+-++|.|...-.+.+|++..+
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHhc
Confidence            67999999999999999999999999987655555 468888899999999999999998774

>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=95.72  E-value=0.022  Score=42.04  Aligned_cols=81  Identities=15%  Similarity=0.103  Sum_probs=49.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhc-cCce---eEEEEccCC--CCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC--
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEA-FGPI---KYCKLQQGS--SPHRHKGYGFIEYETKQASNEAISSMNLFDLGG--  101 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~-~G~v---~~~~i~~~~--~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g--  101 (173)
                      ....+|.|++||+.++|+++.+.++. ++.-   ..+.-..+.  .....-.-|||.|.+.++...-.+.++|+.+.+  
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            34568999999999999999987776 5544   233311221  111124468999999999999999999977643  


Q ss_pred             ---eEEEEEEee
Q psy2141         102 ---QYLRVGRAI  110 (173)
Q Consensus       102 ---~~l~v~~a~  110 (173)
                         .+-.|.+|.
T Consensus        85 g~~~~~~VE~Ap   96 (176)
T PF03467_consen   85 GNEYPAVVEFAP   96 (176)
T ss_dssp             S-EEEEEEEE-S
T ss_pred             CCCcceeEEEcc
Confidence               344666654

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.

>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=95.54  E-value=0.064  Score=39.91  Aligned_cols=62  Identities=13%  Similarity=0.156  Sum_probs=46.1

Q ss_pred             CHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcC--CceeCCeEEEEEEeeCC
Q psy2141          45 TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMN--LFDLGGQYLRVGRAITP  112 (173)
Q Consensus        45 ~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~--g~~i~g~~l~v~~a~~~  112 (173)
                      ....|+++|..|+.+..+..+..      -+-..|.|.+.+.|.++...|+  +..+.|..++|.++...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            44789999999999888877664      3457999999999999999999  99999999999988543

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.

>KOG4676|consensus

Probab=95.52  E-value=0.029  Score=45.93  Aligned_cols=76  Identities=18%  Similarity=0.211  Sum_probs=58.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCC---CCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSS---PHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~---~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ...|.|.||.+.++.++++.+|.-.|.|.++.|.....   -....-.|||-|.+...+..|. .|.++.+-|+.|.|-.
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdraliv~p   85 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDRALIVRP   85 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeeeeEEEEe
Confidence            34789999999999999999999999999998766321   1223458999999999988887 5566666666665544

>KOG2253|consensus

Probab=94.58  E-value=0.02  Score=49.62  Aligned_cols=74  Identities=18%  Similarity=0.216  Sum_probs=64.4

Q ss_pred             hhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q psy2141          27 EEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV  106 (173)
Q Consensus        27 ~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v  106 (173)
                      ....+..++||+|+...+..+-++.+...+|.|..++...         |||..|.......+++..++-..++|..+.+
T Consensus        35 ~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~  105 (668)
T KOG2253|consen   35 QPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIE  105 (668)
T ss_pred             cCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhc
Confidence            3445678999999999999999999999999998876532         9999999999999999999999999988877


Q ss_pred             EEe
Q psy2141         107 GRA  109 (173)
Q Consensus       107 ~~a  109 (173)
                      +..
T Consensus       106 ~~d  108 (668)
T KOG2253|consen  106 NVD  108 (668)
T ss_pred             cch
Confidence            653

>KOG4660|consensus

Probab=94.57  E-value=0.069  Score=45.47  Aligned_cols=86  Identities=14%  Similarity=0.101  Sum_probs=59.0

Q ss_pred             hhhhCCCCeEEEcCCCCCCCHHHHHHHhh-ccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC---
Q psy2141          26 TEEAKLYNRIYVASIHPDLTEEDIKSVFE-AFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG---  101 (173)
Q Consensus        26 ~~~~~~~~~l~V~nLp~~~~e~~L~~~F~-~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g---  101 (173)
                      .+-..+.+++.|.|+|-..|-..|.+.-. ..|.-..+.+..|-.+..+.|||||.|.+.+.+....++.||+.|..   
T Consensus       382 ldge~~rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS  461 (549)
T KOG4660|consen  382 LDGECPRTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNS  461 (549)
T ss_pred             HhCcCchhhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcc
Confidence            33334455566666665544444433322 24666778888888888899999999999999999999999987642   


Q ss_pred             -eEEEEEEeeC
Q psy2141         102 -QYLRVGRAIT  111 (173)
Q Consensus       102 -~~l~v~~a~~  111 (173)
                       +...+.||+-
T Consensus       462 ~Kia~itYArI  472 (549)
T KOG4660|consen  462 EKIASITYARI  472 (549)
T ss_pred             eeeeeeehhhh
Confidence             3336666653

>KOG4285|consensus

Probab=94.18  E-value=0.3  Score=38.89  Aligned_cols=71  Identities=15%  Similarity=0.202  Sum_probs=53.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEE-EEEEee
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYL-RVGRAI  110 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l-~v~~a~  110 (173)
                      +.-|-|-+.|..- ...+..+|++||.|.+....      ....|-+|.|.+..+|++||.. ||+.|+|..+ -|+.+.
T Consensus       197 D~WVTVfGFppg~-~s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkpCt  268 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQ-VSIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKPCT  268 (350)
T ss_pred             cceEEEeccCccc-hhHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhhh-cCeeeccceEEeeeecC
Confidence            5667777888763 35677799999999886543      3456899999999999999955 9999998644 455543

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=94.16  E-value=0.25  Score=31.83  Aligned_cols=56  Identities=13%  Similarity=0.276  Sum_probs=41.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCC
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNL   96 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g   96 (173)
                      ....||. .|.++...||.++|+.||.|.- ..+.|       .-|||...+.+.+..++..+.-
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~V-sWi~d-------TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIYV-SWIND-------TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEEE-EEECT-------TEEEEEECCCHHHHHHHHHHTT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEEE-EEEcC-------CcEEEEeecHHHHHHHHHHhcc
Confidence            4456665 9999999999999999998643 34433       3699999999999999988753

; 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.

>KOG2591|consensus

Probab=93.78  E-value=0.14  Score=43.83  Aligned_cols=70  Identities=13%  Similarity=0.227  Sum_probs=55.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhc--cCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCC--ceeCCeEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEA--FGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNL--FDLGGQYLR  105 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~--~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g--~~i~g~~l~  105 (173)
                      .+.|.|.+.-||..+-+++++.+|..  +-++.+|.+-.+       .--||+|++..+|+.|.++|..  +++-|++|.
T Consensus       173 ~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N-------~nWyITfesd~DAQqAykylreevk~fqgKpIm  245 (684)
T KOG2591|consen  173 HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN-------DNWYITFESDTDAQQAYKYLREEVKTFQGKPIM  245 (684)
T ss_pred             cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec-------CceEEEeecchhHHHHHHHHHHHHHhhcCcchh
Confidence            34667889999999999999999976  557778877554       2469999999999999998865  567777764


Q ss_pred             E
Q psy2141         106 V  106 (173)
Q Consensus       106 v  106 (173)
                      -
T Consensus       246 A  246 (684)
T KOG2591|consen  246 A  246 (684)
T ss_pred             h
Confidence            3

>KOG4574|consensus

Probab=93.63  E-value=0.05  Score=48.53  Aligned_cols=75  Identities=13%  Similarity=0.201  Sum_probs=62.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCcee--CCeEEEEEEeeC
Q psy2141          34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDL--GGQYLRVGRAIT  111 (173)
Q Consensus        34 ~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i--~g~~l~v~~a~~  111 (173)
                      +.++.|.+-..+-..|..++++||.|.+...+++      -..+.|+|...+.|-.|+++|+|+++  -|-+.+|.+++.
T Consensus       300 ~~~~~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  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRD------LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheeccc------ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            4455566667777889999999999999998887      46899999999999999999999875  478899999886


Q ss_pred             CCC
Q psy2141         112 PPN  114 (173)
Q Consensus       112 ~~~  114 (173)
                      -+.
T Consensus       374 ~~~  376 (1007)
T KOG4574|consen  374 LPM  376 (1007)
T ss_pred             ccc
Confidence            543

>KOG2135|consensus

Probab=93.23  E-value=0.068  Score=44.76  Aligned_cols=76  Identities=16%  Similarity=0.215  Sum_probs=59.6

Q ss_pred             CCCeEEEcCCCCCC-CHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          31 LYNRIYVASIHPDL-TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        31 ~~~~l~V~nLp~~~-~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ..+.|-+.-.|+.. +-++|...|.+||.|..|.+-+.      --.|.|+|.+..+|-+|. ..++..|+++.|+|.|-
T Consensus       371 dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~-~s~~avlnnr~iKl~wh  443 (526)
T KOG2135|consen  371 DHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAY-ASHGAVLNNRFIKLFWH  443 (526)
T ss_pred             ccchhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchh-ccccceecCceeEEEEe
Confidence            34455555556654 34789999999999999987554      346899999999997777 44899999999999998


Q ss_pred             eCCC
Q psy2141         110 ITPP  113 (173)
Q Consensus       110 ~~~~  113 (173)
                      ++.+
T Consensus       444 nps~  447 (526)
T KOG2135|consen  444 NPSP  447 (526)
T ss_pred             cCCc
Confidence            8754

>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=92.91  E-value=0.65  Score=29.03  Aligned_cols=59  Identities=22%  Similarity=0.334  Sum_probs=36.1

Q ss_pred             CCCCHHHHHHHhhccC-----ceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          42 PDLTEEDIKSVFEAFG-----PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        42 ~~~~e~~L~~~F~~~G-----~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ..++..+|..++...+     .|-.+++..        .|.||+... +.++.+++.|++..+.|++++|+.|
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 DGLTPRDIVGAICNEAGIPGRDIGRIDIFD--------NFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-S--------S-EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEee--------eEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            3477888888887764     455677743        389999886 5788999999999999999999864

; PDB: 2G0C_A 3MOJ_B.

>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=92.14  E-value=1.4  Score=27.04  Aligned_cols=55  Identities=9%  Similarity=0.103  Sum_probs=42.4

Q ss_pred             CCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q psy2141          43 DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV  106 (173)
Q Consensus        43 ~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v  106 (173)
                      .++-++++..+..|+ ...+.  .|+     . .=||.|.+..+|++|.+..+|..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~-~~~I~--~d~-----t-GfYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYR-WDRIR--DDR-----T-GFYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCC-cceEE--ecC-----C-EEEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            356789999999995 34443  342     2 2489999999999999999999988877654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG4210|consensus

Probab=91.19  E-value=0.13  Score=41.02  Aligned_cols=80  Identities=11%  Similarity=0.031  Sum_probs=65.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      ..+++|+|++.+.+.+.+...++..+|......+........++|++.+.|...+.+..++.......+.+..+......
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            47789999999999988888899999988887777766788899999999999999999997655456666665554443

>KOG0804|consensus

Probab=90.26  E-value=1.2  Score=37.31  Aligned_cols=68  Identities=9%  Similarity=0.157  Sum_probs=57.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccC-ceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFG-PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG  101 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G-~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g  101 (173)
                      .+.|+|-.+|-.++-.||..+...+- .|..+++++|.  --++-..++.|.+.++|..-.+.+||+.+..
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            78899999999999999998887764 67889999973  2245578999999999999999999988764

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

Probab=89.85  E-value=0.55  Score=35.42  Aligned_cols=91  Identities=15%  Similarity=0.192  Sum_probs=56.2

Q ss_pred             CCCCcccccCCCCC--CCCCcch-----------hhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccC
Q psy2141           1 MQHFPHVQVGRPSN--MPQAQSV-----------IDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQG   67 (173)
Q Consensus         1 ~l~gr~i~v~~~~~--~~~~~~~-----------~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~   67 (173)
                      ++.||.|+|.+...  .+.....           .............+++++++..++...+...|..+|.+....+...
T Consensus       181 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  260 (306)
T COG0724         181 ELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPS  260 (306)
T ss_pred             eECCceeEeeccccccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCC
Confidence            36789999987431  1111111           1111222345778999999999999999999999999977777665


Q ss_pred             CCCCCcceEEEEEEcCHHHHHHHH
Q psy2141          68 SSPHRHKGYGFIEYETKQASNEAI   91 (173)
Q Consensus        68 ~~~g~~~g~afv~f~~~~~a~~a~   91 (173)
                      ..........++.+..........
T Consensus       261 ~~~~~~~~~~~~~~~~~~~~~~~~  284 (306)
T COG0724         261 KDGKIPKSRSFVGNEASKDALESN  284 (306)
T ss_pred             CCCcccccccccchhHHHhhhhhh
Confidence            433334444444444444443333

>KOG4454|consensus

Probab=86.70  E-value=0.5  Score=36.03  Aligned_cols=76  Identities=21%  Similarity=0.367  Sum_probs=64.9

Q ss_pred             CCeEEEcC----CCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q psy2141          32 YNRIYVAS----IHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG  107 (173)
Q Consensus        32 ~~~l~V~n----Lp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~  107 (173)
                      ..+++.|+    |...++++.+.+.|+.-|++..+++.++. +|+++.++|+.+........+++...+.+.--+++.+.
T Consensus        80 q~~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~-d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~~~~~~g  158 (267)
T KOG4454|consen   80 QRTLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDN-DGRNRNFGFVTYQRLCAVPFALDLYQGLELFQKKVTIG  158 (267)
T ss_pred             hcccccCCCcchhhhhcchhhheeeecccCCCCCccccccc-cCCccCccchhhhhhhcCcHHhhhhcccCcCCCCcccc
Confidence            56888898    88889999999999999999999999985 68899999999999999999998888877665555544


Q ss_pred             E
Q psy2141         108 R  108 (173)
Q Consensus       108 ~  108 (173)
                      -
T Consensus       159 g  159 (267)
T KOG4454|consen  159 G  159 (267)
T ss_pred             c
Confidence            3

>KOG4410|consensus

Probab=85.78  E-value=2.4  Score=33.67  Aligned_cols=50  Identities=16%  Similarity=0.218  Sum_probs=37.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCH
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETK   84 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~   84 (173)
                      ....-||++||+.++.-.+|+..+.+-+. ..+.|.+.    -+.|-||+.|.+.
T Consensus       328 ~~~~di~~~nl~rd~rv~dlk~~lr~~~~-~pm~iswk----g~~~k~flh~~~~  377 (396)
T KOG4410|consen  328 GAKTDIKLTNLSRDIRVKDLKSELRKREC-TPMSISWK----GHFGKCFLHFGNR  377 (396)
T ss_pred             ccccceeeccCccccchHHHHHHHHhcCC-CceeEeee----cCCcceeEecCCc
Confidence            33556999999999999999999998864 33334332    2467899999664

>smart00596 PRE_C2HC PRE_C2HC domain

Probab=82.20  E-value=3.6  Score=25.50  Aligned_cols=63  Identities=19%  Similarity=0.294  Sum_probs=44.6

Q ss_pred             HHHHHHhhccC-ceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCC
Q psy2141          47 EDIKSVFEAFG-PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITP  112 (173)
Q Consensus        47 ~~L~~~F~~~G-~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~  112 (173)
                      .+|++-|.++| ++..+.-+..+.++.....-+|+.....+...   .|+=+.+.|+++.|......
T Consensus         2 ~~I~~~L~~~G~~v~~i~~m~~~~~r~P~nmf~vel~~~~~~~~---Il~ik~Lg~~~V~VEr~~k~   65 (69)
T smart00596        2 SQIEEALKDIGFPVLFIHNMLNRDTKNPQNMFEVELVPAANGKE---ILNIKTLGGQRVTVERPHKR   65 (69)
T ss_pred             HHHHHHHHHcCCceeEEEcccccCCCCcceeEEEEeeecCCCcc---eEeehhhCCeeEEEecCccc
Confidence            46777888888 77888777776666677788888876543333   45557788999998876543

>PF07530 PRE_C2HC: Associated with zinc fingers; InterPro: IPR006579 This domain is present in proteins found exclusively in the arthropods, including a number of Drosophila species, the silk moth and the gypsy moth

Probab=81.40  E-value=4.9  Score=24.79  Aligned_cols=63  Identities=22%  Similarity=0.310  Sum_probs=45.1

Q ss_pred             HHHHHHhhccC-ceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCC
Q psy2141          47 EDIKSVFEAFG-PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITP  112 (173)
Q Consensus        47 ~~L~~~F~~~G-~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~  112 (173)
                      ++|.+.|...| .|..+.-+..+.++.....-||+.....+   ..+.|+=..+.+..|+|.....+
T Consensus         2 ~~I~~~L~~~G~~v~~i~~~~~~~~k~pl~mf~veL~p~~~---~k~i~~Ik~l~~~~V~vE~~~k~   65 (68)
T PF07530_consen    2 EEIKEELKDQGHPVRNIHNMHSRNTKKPLNMFFVELEPKPN---NKEIYKIKTLCGQRVKVERPRKR   65 (68)
T ss_pred             HHHHHHHHHcCCceEEEEccccCCCCCCceEEEEeeccCcc---ccceeehHhhCCeEEEEecCCCC
Confidence            46777777777 77888777776667777788898877655   23345557788899998876543

These proteins are possibly involved in RNA binding or single strand DNA binding.

>KOG4676|consensus

Probab=81.32  E-value=0.53  Score=38.78  Aligned_cols=66  Identities=15%  Similarity=0.120  Sum_probs=52.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCe
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQ  102 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~  102 (173)
                      .++++|++|+..+...++.+.|..+|.|....+.    .+...-+|-++|........|++. +|.++.-+
T Consensus       151 rRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~a----sk~~s~~c~~sf~~qts~~halr~-~gre~k~q  216 (479)
T KOG4676|consen  151 RRTREVQSLISAAILPESGESFERKGEVSYAHTA----SKSRSSSCSHSFRKQTSSKHALRS-HGRERKRQ  216 (479)
T ss_pred             Hhhhhhhcchhhhcchhhhhhhhhcchhhhhhhh----ccCCCcchhhhHhhhhhHHHHHHh-cchhhhhh
Confidence            3899999999999999999999999998876653    333455777999988888888855 66665533

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	173
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		6e-41
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		3e-40
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		5e-40
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		1e-11
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		5e-11
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		7e-09
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		8e-09
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		2e-07
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		3e-07
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		3e-07
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		3e-07
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		5e-07
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		7e-07
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		7e-07
2u2f_A	85	Solution Structure Of The Second Rna-Binding Domain		8e-07
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		1e-06
2cpj_A	99	Solution Structure Of The N-Terminal Rna Recognitio		2e-06
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		2e-06
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		2e-06
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		2e-06
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		2e-06
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		2e-06
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		3e-06
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		3e-06
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		4e-06
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		6e-06
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		6e-06
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		6e-06
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		7e-06
1x4a_A	109	Solution Structure Of Rrm Domain In Splicing Factor		8e-06
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		1e-05
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		1e-05
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		2e-05
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		2e-05
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		3e-05
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		3e-05
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		3e-05
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		3e-05
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		4e-05
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		5e-05
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		5e-05
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		5e-05
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		7e-05
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		7e-05
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		7e-05
2dnq_A	90	Solution Structure Of Rna Binding Domain 1 In Rna-B		8e-05
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		8e-05
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		9e-05
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		9e-05
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		1e-04
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		1e-04
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		1e-04
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		1e-04
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		2e-04
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		2e-04
1wf1_A	110	Solution Structure Of Rrm Domain In Rna-Binding Pro		2e-04
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		2e-04
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		2e-04
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		2e-04
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		2e-04
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		2e-04
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		2e-04
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		2e-04
4a8x_A	88	Structure Of The Core Asap Complex Length = 88		3e-04
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		3e-04
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		5e-04
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		5e-04
2dgt_A	92	Solution Structure Of The Second Rna Binding Domain		6e-04
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		6e-04
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		6e-04
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		6e-04
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		7e-04
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		8e-04

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score =  163 bits (412), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 72/111 (64%), Positives = 93/111 (83%)
Query: 6   HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
           +++VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DIKSVFEAFG IK C L 
Sbjct: 84  NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLA 143
Query: 66  QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNAL 116
           +  +  +HKGYGFIEYE  Q+S +A+SSMNLFDLGGQYLRVG+A+TPP  L
Sbjct: 144 RDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPL 194

>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 =  160 bits (405), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 72/117 (61%), Positives = 94/117 (80%)
Query: 6   HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
           +++VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DIKSVFEAFG IK C L 
Sbjct: 83  NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLA 142
Query: 66  QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGP 122
           +  +  +HKGYGFIEYE  Q+S +A+SS NLFDLGGQYLRVG+A+TPP  L +   P
Sbjct: 143 RDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKAVTPPXPLLTPATP 199

>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 =  159 bits (403), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 72/118 (61%), Positives = 94/118 (79%)
Query: 6   HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
           +++VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DIKSVFEAFG IK   L 
Sbjct: 99  NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLA 158
Query: 66  QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
           +  +  +HKGYGFIEYE  Q+S +A+SSMNLFDLGGQYLRVG+A+TPP  L +   P 
Sbjct: 159 RDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPATPG 216

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 65.9 bits (159), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 48/74 (64%)
Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           R+YV S+H ++TE+ ++ +FE FG I+  +L   S   R KGYGFI +   + + +A+  
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 94  MNLFDLGGQYLRVG 107
           +N F+L G+ ++VG
Sbjct: 88  LNGFELAGRPMKVG 101

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 63.5 bits (153), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 28/73 (38%), Positives = 45/73 (61%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV S+H ++TE+ ++ +FE FG I    L + S   R KGYGFI +   + +  A+  +
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 95  NLFDLGGQYLRVG 107
           N F+L G+ +RVG
Sbjct: 68  NGFELAGRPMRVG 80

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 56.6 bits (135), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 31/91 (34%), Positives = 46/91 (50%), Gaps = 8/91 (8%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V  + P++T EDIKS F  FG I   ++ +  +  + KGYGF+ +  K  +  AI  M
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 95  NLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
               LGG+ +R   A   P        PAPS
Sbjct: 78  GGQWLGGRQIRTNWATRKP--------PAPS 100

>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 = 56.2 bits (134), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 29/94 (30%), Positives = 48/94 (51%), Gaps = 8/94 (8%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V  + P++T EDIK+ F  FG I   ++ +  +  + KGYGF+ +  K  +  AI  M
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 95  NLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSH 128
               LGG+ +R   A   P        PAP +++
Sbjct: 78  GGQWLGGRQIRTNWATRKP--------PAPKSTY 103

>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 = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 40/73 (54%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +Y+ SI  D TEE I  +    GP+   K+       R KGY FIE+   ++S  A+ ++
Sbjct: 7   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 95  NLFDLGGQYLRVG 107
           N + LG ++L+ G
Sbjct: 67  NGYQLGSRFLKCG 79

>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 = 51.2 bits (121), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 44/80 (55%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V +I  + TEE +K +F   GP+   +L       + KGYGF EY+ ++ +  A+ ++
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 95  NLFDLGGQYLRVGRAITPPN 114
           N  +  G+ LRV  A +  N
Sbjct: 71  NGREFSGRALRVDNAASEKN 90

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 51.2 bits (121), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 40/73 (54%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +Y+ SI  D TEE I  +    GP+   K+       R KGY FIE+   ++S  A+ ++
Sbjct: 5   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 95  NLFDLGGQYLRVG 107
           N + LG ++L+ G
Sbjct: 65  NGYQLGSRFLKCG 77

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 40/73 (54%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +Y+ SI  D TEE I  +    GP+   K+       R KGY FIE+   ++S  A+ ++
Sbjct: 6   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 95  NLFDLGGQYLRVG 107
           N + LG ++L+ G
Sbjct: 66  NGYQLGSRFLKCG 78

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 50.4 bits (119), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 42/76 (55%)
Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++++  +   L ++ +K +  +FGP+K   L + S+    KGY F EY     +++AI+ 
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175
Query: 94  MNLFDLGGQYLRVGRA 109
           +N   LG + L V RA
Sbjct: 176 LNGMQLGDKKLLVQRA 191

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 50.1 bits (118), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 42/76 (55%)
Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++++  +   L ++ +K +  +FGP+K   L + S+    KGY F EY     +++AI+ 
Sbjct: 98  KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 157
Query: 94  MNLFDLGGQYLRVGRA 109
           +N   LG + L V RA
Sbjct: 158 LNGMQLGDKKLLVQRA 173

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 49.7 bits (117), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 42/76 (55%)
Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++++  +   L ++ +K +  +FGP+K   L + S+    KGY F EY     +++AI+ 
Sbjct: 96  KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 155
Query: 94  MNLFDLGGQYLRVGRA 109
           +N   LG + L V RA
Sbjct: 156 LNGMQLGDKKLLVQRA 171

>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of Hu2af65 Length = 85

Iteration: 1
 Score = 49.7 bits (117), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 42/76 (55%)
Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++++  +   L ++ +K +  +FGP+K   L + S+    KGY F EY     +++AI+ 
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 94  MNLFDLGGQYLRVGRA 109
           +N   LG + L V RA
Sbjct: 63  LNGMQLGDKKLLVQRA 78

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 6/74 (8%)
Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           +R++V ++ PD+TEE+++ +FE +G      +      H+ KG+GFI  ET+  +  A  
Sbjct: 23  SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIAKV 76
Query: 93  SMNLFDLGGQYLRV 106
            ++   L G+ LRV
Sbjct: 77  ELDNMPLRGKQLRV 90

>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif Of Nono Length = 99

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 6/74 (8%)
Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           +R++V ++ PD+TEE+++ +FE +G      +      H+ KG+GFI  ET+  +  A  
Sbjct: 16  SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIAKV 69
Query: 93  SMNLFDLGGQYLRV 106
            ++   L G+ LRV
Sbjct: 70  ELDNMPLRGKQLRV 83

>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 = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 37/72 (51%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V  +H + TEEDI   F  +G IK   L         KGY  +EYET + +  A+  +
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 95  NLFDLGGQYLRV 106
           N  DL GQ + V
Sbjct: 70  NGQDLMGQPISV 81

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/68 (36%), Positives = 35/68 (51%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V  +H + TEEDI   F  +G IK   L         KGY  +EYET + +  A+  +
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 95  NLFDLGGQ 102
           N  DL GQ
Sbjct: 70  NGQDLMGQ 77

>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 = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 37/72 (51%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V  +H + TEEDI   F  +G IK   L         KGY  +EYET + +  A+  +
Sbjct: 12  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 95  NLFDLGGQYLRV 106
           N  DL GQ + V
Sbjct: 72  NGQDLMGQPISV 83

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 37/72 (51%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V  +H + TEEDI   F  +G IK   L         KGY  +EYET + +  A+  +
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 95  NLFDLGGQYLRV 106
           N  DL GQ + V
Sbjct: 70  NGQDLMGQPISV 81

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 37/72 (51%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V  +H + TEEDI   F  +G IK   L         KGY  +EYET + +  A+  +
Sbjct: 26  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 95  NLFDLGGQYLRV 106
           N  DL GQ + V
Sbjct: 86  NGQDLMGQPISV 97

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 21/86 (24%), Positives = 48/86 (55%)
Query: 24  EITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYET 83
           ++  E  +   + V  I   + E  ++ +FE +GPI+  K+       + +GYGF+++++
Sbjct: 34  QMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS 93
Query: 84  KQASNEAISSMNLFDLGGQYLRVGRA 109
             ++ +AI+ +N F++  + L+V  A
Sbjct: 94  GSSAQQAIAGLNGFNILNKRLKVALA 119

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 37/72 (51%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V  +H + TEEDI   F  +G IK   L         KGY  +EYET + +  A+  +
Sbjct: 25  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 95  NLFDLGGQYLRV 106
           N  DL GQ + V
Sbjct: 85  NGQDLMGQPISV 96

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 33/94 (35%), Positives = 49/94 (52%), Gaps = 8/94 (8%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPI-KYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           I++ ++ P++ E+ +   F AFG I +  K+ +       KGY FI + +  AS+ AI +
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 94  MNLFDLGGQYLRVGRAITPPNAL-HSSKGPAPST 126
           MN     GQYL   R IT   A    SKG  PS+
Sbjct: 68  MN-----GQYL-CNRPITVSYAFKKDSKGSGPSS 95

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 47.0 bits (110), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           I++ ++   +  + +   F AFG I  CK+      +  KGYGF+ +ET++A+  AI  M
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVV--CDENGSKGYGFVHFETQEAAERAIEKM 65
Query: 95  NLFDLGGQYLRVGR 108
           N   L  + + VGR
Sbjct: 66  NGMLLNDRKVFVGR 79

>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 = 47.0 bits (110), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 8/77 (10%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQASNEAI 91
           I++ ++   +  + +   F AFG I  CK+   + GS     KGYGF+ +ET++A+  AI
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS-----KGYGFVHFETQEAAERAI 155
Query: 92  SSMNLFDLGGQYLRVGR 108
             MN   L  + + VGR
Sbjct: 156 EKMNGMLLNDRKVFVGR 172

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 46.6 bits (109), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           I++ ++   +  + +   F AFG I  CK+      +  KGYGF+ +ET++A+  AI  M
Sbjct: 14  IFIKNLDKSIDNKALYDTFSAFGNILSCKVV--CDENGSKGYGFVHFETQEAAERAIEKM 71
Query: 95  NLFDLGGQYLRVGR 108
           N   L  + + VGR
Sbjct: 72  NGMLLNDRKVFVGR 85

>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 = 46.6 bits (109), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 8/77 (10%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQASNEAI 91
           I++ ++   +  + +   F AFG I  CK+   + GS     KGYGF+ +ET++A+  AI
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS-----KGYGFVHFETQEAAERAI 160
Query: 92  SSMNLFDLGGQYLRVGR 108
             MN   L  + + VGR
Sbjct: 161 EKMNGMLLNDRKVFVGR 177

>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2 Length = 109

Iteration: 1
 Score = 46.6 bits (109), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 7/75 (9%)
Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKL--QQGSSPHRHKGYGFIEYETKQASNEAI 91
           RIYV ++ PD+  +DI+ VF  +G I+   L  ++G  P     + F+E+E  + + +A+
Sbjct: 24  RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPP-----FAFVEFEDPRDAEDAV 78
Query: 92  SSMNLFDLGGQYLRV 106
              + +D  G  LRV
Sbjct: 79  YGRDGYDYDGYRLRV 93

>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 = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 43/83 (51%), Gaps = 2/83 (2%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           IYV ++    T E +K +F  FG +   KL       + KG+GF+E + +  S EAI+ +
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVS-EAIAKL 62
Query: 95  NLFDLGGQYLRVGRAITPPNALH 117
           +  D  G+ +RV  A  P  +L 
Sbjct: 63  DNTDFMGRTIRVTEA-NPKKSLE 84

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/77 (28%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           N+I+V  I  +  E +++  F+ FG +    +   +   R +G+GFI +E +Q+ ++A+ 
Sbjct: 11  NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV- 69
Query: 93  SMNLFDLGGQYLRVGRA 109
           +M+  D+ G+ + V RA
Sbjct: 70  NMHFHDIMGKKVEVKRA 86

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/67 (29%), Positives = 40/67 (59%)
Query: 43  DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQ 102
           ++T+++ KS+F + G I+ CKL +     +  GYGF+ Y     +++AI+++N   L  +
Sbjct: 15  NMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTK 74
Query: 103 YLRVGRA 109
            ++V  A
Sbjct: 75  TIKVSYA 81

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/67 (29%), Positives = 40/67 (59%)
Query: 43  DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQ 102
           ++T+++ KS+F + G I+ CKL +     +  GYGF+ Y     +++AI+++N   L  +
Sbjct: 15  NMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTK 74
Query: 103 YLRVGRA 109
            ++V  A
Sbjct: 75  TIKVSYA 81

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/67 (31%), Positives = 34/67 (50%)
Query: 45  TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYL 104
           TE D++ VF  +GPI    +       R +G+ F+ +E    + EA    N  +L G+ +
Sbjct: 25  TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 84
Query: 105 RVGRAIT 111
           RV  +IT
Sbjct: 85  RVDFSIT 91

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 19/76 (25%), Positives = 41/76 (53%)
Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           +++V  +  D  E+ ++ VF  +G I    + +     R +G+GF+ +E    + +A+ +
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 94  MNLFDLGGQYLRVGRA 109
           MN   + G+ +RV +A
Sbjct: 74  MNGKSVDGRQIRVDQA 89

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 43/75 (57%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV  +   ++E  +  +F   GP+    + +     +H+GYGF+E+ +++ ++ AI  M
Sbjct: 18  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 95  NLFDLGGQYLRVGRA 109
           ++  L G+ +RV +A
Sbjct: 78  DMIKLYGKPIRVNKA 92

>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 = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/67 (31%), Positives = 34/67 (50%)
Query: 45  TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYL 104
           TE D++ VF  +GPI    +       R +G+ F+ +E    + EA    N  +L G+ +
Sbjct: 28  TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87
Query: 105 RVGRAIT 111
           RV  +IT
Sbjct: 88  RVDFSIT 94

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/67 (31%), Positives = 34/67 (50%)
Query: 45  TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYL 104
           TE D++ VF  +GPI    +       R +G+ F+ +E    + EA    N  +L G+ +
Sbjct: 59  TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 118
Query: 105 RVGRAIT 111
           RV  +IT
Sbjct: 119 RVDFSIT 125

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 43.9 bits (102), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 17/83 (20%), Positives = 44/83 (53%), Gaps = 8/83 (9%)
Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++++  ++ D TE++++  F  +G +   K+ +  +  R +G+GF+ +E   + +E + +
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 94  MNLFDLGGQYLRVGRAITPPNAL 116
            ++ D        G+ I P  A+
Sbjct: 65  QHILD--------GKVIDPKRAI 79

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 43.9 bits (102), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 28/108 (25%), Positives = 50/108 (46%), Gaps = 13/108 (12%)
Query: 7   VQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQ 66
           +++  P N P AQ            +  ++VA ++ D TE  ++  FE +GPIK   +  
Sbjct: 86  LKMWDPHNDPNAQ---------GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVY 136
Query: 67  GSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV----GRAI 110
                + +GY FIEYE ++  + A    +   + G+ + V    GR +
Sbjct: 137 SKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTV 184

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 19/75 (25%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           I+V  +  + T ED+K  FE FG +    L    + +RH+G+GF+ +E++    E +  +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIV-EKVCEI 60
Query: 95  NLFDLGGQYLRVGRA 109
           +  ++  + +   +A
Sbjct: 61  HFHEINNKMVECKKA 75

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 43.5 bits (101), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 18/67 (26%), Positives = 36/67 (53%)
Query: 43  DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQ 102
           D+T+ ++ ++F A GPI  C++ +        GY F+++ ++  S  AI  +N   +  +
Sbjct: 14  DMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNK 73
Query: 103 YLRVGRA 109
            L+V  A
Sbjct: 74  RLKVSYA 80

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 43.5 bits (101), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 20/67 (29%), Positives = 40/67 (59%)
Query: 43  DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQ 102
           ++T+E+ +S+F + G I+ CKL +     +  GYGF+ Y   + + +AI+++N   L  +
Sbjct: 13  NMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTK 72
Query: 103 YLRVGRA 109
            ++V  A
Sbjct: 73  TIKVSYA 79

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 43.1 bits (100), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 18/67 (26%), Positives = 36/67 (53%)
Query: 43  DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQ 102
           D+T+ ++ ++F A GPI  C++ +        GY F+++ ++  S  AI  +N   +  +
Sbjct: 14  DMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNK 73
Query: 103 YLRVGRA 109
            L+V  A
Sbjct: 74  RLKVSYA 80

>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 = 8e-05,   Method: Compositional matrix adjust.
 Identities = 24/90 (26%), Positives = 48/90 (53%), Gaps = 11/90 (12%)
Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++++ ++  + TE++I+S+FE +G +  C +         K YGF+  E K A+ +AI +
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRN 61
Query: 94  MNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
           ++ + L G  + V       N   +S GP+
Sbjct: 62  LHHYKLHGVNINVE---ASKNKSKASSGPS 88

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 43.1 bits (100), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 41/75 (54%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV  +  ++ ++ + + F  FG I   ++       +H+G+ F+E+E  + +  AI +M
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 95  NLFDLGGQYLRVGRA 109
           N  +L G+ +RV  A
Sbjct: 70  NESELFGRTIRVNLA 84

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 42.7 bits (99), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V SIH +  E++I+  F  +G IK   L         KGY  +EYET + +  A  ++
Sbjct: 29  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 95  NLFDLGGQYLRV 106
           N  ++ GQ ++V
Sbjct: 89  NGAEIMGQTIQV 100

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 42.7 bits (99), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 41/75 (54%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV  +  ++ ++ + + F  FG I   ++       +H+G+ F+E+E  + +  AI +M
Sbjct: 5   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 95  NLFDLGGQYLRVGRA 109
           N  +L G+ +RV  A
Sbjct: 65  NESELFGRTIRVNLA 79

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 41/75 (54%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV  +  ++ ++ + + F  FG I   ++       +H+G+ F+E+E  + +  AI +M
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 95  NLFDLGGQYLRVGRA 109
           N  +L G+ +RV  A
Sbjct: 68  NESELFGRTIRVNLA 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 = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 41/75 (54%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV  +  ++ ++ + + F  FG I   ++       +H+G+ F+E+E  + +  AI +M
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 95  NLFDLGGQYLRVGRA 109
           N  +L G+ +RV  A
Sbjct: 75  NESELFGRTIRVNLA 89

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V SIH +  E++I+  F  +G IK   L         KGY  +EYET + +  A  ++
Sbjct: 75  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 95  NLFDLGGQYLRV 106
           N  ++ GQ ++V
Sbjct: 135 NGAEIMGQTIQV 146

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/100 (26%), Positives = 47/100 (47%), Gaps = 9/100 (9%)
Query: 7   VQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQ 66
           +++  P N P AQ            +  ++VA ++ D TE  ++  FE +GPIK   +  
Sbjct: 86  LKMWDPHNDPNAQ---------GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVY 136
Query: 67  GSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV 106
                + +GY FIEYE ++  + A    +   + G+ + V
Sbjct: 137 SKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV 176

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 41/75 (54%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV  +  ++ ++ + + F  FG I   ++       +H+G+ F+E+E  + +  AI +M
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 95  NLFDLGGQYLRVGRA 109
           N  +L G+ +RV  A
Sbjct: 126 NESELFGRTIRVNLA 140

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 12  PSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPH 71
           P  M  A S  +   E+ KL+    +  I    TE DI+ +F +FG I+ C++ +G    
Sbjct: 79  PIQMKPADSEKNNAVEDRKLF----IGMISKKCTENDIRVMFSSFGQIEECRILRGPD-G 133
Query: 72  RHKGYGFIEYETKQASNEAISSM 94
             +G  F+ + T+  +  AI +M
Sbjct: 134 LSRGCAFVTFTTRAMAQTAIKAM 156

>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein Np_057951 Length = 110

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/97 (23%), Positives = 51/97 (52%), Gaps = 10/97 (10%)
Query: 17  QAQSVIDEITEEAKLYNRIYVASIHPDLTEE-DIKSVFEAFGPIKYCKLQQGSSPHRHKG 75
           QA +V ++  +   + +R+++ +++  L ++ D++++F  +G +  C +        HKG
Sbjct: 13  QASNVTNK-NDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKG 63
Query: 76  YGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITP 112
           Y F++Y  ++ +  A+   N   L GQ L +  A  P
Sbjct: 64  YAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP 100

>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 = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 12  PSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPH 71
           P  M  A S  +   E+ KL+    +  I    TE DI+ +F +FG I+ C++ +G    
Sbjct: 91  PIQMKPADSEKNNAVEDRKLF----IGMISKKCTENDIRVMFSSFGQIEECRILRGPD-G 145
Query: 72  RHKGYGFIEYETKQASNEAISSM 94
             +G  F+ + T+  +  AI +M
Sbjct: 146 LSRGCAFVTFTTRAMAQTAIKAM 168

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/67 (26%), Positives = 39/67 (58%)
Query: 43  DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQ 102
           ++T+++++S+F + G ++  KL +        GYGF+ Y T + +  AI+++N   L  +
Sbjct: 13  NMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSK 72
Query: 103 YLRVGRA 109
            ++V  A
Sbjct: 73  TIKVSYA 79

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/67 (26%), Positives = 39/67 (58%)
Query: 43  DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQ 102
           ++T+++++S+F + G ++  KL +        GYGF+ Y T + +  AI+++N   L  +
Sbjct: 13  NMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSK 72
Query: 103 YLRVGRA 109
            ++V  A
Sbjct: 73  TIKVSYA 79

>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 = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/67 (26%), Positives = 39/67 (58%)
Query: 43  DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQ 102
           ++T+++++S+F + G ++  KL +        GYGF+ Y T + +  AI+++N   L  +
Sbjct: 15  NMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSK 74
Query: 103 YLRVGRA 109
            ++V  A
Sbjct: 75  TIKVSYA 81

>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4 Rna Binding Protein Length = 105

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 17/63 (26%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
          + +++V  ++   +E+D++ +FEAFG I+ C + +G   +  KG  F++Y +   +  AI
Sbjct: 15 HRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGN-SKGCAFVKYSSHAEAQAAI 73
Query: 92 SSM 94
          +++
Sbjct: 74 NAL 76

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/62 (30%), Positives = 31/62 (50%)
Query: 45  TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYL 104
           TE D++ VF  +GPI    +       R +G+ F+ +E    + EA    N  +L G+ +
Sbjct: 28  TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87
Query: 105 RV 106
           RV
Sbjct: 88  RV 89

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/88 (23%), Positives = 44/88 (50%), Gaps = 1/88 (1%)
Query: 23  DEITEEAKLYNRIYVASIHP-DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY 81
           D++  + +  N   + +  P D T+ ++ ++F A GPI  C++ +        GY F+++
Sbjct: 4   DDLMNDPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDF 63
Query: 82  ETKQASNEAISSMNLFDLGGQYLRVGRA 109
            ++  S  AI  +N   +  + L+V  A
Sbjct: 64  TSEXDSQRAIKVLNGITVRNKRLKVSYA 91

>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex Length = 88

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/81 (22%), Positives = 41/81 (50%), Gaps = 1/81 (1%)
Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ-QGSSPHRHKGYGFIEYETKQASNEAI 91
            ++++  +  ++T++ I  +F  +G IK   +  +   PH  KGY ++E+E    + +A+
Sbjct: 5   TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 92  SSMNLFDLGGQYLRVGRAITP 112
             M+   + GQ +     + P
Sbjct: 65  KHMDGGQIDGQEITATAVLAP 85

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 14/61 (22%), Positives = 37/61 (60%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
          +Y+  + P  T++D+  + + +G I   K     + ++ KGYGF+++++  A+ +A++++
Sbjct: 8  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 95 N 95
Sbjct: 68 K 68

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 45/86 (52%), Gaps = 11/86 (12%)
Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           R++V ++  D+TEED K +FE +G      +      +R +G+GFI  E++  +  A + 
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 77
Query: 94  MNLFDLGGQYLRV-----GRAITPPN 114
           ++   L  + LR+     G A+T  N
Sbjct: 78  LDGTILKSRPLRIRFATHGAALTVKN 103

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/80 (27%), Positives = 45/80 (56%), Gaps = 10/80 (12%)
Query: 35  IYVASIHPDLTEEDIKSVFEAF-----GPIKYCKLQQGSSPHRHKGYGFIEYETKQASNE 89
           ++V  ++ ++ +E +++ F+ F     G + +  +Q GSS    +GYGF+ + ++  +  
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW-DMQTGSS----RGYGFVSFTSQDDAQN 58
Query: 90  AISSMNLFDLGGQYLRVGRA 109
           A+ SM   DL G+ LR+  A
Sbjct: 59  AMDSMQGQDLNGRPLRINWA 78

>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In Rna- Binding Protein 30 Length = 92

Iteration: 1
 Score = 40.0 bits (92), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/94 (23%), Positives = 47/94 (50%), Gaps = 11/94 (11%)
Query: 30  KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNE 89
           K   +++V +I P  T +++++ FE +GP+  C +         K Y F+  E  + + E
Sbjct: 8   KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVE 59
Query: 90  AISSMNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
           AI  ++  +  G+ + V  + +    L ++ GP+
Sbjct: 60  AIRGLDNTEFQGKRMHVQLSTS---RLRTASGPS 90

>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 = 40.0 bits (92), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 18/65 (27%), Positives = 37/65 (56%)
Query: 45  TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYL 104
           T+++++S+F + G ++  KL +        GYGF+ Y T + +  AI+++N   L  + +
Sbjct: 32  TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 91
Query: 105 RVGRA 109
           +V  A
Sbjct: 92  KVSYA 96

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 40.0 bits (92), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 37/72 (51%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           + VA++ P LT++  + +   FG ++ C L       + KGYGF EY  K ++  A S +
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 95  NLFDLGGQYLRV 106
               LG + L V
Sbjct: 158 LGKPLGPRTLYV 169

>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 = 40.0 bits (92), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 37/72 (51%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           + VA++ P LT++  + +   FG ++ C L       + KGYGF EY  K ++  A S +
Sbjct: 96  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 95  NLFDLGGQYLRV 106
               LG + L V
Sbjct: 156 LGKPLGPRTLYV 167

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 37/72 (51%)
Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           + VA++ P LT++  + +   FG ++ C L       + KGYGF EY  K ++  A S +
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 95  NLFDLGGQYLRV 106
               LG + L V
Sbjct: 158 LGKPLGPRTLYV 169

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 39.7 bits (91), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 22/80 (27%), Positives = 45/80 (56%), Gaps = 10/80 (12%)
Query: 35  IYVASIHPDLTEEDIKSVFEAF-----GPIKYCKLQQGSSPHRHKGYGFIEYETKQASNE 89
           ++V  ++ ++ +E +++ F+ F     G + +  +Q GSS    +GYGF+ + ++  +  
Sbjct: 90  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW-DMQTGSS----RGYGFVSFTSQDDAQN 144
Query: 90  AISSMNLFDLGGQYLRVGRA 109
           A+ SM   DL G+ LR+  A
Sbjct: 145 AMDSMQGQDLNGRPLRINWA 164

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	173
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	8e-39
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-21
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-30
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-15
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-30
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-15
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-24
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-21
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	7e-20
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-23
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	5e-23
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-22
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	3e-22
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-22
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	5e-18
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	7e-22
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-21
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-21
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-21
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-20
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-20
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	3e-20
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	3e-20
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-19
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-19
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-19
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	4e-19
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	5e-19
1x5p_A	97	Negative elongation factor E; structure genomics,	5e-19
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	6e-19
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	7e-19
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	8e-19
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	9e-19
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-18
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-18
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-18
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-18
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-18
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-13
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-18
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-18
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-18
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-18
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-18
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-15
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-18
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-18
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	4e-18
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	4e-18
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	6e-18
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	6e-18
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	7e-18
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	7e-18
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	7e-18
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	8e-18
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-16
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	8e-18
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	9e-18
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	9e-18
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-17
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-13
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-17
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-17
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-17
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-17
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-17
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-17
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-17
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	5e-17
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-17
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	6e-14
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	7e-17
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	9e-17
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	9e-17
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-16
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-16
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-16
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-16
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-16
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-16
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	3e-16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-15
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-13
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-16
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	4e-16
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	4e-16
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	5e-16
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	7e-16
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-16
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-15
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	7e-16
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-15
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-15
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-15
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-15
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-15
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	3e-15
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-15
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-15
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-15
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	4e-15
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	4e-15
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	5e-15
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	5e-15
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	6e-15
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	7e-15
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	9e-15
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-14
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-14
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-14
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-14
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-14
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-08
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	4e-14
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	4e-14
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	9e-14
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-13
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-13
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-09
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	5e-13
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	5e-13
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	9e-13
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-12
2div_A	99	TRNA selenocysteine associated protein; structural	1e-12
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-12
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-12
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-12
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-12
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-12
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	3e-12
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	3e-12
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-12
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	8e-12
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	9e-12
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-11
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-06
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-11
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-11
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-11
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	3e-11
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	5e-11
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	5e-11
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	6e-11
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-10
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	1e-10
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-10
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-10
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	8e-10
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	3e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	4e-10
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	4e-10
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	6e-10
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	7e-10
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	8e-10
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	8e-10
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-09
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-09
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-09
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-09
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-09
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	5e-09
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	8e-09
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	1e-08
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-08
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-08
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-08
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	3e-08
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-08
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-07
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-07
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	3e-07
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	4e-07
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	6e-07
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	9e-07
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-06
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-06
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	4e-06
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	6e-06
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-05
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	5e-05
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	8e-05
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	9e-05
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	2e-04
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	2e-04
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	4e-04
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	8e-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 =  130 bits (330), Expect = 8e-39
 Identities = 72/116 (62%), Positives = 93/116 (80%)

Query: 7   VQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQ 66
           ++VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DIKSVFEAFG IK   L +
Sbjct: 100 IKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLAR 159

Query: 67  GSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGP 122
             +  +HKGYGFIEYE  Q+S +A+SSMNLFDLGGQYLRVG+A+TPP  L +   P
Sbjct: 160 DPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPATP 215

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 84.7 bits (210), Expect = 5e-21
 Identities = 34/103 (33%), Positives = 51/103 (49%)

Query: 26  TEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQ 85
                + +R+YV SI+ +L E+ I+  F  FGPIK   +   S   +HKG+ F+EYE  +
Sbjct: 22  QGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPE 81

Query: 86  ASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSH 128
           A+  A+  MN   LGG+ ++VGR      A       A     
Sbjct: 82  AAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA 124

>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 =  108 bits (272), Expect = 1e-30
 Identities = 25/103 (24%), Positives = 49/103 (47%), Gaps = 11/103 (10%)

Query: 7   VQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQ 66
           +++ RP +                  +++++  +   L ++ +K +  +FGP+K   L +
Sbjct: 80  LKIRRPHDYQPLPG-----------AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVK 128

Query: 67  GSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA 109
            S+    KGY F EY     +++AI+ +N   LG + L V RA
Sbjct: 129 DSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 68.8 bits (169), Expect = 2e-15
 Identities = 19/92 (20%), Positives = 39/92 (42%), Gaps = 6/92 (6%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS---SPH--RHKGYGFIEYETKQASN 88
           R+YV +I   +TEE +   F A   +       G+   +    + K + F+E+ +   + 
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 89  EAISSMNLFDLGGQYLRVGRAITPPNALHSSK 120
           +A+ + +     GQ L++ R         + K
Sbjct: 66  QAM-AFDGIIFQGQSLKIRRPHDYQPLPGAHK 96

>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 =  108 bits (272), Expect = 2e-30
 Identities = 26/105 (24%), Positives = 48/105 (45%)

Query: 5   PHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL 64
            +  +   S  P         T      +++++  +   L ++ +K +  +FGP+K   L
Sbjct: 87  DYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNL 146

Query: 65  QQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA 109
            + S+    KGY F EY     +++AI+ +N   LG + L V RA
Sbjct: 147 VKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 191

>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 = 69.7 bits (171), Expect = 2e-15
 Identities = 20/98 (20%), Positives = 41/98 (41%), Gaps = 6/98 (6%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS-----SPHRHKGYGFIEYETKQAS 87
            R+YV +I   +TEE +   F A   +       G+       ++ K + F+E+ +   +
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 88  NEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
            +A+ + +     GQ L++ R          S+ P+  
Sbjct: 65  TQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVY 101

>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 = 93.9 bits (234), Expect = 5e-24
 Identities = 23/91 (25%), Positives = 36/91 (39%), Gaps = 2/91 (2%)

Query: 26  TEEAKLYNRIYVASIHPDLTEED-IKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETK 84
           T        + V  + P   + D +     A     +C+L  G    + KG+  +EYET 
Sbjct: 178 TPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQD-GQLKGFAVLEYETA 236

Query: 85  QASNEAISSMNLFDLGGQYLRVGRAITPPNA 115
           + + EA    +   LGG +LRV      P  
Sbjct: 237 EMAEEAQQQADGLSLGGSHLRVSFCAPGPPG 267

>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 = 87.3 bits (217), Expect = 2e-21
 Identities = 23/95 (24%), Positives = 38/95 (40%)

Query: 27  EEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQA 86
           +       + VA++ P LT++  + +   FG ++ C L       + KGYGF EY  K +
Sbjct: 90  QLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDS 149

Query: 87  SNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKG 121
           +  A S +    LG + L V               
Sbjct: 150 AARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHS 184

>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 = 83.1 bits (206), Expect = 7e-20
 Identities = 15/96 (15%), Positives = 40/96 (41%), Gaps = 7/96 (7%)

Query: 19  QSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGF 78
           +  ++    + +   +I +  +  D+T +++  +   +  +KYC +       ++KG  F
Sbjct: 9   RKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD------KYKGTAF 61

Query: 79  IEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPN 114
           +     + +  AI++ +   L  + L V    T   
Sbjct: 62  VTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDAL 97

>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 = 86.9 bits (216), Expect = 4e-23
 Identities = 26/92 (28%), Positives = 48/92 (52%), Gaps = 9/92 (9%)

Query: 32  YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
            +R++V ++ PD+TEE+++ +FE +G      +       + KG+GFI  ET+  +  A 
Sbjct: 15  RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRLETRTLAEIAK 68

Query: 92  SSMNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
             ++   L G+ LRV  A    +    + GP+
Sbjct: 69  VELDNMPLRGKQLRVRFACHSAS---LTSGPS 97

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 87.0 bits (216), Expect = 5e-23
 Identities = 21/103 (20%), Positives = 42/103 (40%), Gaps = 6/103 (5%)

Query: 12  PSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPH 71
            S   +     D + + +     +Y   I   LT++ ++  F  FG I   ++       
Sbjct: 5   SSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------ 58

Query: 72  RHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPN 114
             KGY F+ + T +++  AI S+N   + G  ++       P+
Sbjct: 59  PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD 101

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 85.1 bits (211), Expect = 2e-22
 Identities = 29/97 (29%), Positives = 42/97 (43%), Gaps = 10/97 (10%)

Query: 12  PSNMPQAQSVIDEITEEAKLYNR-IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSP 70
           P   PQA   +D I   A       Y+ +I    TE D+  +F+ FG I   K       
Sbjct: 9   PQVNPQA---VDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY----- 60

Query: 71  HRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG 107
              KG  FI+Y+T + +   I ++  F   G+ LR G
Sbjct: 61  -PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTG 96

>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 = 84.1 bits (209), Expect = 3e-22
 Identities = 18/83 (21%), Positives = 40/83 (48%), Gaps = 1/83 (1%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQG-SSPHRHKGYGFIEYETKQASNEAI 91
            ++++  +  ++T++ I  +F  +G IK   +      PH  KGY ++E+E    + +A+
Sbjct: 5   TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64

Query: 92  SSMNLFDLGGQYLRVGRAITPPN 114
             M+   + GQ +     + P  
Sbjct: 65  KHMDGGQIDGQEITATAVLAPWP 87

>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 = 87.7 bits (218), Expect = 4e-22
 Identities = 25/91 (27%), Positives = 42/91 (46%), Gaps = 2/91 (2%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             I++ ++   +  + +   F AFG I  CK+      +  KGYGF+ +ET++A+  AI 
Sbjct: 104 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIE 161

Query: 93  SMNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
            MN   L  + + VGR  +           A
Sbjct: 162 KMNGMLLNDRKVFVGRFKSRKEREAELGARA 192

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 76.5 bits (189), Expect = 5e-18
 Identities = 22/87 (25%), Positives = 42/87 (48%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV  +HPD+TE  +   F   GPI   ++ +     R  GY ++ ++    +  A+ +M
Sbjct: 18  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77

Query: 95  NLFDLGGQYLRVGRAITPPNALHSSKG 121
           N   + G+ +R+  +   P+   S  G
Sbjct: 78  NFDVIKGKPVRIMWSQRDPSLRKSGVG 104

>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 = 83.4 bits (207), Expect = 7e-22
 Identities = 25/76 (32%), Positives = 41/76 (53%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            +Y+ SI  D TEE I  +    GP+   K+       R KGY FIE+   ++S  A+ +
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 94  MNLFDLGGQYLRVGRA 109
           +N + LG ++L+ G +
Sbjct: 64  LNGYQLGSRFLKCGYS 79

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 82.7 bits (205), Expect = 2e-21
 Identities = 23/104 (22%), Positives = 43/104 (41%), Gaps = 8/104 (7%)

Query: 11  RPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSP 70
             S +    S +    E      R++V     D+ E ++  +F  FGP+K  K+      
Sbjct: 10  HSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL----- 64

Query: 71  HRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPN 114
               G+ F+E+E  +++ +AI  ++      Q L V  +  P  
Sbjct: 65  ---NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAK 105

>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 = 82.7 bits (205), Expect = 2e-21
 Identities = 29/96 (30%), Positives = 56/96 (58%)

Query: 14  NMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRH 73
           +   A ++ + + + +    R+YV S+H ++TE+ ++ +FE FG I+  +L   S   R 
Sbjct: 8   HSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRS 67

Query: 74  KGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA 109
           KGYGFI +   + + +A+  +N F+L G+ ++VG  
Sbjct: 68  KGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHV 103

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 83.3 bits (206), Expect = 3e-21
 Identities = 21/84 (25%), Positives = 42/84 (50%)

Query: 26  TEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQ 85
              A     +YV  +  ++ ++ + + F  FG I   ++       +H+G+ F+E+E  +
Sbjct: 57  GGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 116

Query: 86  ASNEAISSMNLFDLGGQYLRVGRA 109
            +  AI +MN  +L G+ +RV  A
Sbjct: 117 DAAAAIDNMNESELFGRTIRVNLA 140

>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 = 80.3 bits (199), Expect = 1e-20
 Identities = 20/77 (25%), Positives = 41/77 (53%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             +YV  +  ++ ++ + + F  FG I   ++       +H+G+ F+E+E  + +  AI 
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67

Query: 93  SMNLFDLGGQYLRVGRA 109
           +MN  +L G+ +RV  A
Sbjct: 68  NMNESELFGRTIRVNLA 84

>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 = 82.2 bits (203), Expect = 1e-20
 Identities = 23/82 (28%), Positives = 39/82 (47%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             ++V SIH +  E++I+  F  +G IK   L         KGY  +EYET + +  A  
Sbjct: 73  WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 132

Query: 93  SMNLFDLGGQYLRVGRAITPPN 114
           ++N  ++ GQ ++V        
Sbjct: 133 ALNGAEIMGQTIQVDWCFVKGP 154

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 80.0 bits (198), Expect = 3e-20
 Identities = 28/83 (33%), Positives = 39/83 (46%), Gaps = 2/83 (2%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             ++V  +H + TEEDI   F  +G IK   L         KGY  +EYET + +  A+ 
Sbjct: 24  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83

Query: 93  SMNLFDLGGQYLRVGRAIT--PP 113
            +N  DL GQ + V       PP
Sbjct: 84  GLNGQDLMGQPISVDWCFVRGPP 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 = 79.6 bits (197), Expect = 3e-20
 Identities = 23/76 (30%), Positives = 39/76 (51%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            ++V SIH +  E++I+  F  +G IK   L         KGY  +EYET + +  A  +
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 94  MNLFDLGGQYLRVGRA 109
           +N  ++ GQ ++V   
Sbjct: 88  LNGAEIMGQTIQVDWC 103

>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 = 77.2 bits (191), Expect = 2e-19
 Identities = 28/77 (36%), Positives = 46/77 (59%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           + +YV S+H ++TE+ ++ +FE FG I    L + S   R KGYGFI +   + +  A+ 
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65

Query: 93  SMNLFDLGGQYLRVGRA 109
            +N F+L G+ +RVG  
Sbjct: 66  QLNGFELAGRPMRVGHV 82

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 76.8 bits (190), Expect = 3e-19
 Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 2/77 (2%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            +I+V ++  D T + +K  F   G + Y  ++  +   + KG G +++E+ + +  A  
Sbjct: 9   CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN--GKSKGCGVVKFESPEVAERACR 66

Query: 93  SMNLFDLGGQYLRVGRA 109
            MN   L G+ + V   
Sbjct: 67  MMNGMKLSGREIDVRID 83

>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 = 76.9 bits (190), Expect = 3e-19
 Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 8/83 (9%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            R++V  + P+ +   +   F+ FG I+           +   + +I+YE+  A+  A +
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQAACA 71

Query: 93  SMNLFDLGGQY--LRVGRAITPP 113
            M  F LGG    LRV  A + P
Sbjct: 72  KMRGFPLGGPDRRLRVDFAKSGP 94

>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 = 76.6 bits (189), Expect = 4e-19
 Identities = 19/91 (20%), Positives = 43/91 (47%), Gaps = 5/91 (5%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            R++V++I     + D++ +F  FG I   ++    +    KG+GF+ +E    ++ A  
Sbjct: 16  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEII--FNERGSKGFGFVTFENSADADRARE 73

Query: 93  SMNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
            ++   + G+ + V  A        ++ GP+
Sbjct: 74  KLHGTVVEGRKIEVNNATARVM---TNSGPS 101

>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 = 76.6 bits (189), Expect = 5e-19
 Identities = 22/101 (21%), Positives = 42/101 (41%), Gaps = 8/101 (7%)

Query: 32  YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
              ++V ++   +TEE ++  F  FG ++  K          K Y FI ++ +  + +A+
Sbjct: 11  VKVLFVRNLANTVTEEILEKAFSQFGKLERVKK--------LKDYAFIHFDERDGAVKAM 62

Query: 92  SSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHMPTA 132
             MN  DL G+ + +  A  P       K    + S   + 
Sbjct: 63  EEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGPSSG 103

>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 = 76.2 bits (188), Expect = 5e-19
 Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 8/88 (9%)

Query: 27  EEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQA 86
              +  N +YV     D+T   ++  F  FG I    +         +   F+ YE  ++
Sbjct: 10  RAPRKGNTLYVY--GEDMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMES 61

Query: 87  SNEAISSMNLFDLGGQYLRVGRAITPPN 114
           +++A++ +N   +    L+V  A   P 
Sbjct: 62  ADQAVAELNGTQVESVQLKVNIARKQPM 89

>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 = 76.6 bits (189), Expect = 6e-19
 Identities = 24/106 (22%), Positives = 47/106 (44%), Gaps = 7/106 (6%)

Query: 28  EAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETK 84
           EA    ++++  ++ +  E+ +K+VF   GPI    L   +      + +G+ FI +E  
Sbjct: 3   EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS----KSRGFAFITFENP 58

Query: 85  QASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHMP 130
             +  A   MN   L G+ ++V +A  P       + P  S+ +  
Sbjct: 59  ADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRS 104

>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 = 77.2 bits (190), Expect = 8e-19
 Identities = 14/80 (17%), Positives = 38/80 (47%), Gaps = 5/80 (6%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++YV ++  +  + +++  F  +GP++   +          G+ F+E+E  + + +A+  
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVEFEDPRDAADAVRE 129

Query: 94  MNLFDLGGQYLRVGRAITPP 113
           ++   L G  +RV  +    
Sbjct: 130 LDGRTLCGCRVRVELSNGEK 149

>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 = 75.7 bits (187), Expect = 9e-19
 Identities = 17/78 (21%), Positives = 37/78 (47%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           + +YV+++   LT  D+  +F  +G +    + +     + KG  FI +  K ++     
Sbjct: 17  STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76

Query: 93  SMNLFDLGGQYLRVGRAI 110
           ++N   L G+ ++   AI
Sbjct: 77  AINNKQLFGRVIKASIAI 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 = 75.8 bits (187), Expect = 1e-18
 Identities = 19/80 (23%), Positives = 39/80 (48%), Gaps = 3/80 (3%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ---QGSSPHRHKGYGFIEYETKQASNE 89
           + +++ +++   TEE +K VF   G IK C +      +      G+GF+EY+  + + +
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 90  AISSMNLFDLGGQYLRVGRA 109
           A+  +    + G  L V  +
Sbjct: 66  ALKQLQGHTVDGHKLEVRIS 85

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 75.4 bits (186), Expect = 1e-18
 Identities = 15/83 (18%), Positives = 47/83 (56%), Gaps = 1/83 (1%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           ++++++ +    T+E+++ + +A G +K  +L    +  + KG  ++EYE +  +++A+ 
Sbjct: 18  HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRA-GKPKGLAYVEYENESQASQAVM 76

Query: 93  SMNLFDLGGQYLRVGRAITPPNA 115
            M+   +    ++V  + + P++
Sbjct: 77  KMDGMTIKENIIKVAISNSGPSS 99

>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 = 75.3 bits (186), Expect = 1e-18
 Identities = 21/84 (25%), Positives = 43/84 (51%)

Query: 26  TEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQ 85
           +  A     +YV  +  ++ ++ + + F  FG I   ++       +H+G+ F+E+E  +
Sbjct: 6   SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 65

Query: 86  ASNEAISSMNLFDLGGQYLRVGRA 109
            +  AI +MN  +L G+ +RV  A
Sbjct: 66  DAAAAIDNMNESELFGRTIRVNLA 89

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 75.4 bits (186), Expect = 1e-18
 Identities = 16/95 (16%), Positives = 41/95 (43%), Gaps = 5/95 (5%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++YV ++     + +++  F  +GP++   +          G+ F+E+E  + + +A+  
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWI-----ARNPPGFAFVEFEDPRDAEDAVRG 56

Query: 94  MNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSH 128
           ++   + G  +RV  +   P      + PA     
Sbjct: 57  LDGKVICGSRVRVELSTGMPRRSRFDRPPARRKLL 91

>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 = 76.8 bits (190), Expect = 1e-18
 Identities = 19/75 (25%), Positives = 39/75 (52%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           + V  +  D+T+ ++ ++F A GPI  C++ +        GY F+++ ++  S  AI  +
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65

Query: 95  NLFDLGGQYLRVGRA 109
           N   +  + L+V  A
Sbjct: 66  NGITVRNKRLKVSYA 80

>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 = 64.1 bits (157), Expect = 1e-13
 Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 10/81 (12%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKL----QQGSSPHRHKGYGFIEYETKQASNEA 90
           +YV ++   +T++ + ++F  +G I    +      G      +G  F+ Y  ++ + EA
Sbjct: 92  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRP----RGVAFVRYNKREEAQEA 147

Query: 91  ISSMN--LFDLGGQYLRVGRA 109
           IS++N  + + G Q L V  A
Sbjct: 148 ISALNNVIPEGGSQPLSVRLA 168

>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 = 75.4 bits (186), Expect = 2e-18
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 3/77 (3%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            RIYV ++ PD+  +DI+ VF  +G I+   L+          + F+E+E  + + +A+ 
Sbjct: 23  CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVY 79

Query: 93  SMNLFDLGGQYLRVGRA 109
             + +D  G  LRV   
Sbjct: 80  GRDGYDYDGYRLRVEFP 96

>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 = 75.4 bits (186), Expect = 2e-18
 Identities = 22/93 (23%), Positives = 41/93 (44%), Gaps = 5/93 (5%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             +Y+ ++ P +TE D+ S+F  F   K   +Q      R +G  FI +  K+ + +A+ 
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85

Query: 93  SMNLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
            +N + L G+ L +             +   PS
Sbjct: 86  LVNGYKLYGKILVIEFGKNK-----KQRSSGPS 113

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 74.6 bits (184), Expect = 2e-18
 Identities = 16/80 (20%), Positives = 39/80 (48%), Gaps = 7/80 (8%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQASNE 89
             ++V ++   + EE +  +F   GP+    +   ++G    + K +GF+ ++  ++ + 
Sbjct: 17  RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG----KPKSFGFVCFKHPESVSY 72

Query: 90  AISSMNLFDLGGQYLRVGRA 109
           AI+ +N   L G+ + V   
Sbjct: 73  AIALLNGIRLYGRPINVSGP 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 = 74.5 bits (184), Expect = 2e-18
 Identities = 20/77 (25%), Positives = 34/77 (44%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             + V  +    TE D++ VF  +GPI    +       R +G+ F+ +E    + EA  
Sbjct: 16  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75

Query: 93  SMNLFDLGGQYLRVGRA 109
             N  +L G+ +RV   
Sbjct: 76  RANGMELDGRRIRVSGP 92

>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 = 76.5 bits (189), Expect = 3e-18
 Identities = 16/100 (16%), Positives = 45/100 (45%), Gaps = 8/100 (8%)

Query: 10  GRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSS 69
           G    + + +      +++ +    +   ++  ++TE+++K VFE    I+    Q G S
Sbjct: 80  GNEIKLEKPKG---RDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-QDGKS 135

Query: 70  PHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA 109
               KG  +IE++++  + + +      ++ G+ + +   
Sbjct: 136 ----KGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT 171

>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 = 68.8 bits (169), Expect = 2e-15
 Identities = 10/95 (10%), Positives = 43/95 (45%), Gaps = 3/95 (3%)

Query: 20  SVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFI 79
           S + E +E    +N +++ +++P+ +  ++K             +    +   ++ +G++
Sbjct: 2   SHMVEGSESTTPFN-LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT-GTNRKFGYV 59

Query: 80  EYETKQASNEAISSMNLFDLGGQYLRVGRAITPPN 114
           ++E+ +   +A+  +    + G  +++ +     +
Sbjct: 60  DFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDS 93

>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 = 74.1 bits (183), Expect = 3e-18
 Identities = 15/76 (19%), Positives = 40/76 (52%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            +Y+  + P  T++D+  + + +G I   K     + ++ KGYGF+++++  A+ +A+++
Sbjct: 7   GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66

Query: 94  MNLFDLGGQYLRVGRA 109
           +    +  Q  +    
Sbjct: 67  LKASGVQAQMAKQSGP 82

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 74.7 bits (184), Expect = 3e-18
 Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            R++V++I     + D++ +F  FG I   ++    +    KG+GF+ +E    ++ A  
Sbjct: 30  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEII--FNERGSKGFGFVTFENSADADRARE 87

Query: 93  SMNLFDLGGQYLRVGRA 109
            ++   + G+ + V  A
Sbjct: 88  KLHGTVVEGRKIEVNNA 104

>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 = 73.8 bits (182), Expect = 4e-18
 Identities = 19/90 (21%), Positives = 39/90 (43%), Gaps = 9/90 (10%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV ++    +EE I+  F    P    +++      + + Y F+ +  ++ + EA+ ++
Sbjct: 18  LYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKAL 71

Query: 95  NLFDLGGQYLRVGRAITPPNALHSSKGPAP 124
           N   L G  + V  A         S GP+ 
Sbjct: 72  NGKVLDGSPIEVTLAKPVDK---DSSGPSS 98

>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 = 74.2 bits (183), Expect = 4e-18
 Identities = 21/83 (25%), Positives = 38/83 (45%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             I V ++  D  E D++ +F  FG I    L +  +  + KG+ FI +  ++ +  AI+
Sbjct: 16  ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75

Query: 93  SMNLFDLGGQYLRVGRAITPPNA 115
            ++ F      L V  A    N+
Sbjct: 76  GVSGFGYDHLILNVEWAKPSTNS 98

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 73.4 bits (181), Expect = 6e-18
 Identities = 23/90 (25%), Positives = 48/90 (53%), Gaps = 11/90 (12%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++++ ++  + TE++I+S+FE +G +  C +         K YGF+  E K A+ +AI +
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDI--------IKNYGFVHIEDKTAAEDAIRN 61

Query: 94  MNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
           ++ + L G  + V  +        +S GP+
Sbjct: 62  LHHYKLHGVNINVEASKNKSK---ASSGPS 88

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 73.9 bits (182), Expect = 6e-18
 Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 4/78 (5%)

Query: 32  YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
              + ++++    TEE ++ VFE    IK  + Q G S    KGY FIE+ + + + EA+
Sbjct: 15  SKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKS----KGYAFIEFASFEDAKEAL 70

Query: 92  SSMNLFDLGGQYLRVGRA 109
           +S N  ++ G+ +R+   
Sbjct: 71  NSCNKREIEGRAIRLELQ 88

>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 = 74.3 bits (183), Expect = 7e-18
 Identities = 14/77 (18%), Positives = 35/77 (45%), Gaps = 1/77 (1%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            ++ V+++   +++ DI+ +F  FG +K   +    S  R  G   + +E +  + +A+ 
Sbjct: 36  AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKAMK 94

Query: 93  SMNLFDLGGQYLRVGRA 109
                 L G+ + +   
Sbjct: 95  QYKGVPLDGRPMDIQLV 111

>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 = 74.3 bits (183), Expect = 7e-18
 Identities = 30/96 (31%), Positives = 41/96 (42%), Gaps = 1/96 (1%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             ++V  +H + TEEDI   F  +G IK   L         KGY  +EYET + +  A+ 
Sbjct: 23  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82

Query: 93  SMNLFDLGGQYLRVGRAIT-PPNALHSSKGPAPSTS 127
            +N  DL GQ + V       P       G   S S
Sbjct: 83  GLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRS 118

>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 = 73.1 bits (180), Expect = 7e-18
 Identities = 17/95 (17%), Positives = 42/95 (44%), Gaps = 12/95 (12%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           N++Y+ ++ P +T +D++ +F         ++          GY F++Y  +  +  AI 
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL------LKSGYAFVDYPDQNWAIRAIE 62

Query: 93  SMN-LFDLGGQYLRVGRAITPPNALHSSKGPAPST 126
           +++   +L G+ + V  +          +   PS+
Sbjct: 63  TLSGKVELHGKIMEVDYS-VSK----KLRSSGPSS 92

>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 = 75.3 bits (186), Expect = 8e-18
 Identities = 27/108 (25%), Positives = 47/108 (43%), Gaps = 14/108 (12%)

Query: 8   QVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL--- 64
            +  P  M  A S  +   E+ KL+    +  I    TE DI+ +F +FG I+ C++   
Sbjct: 75  GMHHPIQMKPADSEKNNAVEDRKLF----IGMISKKCTENDIRVMFSSFGQIEECRILRG 130

Query: 65  QQGSSPHRHKGYGFIEYETKQASNEAISSMN---LFDLGGQYLRVGRA 109
             G S    +G  F+ + T+  +  AI +M+     +     + V  A
Sbjct: 131 PDGLS----RGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 71.1 bits (175), Expect = 3e-16
 Identities = 14/77 (18%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQ--GSSPHRHKGYGFIEYETKQASNEAIS 92
           ++V  +    +E+D++ +FE +G +    + +    +P + KG  F+ + T++A+ EA +
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65

Query: 93  SMNLFDLGGQYLRVGRA 109
           +++   +        + 
Sbjct: 66  ALHNMKVLPGMHHPIQM 82

>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 = 73.8 bits (182), Expect = 8e-18
 Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 2/76 (2%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           I++ ++   +  + +   F AFG I  CK+      +  KGYGF+ +ET++A+  AI  M
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIEKM 65

Query: 95  NLFDLGGQYLRVGRAI 110
           N   L  + + VGR  
Sbjct: 66  NGMLLNDRKVFVGRFK 81

>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 = 73.5 bits (181), Expect = 9e-18
 Identities = 16/77 (20%), Positives = 36/77 (46%), Gaps = 1/77 (1%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            ++ V+++   +++ DI+ +F  FG +K   +    S  R  G   + +E K  + +A+ 
Sbjct: 30  GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALKAMK 88

Query: 93  SMNLFDLGGQYLRVGRA 109
             N   L G+ + +   
Sbjct: 89  QYNGVPLDGRPMNIQLV 105

>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 = 73.6 bits (181), Expect = 9e-18
 Identities = 15/77 (19%), Positives = 37/77 (48%), Gaps = 3/77 (3%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +Y+ ++   +T E++  +F  +GPI+  ++         +G  ++ YE    +  A+  +
Sbjct: 11  LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNAVDHL 67

Query: 95  NLFDLGGQYLRVGRAIT 111
           + F++  +YL V     
Sbjct: 68  SGFNVSNRYLVVLYYNA 84

>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 = 74.5 bits (184), Expect = 1e-17
 Identities = 21/75 (28%), Positives = 43/75 (57%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           + V  +  ++T+E+ +S+F + G I+ CKL +     +  GYGF+ Y   + + +AI+++
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 95  NLFDLGGQYLRVGRA 109
           N   L  + ++V  A
Sbjct: 65  NGLRLQTKTIKVSYA 79

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 64.1 bits (157), Expect = 1e-13
 Identities = 16/78 (20%), Positives = 37/78 (47%), Gaps = 2/78 (2%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            +YV+ +   +T+++++ +F  +G I   ++         +G GFI ++ +  + EAI  
Sbjct: 90  NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 149

Query: 94  MN--LFDLGGQYLRVGRA 109
           +N        + + V  A
Sbjct: 150 LNGQKPSGATEPITVKFA 167

>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 = 72.1 bits (178), Expect = 1e-17
 Identities = 17/82 (20%), Positives = 39/82 (47%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             ++V  ++ ++ +E +++ F+ F       +         +GYGF+ + ++  +  A+ 
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 93  SMNLFDLGGQYLRVGRAITPPN 114
           SM   DL G+ LR+  A    +
Sbjct: 62  SMQGQDLNGRPLRINWAAKLEH 83

>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 = 72.4 bits (178), Expect = 2e-17
 Identities = 23/96 (23%), Positives = 47/96 (48%), Gaps = 8/96 (8%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++++  I  +L E+D+K +FE FG I    + +      HKG  F+ Y  ++++ +A S+
Sbjct: 15  KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74

Query: 94  MN---LFDLGGQYLRVGRAITPPNALHSSKGPAPST 126
           ++         + ++V  A +      S  G  PS+
Sbjct: 75  LHEQKTLPGMNRPIQVKPADS-----ESRGGSGPSS 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 = 72.8 bits (179), Expect = 2e-17
 Identities = 29/94 (30%), Positives = 46/94 (48%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            ++V  + P++T EDIK+ F  FG I   ++ +  +  + KGYGF+ +  K  +  AI  
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76

Query: 94  MNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTS 127
           M    LGG+ +R   A   P A  S+       S
Sbjct: 77  MGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQS 110

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 72.4 bits (178), Expect = 2e-17
 Identities = 9/74 (12%), Positives = 33/74 (44%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             +  A ++ ++ E  +K +   +G ++  ++       +H G   + + + + + E + 
Sbjct: 7   KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 93  SMNLFDLGGQYLRV 106
           +++L  + G  +  
Sbjct: 67  NLHLTSVMGNIIHA 80

>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 = 71.9 bits (177), Expect = 3e-17
 Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 2/80 (2%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV ++  D+TE  I  +F   GP K CK+   +    +  Y F+E+   + +  A+++M
Sbjct: 18  LYVGNLSRDVTEVLILQLFSQIGPCKSCKM--ITEHTSNDPYCFVEFYEHRDAAAALAAM 75

Query: 95  NLFDLGGQYLRVGRAITPPN 114
           N   + G+ ++V  A TP +
Sbjct: 76  NGRKILGKEVKVNWATTPSS 95

>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 = 71.4 bits (176), Expect = 3e-17
 Identities = 22/76 (28%), Positives = 38/76 (50%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            ++V  + P++T   I + F  FG I   ++ +  +  + KGYGF+ +  K  +  AI  
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 94  MNLFDLGGQYLRVGRA 109
           M    LGG+ +R   A
Sbjct: 68  MGGQWLGGRQIRTNWA 83

>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 = 76.8 bits (188), Expect = 3e-17
 Identities = 20/71 (28%), Positives = 37/71 (52%)

Query: 32  YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
           +  ++VA ++ D TE  ++  FE +GPIK   +       + +GY FIEYE ++  + A 
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161

Query: 92  SSMNLFDLGGQ 102
              +   + G+
Sbjct: 162 KHADGKKIDGR 172

>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 = 71.5 bits (176), Expect = 5e-17
 Identities = 27/99 (27%), Positives = 44/99 (44%), Gaps = 4/99 (4%)

Query: 27  EEAKL-YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQ 85
            E K+  N ++V  I   + E +I+S F  +G +K  K+    +    KGYGF+ +    
Sbjct: 3   PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT-GVSKGYGFVSFYNDV 61

Query: 86  ASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAP 124
              + + S   F   G+ L++G AI   N       P P
Sbjct: 62  DVQKIVESQINFH--GKKLKLGPAIRKQNLSTYHVQPRP 98

>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 = 74.7 bits (184), Expect = 5e-17
 Identities = 23/106 (21%), Positives = 46/106 (43%), Gaps = 9/106 (8%)

Query: 9   VGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS 68
           +G   ++       ++         R++V ++  D+TEED K +FE +G      +    
Sbjct: 2   MGFTIDIKSFLKPGEK---TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN--- 55

Query: 69  SPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPN 114
              R +G+GFI  E++  +  A + ++   L  + LR+  A     
Sbjct: 56  ---RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGAA 98

>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 = 66.6 bits (163), Expect = 6e-14
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 12/83 (14%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQASNE 89
             + V ++ P ++ E ++  F  FGP++   +    +G    R  G GF+E+  K  + +
Sbjct: 97  AALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRG----RATGKGFVEFAAKPPARK 152

Query: 90  AISSMNLFDLGGQYLRVGRAITP 112
           A+         G +L +     P
Sbjct: 153 ALERCG----DGAFL-LTTTPRP 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 = 71.1 bits (175), Expect = 7e-17
 Identities = 20/75 (26%), Positives = 43/75 (57%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV  +   ++E  +  +F   GP+    + +     +H+GYGF+E+ +++ ++ AI  M
Sbjct: 18  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77

Query: 95  NLFDLGGQYLRVGRA 109
           ++  L G+ +RV +A
Sbjct: 78  DMIKLYGKPIRVNKA 92

>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 = 70.0 bits (172), Expect = 9e-17
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 7/74 (9%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV  +   +TE D+++ F  FG I+   + Q       +   FI++ T+QA+  A    
Sbjct: 15  LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKS 68

Query: 95  -NLFDLGGQYLRVG 107
            N   + G+ L V 
Sbjct: 69  FNKLIVNGRRLNVK 82

>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 = 70.7 bits (174), Expect = 9e-17
 Identities = 17/93 (18%), Positives = 42/93 (45%), Gaps = 5/93 (5%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            + V ++    + + ++ VFE +G +    + +       +G+ F+ +  ++ + +A ++
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74

Query: 94  MNLFDLGGQYLRVGRAITPPNALHSSKGPAPST 126
           M+  +L G+ LRV  A              PS+
Sbjct: 75  MDGAELDGRELRVQVARYGRR-----DLSGPSS 102

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 70.8 bits (174), Expect = 1e-16
 Identities = 18/75 (24%), Positives = 38/75 (50%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +++  +  +  ++D+  +F  FG +   K+      +  K +GF+ Y+   ++  AI SM
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87

Query: 95  NLFDLGGQYLRVGRA 109
           N F +G + L+V   
Sbjct: 88  NGFQIGMKRLKVQLK 102

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 69.9 bits (172), Expect = 1e-16
 Identities = 20/92 (21%), Positives = 41/92 (44%), Gaps = 14/92 (15%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           +I+V ++    T ++++S+FE  G +  C +         K Y F+  E +  +  AI+ 
Sbjct: 11  KIFVGNVSAACTSQELRSLFERRGRVIECDV--------VKDYAFVHMEKEADAKAAIAQ 62

Query: 94  MNLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
           +N  ++ G+ + V  +          K   PS
Sbjct: 63  LNGKEVKGKRINVELSTKGQ------KKSGPS 88

>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 = 69.6 bits (171), Expect = 2e-16
 Identities = 20/91 (21%), Positives = 45/91 (49%), Gaps = 11/91 (12%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            +++V +I P  T +++++ FE +GP+  C +         K Y F+  E  + + EAI 
Sbjct: 11  TKLHVGNISPTCTNQELRAKFEEYGPVIECDI--------VKDYAFVHMERAEDAVEAIR 62

Query: 93  SMNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
            ++  +  G+ + V  + +      ++ GP+
Sbjct: 63  GLDNTEFQGKRMHVQLSTSRL---RTASGPS 90

>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 = 70.5 bits (173), Expect = 2e-16
 Identities = 23/102 (22%), Positives = 52/102 (50%)

Query: 8   QVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQG 67
           Q+ +     Q      ++  E  +   + V  I   + E  ++ +FE +GPI+  K+   
Sbjct: 18  QLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCD 77

Query: 68  SSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA 109
               + +GYGF+++++  ++ +AI+ +N F++  + L+V  A
Sbjct: 78  RETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA 119

>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 = 69.7 bits (171), Expect = 2e-16
 Identities = 21/88 (23%), Positives = 44/88 (50%), Gaps = 6/88 (6%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            +++ ++  D  EE +  V + FG +KY ++         KG  F ++ T++A+ + +++
Sbjct: 17  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76

Query: 94  MNL------FDLGGQYLRVGRAITPPNA 115
            +L        L G+ L+V  A+T   A
Sbjct: 77  ASLEAEGGGLKLDGRQLKVDLAVTRDEA 104

>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 = 70.0 bits (172), Expect = 2e-16
 Identities = 12/78 (15%), Positives = 33/78 (42%), Gaps = 7/78 (8%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQASNEAI 91
           +Y++++   + E++++++ + FG +   ++     G+S    +G GF   E+ +     I
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTS----RGVGFARMESTEKCEAVI 83

Query: 92  SSMNLFDLGGQYLRVGRA 109
              N   +          
Sbjct: 84  GHFNGKFIKTPPGVSAPT 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 = 69.6 bits (171), Expect = 3e-16
 Identities = 19/82 (23%), Positives = 42/82 (51%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            +++V  +  D  E+ ++ VF  +G I    + +     R +G+GF+ +E    + +A+ 
Sbjct: 13  GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72

Query: 93  SMNLFDLGGQYLRVGRAITPPN 114
           +MN   + G+ +RV +A    +
Sbjct: 73  AMNGKSVDGRQIRVDQAGKSSD 94

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 73.1 bits (180), Expect = 3e-16
 Identities = 12/76 (15%), Positives = 29/76 (38%), Gaps = 3/76 (3%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           + V ++     +  +   F+  GPI +  +    S  ++  +  IE+     +  AI+  
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVAD--SLKKNFRFARIEFARYDGALAAITKT 101

Query: 95  NLFDLGGQYLRVGRAI 110
           +   +G   + V    
Sbjct: 102 H-KVVGQNEIIVSHLT 116

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 70.8 bits (174), Expect = 3e-15
 Identities = 8/77 (10%), Positives = 30/77 (38%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             +++ +  P  T+ +I+ + +    +           +  + + +I+  +K+ +   + 
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177

Query: 93  SMNLFDLGGQYLRVGRA 109
            +N   + G  L    +
Sbjct: 178 KLNGLKIEGYTLVTKVS 194

>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 = 65.0 bits (159), Expect = 2e-13
 Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 3/77 (3%)

Query: 35  IYVASIHPDLTEED-IKSVFEAFGPIKYCKLQQGSSPH-RHKGYGFIEYETKQASNEAIS 92
           I + ++  +L +E+ ++  FE FG I+   +  G   H  +    F+ +E K ++  A+ 
Sbjct: 213 IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL- 271

Query: 93  SMNLFDLGGQYLRVGRA 109
            MN   LG + + V  A
Sbjct: 272 QMNRSLLGNREISVSLA 288

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 71.0 bits (174), Expect = 4e-16
 Identities = 14/79 (17%), Positives = 36/79 (45%), Gaps = 1/79 (1%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            ++ V+++   +++ DI+ +F  FG +K   +    S  R  G   + +E +  + +A+ 
Sbjct: 89  AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKAMK 147

Query: 93  SMNLFDLGGQYLRVGRAIT 111
                 L G+ + +    +
Sbjct: 148 QYKGVPLDGRPMDIQLVAS 166

>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 = 68.8 bits (169), Expect = 4e-16
 Identities = 15/89 (16%), Positives = 41/89 (46%), Gaps = 5/89 (5%)

Query: 26  TEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQ 85
           +++ +    +   ++  ++TE+++K VFE    I+    Q G S    KG  +IE++++ 
Sbjct: 10  SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-QDGKS----KGIAYIEFKSEA 64

Query: 86  ASNEAISSMNLFDLGGQYLRVGRAITPPN 114
            + + +      ++ G+ + +        
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYYTGEKGG 93

>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 = 68.9 bits (169), Expect = 4e-16
 Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 9/83 (10%)

Query: 33  NRIYVASIHPDL-TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
           +R+++ +++  L  + D++++F  +G +  C +        HKGY F++Y  ++ +  A+
Sbjct: 28  SRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAV 79

Query: 92  SSMNLFDLGGQYLRVGRAITPPN 114
              N   L GQ L +  A  P  
Sbjct: 80  LGENGRVLAGQTLDINMAGEPKP 102

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 69.3 bits (170), Expect = 5e-16
 Identities = 18/75 (24%), Positives = 37/75 (49%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +++  +  + T+ D+ S F  FG +   K+         K +GF+ ++   ++  AI +M
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102

Query: 95  NLFDLGGQYLRVGRA 109
           N F +G + L+V   
Sbjct: 103 NGFQVGTKRLKVQLK 117

>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 = 68.4 bits (168), Expect = 7e-16
 Identities = 24/77 (31%), Positives = 42/77 (54%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             ++V +I  + TEE +K +F   GP+   +L       + KGYGF EY+ ++ +  A+ 
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68

Query: 93  SMNLFDLGGQYLRVGRA 109
           ++N  +  G+ LRV  A
Sbjct: 69  NLNGREFSGRALRVDNA 85

>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 = 69.9 bits (172), Expect = 7e-16
 Identities = 18/80 (22%), Positives = 39/80 (48%), Gaps = 1/80 (1%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV ++   +TE+ +K  F+  GPI   K+    + +++  Y F+EY     +N A+ ++
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTL 61

Query: 95  NLFDLGGQYLRVGRAITPPN 114
           N   +    +++  A     
Sbjct: 62  NGKQIENNIVKINWAFQSQQ 81

>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 = 68.7 bits (169), Expect = 2e-15
 Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 8/80 (10%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKL----QQGSSPHRHKGYGFIEYETKQASNE 89
            ++V  ++ ++ +E +++ F+ F       +    Q GSS    +GYGF+ + ++  +  
Sbjct: 89  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSS----RGYGFVSFTSQDDAQN 144

Query: 90  AISSMNLFDLGGQYLRVGRA 109
           A+ SM   DL G+ LR+  A
Sbjct: 145 AMDSMQGQDLNGRPLRINWA 164

>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 = 69.0 bits (169), Expect = 7e-16
 Identities = 22/79 (27%), Positives = 37/79 (46%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             + V  +    TE D++ VF  +GPI    +       R +G+ F+ +E    + EA  
Sbjct: 47  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 106

Query: 93  SMNLFDLGGQYLRVGRAIT 111
             N  +L G+ +RV  +IT
Sbjct: 107 RANGMELDGRRIRVDFSIT 125

>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 = 67.6 bits (166), Expect = 1e-15
 Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 6/78 (7%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKL--QQGSSPHRHKGYGFIEYETKQASNEAI 91
            +YV ++   + +E ++  F  FG I   K+  + G S    KG+GF+ + + + + +A+
Sbjct: 17  NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRS----KGFGFVCFSSPEEATKAV 72

Query: 92  SSMNLFDLGGQYLRVGRA 109
           + MN   +  + L V  A
Sbjct: 73  TEMNGRIVATKPLYVALA 90

>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 = 67.7 bits (166), Expect = 1e-15
 Identities = 21/79 (26%), Positives = 45/79 (56%), Gaps = 2/79 (2%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQ-GSSPHRHKGYGFIEYETKQASNEAI 91
           ++I V +I     + +I+ +F  FG +K  +L +  +    H+G+GF+++ TKQ + +A 
Sbjct: 16  SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75

Query: 92  SSM-NLFDLGGQYLRVGRA 109
           +++ +   L G+ L +  A
Sbjct: 76  NALCHSTHLYGRRLVLEWA 94

>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 = 67.3 bits (165), Expect = 2e-15
 Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 4/83 (4%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            +++V  ++   +EED+  +F+ FG I  C + +G      KG  F+++ +   +  AI 
Sbjct: 16  RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDG-SSKGCAFVKFSSHTEAQAAIH 74

Query: 93  SMN---LFDLGGQYLRVGRAITP 112
           +++           L V  A T 
Sbjct: 75  ALHGSQTMPGASSSLVVKFADTD 97

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 67.2 bits (165), Expect = 2e-15
 Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYC-KLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            I++ ++ P++ E+ +   F AFG I    K+ +       KGY FI + +  AS+ AI 
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 93  SMNLFDLGGQYLRVGRAI 110
           +MN   L  + + V  A 
Sbjct: 67  AMNGQYLCNRPITVSYAF 84

>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 = 67.3 bits (165), Expect = 2e-15
 Identities = 18/87 (20%), Positives = 38/87 (43%), Gaps = 7/87 (8%)

Query: 26  TEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYE 82
            +  +L + ++VA++   +  + +K VF   G +    +   + G S    +G G + +E
Sbjct: 9   LQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKS----RGIGTVTFE 64

Query: 83  TKQASNEAISSMNLFDLGGQYLRVGRA 109
               + +AIS  N   L  + + V   
Sbjct: 65  QSIEAVQAISMFNGQLLFDRPMHVKMD 91

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 67.8 bits (166), Expect = 3e-15
 Identities = 20/88 (22%), Positives = 44/88 (50%), Gaps = 2/88 (2%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             + V ++    + + ++ VFE +G +    + +       +G+ F+ +  K+ + +A+ 
Sbjct: 48  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107

Query: 93  SMNLFDLGGQYLRVGRAIT--PPNALHS 118
           +M+   L G+ LRV  A    PP++ HS
Sbjct: 108 AMDGAVLDGRELRVQMARYGRPPDSHHS 135

>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 = 66.5 bits (163), Expect = 3e-15
 Identities = 15/81 (18%), Positives = 40/81 (49%), Gaps = 7/81 (8%)

Query: 33  NRIYVASIHPDLTEEDIK----SVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASN 88
           + IY+ +++  + ++++K    ++F  FG I    + +     + +G  F+ ++   ++ 
Sbjct: 9   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKEVSSAT 65

Query: 89  EAISSMNLFDLGGQYLRVGRA 109
            A+ SM  F    + +R+  A
Sbjct: 66  NALRSMQGFPFYDKPMRIQYA 86

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 66.5 bits (163), Expect = 3e-15
 Identities = 17/77 (22%), Positives = 39/77 (50%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            R++V ++    +EED++ +F A+GP+        S   + KG+ F+ +   + + +A +
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 93  SMNLFDLGGQYLRVGRA 109
            ++     G+ L V  +
Sbjct: 69  EVDGQVFQGRMLHVLPS 85

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 66.5 bits (163), Expect = 3e-15
 Identities = 14/75 (18%), Positives = 37/75 (49%), Gaps = 9/75 (12%)

Query: 33  NRIYVASIHP-DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
           +R+++ ++   ++++ED+  +F  +G I    +           +GFI+++  Q+  +AI
Sbjct: 11  SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 62

Query: 92  SSMNLFDLGGQYLRV 106
              +     G+ L +
Sbjct: 63  ECESQEMNFGKKLIL 77

>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 = 66.7 bits (163), Expect = 4e-15
 Identities = 23/102 (22%), Positives = 38/102 (37%), Gaps = 13/102 (12%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPH--------RHKGYGFIEYETK 84
           + IYV  ++  +T +D+   F+  G +K  K       H        + KG   + YE  
Sbjct: 16  SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75

Query: 85  QASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPST 126
             +  A+   +  D  G  L+V  A   P          PS+
Sbjct: 76  PTAKAAVEWFDGKDFQGSKLKVSLARKKPP-----MNSGPSS 112

>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 = 65.9 bits (161), Expect = 4e-15
 Identities = 18/80 (22%), Positives = 37/80 (46%), Gaps = 6/80 (7%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS-----SPHRHKGYGFIEYETKQASN 88
           R+YV +I   +TEE +   F A   +       G+       ++ K + F+E+ +   + 
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 89  EAISSMNLFDLGGQYLRVGR 108
           +A+ + +     GQ L++ R
Sbjct: 68  QAM-AFDGIIFQGQSLKIRR 86

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 66.3 bits (162), Expect = 5e-15
 Identities = 12/78 (15%), Positives = 31/78 (39%), Gaps = 1/78 (1%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
               + S    + ++ + S+F   G +   +     +  + KG+ F+E  +   + + I 
Sbjct: 13  GAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72

Query: 93  SMNLFDLGGQY-LRVGRA 109
           S +   L  ++ L +   
Sbjct: 73  SFHGKRLDLKHRLFLYTM 90

>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 = 67.6 bits (165), Expect = 5e-15
 Identities = 20/88 (22%), Positives = 44/88 (50%), Gaps = 2/88 (2%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             + V ++    + + ++ VFE +G +    + +       +G+ F+ +  K+ + +A+ 
Sbjct: 71  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130

Query: 93  SMNLFDLGGQYLRVGRAIT--PPNALHS 118
           +M+   L G+ LRV  A    PP++ HS
Sbjct: 131 AMDGAVLDGRELRVQMARYGRPPDSHHS 158

>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 = 67.1 bits (164), Expect = 6e-15
 Identities = 18/82 (21%), Positives = 32/82 (39%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             +YV ++    TEE I  +F   G IK   +          G+ F+EY ++  +  A+ 
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99

Query: 93  SMNLFDLGGQYLRVGRAITPPN 114
            +N   L  + +R         
Sbjct: 100 YINGTRLDDRIIRTDWDAGFKE 121

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 65.5 bits (160), Expect = 7e-15
 Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 3/74 (4%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            ++ + +I P L  E + S+   +G ++ C+     +         + Y +K  + +A+ 
Sbjct: 16  RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQ---VNTDSETAVVNVTYSSKDQARQALD 72

Query: 93  SMNLFDLGGQYLRV 106
            +N F L    L+V
Sbjct: 73  KLNGFQLENFTLKV 86

>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 = 65.4 bits (160), Expect = 9e-15
 Identities = 17/85 (20%), Positives = 34/85 (40%), Gaps = 8/85 (9%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPH--------RHKGYGFIEYETK 84
           N I+V  +  ++T E +   F+  G IK  K       +        + KG   + ++  
Sbjct: 14  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73

Query: 85  QASNEAISSMNLFDLGGQYLRVGRA 109
            ++  AI   +  +  G  ++V  A
Sbjct: 74  PSAKAAIDWFDGKEFSGNPIKVSFA 98

>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 = 64.7 bits (158), Expect = 1e-14
 Identities = 17/91 (18%), Positives = 36/91 (39%), Gaps = 10/91 (10%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           + I V ++  D   +++  + + +  +KYC +       R+K   F+     + +  AI 
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQ 58

Query: 93  SMNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
             + +   G+ L V      P       GP+
Sbjct: 59  MFHQYSFRGKDLIVQLQ---PTDALLCSGPS 86

>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 = 65.0 bits (159), Expect = 1e-14
 Identities = 14/75 (18%), Positives = 37/75 (49%), Gaps = 9/75 (12%)

Query: 33  NRIYVASI-HPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
           +R+++ ++   ++++ED+  +F  +G I    +           +GFI+++  Q+  +AI
Sbjct: 23  SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 74

Query: 92  SSMNLFDLGGQYLRV 106
              +     G+ L +
Sbjct: 75  EXESQEMNFGKKLIL 89

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 65.1 bits (159), Expect = 2e-14
 Identities = 17/85 (20%), Positives = 34/85 (40%), Gaps = 8/85 (9%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPH--------RHKGYGFIEYETK 84
           N I+V  +  ++T E +   F+  G IK  K       +        + KG   + ++  
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67

Query: 85  QASNEAISSMNLFDLGGQYLRVGRA 109
            ++  AI   +  +  G  ++V  A
Sbjct: 68  PSAKAAIDWFDGKEFSGNPIKVSFA 92

>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 = 64.8 bits (158), Expect = 2e-14
 Identities = 17/99 (17%), Positives = 35/99 (35%), Gaps = 6/99 (6%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGP-IKYCKL-QQGSSPHRHKGYGFIEYETKQASNEA 90
            R+++  I      E+I          +    +    +   +++G+ F+EYE+ +A+  A
Sbjct: 9   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68

Query: 91  ISSMNL--FDLGGQYLRVGRAITP--PNALHSSKGPAPS 125
              +      L G  + V  A      +         PS
Sbjct: 69  RRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSGPS 107

>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 = 66.7 bits (162), Expect = 3e-14
 Identities = 11/75 (14%), Positives = 31/75 (41%)

Query: 32  YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
            N ++  +   ++TEE+   + +  G  +   ++  S        G +E+++K  + E +
Sbjct: 123 SNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETL 182

Query: 92  SSMNLFDLGGQYLRV 106
             +N + +       
Sbjct: 183 GFLNHYQMKNPNGPY 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 = 49.7 bits (118), Expect = 5e-08
 Identities = 17/96 (17%), Positives = 34/96 (35%), Gaps = 6/96 (6%)

Query: 35  IYVASIHPD-LTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           + V  +    +  + + +VF  +G ++  K           G   +E     A + AI+ 
Sbjct: 7   LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKF-----MKSKPGAAMVEMADGYAVDRAITH 61

Query: 94  MNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHM 129
           +N   + GQ + V  +  P      S G    +   
Sbjct: 62  LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSY 97

>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 = 63.8 bits (156), Expect = 4e-14
 Identities = 6/76 (7%), Positives = 35/76 (46%), Gaps = 2/76 (2%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            +++ +++P+ +  ++K             +    +   ++ +G++++E+ +   +A+  
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT-GTNRKFGYVDFESAEDLEKAL-E 76

Query: 94  MNLFDLGGQYLRVGRA 109
           +    + G  +++ + 
Sbjct: 77  LTGLKVFGNEIKLEKP 92

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 64.1 bits (156), Expect = 4e-14
 Identities = 14/85 (16%), Positives = 30/85 (35%), Gaps = 6/85 (7%)

Query: 33  NRIYVASIHPDLTEEDI---KSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQA 86
           N ++V  +   L + ++      F  FG I    +      +         ++ Y   + 
Sbjct: 16  NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75

Query: 87  SNEAISSMNLFDLGGQYLRVGRAIT 111
           +  AI  +N   + G+ L+     T
Sbjct: 76  ALRAIQCVNNVVVDGRTLKASLGTT 100

>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 = 64.1 bits (156), Expect = 9e-14
 Identities = 25/119 (21%), Positives = 47/119 (39%), Gaps = 5/119 (4%)

Query: 8   QVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ-- 65
           + GR S        +    E  +   RIYV ++   + E+D+K +F  +        +  
Sbjct: 21  EKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIM 80

Query: 66  ---QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKG 121
              +     R KG  FI    ++A+ +A+   N + L G+ + V  A +        +G
Sbjct: 81  FDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARPKQDPKEG 139

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 62.1 bits (151), Expect = 2e-13
 Identities = 14/80 (17%), Positives = 35/80 (43%), Gaps = 3/80 (3%)

Query: 28  EAKLYNR-IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQA 86
           +  + NR +Y+     D T +DIK   E  G +   ++++       KG  F+ +++ ++
Sbjct: 6   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIES 64

Query: 87  SNEAISSMNLFDLGGQYLRV 106
           + + + +          L +
Sbjct: 65  AKKFVETPGQ-KYKETDLLI 83

>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 = 63.3 bits (155), Expect = 3e-13
 Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            +I+V  I PD+  ++ +  F  +G I   +L       + +G+GF+ Y++  A +    
Sbjct: 88  GKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC- 146

Query: 93  SMNLFDLGGQYLRVGRAI 110
                D   + + + RA 
Sbjct: 147 QNKFIDFKDRKIEIKRAE 164

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 53.7 bits (130), Expect = 1e-09
 Identities = 18/87 (20%), Positives = 46/87 (52%), Gaps = 2/87 (2%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++++  ++ D TE++++  F  +G +   K+ +  +  R +G+GF+ +E   + +E + +
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64

Query: 94  MNLFDLGGQYLRVGRAITPPNALHSSK 120
            ++ D  G+ +   RAI       + K
Sbjct: 65  QHILD--GKVIDPKRAIPRDEQDKTGK 89

>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 = 60.6 bits (148), Expect = 5e-13
 Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            IYV ++    T E +K +F  FG +   KL       + KG+GF+E + +   +EAI+ 
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESV-SEAIAK 61

Query: 94  MNLFDLGGQYLRVGRA 109
           ++  D  G+ +RV  A
Sbjct: 62  LDNTDFMGRTIRVTEA 77

>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 = 61.2 bits (149), Expect = 5e-13
 Identities = 18/104 (17%), Positives = 41/104 (39%), Gaps = 1/104 (0%)

Query: 11  RPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSP 70
             S     +  +D ++ E +    ++   +   +   D++  F A G ++  ++    + 
Sbjct: 4   GSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNS 63

Query: 71  HRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPN 114
            R KG  ++E+   Q+   AI  +    L G  + V  +    N
Sbjct: 64  RRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKN 106

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 61.5 bits (149), Expect = 9e-13
 Identities = 17/107 (15%), Positives = 41/107 (38%), Gaps = 2/107 (1%)

Query: 5   PHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGP--IKYC 62
           P  Q   P    +  +++   +        +YV S     T++ +  V  + G   +   
Sbjct: 28  PVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVEL 87

Query: 63  KLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA 109
           K  +  +  + KGY  +   ++ + ++ +  +    L G+ + V  A
Sbjct: 88  KFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPA 134

>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 = 60.5 bits (147), Expect = 1e-12
 Identities = 17/104 (16%), Positives = 43/104 (41%), Gaps = 1/104 (0%)

Query: 6   HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
           H ++   +        +    ++      +YV ++    T +D+++ F + G I    + 
Sbjct: 10  HSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITIL 69

Query: 66  QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA 109
                   KGY +IE+  + + + A+ +M+     G+ ++V   
Sbjct: 70  CDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPK 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 = 59.6 bits (145), Expect = 1e-12
 Identities = 13/73 (17%), Positives = 27/73 (36%), Gaps = 1/73 (1%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFG-PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           +++  + P + E  I   F   G  +   K+ +        GY F+E+     + + +  
Sbjct: 12  LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71

Query: 94  MNLFDLGGQYLRV 106
           +N   L G     
Sbjct: 72  INGKPLPGATPAK 84

>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 = 59.5 bits (145), Expect = 1e-12
 Identities = 14/78 (17%), Positives = 34/78 (43%), Gaps = 2/78 (2%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGP--IKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
            +Y+ ++    T+ED+     + G   I   K  +  +  + KG+  +   ++ +S + +
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 92  SSMNLFDLGGQYLRVGRA 109
             +   +L GQ   V  +
Sbjct: 63  DLLPKRELHGQNPVVTPS 80

>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 = 59.4 bits (145), Expect = 1e-12
 Identities = 14/76 (18%), Positives = 35/76 (46%), Gaps = 1/76 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            IYV ++    T E++++ F   G +    +         KG+ +IE+  K++   ++ +
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 66

Query: 94  MNLFDLGGQYLRVGRA 109
           ++     G+ ++V   
Sbjct: 67  LDESLFRGRQIKVIPK 82

>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 = 59.8 bits (145), Expect = 1e-12
 Identities = 19/99 (19%), Positives = 37/99 (37%), Gaps = 12/99 (12%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           NR+ V+ + P  + +D+K      G + Y  +          G G +E+  K+    A+ 
Sbjct: 16  NRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-------YRDGTGVVEFVRKEDMTYAVR 68

Query: 93  SMNLFDLGGQ-----YLRVGRAITPPNALHSSKGPAPST 126
            ++            Y+RV        +   S+   PS+
Sbjct: 69  KLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSSGPSS 107

>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 = 59.4 bits (144), Expect = 2e-12
 Identities = 14/74 (18%), Positives = 27/74 (36%), Gaps = 8/74 (10%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           ++V  +   + E D+    E FG I Y  +         K    +E+E   ++ E ++  
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMM------MPFKRQALVEFENIDSAKECVTFA 71

Query: 95  NL--FDLGGQYLRV 106
                 + GQ    
Sbjct: 72  ADVPVYIAGQQAFF 85

>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 = 59.4 bits (144), Expect = 2e-12
 Identities = 15/108 (13%), Positives = 32/108 (29%), Gaps = 8/108 (7%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             I   ++       +I+  F  FG +    L +G           +E+     + +A  
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG------GITAIVEFLEPLEARKAFR 64

Query: 93  SMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHMPTAAAVAAAAA 140
            +         L +  A  P     ++     S    P   A +  ++
Sbjct: 65  HLAYSKFHHVPLYLEWA--PIGVFGAAPQKKDSQHEQPAEKAESGPSS 110

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 58.7 bits (142), Expect = 3e-12
 Identities = 22/83 (26%), Positives = 33/83 (39%), Gaps = 5/83 (6%)

Query: 27  EEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQA 86
           E A L   +YV ++  D    D+K      G +      QG      +   F+ Y    A
Sbjct: 14  EGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGP-----RRRAFLHYPDSAA 68

Query: 87  SNEAISSMNLFDLGGQYLRVGRA 109
           + +A+S +    LG   LRV  A
Sbjct: 69  AQQAVSCLQGLRLGTDTLRVALA 91

>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 = 59.1 bits (143), Expect = 3e-12
 Identities = 18/98 (18%), Positives = 36/98 (36%), Gaps = 12/98 (12%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           NR+ V+ + P  + +D+K      G + Y  +          G G +E+  K+    A+ 
Sbjct: 17  NRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-------YRDGTGVVEFVRKEDMTYAVR 69

Query: 93  SMNLFDLGGQ-----YLRVGRAITPPNALHSSKGPAPS 125
            ++            Y+RV        +   S+  + S
Sbjct: 70  KLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRS 107

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 58.1 bits (141), Expect = 4e-12
 Identities = 10/83 (12%), Positives = 34/83 (40%), Gaps = 6/83 (7%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFG--PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEA 90
           + I + +I P    + I +    +    +   +L +     +++G+ F++  +   +++ 
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 91  ISSMN----LFDLGGQYLRVGRA 109
           +  +        + G+ + V  A
Sbjct: 70  LQILQSLHPPLKIDGKTIGVDFA 92

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 57.7 bits (140), Expect = 8e-12
 Identities = 11/83 (13%), Positives = 33/83 (39%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             I V ++   ++ ++I   F  +  I      + +      G   + +E++  +  A+ 
Sbjct: 16  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75

Query: 93  SMNLFDLGGQYLRVGRAITPPNA 115
            +N   +G + +++     P + 
Sbjct: 76  DLNDRPIGSRKVKLVLGSGPSSG 98

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 58.4 bits (141), Expect = 9e-12
 Identities = 12/88 (13%), Positives = 39/88 (44%), Gaps = 7/88 (7%)

Query: 33  NRIYVASIHPDLTEEDIK----SVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASN 88
             + + +I+P++ +E ++    ++  + G I    +        + G  +I + T++++ 
Sbjct: 30  QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQ 86

Query: 89  EAISSMNLFDLGGQYLRVGRAITPPNAL 116
             + +   +   G  L +  + TP + +
Sbjct: 87  AFVEAFQGYPFQGNPLVITFSETPQSQV 114

>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 = 59.6 bits (145), Expect = 1e-11
 Identities = 14/78 (17%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            +I+V  I  D  E  ++  FE +G I+  ++       + +G+ F+ ++   + ++ + 
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV- 163

Query: 93  SMNLFDLGGQYLRVGRAI 110
                 + G    V +A+
Sbjct: 164 IQKYHTVNGHNCEVRKAL 181

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 19/87 (21%), Positives = 46/87 (52%), Gaps = 1/87 (1%)

Query: 24  EITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYET 83
           E  +E +   ++++  +  + T+E ++S FE +G +  C + +  +  R +G+GF+ Y T
Sbjct: 5   ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT 64

Query: 84  KQASNEAISSMNLFDLGGQYLRVGRAI 110
            +  + A+ +     + G+ +   RA+
Sbjct: 65  VEEVDAAM-NARPHKVDGRVVEPKRAV 90

>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 = 60.1 bits (145), Expect = 1e-11
 Identities = 16/108 (14%), Positives = 39/108 (36%), Gaps = 6/108 (5%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGP--IKYCKLQQGSSPHRHKGYGFIEYETKQASNEA 90
             +Y+ ++    T+ED+     + G   I   K  +  +  + KG+  +   ++ +S + 
Sbjct: 69  IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 128

Query: 91  ISSMNLFDLGGQYLRVG----RAITPPNALHSSKGPAPSTSHMPTAAA 134
           +  +   +L GQ   V     + ++           +   S    A  
Sbjct: 129 MDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGP 176

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 57.1 bits (138), Expect = 1e-11
 Identities = 13/74 (17%), Positives = 27/74 (36%), Gaps = 8/74 (10%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +++  +   + E D+    + FGPI Y  +         K    +E+E    +  A++  
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNAVNYA 77

Query: 95  NL--FDLGGQYLRV 106
                 + G    V
Sbjct: 78  ADNQIYIAGHPAFV 91

>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 = 56.9 bits (138), Expect = 2e-11
 Identities = 19/95 (20%), Positives = 40/95 (42%), Gaps = 8/95 (8%)

Query: 32  YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
              ++V  +  D TEE +K   E+F      ++         KG+GF+++ +++ +  A 
Sbjct: 15  SKTLFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAK 71

Query: 92  SSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPST 126
            +M   ++ G  + +  A           G  PS+
Sbjct: 72  EAMEDGEIDGNKVTLDWAKPKGE-----GGSGPSS 101

>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 = 55.8 bits (135), Expect = 3e-11
 Identities = 11/81 (13%), Positives = 32/81 (39%), Gaps = 8/81 (9%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKY----CKLQQGSSPHRHKGYGFIEYETKQASN 88
             I V ++   ++ ++I   F  +  I         ++G       G   + +E++  + 
Sbjct: 16  TVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKG----MPTGEAMVAFESRDEAT 71

Query: 89  EAISSMNLFDLGGQYLRVGRA 109
            A+  +N   +G + +++   
Sbjct: 72  AAVIDLNDRPIGSRKVKLSGP 92

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 55.7 bits (135), Expect = 5e-11
 Identities = 18/82 (21%), Positives = 39/82 (47%), Gaps = 2/82 (2%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
              YV ++  +  + DI ++F+    I+  +L +     + KG+ ++E++   +  EA+ 
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL- 73

Query: 93  SMNLFDLGGQYLRVGRAITPPN 114
           + +   LG + LRV  A     
Sbjct: 74  TYDGALLGDRSLRVDIAEGRKQ 95

>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 = 56.1 bits (135), Expect = 5e-11
 Identities = 14/71 (19%), Positives = 26/71 (36%), Gaps = 9/71 (12%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +    +   ++   +  V E  G +    +        +K Y F  Y T + S  A  ++
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMP------PNKPYSFARYRTTEESKRAYVTL 83

Query: 95  N---LFDLGGQ 102
           N   + D  GQ
Sbjct: 84  NGKEVVDDLGQ 94

>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 = 55.3 bits (134), Expect = 6e-11
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 1/81 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
             ++ ++  D+TEE IK  F           ++ S+P R KG+G+ E+E   +   A+ S
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 75

Query: 94  MNLFDLGGQYLRVGRAITPPN 114
           +N   LG + +RV  A    +
Sbjct: 76  LNEESLGNKRIRVDVADQAQD 96

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 54.6 bits (132), Expect = 1e-10
 Identities = 18/89 (20%), Positives = 29/89 (32%), Gaps = 6/89 (6%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            ++V+     +    +   F AFGP+    +           +  +E     A    +S 
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVM-----DKDKGVFAIVEMGDVGAREAVLSQ 64

Query: 94  MNLFDLGGQYLRVGRAITPPNALHSSKGP 122
                LGG  LRV           +SK P
Sbjct: 65  SQH-SLGGHRLRVRPREQKEFQSPASKSP 92

>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 = 54.6 bits (132), Expect = 1e-10
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 1/81 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
             ++ ++  D+TEE IK  F           ++ S+P R KG+G+ E+E   +   A+ S
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 79

Query: 94  MNLFDLGGQYLRVGRAITPPN 114
           +N   LG + +RV  A    +
Sbjct: 80  LNEESLGNRRIRVDVADQAQD 100

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 54.7 bits (132), Expect = 1e-10
 Identities = 20/94 (21%), Positives = 38/94 (40%), Gaps = 9/94 (9%)

Query: 23  DEITEEAKLYNRIYVASI------HPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGY 76
           D   E   + + I V ++        +  +  I  +F  FG I      +     + KGY
Sbjct: 6   DRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGY 63

Query: 77  GFIEYETKQASNEAISSMNLFDLGGQY-LRVGRA 109
            F+EY +   + +A+ + + + L  Q+  RV   
Sbjct: 64  IFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLF 97

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 56.4 bits (136), Expect = 2e-10
 Identities = 14/98 (14%), Positives = 38/98 (38%), Gaps = 6/98 (6%)

Query: 35  IYVASIHPD-LTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           + V++++P+ +T + +  +F  +G ++  K+         K    ++      +  A+S 
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKIL-----FNKKENALVQMADGNQAQLAMSH 60

Query: 94  MNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHMPT 131
           +N   L G+ +R+  +      L          +    
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYG 98

>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 = 54.5 bits (131), Expect = 8e-10
 Identities = 16/75 (21%), Positives = 38/75 (50%), Gaps = 5/75 (6%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             +++++I P ++EED+K +F + G +            + +    I+  + + + +A+ 
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF----FQKDRKMALIQMGSVEEAVQALI 176

Query: 93  SMNLFDLG-GQYLRV 106
            ++  DLG   +LRV
Sbjct: 177 DLHNHDLGENHHLRV 191

>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 = 53.4 bits (129), Expect = 3e-10
 Identities = 26/94 (27%), Positives = 50/94 (53%), Gaps = 6/94 (6%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           N+I+V  I  +  E +++  F+ FG +    +   +   R +G+GFI +E +Q+ ++A+ 
Sbjct: 11  NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV- 69

Query: 93  SMNLFDLGGQYLRVGRAITPPNALHSSKGPAPST 126
           +M+  D+ G+ + V RA         SK   PS+
Sbjct: 70  NMHFHDIMGKKVEVKRAEPRD-----SKSSGPSS 98

>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-10
 Identities = 18/106 (16%), Positives = 44/106 (41%), Gaps = 7/106 (6%)

Query: 33  NRIYVASIHPDLTEEDIKS----VFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASN 88
           + IY+ +++  + ++++K     +F  FG I    + +     + +G  F+ ++   ++ 
Sbjct: 10  HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRS---LKMRGQAFVIFKEVSSAT 66

Query: 89  EAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHMPTAAA 134
            A+ SM  F    + +R+  A T  + +   KG             
Sbjct: 67  NALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRK 112

>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 = 49.1 bits (116), Expect = 1e-07
 Identities = 11/79 (13%), Positives = 32/79 (40%), Gaps = 6/79 (7%)

Query: 32  YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
            + +++ ++  +  E  +  +F  F   K  +L  G          F+E++ +  +  A 
Sbjct: 207 NHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAAR 261

Query: 92  SSMNLFDL-GGQYLRVGRA 109
            ++  F +     +++  A
Sbjct: 262 DALQGFKITQNNAMKISFA 280

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 53.7 bits (129), Expect = 4e-10
 Identities = 17/74 (22%), Positives = 35/74 (47%), Gaps = 8/74 (10%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS-- 92
           I++  +  D+TE ++ S+   FG +    +       + K   FIE  T++A+N  ++  
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVNYY 72

Query: 93  SMNLFDLGGQYLRV 106
           +     L GQ + +
Sbjct: 73  TSVTPVLRGQPIYI 86

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 53.7 bits (129), Expect = 4e-10
 Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 5/82 (6%)

Query: 33  NRIYVASIHPDLTEEDIKSVF-EAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
            RI + ++    + +D+K +  E      +  +          G G +E+ +++   EA+
Sbjct: 29  YRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEAL 84

Query: 92  SSMNLFDLGGQYLRVGRAITPP 113
             +N  +  G  + V R   PP
Sbjct: 85  ERLNNIEFRGSVITVERDDNPP 106

>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 = 52.2 bits (126), Expect = 6e-10
 Identities = 15/92 (16%), Positives = 36/92 (39%), Gaps = 10/92 (10%)

Query: 32  YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
            + ++V     D+TE++++  F  +G +    +     P   + + F+ +   Q +    
Sbjct: 5   SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIAQSLC 59

Query: 92  SSMNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
               +    G  + +  A    N   S+ GP+
Sbjct: 60  GEDLIIK--GISVHISNAEPKHN---SNSGPS 86

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 52.0 bits (125), Expect = 7e-10
 Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 9/81 (11%)

Query: 33  NRIYVASI------HPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQA 86
           + I V ++        +  +  I  +F  FG I      +     + KGY F+EY +   
Sbjct: 2   SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAH 59

Query: 87  SNEAISSMNLFDLGGQY-LRV 106
           + +A+ + + + L  Q+  RV
Sbjct: 60  AVDAVKNADGYKLDKQHTFRV 80

>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 = 52.5 bits (126), Expect = 8e-10
 Identities = 11/74 (14%), Positives = 33/74 (44%), Gaps = 8/74 (10%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +++  +  ++TE ++ ++   FG +    +       + K   F+E  T++A+   ++  
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILM------LKGKNQAFLELATEEAAITMVNYY 71

Query: 95  NL--FDLGGQYLRV 106
           +     L  Q + +
Sbjct: 72  SAVTPHLRNQPIYI 85

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 52.3 bits (126), Expect = 8e-10
 Identities = 22/98 (22%), Positives = 41/98 (41%), Gaps = 10/98 (10%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGP-IKYCKL---QQGSSPHRHKGYGFIEYETKQASNE 89
            ++V  + PD+ +  +   F    P  +  K+   Q G S    KGYGF+++  +     
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVS----KGYGFVKFTDELEQKR 66

Query: 90  AISSMN-LFDLGGQYLRVGRAITPPNALHSSKGPAPST 126
           A++       LG + +R+  A  P  +        PS+
Sbjct: 67  ALTECQGAVGLGSKPVRLSVA-IPKASRVKPVESGPSS 103

>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 = 52.6 bits (126), Expect = 1e-09
 Identities = 17/76 (22%), Positives = 35/76 (46%), Gaps = 8/76 (10%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             I++  +  D+TE ++ S+   FG +    +       + K   FIE  T++A+N  ++
Sbjct: 32  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVN 85

Query: 93  --SMNLFDLGGQYLRV 106
             +     L GQ + +
Sbjct: 86  YYTSVTPVLRGQPIYI 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 = 54.2 bits (130), Expect = 1e-09
 Identities = 17/130 (13%), Positives = 42/130 (32%), Gaps = 6/130 (4%)

Query: 3   HFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPD-LTEEDIKSVFEAFGPIKY 61
           H  H               I          + + V++++P+ +T + +  +F  +G ++ 
Sbjct: 5   HHHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQR 64

Query: 62  CKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKG 121
            K+         K    ++      +  A+S +N   L G+ +R+  +      L     
Sbjct: 65  VKIL-----FNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQ 119

Query: 122 PAPSTSHMPT 131
                +    
Sbjct: 120 EDQGLTKDYG 129

>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 = 52.7 bits (126), Expect = 4e-09
 Identities = 16/76 (21%), Positives = 38/76 (50%), Gaps = 5/76 (6%)

Query: 32  YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
              +++++I P ++EED+K +F + G +            + +    I+  + + + +A+
Sbjct: 151 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF----FQKDRKMALIQMGSVEEAVQAL 206

Query: 92  SSMNLFDLG-GQYLRV 106
             ++  DLG   +LRV
Sbjct: 207 IDLHNHDLGENHHLRV 222

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 54.0 bits (129), Expect = 2e-09
 Identities = 14/87 (16%), Positives = 28/87 (32%), Gaps = 6/87 (6%)

Query: 31  LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEA 90
           +   +    + P   E  I+ VF   G I   +          K  GF++++ +  +  A
Sbjct: 142 IDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRY------VESKNCGFVKFKYQANAEFA 195

Query: 91  ISSMNLFDLGGQYLRVGRAITPPNALH 117
             +M+   L     +          L 
Sbjct: 196 KEAMSNQTLLLPSDKEWDDRREGTGLL 222

>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 = 51.1 bits (123), Expect = 2e-09
 Identities = 10/85 (11%), Positives = 30/85 (35%), Gaps = 7/85 (8%)

Query: 26  TEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQ 85
                  ++++V     D+T E+++  F  +G +    +     P   + + F+ +   +
Sbjct: 5   HHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFI-----PKPFRAFAFVTFADDK 59

Query: 86  ASNEAISSMNLFDLGGQYLRVGRAI 110
            +        +    G  + +  A 
Sbjct: 60  VAQSLCGEDLIIK--GISVHISNAE 82

>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 = 50.8 bits (122), Expect = 5e-09
 Identities = 18/83 (21%), Positives = 34/83 (40%), Gaps = 1/83 (1%)

Query: 32  YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
           + +I+V  +    T+  ++  FE FG I+   +       + +GYGF+    + A+  A 
Sbjct: 17  FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 76

Query: 92  SSMNLFDLGGQYLRVGRAITPPN 114
              N   + G+   V  A     
Sbjct: 77  KDPNP-IIDGRKANVNLAYLGAK 98

>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 = 49.0 bits (118), Expect = 8e-09
 Identities = 16/76 (21%), Positives = 37/76 (48%), Gaps = 1/76 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           +I+V  + PD  EE I+  F  FG ++  +L   +  ++ +G+ FI ++ ++   + +  
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 94  MNLFDLGGQYLRVGRA 109
               ++G     +  A
Sbjct: 61  KYH-NVGLSKCEIKVA 75

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 49.6 bits (118), Expect = 1e-08
 Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ--QGSSPHRHKGYGFIEYETKQASNEA 90
            +++V  + PD+ E++I + F  FGP+        +  S    KGY F+ ++ + +    
Sbjct: 9   RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68

Query: 91  ISSMNLFDLGGQYLRV 106
           I +    D G  YL V
Sbjct: 69  IDACLEED-GKLYLCV 83

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 48.8 bits (117), Expect = 2e-08
 Identities = 17/101 (16%), Positives = 38/101 (37%), Gaps = 8/101 (7%)

Query: 27  EEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQA 86
              +  + + V  +    TE+D+K  F  FG +   ++++       KG+GF+ +   + 
Sbjct: 10  RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 69

Query: 87  SNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTS 127
             + +S  ++ D        GR              +  +S
Sbjct: 70  QVKVMSQRHMID--------GRWCDCKLPNSKQSQDSGPSS 102

>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 = 49.0 bits (117), Expect = 2e-08
 Identities = 8/78 (10%), Positives = 28/78 (35%), Gaps = 1/78 (1%)

Query: 32  YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
               ++ +I   +T+ D+    E     +        +  +  G   ++++ +  + ++ 
Sbjct: 15  KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE 74

Query: 92  SSMNLFDLGGQYLRVGRA 109
             ++   L G+   V   
Sbjct: 75  -RLHRKKLNGREAFVHVV 91

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 47.8 bits (115), Expect = 2e-08
 Identities = 18/76 (23%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           +I+V  +  + T ED+K  FE FG +    L    + +RH+G+GF+ +E++    +    
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-E 59

Query: 94  MNLFDLGGQYLRVGRA 109
           ++  ++  + +   +A
Sbjct: 60  IHFHEINNKMVECKKA 75

>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 = 50.2 bits (119), Expect = 3e-08
 Identities = 12/75 (16%), Positives = 31/75 (41%), Gaps = 2/75 (2%)

Query: 32  YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
              +Y+     D T +DIK   E  G +   ++++       KG  F+ +++ +++ + +
Sbjct: 109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFV 167

Query: 92  SSMNLFDLGGQYLRV 106
            +          L +
Sbjct: 168 ETPGQ-KYKETDLLI 181

>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 = 48.3 bits (115), Expect = 4e-08
 Identities = 10/75 (13%), Positives = 32/75 (42%), Gaps = 1/75 (1%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           + +  +    T+E+I   F     +            +  G  F+++ +++ + +A+   
Sbjct: 45  VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKAL-GK 103

Query: 95  NLFDLGGQYLRVGRA 109
           +   +G +Y+ V ++
Sbjct: 104 HKERIGHRYIEVFKS 118

>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 = 46.3 bits (110), Expect = 2e-07
 Identities = 9/75 (12%), Positives = 32/75 (42%), Gaps = 1/75 (1%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           + +  +    ++E+I   F     +            R  G  F+++ +++ + +A+   
Sbjct: 18  VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL-KK 76

Query: 95  NLFDLGGQYLRVGRA 109
           +   +G +Y+ + ++
Sbjct: 77  HKERIGHRYIEIFKS 91

>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 = 45.4 bits (108), Expect = 2e-07
 Identities = 16/83 (19%), Positives = 38/83 (45%), Gaps = 7/83 (8%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGP--IKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           + +     ++TE+++        P  I+  +   G       GY F+++  ++   +A+ 
Sbjct: 13  VKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHG----NKTGYIFVDFSNEEEVKQAL- 67

Query: 93  SMNLFDLGGQYLRVGRAITPPNA 115
             N   +GG+Y+ V R  + P++
Sbjct: 68  KCNREYMGGRYIEVFREKSGPSS 90

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 45.9 bits (109), Expect = 3e-07
 Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 7/77 (9%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGP--IKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           + V  +     E D++  F       +   K   G    R+ G G +++ + Q + EA+ 
Sbjct: 19  VSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVG----RNNGNGLVKFLSPQDTFEAL- 73

Query: 93  SMNLFDLGGQYLRVGRA 109
             N   +  +Y+ V  A
Sbjct: 74  KRNRMLMIQRYVEVSPA 90

>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 = 46.0 bits (109), Expect = 4e-07
 Identities = 18/89 (20%), Positives = 40/89 (44%), Gaps = 5/89 (5%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +++  +    TE DI + F    P++   ++ G    R  G   +E+ T + +  A+ S 
Sbjct: 49  VHMRGLPYKATENDIYNFFSPLNPVR-VHIEIGPD-GRVTGEADVEFATHEEAVAAM-SK 105

Query: 95  NLFDLGGQYLRVGRAITPP--NALHSSKG 121
           +  ++  +Y+ +    T    N  +SS+ 
Sbjct: 106 DRANMQHRYIELFLNSTTGASNGAYSSQV 134

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 44.5 bits (106), Expect = 6e-07
 Identities = 13/70 (18%), Positives = 35/70 (50%)

Query: 26 TEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQ 85
          ++  +   +++V  +  D +++D+K  F  FG +  C ++   +  R +G+GFI ++   
Sbjct: 5  SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAA 64

Query: 86 ASNEAISSMN 95
          +  + +    
Sbjct: 65 SVEKVLDQKE 74

>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 = 44.8 bits (106), Expect = 9e-07
 Identities = 11/79 (13%), Positives = 29/79 (36%), Gaps = 9/79 (11%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGP----IKYCKLQQGSSPHRHKGYGFIEYETKQASNEA 90
           +Y+  +  +   + +   F+        I       G    +  G GF+E+  +     A
Sbjct: 28  VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNG----KATGEGFVEFRNEADYKAA 83

Query: 91  ISSMNLFDLGGQYLRVGRA 109
           +   +   +G ++++V   
Sbjct: 84  L-CRHKQYMGNRFIQVHPI 101

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 43.2 bits (103), Expect = 1e-06
 Identities = 13/76 (17%), Positives = 37/76 (48%), Gaps = 1/76 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++++  +    T+E ++  F  FG +K C + +     R +G+GF+ +  +   ++ + +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-A 60

Query: 94  MNLFDLGGQYLRVGRA 109
            +  +L  + +    A
Sbjct: 61  QSRHELDSKTIDPKVA 76

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 42.8 bits (101), Expect = 3e-06
 Identities = 13/74 (17%), Positives = 31/74 (41%), Gaps = 7/74 (9%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGP--IKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           +++  +    TE DI + F    P  +       G    R  G   +E+ T + +  A+ 
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDG----RVTGEADVEFATHEDAVAAM- 72

Query: 93  SMNLFDLGGQYLRV 106
           + +  ++  +Y+ +
Sbjct: 73  AKDKANMQHRYVEL 86

>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 = 42.6 bits (101), Expect = 4e-06
 Identities = 15/88 (17%), Positives = 45/88 (51%), Gaps = 1/88 (1%)

Query: 23  DEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYE 82
           +    E + + ++++  +  + TEE +++ +E +G +  C + +  +  R +G+GF+ + 
Sbjct: 18  ERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFS 77

Query: 83  TKQASNEAISSMNLFDLGGQYLRVGRAI 110
           +    + A+ +     + G+ +   RA+
Sbjct: 78  SMAEVDAAM-AARPHSIDGRVVEPKRAV 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 = 42.2 bits (100), Expect = 6e-06
 Identities = 12/77 (15%), Positives = 36/77 (46%), Gaps = 1/77 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           +++V  +    T+E ++S F  +G +  C + +  + ++ +G+GF++++        + +
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL-A 76

Query: 94  MNLFDLGGQYLRVGRAI 110
                L G+ +      
Sbjct: 77  SRPHTLDGRNIDPKPCT 93

>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 = 41.5 bits (98), Expect = 1e-05
 Identities = 13/77 (16%), Positives = 37/77 (48%), Gaps = 1/77 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++++  +    T+E ++  F  FG +K C + +     R +G+GF+ +  +   ++ + +
Sbjct: 27  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-A 85

Query: 94  MNLFDLGGQYLRVGRAI 110
            +  +L  + +    A 
Sbjct: 86  QSRHELDSKTIDPKVAF 102

>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 = 39.9 bits (93), Expect = 5e-05
 Identities = 14/59 (23%), Positives = 28/59 (47%), Gaps = 7/59 (11%)

Query: 35 IYVASI-HPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
          I+++++ H   ++  +  + E +G IK   L       R K   FIE ET++ +   + 
Sbjct: 28 IHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL------MRMKSQAFIEMETREDAMAMVD 80

>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 = 39.1 bits (91), Expect = 8e-05
 Identities = 18/93 (19%), Positives = 35/93 (37%), Gaps = 11/93 (11%)

Query: 23  DEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGP------IKYCKLQQGSSPHRHKGY 76
            ++ EE      I    +    T ED+ + F           I +   + G    + +G 
Sbjct: 2   SKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDG----KRRGD 57

Query: 77  GFIEYETKQASNEAISSMNLFDLGGQYLRVGRA 109
             IE E++Q   +A+   +   +G +Y+ V   
Sbjct: 58  ALIEMESEQDVQKAL-EKHRMYMGQRYVEVYEI 89

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 39.1 bits (91), Expect = 9e-05
 Identities = 14/78 (17%), Positives = 31/78 (39%), Gaps = 4/78 (5%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ---QGSSPHRHKGYGFIEYETKQASNEAI 91
           + +  +    T E++ + F    PI   K           R  G  F+ +  ++ +  A+
Sbjct: 26  VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85

Query: 92  SSMNLFDLGGQYLRVGRA 109
              +   LG +Y+ + R+
Sbjct: 86  -RKHKDLLGKRYIELFRS 102

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 17/103 (16%), Positives = 39/103 (37%), Gaps = 7/103 (6%)

Query: 7   VQVGRPSNMPQAQSVIDEIT-EEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
           VQ G  +    A +V   +         RI V ++   +T + +  +F  FG +      
Sbjct: 2   VQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKII-- 59

Query: 66  QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDL--GGQYLRV 106
             +    ++    ++Y    ++  A  S++  ++      LR+
Sbjct: 60  --TFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI 100

>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 = 38.5 bits (89), Expect = 2e-04
 Identities = 12/75 (16%), Positives = 31/75 (41%), Gaps = 6/75 (8%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           RI V ++   +T + +  +F  FG +        +    ++    ++Y    ++  A  S
Sbjct: 48  RIIVENLFYPVTLDVLHQIFSKFGTVLKII----TFTKNNQFQALLQYADPVSAQHAKLS 103

Query: 94  MNLFDL--GGQYLRV 106
           ++  ++      LR+
Sbjct: 104 LDGQNIYNACCTLRI 118

>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 = 36.9 bits (85), Expect = 4e-04
 Identities = 14/85 (16%), Positives = 38/85 (44%), Gaps = 7/85 (8%)

Query: 35  IYVASIHPDLTEEDIK----SVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEA 90
           + V++I   L+ ++++      F   G +K  +L   +    ++    ++ E  Q +  A
Sbjct: 12  VQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHT---DYQLKAVVQMENLQDAIGA 68

Query: 91  ISSMNLFDLGGQYLRVGRAITPPNA 115
           ++S++ + +G + + V  A      
Sbjct: 69  VNSLHRYKIGSKKILVSLATGASGP 93

>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 = 36.9 bits (85), Expect = 8e-04
 Identities = 11/78 (14%), Positives = 30/78 (38%), Gaps = 11/78 (14%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGP------IKYCKLQQGSSPHRHKGYGFIEYETKQASN 88
           + +  +    + ED+++             + +   ++G    R  G  F+E  ++    
Sbjct: 47  VKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREG----RQSGEAFVELGSEDDVK 102

Query: 89  EAISSMNLFDLGGQYLRV 106
            A+   +   +G +Y+ V
Sbjct: 103 MAL-KKDRESMGHRYIEV 119

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	173
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.91
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.89
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.89
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.89
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.88
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.88
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.88
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.88
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.88
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.88
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.88
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.88
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.87
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.87
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.87
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.87
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.87
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.87
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.87
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.87
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.87
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.87
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.87
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.87
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.87
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.87
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.87
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.86
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.86
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.86
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.86
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.86
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.86
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.86
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.86
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.86
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.86
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.86
2div_A	99	TRNA selenocysteine associated protein; structural	99.86
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.86
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.86
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.86
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.86
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.86
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.86
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.86
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.86
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.85
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.85
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.85
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.85
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.85
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.85
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.85
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.85
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.85
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.85
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.85
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.85
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.85
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.85
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.85
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.85
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.84
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.84
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.84
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.84
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.84
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.84
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.84
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.84
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.84
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.84
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.84
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.84
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.84
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.84
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.84
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.84
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.84
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.83
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.83
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.83
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.83
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.83
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.83
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.83
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.83
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.83
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.83
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.83
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.83
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.82
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.82
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.82
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.71
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.82
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.82
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.82
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.82
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.82
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.82
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.82
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.82
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.82
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.81
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.81
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.81
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.81
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.81
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.81
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.81
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.81
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.81
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.81
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.81
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.81
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.81
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.81
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.81
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.81
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.8
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.8
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.8
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.8
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.8
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.8
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.8
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.8
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.8
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.8
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.8
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.8
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.8
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.8
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.8
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.8
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.79
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.79
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.79
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.79
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.79
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.79
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.79
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.79
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.79
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.78
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.78
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.78
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.78
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.78
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.78
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.77
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.77
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.77
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.77
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.77
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.76
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.76
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.76
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.76
1x5p_A	97	Negative elongation factor E; structure genomics,	99.76
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.76
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.76
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.76
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.76
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.76
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.75
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.75
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.75
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.75
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.74
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.74
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.74
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.74
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.73
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.73
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.73
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.73
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.73
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.72
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.72
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.72
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.72
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.71
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.71
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.71
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.7
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.7
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.68
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.68
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.67
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.65
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.65
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.63
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.63
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.62
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.61
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.59
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.58
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.57
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.52
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.52
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.43
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.31
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.23
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.13
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.09
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.84
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.07
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.69
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.59
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.2
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.06
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.9
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.81
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.3
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.23
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	96.1
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.1
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	95.43
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	88.96
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	86.19

>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=99.91  E-value=4.2e-24  Score=142.83  Aligned_cols=82  Identities=23%  Similarity=0.445  Sum_probs=78.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||.++++++|+++|++||.|..+++++++.+|+++|||||+|.+.++|++|++.|||..++|++|+|+++
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            34679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eC
Q psy2141         110 IT  111 (173)
Q Consensus       110 ~~  111 (173)
                      +|
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            75

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.89  E-value=8.8e-23  Score=138.93  Aligned_cols=83  Identities=12%  Similarity=0.283  Sum_probs=79.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||+++++++|+++|++||.|.+++|++|+.+++++|||||+|.+.++|++|++.|||..+.|+.|+|.++
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            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             eCC
Q psy2141         110 ITP  112 (173)
Q Consensus       110 ~~~  112 (173)
                      ...
T Consensus        84 ~~~   86 (110)
T 3s8s_A           84 IKG   86 (110)
T ss_dssp             STT
T ss_pred             CCC
Confidence            643

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.89  E-value=2.5e-23  Score=136.93  Aligned_cols=84  Identities=18%  Similarity=0.353  Sum_probs=77.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccC-ceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFG-PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMN-LFDLGGQYLRVGRA  109 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G-~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~-g~~i~g~~l~v~~a  109 (173)
                      +++|||+|||.+++|++|+++|++|| .|.++++++++.+|+++|||||+|.+.++|++|++.++ +..++|++|+|+++
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            47899999999999999999999999 89999999999999999999999999999999999874 57899999999999


Q ss_pred             eCCCCC
Q psy2141         110 ITPPNA  115 (173)
Q Consensus       110 ~~~~~~  115 (173)
                      .+++..
T Consensus        81 ~~~~~~   86 (91)
T 2lxi_A           81 DPKPKI   86 (91)
T ss_dssp             CSCCCC
T ss_pred             CCCCCC
Confidence            876543

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.89  E-value=1.6e-22  Score=151.47  Aligned_cols=118  Identities=61%  Similarity=1.003  Sum_probs=104.1

Q ss_pred             CCCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEE
Q psy2141           1 MQHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIE   80 (173)
Q Consensus         1 ~l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~   80 (173)
                      .++|+.|+|.++.......+..+.......+.++|||+|||.++++++|+++|++||.|..+++.+++.+|+++|||||+
T Consensus        94 ~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~  173 (216)
T 2qfj_A           94 MLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIE  173 (216)
T ss_dssp             CCC-CCCEEECCSCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEE
T ss_pred             eeCCeeEEEecCCCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEE
Confidence            47899999999886655555555666667789999999999999999999999999999999999998899999999999


Q ss_pred             EcCHHHHHHHHHhcCCceeCCeEEEEEEeeCCCCCCCC
Q psy2141          81 YETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHS  118 (173)
Q Consensus        81 f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~~~~~~~  118 (173)
                      |.+.++|.+|++.|||..++|++|+|.++.+++.....
T Consensus       174 F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~~~~~~  211 (216)
T 2qfj_A          174 YEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLT  211 (216)
T ss_dssp             ESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCSSTTSC
T ss_pred             ecCHHHHHHHHHHccCCEeCCcEEEEEEecCCCCCCCC
Confidence            99999999999999999999999999999877555433

>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=99.88  E-value=1.9e-22  Score=131.04  Aligned_cols=84  Identities=27%  Similarity=0.497  Sum_probs=77.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+.+++.+++++|||||+|.+.++|++|++.|||..++|+.|+|.++
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            46789999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             eCCC
Q psy2141         110 ITPP  113 (173)
Q Consensus       110 ~~~~  113 (173)
                      +++|
T Consensus        84 ~~kp   87 (87)
T 3bs9_A           84 TRKP   87 (87)
T ss_dssp             C---
T ss_pred             CCCC
Confidence            8754

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.88  E-value=5e-23  Score=136.61  Aligned_cols=82  Identities=12%  Similarity=0.364  Sum_probs=77.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCc--eeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCc----eeCCeE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGP--IKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLF----DLGGQY  103 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~--v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~----~i~g~~  103 (173)
                      ....+|||+|||+++++++|+++|++||.  +..|++++|+.+|++||||||+|.+.++|++|++.|||.    .++|++
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~   86 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKT   86 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEE
Confidence            46789999999999999999999999995  679999999999999999999999999999999999996    599999


Q ss_pred             EEEEEeeC
Q psy2141         104 LRVGRAIT  111 (173)
Q Consensus       104 l~v~~a~~  111 (173)
                      |.|+|++.
T Consensus        87 i~V~~Aks   94 (95)
T 2lkz_A           87 IGVDFAKS   94 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEccC
Confidence            99999874

>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=99.88  E-value=4e-22  Score=128.37  Aligned_cols=81  Identities=21%  Similarity=0.437  Sum_probs=78.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCC
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITP  112 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~  112 (173)
                      .+|||+|||.++++++|+++|++||.|..+.+++++.+++++|||||+|.+.++|++|++.|||..++|++|+|++++++
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            58999999999999999999999999999999999889999999999999999999999999999999999999999876


Q ss_pred             C
Q psy2141         113 P  113 (173)
Q Consensus       113 ~  113 (173)
                      +
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.88  E-value=5.4e-22  Score=131.01  Aligned_cols=89  Identities=31%  Similarity=0.578  Sum_probs=83.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+.+++.+++++|||||+|.+.++|++|++.||+..+.|++|+|.++
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            46799999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             eCCCCCCCC
Q psy2141         110 ITPPNALHS  118 (173)
Q Consensus       110 ~~~~~~~~~  118 (173)
                      +++......
T Consensus        83 ~~~~~~~~~   91 (95)
T 2dnz_A           83 TERLDGGSG   91 (95)
T ss_dssp             SCCCCCCCC
T ss_pred             ccccCCCCC
Confidence            877655433

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.88  E-value=1.1e-21  Score=133.93  Aligned_cols=87  Identities=31%  Similarity=0.525  Sum_probs=82.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||..+++++|+++|++||.|..+++++++.++.++|||||+|.+.++|++|++.|||..++|+.|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (115)
T 2dgo_A           13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   92 (115)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            56889999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      ++++...
T Consensus        93 ~~~~~~~   99 (115)
T 2dgo_A           93 TRKPPAP   99 (115)
T ss_dssp             SCCCCCS
T ss_pred             cCCCCCC
Confidence            8765543

>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=99.88  E-value=7.7e-22  Score=131.28  Aligned_cols=87  Identities=21%  Similarity=0.350  Sum_probs=82.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+++++.+++++|||||+|.+.++|++|++.|||..+.|++|+|.++
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            46789999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      ++++...
T Consensus        86 ~~~~~~~   92 (99)
T 1whw_A           86 TIKKEAS   92 (99)
T ss_dssp             CCCSTTC
T ss_pred             CCCcccc
Confidence            8876543

>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=99.88  E-value=6.9e-22  Score=135.60  Aligned_cols=89  Identities=24%  Similarity=0.433  Sum_probs=82.6

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ..+.++|||+|||.++++++|+++|++||.|..+.+..++ +|+++|||||+|.+.++|++|++.|||..+.|+.|+|.+
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            3567999999999999999999999999999999999997 999999999999999999999999999999999999999


Q ss_pred             eeCCCCCCCC
Q psy2141         109 AITPPNALHS  118 (173)
Q Consensus       109 a~~~~~~~~~  118 (173)
                      +++++.....
T Consensus        83 a~~~~~~~~~   92 (116)
T 2fy1_A           83 AKKPSFQSGG   92 (116)
T ss_dssp             CCCSSCSSSS
T ss_pred             CCCCCCCCCC
Confidence            9876655444

>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=99.88  E-value=6.1e-22  Score=131.18  Aligned_cols=84  Identities=30%  Similarity=0.502  Sum_probs=79.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      +.++|||+|||.++++++|+++|++||.|..+++.+++.+|+++|||||+|.+.++|++|++.|||..++|+.|+|.++.
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            46899999999999999999999999999999999999899999999999999999999999999999999999999998


Q ss_pred             CCCC
Q psy2141         111 TPPN  114 (173)
Q Consensus       111 ~~~~  114 (173)
                      +++.
T Consensus        81 ~~~~   84 (96)
T 2x1f_A           81 NSDI   84 (96)
T ss_dssp             CSSG
T ss_pred             CCCC
Confidence            7543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.87  E-value=8.1e-22  Score=131.22  Aligned_cols=86  Identities=26%  Similarity=0.503  Sum_probs=81.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+++++.+++++|||||+|.+.++|++|++ |++..++|++|+|.++
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            467999999999999999999999999999999999999899999999999999999999998 9999999999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      .++....
T Consensus        87 ~~~~~~~   93 (99)
T 2dgs_A           87 EPRDSKS   93 (99)
T ss_dssp             CCCCCCC
T ss_pred             CCCcccC
Confidence            8765554

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=6.2e-22  Score=132.71  Aligned_cols=87  Identities=24%  Similarity=0.395  Sum_probs=82.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..|.+++++.+++++|||||+|.+.++|++|++.||+..+.|+.|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   92 (103)
T 2cq0_A           13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   92 (103)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEC
Confidence            56899999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      ++++...
T Consensus        93 ~~~~~~~   99 (103)
T 2cq0_A           93 KPSTNSG   99 (103)
T ss_dssp             SCCCCSC
T ss_pred             CCCCCCC
Confidence            8765543

>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=99.87  E-value=9.7e-22  Score=134.35  Aligned_cols=88  Identities=20%  Similarity=0.389  Sum_probs=82.5

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ..+.++|||+|||.++++++|+++|++||.|..+++++++.+++++|||||+|.+.++|++|++.||+..+.|++|+|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eeCCCCCC
Q psy2141         109 AITPPNAL  116 (173)
Q Consensus       109 a~~~~~~~  116 (173)
                      ++++....
T Consensus       102 a~~~~~~~  109 (115)
T 2cpz_A          102 KRSKNDSK  109 (115)
T ss_dssp             CCCSCCCC
T ss_pred             cCCCCcCC
Confidence            98765544

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=1.2e-21  Score=129.52  Aligned_cols=87  Identities=26%  Similarity=0.398  Sum_probs=81.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEE-EEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYC-KLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~-~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+ ++++++.++.++|||||+|.+.++|++|++.|||..+.|++|+|.+
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 9999988999999999999999999999999999999999999999


Q ss_pred             eeCCCCCC
Q psy2141         109 AITPPNAL  116 (173)
Q Consensus       109 a~~~~~~~  116 (173)
                      +.+++...
T Consensus        83 a~~~~~~~   90 (96)
T 1x5t_A           83 AFKKDSKG   90 (96)
T ss_dssp             SCCCCCCC
T ss_pred             ecccCCCC
Confidence            98765443

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=8.4e-22  Score=131.78  Aligned_cols=87  Identities=23%  Similarity=0.405  Sum_probs=82.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||..+++++|+++|++||.|..+.+++++.+++++|||||+|.+.++|++|++.||+..+.|++|+|.++
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            46899999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      ++++...
T Consensus        90 ~~~~~~~   96 (102)
T 2cqb_A           90 KPMRIKE   96 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            8765554

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=9e-22  Score=131.62  Aligned_cols=88  Identities=22%  Similarity=0.450  Sum_probs=82.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+++++++.+++++|||||+|.+.++|++|++.||+..+.|++|+|.++
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 1x5s_A           10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   89 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            46899999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             eCCCCCCC
Q psy2141         110 ITPPNALH  117 (173)
Q Consensus       110 ~~~~~~~~  117 (173)
                      ++++....
T Consensus        90 ~~~~~~~~   97 (102)
T 1x5s_A           90 GKSSDNRS   97 (102)
T ss_dssp             ECCCCCCC
T ss_pred             CCCCCCCC
Confidence            98765543

>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=99.87  E-value=5.8e-22  Score=128.20  Aligned_cols=81  Identities=25%  Similarity=0.472  Sum_probs=78.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+++++.+++++|||||+|.+.++|++|++.|||..++|++|+|+++
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            46899999999999999999999999999999999999889999999999999999999999999999999999999997


Q ss_pred             e
Q psy2141         110 I  110 (173)
Q Consensus       110 ~  110 (173)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.87  E-value=8.9e-23  Score=133.83  Aligned_cols=83  Identities=17%  Similarity=0.242  Sum_probs=73.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccC--ceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFG--PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G--~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      .+|||+|||+++++++|+++|++||  .|.++++++++.+|+++|||||+|.+.++|++|++.|||..++|+.|+|.++.
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  99999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCC
Q psy2141         111 TPPNA  115 (173)
Q Consensus       111 ~~~~~  115 (173)
                      +++..
T Consensus        82 ~~~~~   86 (90)
T 3p5t_L           82 KLEHH   86 (90)
T ss_dssp             -----
T ss_pred             CCccc
Confidence            76443

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.87  E-value=1.4e-21  Score=130.27  Aligned_cols=84  Identities=18%  Similarity=0.407  Sum_probs=79.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+..++ +|+++|||||+|.+.++|++|++.||+..+.|++|+|.++
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   93 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS   93 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            467899999999999999999999999999999999997 9999999999999999999999999999999999999999


Q ss_pred             eCCCC
Q psy2141         110 ITPPN  114 (173)
Q Consensus       110 ~~~~~  114 (173)
                      ++++.
T Consensus        94 ~~~~~   98 (100)
T 2do4_A           94 NSGPS   98 (100)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            87654

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.87  E-value=2.9e-21  Score=133.74  Aligned_cols=86  Identities=15%  Similarity=0.299  Sum_probs=80.4

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ..+.++|||+|||..+++++|+++|++||.|..+++.+++ +|+++|||||+|.+.++|++|++.|||..++|+.|+|.+
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            3567899999999999999999999999999999999997 999999999999999999999999999999999999999


Q ss_pred             eeCCCCC
Q psy2141         109 AITPPNA  115 (173)
Q Consensus       109 a~~~~~~  115 (173)
                      +.+....
T Consensus       111 a~~~~~~  117 (124)
T 2kt5_A          111 VASQIDL  117 (124)
T ss_dssp             ECCTTCC
T ss_pred             eCCCCCC
Confidence            9865444

>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=99.87  E-value=1.2e-21  Score=131.76  Aligned_cols=87  Identities=24%  Similarity=0.478  Sum_probs=82.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+++++.+++++|||||+|.+.++|++|++.||+..+.|++|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   92 (105)
T 1x5u_A           13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   92 (105)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            56899999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      ++++...
T Consensus        93 ~~~~~~~   99 (105)
T 1x5u_A           93 SAHNKNL   99 (105)
T ss_dssp             TTTSCCC
T ss_pred             CCCCcCC
Confidence            8766554

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.87  E-value=3.2e-21  Score=135.90  Aligned_cols=91  Identities=23%  Similarity=0.479  Sum_probs=84.0

Q ss_pred             hhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q psy2141          28 EAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG  107 (173)
Q Consensus        28 ~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~  107 (173)
                      +..+.++|||+|||.++++++|+++|+.||.|..+++++++.+++++|||||+|.+.++|++|++.|||..+.|+.|+|.
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            44568999999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             EeeCCCCCCCC
Q psy2141         108 RAITPPNALHS  118 (173)
Q Consensus       108 ~a~~~~~~~~~  118 (173)
                      ++++.......
T Consensus       118 ~a~~~~~~~~~  128 (139)
T 1u6f_A          118 LAASGHQRPGI  128 (139)
T ss_dssp             ESSCCCCCCCS
T ss_pred             ECCCCCCCCCC
Confidence            99876655433

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.87  E-value=1.6e-22  Score=141.53  Aligned_cols=88  Identities=14%  Similarity=0.317  Sum_probs=82.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeE--EEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCc----eeCCeE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKY--CKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLF----DLGGQY  103 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~--~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~----~i~g~~  103 (173)
                      .+.++|||+|||+++++++|+++|++||.|..  |+|++|+.+|+++|||||+|.+. +|.+|++.|||.    .++|++
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~   99 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKT   99 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEE
Confidence            56789999999999999999999999999976  99999999999999999999999 999999999999    999999


Q ss_pred             EEEEEeeCCCCCCCC
Q psy2141         104 LRVGRAITPPNALHS  118 (173)
Q Consensus       104 l~v~~a~~~~~~~~~  118 (173)
                      |+|+++++.......
T Consensus       100 l~V~~a~~~~~~~~~  114 (131)
T 2m2b_A          100 INVEFAKGSKRDMAS  114 (131)
T ss_dssp             CCCEECCCSCCCCCC
T ss_pred             EEEEECCCCCCCCCC
Confidence            999999887665544

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.87  E-value=8.4e-22  Score=132.07  Aligned_cols=87  Identities=18%  Similarity=0.349  Sum_probs=81.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+.+++.+++++|||||+|.+.++|++|++.|||..+.|+.|+|.++
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2dnm_A           11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVA   90 (103)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEC
Confidence            56899999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      ++.....
T Consensus        91 ~~~~~~~   97 (103)
T 2dnm_A           91 RYGRRDL   97 (103)
T ss_dssp             SSCCSCC
T ss_pred             CcCCCCC
Confidence            8765443

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=3.7e-21  Score=131.61  Aligned_cols=85  Identities=21%  Similarity=0.404  Sum_probs=79.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+++++++.+++++|||||+|.+.++|++|++.|++ .+.|++|+|.++
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~a   93 (116)
T 2cqd_A           15 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLA   93 (116)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEEc
Confidence            5689999999999999999999999999999999999999999999999999999999999999998 899999999999


Q ss_pred             eCCCCC
Q psy2141         110 ITPPNA  115 (173)
Q Consensus       110 ~~~~~~  115 (173)
                      ......
T Consensus        94 ~~~~~~   99 (116)
T 2cqd_A           94 YLGAKP   99 (116)
T ss_dssp             TTTCCC
T ss_pred             ccCCCc
Confidence            765433

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.86  E-value=1.6e-21  Score=128.42  Aligned_cols=81  Identities=21%  Similarity=0.399  Sum_probs=78.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+.+++.+++++|||||+|.+.++|++|++.||+..+.|++|+|+++
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA   93 (94)
T ss_dssp             CCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEec
Confidence            46789999999999999999999999999999999999989999999999999999999999999999999999999997


Q ss_pred             e
Q psy2141         110 I  110 (173)
Q Consensus       110 ~  110 (173)
                      +
T Consensus        94 k   94 (94)
T 2e5h_A           94 I   94 (94)
T ss_dssp             C
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=99.86  E-value=4.8e-21  Score=130.52  Aligned_cols=83  Identities=19%  Similarity=0.246  Sum_probs=78.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+++++++ +++++|||||+|.+.++|++|++.||+..+.|+.|+|.++
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            568899999999999999999999999999999999997 6999999999999999999999999999999999999998


Q ss_pred             eCCC
Q psy2141         110 ITPP  113 (173)
Q Consensus       110 ~~~~  113 (173)
                      +...
T Consensus        92 ~~~~   95 (114)
T 2do0_A           92 ERAL   95 (114)
T ss_dssp             SCCC
T ss_pred             ccCC
Confidence            7543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=1.1e-21  Score=132.00  Aligned_cols=85  Identities=31%  Similarity=0.418  Sum_probs=80.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||..+++++|+++|++||.|..+.+.+++.+|.++|||||+|.+.++|++|++.|||..++|+.|+|.++
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            45688999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCCCC
Q psy2141         110 ITPPN  114 (173)
Q Consensus       110 ~~~~~  114 (173)
                      .+++.
T Consensus       101 ~~~~~  105 (106)
T 1p27_B          101 FVRGP  105 (106)
T ss_dssp             EESSC
T ss_pred             cCCCC
Confidence            87643

>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=99.86  E-value=1.9e-21  Score=131.85  Aligned_cols=87  Identities=23%  Similarity=0.437  Sum_probs=82.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcC------CceeCCeE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMN------LFDLGGQY  103 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~------g~~i~g~~  103 (173)
                      .+.++|||+|||+++++++|+++|++||.|..|++++++.++.++|||||+|.+.++|++|++.||      +..++|++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~   92 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   92 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEE
Confidence            568899999999999999999999999999999999999999999999999999999999999999      99999999


Q ss_pred             EEEEEeeCCCCCC
Q psy2141         104 LRVGRAITPPNAL  116 (173)
Q Consensus       104 l~v~~a~~~~~~~  116 (173)
                      |+|.++.++....
T Consensus        93 l~v~~a~~~~~~~  105 (111)
T 1x4h_A           93 LKVDLAVTRDEAA  105 (111)
T ss_dssp             EEEECCCCCCCCC
T ss_pred             EEEEECCCCccCC
Confidence            9999998765544

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.86  E-value=1.8e-21  Score=129.29  Aligned_cols=87  Identities=22%  Similarity=0.429  Sum_probs=80.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCC---CCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSS---PHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV  106 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~---~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v  106 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+.+++.   +++++|||||+|.+.++|++|++.|||..+.|++|+|
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            4678999999999999999999999999999999998875   5689999999999999999999999999999999999


Q ss_pred             EEeeCCCCCC
Q psy2141         107 GRAITPPNAL  116 (173)
Q Consensus       107 ~~a~~~~~~~  116 (173)
                      .+++++....
T Consensus        83 ~~a~~~~~~~   92 (98)
T 2cpf_A           83 RISERATKPA   92 (98)
T ss_dssp             ECSSCSSCCC
T ss_pred             EEccCCCCCC
Confidence            9998765443

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=1.4e-21  Score=128.87  Aligned_cols=82  Identities=24%  Similarity=0.416  Sum_probs=78.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||..+++++|+++|++||.|..+.+++++.+++++|||||+|.+.++|++|++.|||..++|++|+|.++
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   92 (95)
T 2cqc_A           13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGP   92 (95)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            45789999999999999999999999999999999999989999999999999999999999999999999999999998


Q ss_pred             eC
Q psy2141         110 IT  111 (173)
Q Consensus       110 ~~  111 (173)
                      +.
T Consensus        93 ~~   94 (95)
T 2cqc_A           93 SS   94 (95)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>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=99.86  E-value=1.7e-21  Score=133.33  Aligned_cols=83  Identities=29%  Similarity=0.508  Sum_probs=75.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      ...+|||+|||+++++++|+++|++||.|..|+|++++  +.++|||||+|.+.++|++|++.|+|..++|++|+|.++.
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            35789999999999999999999999999999999985  4589999999999999999999999999999999999988


Q ss_pred             CCCCC
Q psy2141         111 TPPNA  115 (173)
Q Consensus       111 ~~~~~  115 (173)
                      ++...
T Consensus        82 ~~~~~   86 (115)
T 4f25_A           82 SRKER   86 (115)
T ss_dssp             CCCC-
T ss_pred             Ccccc
Confidence            76544

>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=99.86  E-value=6.6e-22  Score=134.06  Aligned_cols=87  Identities=32%  Similarity=0.614  Sum_probs=81.7

Q ss_pred             hhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q psy2141          27 EEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV  106 (173)
Q Consensus        27 ~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v  106 (173)
                      ....+.++|||+|||..+++++|+++|++||.|..+++++++.+|+++|||||+|.+.++|++|++.|+|..++|++|+|
T Consensus        21 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  100 (108)
T 2jrs_A           21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV  100 (108)
T ss_dssp             CSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            33457889999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEeeCCC
Q psy2141         107 GRAITPP  113 (173)
Q Consensus       107 ~~a~~~~  113 (173)
                      .++++++
T Consensus       101 ~~a~~k~  107 (108)
T 2jrs_A          101 GHVTERT  107 (108)
T ss_dssp             ECSCSSC
T ss_pred             EEcccCC
Confidence            9998764

>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=99.86  E-value=2.1e-21  Score=131.60  Aligned_cols=85  Identities=27%  Similarity=0.386  Sum_probs=80.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||..+++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|++.|||..++|++|+|.++
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  103 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  103 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEc
Confidence            45789999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             eCCCC
Q psy2141         110 ITPPN  114 (173)
Q Consensus       110 ~~~~~  114 (173)
                      .+++.
T Consensus       104 ~~~~~  108 (110)
T 1oo0_B          104 FVKGP  108 (110)
T ss_dssp             EESSC
T ss_pred             ccCCC
Confidence            87653

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.86  E-value=2.9e-21  Score=130.17  Aligned_cols=88  Identities=24%  Similarity=0.445  Sum_probs=82.3

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccC-CCCCCcceEEEEEEcCHHHHHHHHHhc-CCceeCCeEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQG-SSPHRHKGYGFIEYETKQASNEAISSM-NLFDLGGQYLRV  106 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~-~~~g~~~g~afv~f~~~~~a~~a~~~l-~g~~i~g~~l~v  106 (173)
                      ..+.++|||+|||..+++++|+++|++||.|..|.++++ +.+++++|||||+|.+.++|++|++.| |+..+.|++|+|
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            356899999999999999999999999999999999999 789999999999999999999999999 999999999999


Q ss_pred             EEeeCCCCCC
Q psy2141         107 GRAITPPNAL  116 (173)
Q Consensus       107 ~~a~~~~~~~  116 (173)
                      .++++++...
T Consensus        92 ~~a~~~~~~~  101 (107)
T 2cph_A           92 EWADSEVTVQ  101 (107)
T ss_dssp             EECCCCCCCC
T ss_pred             EeCCCCCCCC
Confidence            9998765544

>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=99.86  E-value=1.6e-21  Score=131.23  Aligned_cols=87  Identities=22%  Similarity=0.320  Sum_probs=81.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCcee---CCeEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDL---GGQYLRV  106 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i---~g~~l~v  106 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+++++++.+++++|||||+|.+.++|++|++.||+..+   .|++|+|
T Consensus        11 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v   90 (106)
T 2dgp_A           11 HDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQV   90 (106)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEE
Confidence            4678999999999999999999999999999999999998999999999999999999999999999988   8999999


Q ss_pred             EEeeCCCCCC
Q psy2141         107 GRAITPPNAL  116 (173)
Q Consensus       107 ~~a~~~~~~~  116 (173)
                      .++.++....
T Consensus        91 ~~a~~~~~~~  100 (106)
T 2dgp_A           91 KPADSESRGG  100 (106)
T ss_dssp             EECCCCSCCC
T ss_pred             EECCcccccC
Confidence            9998766544

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=1.6e-21  Score=129.70  Aligned_cols=84  Identities=17%  Similarity=0.309  Sum_probs=79.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCcee-EEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeE----E
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIK-YCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQY----L  104 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~-~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~----l  104 (173)
                      .+.++|||+|||.++++++|+++|++||.|. .+++++++.+++++|||||+|.+.++|++|++.|||..+.|+.    |
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            4689999999999999999999999999999 9999999999999999999999999999999999999999999    9


Q ss_pred             EEEEeeCCC
Q psy2141         105 RVGRAITPP  113 (173)
Q Consensus       105 ~v~~a~~~~  113 (173)
                      +|.|+++..
T Consensus        87 ~v~~a~~~~   95 (99)
T 2div_A           87 KLNYATYSG   95 (99)
T ss_dssp             CEEETTCCS
T ss_pred             EEeecCCCC
Confidence            999987653

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.86  E-value=3.5e-21  Score=130.64  Aligned_cols=92  Identities=14%  Similarity=0.355  Sum_probs=76.9

Q ss_pred             hhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2141          22 IDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG  101 (173)
Q Consensus        22 ~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g  101 (173)
                      .+...++..+.++|||+|||.++++++|+++|+.||.|..+++++++.+|+++|||||+|.+.++|++|++.+ +..++|
T Consensus        15 ~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g   93 (109)
T 2rs2_A           15 VPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDS   93 (109)
T ss_dssp             -----------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETT
T ss_pred             CccccccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCC
Confidence            3444555677899999999999999999999999999999999999989999999999999999999999986 499999


Q ss_pred             eEEEEEEeeCCCC
Q psy2141         102 QYLRVGRAITPPN  114 (173)
Q Consensus       102 ~~l~v~~a~~~~~  114 (173)
                      +.|+|.++.+++.
T Consensus        94 ~~l~V~~a~~~~~  106 (109)
T 2rs2_A           94 KTIDPKVAFPRRA  106 (109)
T ss_dssp             EEEEEEECCCCCC
T ss_pred             EEEEEEEccCCCC
Confidence            9999999987654

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=2.6e-21  Score=131.78  Aligned_cols=88  Identities=22%  Similarity=0.323  Sum_probs=82.3

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCcee--------EEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeC
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIK--------YCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLG  100 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~--------~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~  100 (173)
                      ..+.++|||+|||.++++++|+++|++||.|.        .+++.+++.+++++|||||+|.+.++|++|++.|||..+.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   91 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   91 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccC
Confidence            35789999999999999999999999999999        6999999889999999999999999999999999999999


Q ss_pred             CeEEEEEEeeCCCCCC
Q psy2141         101 GQYLRVGRAITPPNAL  116 (173)
Q Consensus       101 g~~l~v~~a~~~~~~~  116 (173)
                      |++|+|.+++++....
T Consensus        92 g~~l~V~~a~~~~~~~  107 (113)
T 2cpe_A           92 GSKLKVSLARKKPPMN  107 (113)
T ss_dssp             TEECEEECSSCCCCST
T ss_pred             CCEEEEEECCCCCCCC
Confidence            9999999998765543

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.86  E-value=1.3e-21  Score=134.24  Aligned_cols=83  Identities=23%  Similarity=0.415  Sum_probs=78.3

Q ss_pred             hhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q psy2141          28 EAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG  107 (173)
Q Consensus        28 ~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~  107 (173)
                      +..+.++|||+|||.++++++|+++|++||.|..+++++++.+|+++|||||+|.+.++|++|++.|||..++|++|+|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             Eee
Q psy2141         108 RAI  110 (173)
Q Consensus       108 ~a~  110 (173)
                      +++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            874

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.86  E-value=1.5e-21  Score=129.98  Aligned_cols=81  Identities=21%  Similarity=0.320  Sum_probs=77.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeE--------EEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKY--------CKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG  101 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~--------~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g  101 (173)
                      .+.++|||+|||.++++++|+++|++||.|..        +++.+++.+|+++|||||+|.+.++|++|++.|||..+.|
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g   90 (99)
T 2la6_A           11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   90 (99)
T ss_dssp             CCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            46899999999999999999999999999999        9999999899999999999999999999999999999999


Q ss_pred             eEEEEEEee
Q psy2141         102 QYLRVGRAI  110 (173)
Q Consensus       102 ~~l~v~~a~  110 (173)
                      +.|+|++++
T Consensus        91 ~~l~V~~A~   99 (99)
T 2la6_A           91 NPIKVSFAT   99 (99)
T ss_dssp             SBCEEEECC
T ss_pred             cEEEEEecC
Confidence            999999874

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.86  E-value=1.9e-21  Score=130.48  Aligned_cols=86  Identities=19%  Similarity=0.339  Sum_probs=80.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhc-cCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCce-eCCeEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEA-FGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFD-LGGQYLRVG  107 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~-~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~-i~g~~l~v~  107 (173)
                      .+.++|||+|||.++++++|+++|++ ||.|..+++++++ +|+++|||||+|.+.++|++|++.|++.. ++|++|+|.
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            56899999999999999999999999 9999999999998 99999999999999999999999999999 999999999


Q ss_pred             EeeCCCCCC
Q psy2141         108 RAITPPNAL  116 (173)
Q Consensus       108 ~a~~~~~~~  116 (173)
                      ++.++....
T Consensus        86 ~a~~~~~~~   94 (104)
T 2dhg_A           86 VAIPKASRV   94 (104)
T ss_dssp             BCCCCCSCC
T ss_pred             EccCCCcCC
Confidence            998765543

>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=99.86  E-value=3.2e-21  Score=129.57  Aligned_cols=86  Identities=22%  Similarity=0.358  Sum_probs=80.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC---eEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG---QYLRV  106 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g---~~l~v  106 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+.+++ +++++|||||+|.+.++|++|++.|||..+.|   ++|+|
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            468999999999999999999999999999999999997 89999999999999999999999999999998   99999


Q ss_pred             EEeeCCCCCC
Q psy2141         107 GRAITPPNAL  116 (173)
Q Consensus       107 ~~a~~~~~~~  116 (173)
                      .++++++...
T Consensus        92 ~~a~~~~~~~  101 (105)
T 2dnh_A           92 KFADTDKESG  101 (105)
T ss_dssp             EESCSSCCCS
T ss_pred             EECccCcccC
Confidence            9998766543

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.86  E-value=6.2e-21  Score=127.86  Aligned_cols=85  Identities=21%  Similarity=0.367  Sum_probs=79.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++|| |..+++++++.+++++|||||+|.+.++|++|+ .||+..+.|++|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a   90 (103)
T 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIA   90 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEe
Confidence            4678999999999999999999999997 999999999989999999999999999999999 89999999999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      .+++...
T Consensus        91 ~~~~~~~   97 (103)
T 2dng_A           91 EGRKQDK   97 (103)
T ss_dssp             CCCCCCC
T ss_pred             cCCCCCC
Confidence            8765544

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.86  E-value=3.3e-21  Score=133.30  Aligned_cols=86  Identities=20%  Similarity=0.322  Sum_probs=80.1

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ..+.++|||+|||.++++++|+++|++||.|..+.+++++.+|+++|||||+|.+.++|++|+ .|||..++|+.|+|.+
T Consensus        33 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~  111 (124)
T 2jwn_A           33 EIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLP  111 (124)
T ss_dssp             HHHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEE
Confidence            345799999999999999999999999999999999999889999999999999999999999 8999999999999999


Q ss_pred             eeCCCCC
Q psy2141         109 AITPPNA  115 (173)
Q Consensus       109 a~~~~~~  115 (173)
                      +++....
T Consensus       112 a~~~~~~  118 (124)
T 2jwn_A          112 KRTNMPG  118 (124)
T ss_dssp             SSCCCSS
T ss_pred             CCCCCCC
Confidence            9865444

>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=99.85  E-value=4.4e-21  Score=125.04  Aligned_cols=81  Identities=19%  Similarity=0.336  Sum_probs=77.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      ..++|||+|||.++++++|+++|++||.|..+++.+++.+++++|||||+|.+.++|++|+ .|||..+.|+.|+|.+++
T Consensus         5 ~~~~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            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            4589999999999999999999999999999999999889999999999999999999999 999999999999999987


Q ss_pred             CC
Q psy2141         111 TP  112 (173)
Q Consensus       111 ~~  112 (173)
                      +.
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>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=99.85  E-value=3e-21  Score=125.50  Aligned_cols=83  Identities=19%  Similarity=0.422  Sum_probs=77.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCC-cceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHR-HKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~-~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ..++|||+|||.++++++|+++|++||.|..+.+..++.++. ++|||||+|.+.++|++|++.|||..++|+.|+|.++
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            468999999999999999999999999999999999877666 8999999999999999999999999999999999999


Q ss_pred             eCCC
Q psy2141         110 ITPP  113 (173)
Q Consensus       110 ~~~~  113 (173)
                      .++.
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.85  E-value=5.8e-21  Score=126.58  Aligned_cols=83  Identities=17%  Similarity=0.261  Sum_probs=76.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIK----SVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLR  105 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~----~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~  105 (173)
                      .+.++|||+|||+++++++|+    ++|++||.|..+++++++.+   +|||||+|.+.++|++|++.|||..++|++|+
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            356799999999999999999    99999999999999998754   88999999999999999999999999999999


Q ss_pred             EEEeeCCCCC
Q psy2141         106 VGRAITPPNA  115 (173)
Q Consensus       106 v~~a~~~~~~  115 (173)
                      |+++++.+..
T Consensus        84 V~~a~~~~~~   93 (96)
T 2dgx_A           84 VSLATGASGP   93 (96)
T ss_dssp             EEECCCSSCC
T ss_pred             EEEcCCCCCC
Confidence            9999876543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=5.5e-21  Score=128.08  Aligned_cols=86  Identities=22%  Similarity=0.377  Sum_probs=80.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+..+  ++.++|||||+|.+.++|++|++.||+..+.|++|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2d9p_A           13 YQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA   90 (103)
T ss_dssp             SSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            46899999999999999999999999999999999998  8999999999999999999999999999999999999999


Q ss_pred             eCCCCCCC
Q psy2141         110 ITPPNALH  117 (173)
Q Consensus       110 ~~~~~~~~  117 (173)
                      +++.....
T Consensus        91 ~~~~~~~~   98 (103)
T 2d9p_A           91 QRKEERQS   98 (103)
T ss_dssp             SSCCCCCC
T ss_pred             cccccCCC
Confidence            88765543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.85  E-value=3.3e-22  Score=133.67  Aligned_cols=81  Identities=16%  Similarity=0.167  Sum_probs=77.7

Q ss_pred             CCCeEEEcCCCC------CCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC-eE
Q psy2141          31 LYNRIYVASIHP------DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG-QY  103 (173)
Q Consensus        31 ~~~~l~V~nLp~------~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g-~~  103 (173)
                      ..++|||+|||.      ++++++|+++|++||.|..+++++++.+|+++|||||+|.+.++|++|++.|||..+.| ++
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            468999999999      99999999999999999999999999999999999999999999999999999999999 99


Q ss_pred             EEEEEeeC
Q psy2141         104 LRVGRAIT  111 (173)
Q Consensus       104 l~v~~a~~  111 (173)
                      |+|.++.+
T Consensus        85 l~V~~a~~   92 (100)
T 3ns6_A           85 LFLYTMKD   92 (100)
T ss_dssp             CEEEESHH
T ss_pred             EEEEECch
Confidence            99999865

>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=99.85  E-value=7.1e-21  Score=123.67  Aligned_cols=80  Identities=20%  Similarity=0.488  Sum_probs=75.3

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ..+.++|||+|||.++++++|+++|++||.|..+++++++.+|+++|||||+|.+.++|++|++. ++..++|+.|+|++
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 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ-KEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS-SCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh-CCCEECCEEEEEEe
Confidence            45789999999999999999999999999999999999998999999999999999999999965 88899999999987


Q ss_pred             e
Q psy2141         109 A  109 (173)
Q Consensus       109 a  109 (173)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.85  E-value=6.6e-21  Score=127.94  Aligned_cols=85  Identities=28%  Similarity=0.412  Sum_probs=79.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCC-CCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSP-HRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~-g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      .+.++|||+|||.++++++|+++|+.|| |..+.+++++.+ ++++|||||+|.+.++|++|+ .||+..+.|+.|+|.+
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            4678999999999999999999999999 999999999887 999999999999999999999 9999999999999999


Q ss_pred             eeCCCCCC
Q psy2141         109 AITPPNAL  116 (173)
Q Consensus       109 a~~~~~~~  116 (173)
                      +.+++...
T Consensus        91 a~~~~~~~   98 (104)
T 1wi8_A           91 ADQAQDKD   98 (104)
T ss_dssp             CCCCCCCC
T ss_pred             ccCCCCCC
Confidence            98776554

>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=99.85  E-value=1.4e-20  Score=126.10  Aligned_cols=86  Identities=27%  Similarity=0.444  Sum_probs=78.7

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ..+.++|||+|||.++++++|+++|++||.|..|++++++.  .++|||||+|.+.++|++|++.||+..+.|++|+|.+
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 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            35689999999999999999999999999999999999853  3689999999999999999999999999999999999


Q ss_pred             eeCCCCCC
Q psy2141         109 AITPPNAL  116 (173)
Q Consensus       109 a~~~~~~~  116 (173)
                      ++++....
T Consensus        90 a~~~~~~~   97 (103)
T 2cqi_A           90 ATTPSSQK   97 (103)
T ss_dssp             CCCTTCCC
T ss_pred             CCCCcccc
Confidence            98765543

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.85  E-value=4.4e-21  Score=138.16  Aligned_cols=81  Identities=17%  Similarity=0.222  Sum_probs=76.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccC--ceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFG--PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G--~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ..++|||+|||+++++++|+++|+.||  .|..+++++|+.+|+++|||||+|.+.++|++|++.|||..|+|+.|+|.+
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            468999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             eeC
Q psy2141         109 AIT  111 (173)
Q Consensus       109 a~~  111 (173)
                      +.+
T Consensus       134 a~~  136 (156)
T 3n9u_C          134 ATR  136 (156)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            864

>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=99.85  E-value=1.6e-21  Score=133.04  Aligned_cols=85  Identities=18%  Similarity=0.300  Sum_probs=79.7

Q ss_pred             hhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q psy2141          28 EAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG  107 (173)
Q Consensus        28 ~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~  107 (173)
                      +....++|||+|||.++++++|+++|+.||.|..+.+++++.+++++|||||+|.+.++|++|+ .||+..+.|+.|+|.
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   99 (114)
T 2cq4_A           21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQ   99 (114)
T ss_dssp             THHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEE
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEE
Confidence            3445789999999999999999999999999999999999989999999999999999999999 999999999999999


Q ss_pred             EeeCCC
Q psy2141         108 RAITPP  113 (173)
Q Consensus       108 ~a~~~~  113 (173)
                      ++++++
T Consensus       100 ~a~~~~  105 (114)
T 2cq4_A          100 ASQAEK  105 (114)
T ss_dssp             EHHHHH
T ss_pred             ecCCCc
Confidence            987643

>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=99.85  E-value=2e-20  Score=125.31  Aligned_cols=86  Identities=20%  Similarity=0.338  Sum_probs=79.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+++++++.  .++|||||+|.+.++|++|++.||+..++|++|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   90 (103)
T 2cq3_A           13 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   90 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            5689999999999999999999999999999999999853  38999999999999999999999999999999999999


Q ss_pred             eCCCCCCC
Q psy2141         110 ITPPNALH  117 (173)
Q Consensus       110 ~~~~~~~~  117 (173)
                      .+++....
T Consensus        91 ~~~~~~~~   98 (103)
T 2cq3_A           91 TARVMTNS   98 (103)
T ss_dssp             CSSCCCCC
T ss_pred             ccCCCCCC
Confidence            87765543

>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=99.85  E-value=5.2e-21  Score=126.24  Aligned_cols=81  Identities=19%  Similarity=0.360  Sum_probs=76.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||..+++++|+++|++||.|..+++.+++. ++++|||||+|.+.++|++|++.||+..+.|++|+|.++
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGP   92 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEc
Confidence            4578999999999999999999999999999999999974 999999999999999999999999999999999999998


Q ss_pred             eC
Q psy2141         110 IT  111 (173)
Q Consensus       110 ~~  111 (173)
                      +.
T Consensus        93 ~~   94 (95)
T 2ywk_A           93 SS   94 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.85  E-value=1.6e-20  Score=134.90  Aligned_cols=88  Identities=22%  Similarity=0.261  Sum_probs=82.4

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ..+.++|||+|||.++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|++.||+..|.|++|+|.+
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            35689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeCCCCCC
Q psy2141         109 AITPPNAL  116 (173)
Q Consensus       109 a~~~~~~~  116 (173)
                      +++.....
T Consensus       116 a~~~~~~~  123 (156)
T 1h2v_Z          116 DAGFKEGR  123 (156)
T ss_dssp             ESCCCTTC
T ss_pred             CCCCCCcC
Confidence            98765443

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=7.9e-21  Score=129.98  Aligned_cols=86  Identities=16%  Similarity=0.512  Sum_probs=80.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|+.||.|..+.+++++.+++++|||||+|.+.++|++|++. ++..++|+.|+|.++
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a  103 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRA  103 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEEC
Confidence            4568999999999999999999999999999999999998999999999999999999999988 999999999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      .++....
T Consensus       104 ~~~~~~~  110 (116)
T 1x4b_A          104 VAREESG  110 (116)
T ss_dssp             SSCCCCC
T ss_pred             CCCccCC
Confidence            8776554

>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=99.85  E-value=2.3e-21  Score=135.43  Aligned_cols=85  Identities=26%  Similarity=0.417  Sum_probs=80.7

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ..+.++|||+|||.++++++|+++|++||.|..+++++++.+++++|||||+|.+.++|++|++.|||..|+|++|+|.+
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            35688999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeCCC
Q psy2141         109 AITPP  113 (173)
Q Consensus       109 a~~~~  113 (173)
                      +++++
T Consensus       123 a~~~~  127 (129)
T 2kxn_B          123 SITKR  127 (129)
T ss_dssp             CSSSS
T ss_pred             ecCCC
Confidence            98654

>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=99.85  E-value=9.9e-21  Score=127.58  Aligned_cols=81  Identities=19%  Similarity=0.340  Sum_probs=77.5

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ..+.++|||+|||..+++++|+++|++||.|..+++++++ +|+++|||||+|.+.++|++|++.|||..+.|++|+|++
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            3568899999999999999999999999999999999997 999999999999999999999999999999999999999


Q ss_pred             ee
Q psy2141         109 AI  110 (173)
Q Consensus       109 a~  110 (173)
                      +.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=5.4e-21  Score=128.54  Aligned_cols=86  Identities=15%  Similarity=0.401  Sum_probs=80.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..|.+++++.+++++|||||+|.+.++|++|++. ++..+.|+.|+|.++
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~a   92 (105)
T 2dh8_A           14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPC   92 (105)
T ss_dssp             SSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEc
Confidence            5689999999999999999999999999999999999999999999999999999999999999 999999999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      .++....
T Consensus        93 ~~~~~~~   99 (105)
T 2dh8_A           93 TPRGMQP   99 (105)
T ss_dssp             CCSSCCT
T ss_pred             cCCCCCC
Confidence            8765443

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.84  E-value=9.9e-21  Score=124.16  Aligned_cols=84  Identities=21%  Similarity=0.351  Sum_probs=78.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+++.++  +++++|||||+|.+.++|++|++.||+..+.|+.|+|.++
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            46799999999999999999999999999999999885  7899999999999999999999999999999999999999


Q ss_pred             eCCCCC
Q psy2141         110 ITPPNA  115 (173)
Q Consensus       110 ~~~~~~  115 (173)
                      ++....
T Consensus        84 ~~~~~~   89 (92)
T 2dgv_A           84 RNASGP   89 (92)
T ss_dssp             SCCSSC
T ss_pred             CCCCCC
Confidence            876443

>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=99.84  E-value=3.6e-21  Score=127.75  Aligned_cols=84  Identities=13%  Similarity=0.164  Sum_probs=78.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||.++++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|++.|||..+.|++|+|.++
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   92 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   92 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            35689999999999999999999999999998888888889999999999999999999999999999999999999998


Q ss_pred             eCCC
Q psy2141         110 ITPP  113 (173)
Q Consensus       110 ~~~~  113 (173)
                      ..++
T Consensus        93 ~~~~   96 (98)
T 2cqp_A           93 SGPS   96 (98)
T ss_dssp             SCSS
T ss_pred             CCCC
Confidence            7543

>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=99.84  E-value=2.7e-21  Score=129.11  Aligned_cols=83  Identities=29%  Similarity=0.458  Sum_probs=75.7

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCC-CCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS-SPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG  107 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~-~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~  107 (173)
                      ....++|||+|||.++++++|+++|++|| |..+++++++ .+|+++|||||+|.+.++|++|+ .|||..++|+.|+|+
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            35689999999999999999999999999 9999999998 68999999999999999999999 899999999999999


Q ss_pred             EeeCCC
Q psy2141         108 RAITPP  113 (173)
Q Consensus       108 ~a~~~~  113 (173)
                      +++++.
T Consensus        94 ~a~~~~   99 (100)
T 2j76_E           94 VADQAQ   99 (100)
T ss_dssp             ECCCSC
T ss_pred             eccCCC
Confidence            998654

>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=99.84  E-value=7.2e-21  Score=131.92  Aligned_cols=87  Identities=30%  Similarity=0.402  Sum_probs=81.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|++.|||..|.|+.|+|.++
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   99 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC   99 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEe
Confidence            45789999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      .+++...
T Consensus       100 ~~~~~~~  106 (126)
T 3ex7_B          100 FVRGPPK  106 (126)
T ss_dssp             EESSSCC
T ss_pred             cCCCCCC
Confidence            8765543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=2.7e-20  Score=121.95  Aligned_cols=82  Identities=16%  Similarity=0.340  Sum_probs=77.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||+++++++|+++|+.| .|..++++++ .+|+++|||||+|.+.++|++|++ ||+..++|+.|+|.++
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            467899999999999999999999999 9999999999 799999999999999999999999 9999999999999999


Q ss_pred             eCCCC
Q psy2141         110 ITPPN  114 (173)
Q Consensus       110 ~~~~~  114 (173)
                      .+++.
T Consensus        85 ~~~~~   89 (91)
T 2dgw_A           85 KSGPS   89 (91)
T ss_dssp             SSCCC
T ss_pred             CcCCC
Confidence            87654

>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=99.84  E-value=1.9e-20  Score=134.49  Aligned_cols=86  Identities=19%  Similarity=0.351  Sum_probs=81.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+++++++.+|+++|||||+|.+.++|++|++.|||..++|++|+|.++
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  147 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  147 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45789999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             eCCCCC
Q psy2141         110 ITPPNA  115 (173)
Q Consensus       110 ~~~~~~  115 (173)
                      ++....
T Consensus       148 ~~~~~~  153 (158)
T 2kn4_A          148 RYGRPP  153 (158)
T ss_dssp             CCSSCC
T ss_pred             CCCCCC
Confidence            875433

>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=99.84  E-value=2e-20  Score=126.47  Aligned_cols=86  Identities=17%  Similarity=0.262  Sum_probs=79.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCc-eeEEEEc-cCCCCCCcceEEEEEEcCHHHHHHHHHhcC--CceeCCeEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGP-IKYCKLQ-QGSSPHRHKGYGFIEYETKQASNEAISSMN--LFDLGGQYLR  105 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~-v~~~~i~-~~~~~g~~~g~afv~f~~~~~a~~a~~~l~--g~~i~g~~l~  105 (173)
                      .+.++|||+|||.++++++|+++|++||. |..+.++ .++.+|+++|||||+|.+.++|++|++.|+  +..+.|+.|+
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            35789999999999999999999999998 9999998 888889999999999999999999999996  5899999999


Q ss_pred             EEEeeCCCCC
Q psy2141         106 VGRAITPPNA  115 (173)
Q Consensus       106 v~~a~~~~~~  115 (173)
                      |.++++++..
T Consensus        86 V~~a~~~~~~   95 (109)
T 2dis_A           86 VDWAEPEIDV   95 (109)
T ss_dssp             EEESCSSCST
T ss_pred             EEEcCCCCCc
Confidence            9999876553

>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=99.84  E-value=1.2e-20  Score=128.28  Aligned_cols=87  Identities=17%  Similarity=0.276  Sum_probs=79.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH---HHhhccCceeEEEEccCCCCC---CcceEEEEEEcCHHHHHHHHHhcCCceeCCeE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIK---SVFEAFGPIKYCKLQQGSSPH---RHKGYGFIEYETKQASNEAISSMNLFDLGGQY  103 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~---~~F~~~G~v~~~~i~~~~~~g---~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~  103 (173)
                      ...++|||+|||+++++++|+   ++|++||.|..+.+.+++.++   +++|||||+|.+.++|++|++.|||..++|++
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            357899999999999999999   999999999999999987644   55699999999999999999999999999999


Q ss_pred             EEEEEeeCCCCCC
Q psy2141         104 LRVGRAITPPNAL  116 (173)
Q Consensus       104 l~v~~a~~~~~~~  116 (173)
                      |+|.++.+++...
T Consensus        93 l~V~~a~~k~~~~  105 (111)
T 2cpi_A           93 LKASLGTTKYCSY  105 (111)
T ss_dssp             EEEESCCCCSCSS
T ss_pred             EEEEecccccccc
Confidence            9999998876443

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=4.7e-21  Score=128.85  Aligned_cols=80  Identities=15%  Similarity=0.173  Sum_probs=75.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||+++++++|+++|++||.|..|.+++++. |+++|||||+|.+.++|++|+. +++..++|+.|.|.++
T Consensus         9 ~~~~~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            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            3468999999999999999999999999999999999976 9999999999999999999998 8999999999999987


Q ss_pred             eC
Q psy2141         110 IT  111 (173)
Q Consensus       110 ~~  111 (173)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            53

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.84  E-value=2e-20  Score=134.14  Aligned_cols=100  Identities=19%  Similarity=0.345  Sum_probs=89.7

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY   81 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f   81 (173)
                      ++|+.|+|.++.....         ....+.++|||+|||..+++++|+++|++||.|..+.+.+++.+|.++|+|||+|
T Consensus        66 ~~g~~i~v~~~~~~~~---------~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f  136 (166)
T 3md3_A           66 IENNIVKINWAFQSQQ---------SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSF  136 (166)
T ss_dssp             ETTEECEEEECCCCCC---------CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEE
T ss_pred             cCCCeeEEEEcCCCCC---------CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEe
Confidence            5788999987754322         1224678999999999999999999999999999999999988999999999999


Q ss_pred             cCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          82 ETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        82 ~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      .+.++|.+|++.|||..++|++|+|.|++
T Consensus       137 ~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          137 TSQDDAQNAMDSMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             SCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             CCHHHHHHHHHHhCCCccCCcEEEEEecC
Confidence            99999999999999999999999999985

>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=99.84  E-value=5.5e-21  Score=128.12  Aligned_cols=83  Identities=29%  Similarity=0.531  Sum_probs=79.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      +.++|||+|||..+++++|+++|++||.|..+.+.+++.+|+++|||||+|.+.++|++|++.|||..+.|+.|+|.++.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            46899999999999999999999999999999999998899999999999999999999999999999999999999987


Q ss_pred             CCC
Q psy2141         111 TPP  113 (173)
Q Consensus       111 ~~~  113 (173)
                      +..
T Consensus        87 ~~~   89 (104)
T 1p1t_A           87 SEK   89 (104)
T ss_dssp             CTT
T ss_pred             Ccc
Confidence            653

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.3e-21  Score=126.72  Aligned_cols=81  Identities=19%  Similarity=0.446  Sum_probs=76.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.|||..+.|+.|+++++
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            46799999999999999999999999999999999999989999999999999999999999999999999999988765


Q ss_pred             e
Q psy2141         110 I  110 (173)
Q Consensus       110 ~  110 (173)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.84  E-value=3.9e-20  Score=123.85  Aligned_cols=85  Identities=16%  Similarity=0.326  Sum_probs=78.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+++++.+++++|||||+|.+.++|++|++  ++..++|+.|+|.++
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~a   90 (103)
T 2cqg_A           13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLP   90 (103)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEec
Confidence            568899999999999999999999999999999999999899999999999999999999998  478999999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      .++....
T Consensus        91 ~~~~~~~   97 (103)
T 2cqg_A           91 NSKQSQD   97 (103)
T ss_dssp             CTTCCCC
T ss_pred             CCCCcCC
Confidence            8765543

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.84  E-value=4.6e-21  Score=121.21  Aligned_cols=75  Identities=24%  Similarity=0.584  Sum_probs=72.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        34 ~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      +|||+|||.++++++|+++|++||.|..+.+.+++.+|+++|||||+|.+.++|++|++ |++..++|++|+|+++
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            58999999999999999999999999999999998899999999999999999999997 9999999999999875

>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=99.84  E-value=3.4e-20  Score=125.43  Aligned_cols=84  Identities=26%  Similarity=0.455  Sum_probs=76.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+..+   +.++|||||+|.+.++|++|++.||+..+.|+.|+|+++
T Consensus        20 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   96 (109)
T 1x4a_A           20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   96 (109)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            46789999999999999999999999999999999654   557999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      ++.....
T Consensus        97 ~~~~~~~  103 (109)
T 1x4a_A           97 RSGRGTG  103 (109)
T ss_dssp             CCCCCCC
T ss_pred             ccCCCCC
Confidence            8765543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1e-20  Score=128.30  Aligned_cols=84  Identities=21%  Similarity=0.390  Sum_probs=77.6

Q ss_pred             hhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q psy2141          27 EEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV  106 (173)
Q Consensus        27 ~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v  106 (173)
                      ....+.++|||+|||.++++++|+++|++||.|..+++.+++  +.++|||||+|.+.++|++|++.|||..++|++|+|
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  101 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV  101 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            344578999999999999999999999999999999999985  458999999999999999999999999999999999


Q ss_pred             EEeeCC
Q psy2141         107 GRAITP  112 (173)
Q Consensus       107 ~~a~~~  112 (173)
                      .+++++
T Consensus       102 ~~a~~~  107 (109)
T 2err_A          102 NNATAR  107 (109)
T ss_dssp             EECCCS
T ss_pred             EECCCC
Confidence            998765

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=1.2e-20  Score=126.87  Aligned_cols=80  Identities=23%  Similarity=0.227  Sum_probs=73.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCC--ceeCCeEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNL--FDLGGQYLRVG  107 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g--~~i~g~~l~v~  107 (173)
                      .+.++|||+|||++++|++|+++|++||.|..++++++      ||||||+|.+.++|++|++.|++  ..+.|++|+|.
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            46899999999999999999999999999999999876      79999999999999999998864  78999999999


Q ss_pred             EeeCCCCC
Q psy2141         108 RAITPPNA  115 (173)
Q Consensus       108 ~a~~~~~~  115 (173)
                      ++++++..
T Consensus        88 ~A~~~~~~   95 (105)
T 1sjq_A           88 FSNHKELK   95 (105)
T ss_dssp             CCSSSSCC
T ss_pred             EcCCCCCC
Confidence            99865443

>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=99.83  E-value=6e-21  Score=125.94  Aligned_cols=82  Identities=12%  Similarity=0.167  Sum_probs=75.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..+.|++|+|.++
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            35689999999999999999999999999999988888889999999999999999999999999999999999999987


Q ss_pred             eC
Q psy2141         110 IT  111 (173)
Q Consensus       110 ~~  111 (173)
                      ..
T Consensus        93 ~s   94 (95)
T 2ek1_A           93 SS   94 (95)
T ss_dssp             C-
T ss_pred             cC
Confidence            53

>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=99.83  E-value=2.2e-21  Score=126.85  Aligned_cols=82  Identities=29%  Similarity=0.492  Sum_probs=74.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCC
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITP  112 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~  112 (173)
                      ++|||+|||.++++++|+++|++||.|..+.+.+++.+|+++|||||+|.+.+ |.+|++.|||..++|++|+|+++.+.
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            68999999999999999999999999999999999989999999999999999 99999999999999999999999875


Q ss_pred             CCC
Q psy2141         113 PNA  115 (173)
Q Consensus       113 ~~~  115 (173)
                      ...
T Consensus        81 ~~~   83 (90)
T 2ki2_A           81 KSL   83 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            444

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.83  E-value=2.3e-20  Score=124.43  Aligned_cols=78  Identities=17%  Similarity=0.277  Sum_probs=71.8

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCce--eCCeEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFD--LGGQYLRV  106 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~--i~g~~l~v  106 (173)
                      ..+.++|||+|||+++++++|+++|++||.|..++++++      ||+|||+|.+.++|.+|++.|++..  +.|++|+|
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V   91 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEE
Confidence            357899999999999999999999999999999999864      7899999999999999999999875  78999999


Q ss_pred             EEeeCC
Q psy2141         107 GRAITP  112 (173)
Q Consensus       107 ~~a~~~  112 (173)
                      ++++.+
T Consensus        92 ~~S~~k   97 (100)
T 3r27_A           92 NYSTSQ   97 (100)
T ss_dssp             EECSCS
T ss_pred             Eecccc
Confidence            998764

>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=99.83  E-value=2.4e-20  Score=134.84  Aligned_cols=97  Identities=26%  Similarity=0.482  Sum_probs=88.5

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY   81 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f   81 (173)
                      ++|++|+|.++.....           ....++|||+|||..+++++|+++|++||.|..+.+.+++.+|.++|||||+|
T Consensus        75 ~~g~~i~v~~~~~~~~-----------~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f  143 (172)
T 2g4b_A           75 FQGQSLKIRRPHDYQP-----------LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY  143 (172)
T ss_dssp             ETTEECEEECCSSCCC-----------CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEE
T ss_pred             ecCceeeecCCcccCC-----------CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEe
Confidence            6799999998764321           13478999999999999999999999999999999999988999999999999


Q ss_pred             cCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          82 ETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        82 ~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|.+|++.|||..++|++|+|+++
T Consensus       144 ~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          144 VDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             SSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            9999999999999999999999999987

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.83  E-value=2.6e-20  Score=137.55  Aligned_cols=113  Identities=23%  Similarity=0.411  Sum_probs=93.9

Q ss_pred             CCCcccccCCCCCCCCCcchhh---------hhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCC
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVID---------EITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHR   72 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~---------~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~   72 (173)
                      |+|+.|+|.++...........         .......+.++|||+|||..+++++|+++|++||.|..+.+.+++.+|.
T Consensus        75 ~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~  154 (198)
T 2yh0_A           75 FQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGL  154 (198)
T ss_dssp             ETTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCS
T ss_pred             EcCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCC
Confidence            6899999998765421111000         0011124679999999999999999999999999999999999988999


Q ss_pred             cceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCCCC
Q psy2141          73 HKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPN  114 (173)
Q Consensus        73 ~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~~~  114 (173)
                      ++|||||+|.+.++|++|++.|||..++|+.|+|.+++++..
T Consensus       155 ~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          155 SKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             EEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             cceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            999999999999999999999999999999999999987643

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=5.1e-20  Score=122.89  Aligned_cols=83  Identities=25%  Similarity=0.358  Sum_probs=75.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|   +++.+ .+++++|||||+|.+.++|++|++.||+..+.|+.|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   88 (101)
T 2fc9_A           13 GESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQ   88 (101)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEc
Confidence            568999999999999999999999999987   56666 68999999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      ++++...
T Consensus        89 ~~~~~~~   95 (101)
T 2fc9_A           89 GPRGSPN   95 (101)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            8765543

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.83  E-value=3.8e-20  Score=130.14  Aligned_cols=82  Identities=26%  Similarity=0.485  Sum_probs=77.5

Q ss_pred             hhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q psy2141          28 EAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG  107 (173)
Q Consensus        28 ~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~  107 (173)
                      ...+.++|||+|||..+++++|+++|++||.|..+++++++.+++++|||||+|.+.++|++|++.|||..++|++|+|+
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             Ee
Q psy2141         108 RA  109 (173)
Q Consensus       108 ~a  109 (173)
                      ++
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            75

>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=99.83  E-value=1.7e-20  Score=125.86  Aligned_cols=80  Identities=15%  Similarity=0.131  Sum_probs=72.8

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCC--ceeCCeEEEE
Q psy2141          30 KLYNRIYVASIHP-DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNL--FDLGGQYLRV  106 (173)
Q Consensus        30 ~~~~~l~V~nLp~-~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g--~~i~g~~l~v  106 (173)
                      .+.++|||+|||+ ++++++|+++|++||.|..+.++++      +|||||+|.+.++|++|++.|++  ..+.|++|+|
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            4689999999999 9999999999999999999999876      58999999999999999999986  4599999999


Q ss_pred             EEeeCCCCC
Q psy2141         107 GRAITPPNA  115 (173)
Q Consensus       107 ~~a~~~~~~  115 (173)
                      .+++..+..
T Consensus        87 ~~a~~~~~~   95 (102)
T 1x4d_A           87 HLSQKYKRI   95 (102)
T ss_dssp             EEECCCTTS
T ss_pred             EECCCCCCC
Confidence            999865443

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.83  E-value=9.7e-21  Score=133.20  Aligned_cols=86  Identities=19%  Similarity=0.351  Sum_probs=80.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+++++.+++++|||||+|.+.++|++|++.|||..+.|++|+|.++
T Consensus        45 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a  124 (135)
T 2lea_A           45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  124 (135)
T ss_dssp             GGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45789999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             eCCCCC
Q psy2141         110 ITPPNA  115 (173)
Q Consensus       110 ~~~~~~  115 (173)
                      ++....
T Consensus       125 ~~~~~~  130 (135)
T 2lea_A          125 RYGRPP  130 (135)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            865443

>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=99.83  E-value=7.1e-20  Score=121.38  Aligned_cols=79  Identities=28%  Similarity=0.524  Sum_probs=73.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeC--CeEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLG--GQYLRVG  107 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~--g~~l~v~  107 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+..+      +|||||+|.+.++|++|++.||+..+.  |++|+|.
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            45789999999999999999999999999999999764      789999999999999999999999999  9999999


Q ss_pred             EeeCCCC
Q psy2141         108 RAITPPN  114 (173)
Q Consensus       108 ~a~~~~~  114 (173)
                      ++++++.
T Consensus        89 ~a~~~~~   95 (97)
T 1why_A           89 FAKSGPS   95 (97)
T ss_dssp             ECCCCCC
T ss_pred             ECCCCCC
Confidence            9987654

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.83  E-value=7.9e-21  Score=120.57  Aligned_cols=76  Identities=17%  Similarity=0.476  Sum_probs=73.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ++|||+|||.++++++|+++|++||.|..+.+.+++.+|+++|||||+|.+.++|++|++.++ ..++|++|+|+++
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            579999999999999999999999999999999998899999999999999999999999999 9999999999986

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.82  E-value=3.7e-20  Score=119.93  Aligned_cols=74  Identities=12%  Similarity=0.222  Sum_probs=69.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      ....|||+||++.++|++|+++|.+||+|..+++..      +||||||+|.+.++|++|++.||+..++|++|+|+++.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            467899999999999999999999999999999966      48999999999999999999999999999999999983

>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=99.82  E-value=4.2e-20  Score=125.91  Aligned_cols=82  Identities=15%  Similarity=0.284  Sum_probs=77.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCcee--------CC
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDL--------GG  101 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i--------~g  101 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+++++++ ++.++|||||+|.+.++|++|++.|||..+        .+
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~  101 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT  101 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCC
Confidence            467899999999999999999999999999999999997 999999999999999999999999999999        57


Q ss_pred             eEEEEEEeeCC
Q psy2141         102 QYLRVGRAITP  112 (173)
Q Consensus       102 ~~l~v~~a~~~  112 (173)
                      ++|.|.|+.++
T Consensus       102 ~~l~v~~a~p~  112 (114)
T 1x5o_A          102 EPLLCKFSGPS  112 (114)
T ss_dssp             SCBEEEECCCS
T ss_pred             CceeEEccCCC
Confidence            88999998854

>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=99.82  E-value=6e-20  Score=133.14  Aligned_cols=86  Identities=27%  Similarity=0.380  Sum_probs=79.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|++|++.|||..|.|++|.|.|+
T Consensus        70 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  149 (165)
T 1rk8_A           70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  149 (165)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            44678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCCCCC
Q psy2141         110 ITPPNA  115 (173)
Q Consensus       110 ~~~~~~  115 (173)
                      .+++..
T Consensus       150 ~~~~~~  155 (165)
T 1rk8_A          150 FVKGPK  155 (165)
T ss_dssp             EECC--
T ss_pred             cCCCCC
Confidence            876544

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.71  E-value=6.4e-22  Score=135.50  Aligned_cols=91  Identities=19%  Similarity=0.283  Sum_probs=83.7

Q ss_pred             hhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeE--------EEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCcee
Q psy2141          28 EAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKY--------CKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDL   99 (173)
Q Consensus        28 ~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~--------~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i   99 (173)
                      +..+.++|||+|||.++++++|+++|++||.|..        +++++++.+++++|||||+|.+.++|++|++.|||..+
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            3457899999999999999999999999999998        99999988999999999999999999999999999999


Q ss_pred             CCeEEEEEEeeCCCCCCCC
Q psy2141         100 GGQYLRVGRAITPPNALHS  118 (173)
Q Consensus       100 ~g~~l~v~~a~~~~~~~~~  118 (173)
                      .|++|+|.++++++.....
T Consensus        83 ~g~~l~V~~a~~~~~~~~g  101 (116)
T 2lcw_A           83 SGNPIKVSFATRRADFNRG  101 (116)
Confidence            9999999999887665433

>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=99.82  E-value=3.9e-20  Score=126.34  Aligned_cols=81  Identities=10%  Similarity=0.074  Sum_probs=76.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCce-eEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPI-KYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v-~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      .+.++|||+|||+++++++|+++|+.||.| ..++|++++ +|+++|||||+|.+.++|++|++. |+..++|+.|+|.+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHV   90 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEE
Confidence            467899999999999999999999999999 899999998 999999999999999999999987 99999999999999


Q ss_pred             eeCC
Q psy2141         109 AITP  112 (173)
Q Consensus       109 a~~~  112 (173)
                      +.++
T Consensus        91 a~~~   94 (114)
T 2cpy_A           91 VTLE   94 (114)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8754

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.82  E-value=2.7e-20  Score=125.33  Aligned_cols=81  Identities=22%  Similarity=0.297  Sum_probs=75.0

Q ss_pred             CCCCeEEEcCCCCCC------CHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCe-
Q psy2141          30 KLYNRIYVASIHPDL------TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQ-  102 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~------~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~-  102 (173)
                      ...++|||+|||..+      ++++|+++|++||.|..+.+.  +.+|+++|||||+|.+.++|++|++.|||..+.|+ 
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~   90 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   90 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTC
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCc
Confidence            457899999999999      789999999999999999988  36899999999999999999999999999999998 


Q ss_pred             EEEEEEeeCC
Q psy2141         103 YLRVGRAITP  112 (173)
Q Consensus       103 ~l~v~~a~~~  112 (173)
                      +|+|.++...
T Consensus        91 ~l~V~~a~~~  100 (105)
T 2nlw_A           91 TFRVNLFTDF  100 (105)
T ss_dssp             EEEEECSCCC
T ss_pred             eEEEEEcchH
Confidence            9999998754

>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=99.82  E-value=3e-19  Score=120.80  Aligned_cols=85  Identities=22%  Similarity=0.422  Sum_probs=77.5

Q ss_pred             hhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q psy2141          26 TEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLR  105 (173)
Q Consensus        26 ~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~  105 (173)
                      .......++|||+|||..+++++|+++|++||.|..+++.++      +|||||+|.+.++|++|++.|+|..+.|++|+
T Consensus        19 ~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   92 (109)
T 1x4g_A           19 NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVK   92 (109)
T ss_dssp             HHSCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             cCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            334556889999999999999999999999999999999876      78999999999999999999999999999999


Q ss_pred             EEEeeCCCCCC
Q psy2141         106 VGRAITPPNAL  116 (173)
Q Consensus       106 v~~a~~~~~~~  116 (173)
                      |.++++.+...
T Consensus        93 v~~a~~~~~~~  103 (109)
T 1x4g_A           93 CYWGKESPDMT  103 (109)
T ss_dssp             EECCCCCCSSC
T ss_pred             EEecCCCCCCC
Confidence            99998766543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=1.1e-19  Score=121.37  Aligned_cols=84  Identities=18%  Similarity=0.345  Sum_probs=77.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|+.|+   .+.+++++.+++++|||||+|.+.++|++|++.||+..+.|+.|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2fc8_A           13 QPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA   89 (102)
T ss_dssp             CCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEe
Confidence            5689999999999999999999999873   6778888889999999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      +++....
T Consensus        90 ~~~~~~~   96 (102)
T 2fc8_A           90 KPKGEGG   96 (102)
T ss_dssp             CCCCSSS
T ss_pred             cCCCCCC
Confidence            8876553

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.82  E-value=5e-20  Score=128.26  Aligned_cols=83  Identities=14%  Similarity=0.326  Sum_probs=74.8

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHH----HHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIK----SVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYL  104 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~----~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l  104 (173)
                      ..+.++|||+|||+.+++++|+    ++|++||.|..|.+..   +++++|||||+|.+.++|.+|++.|||..+.|++|
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l  102 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL  102 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEE
Confidence            3568899999999999999876    6999999999988753   57889999999999999999999999999999999


Q ss_pred             EEEEeeCCCC
Q psy2141         105 RVGRAITPPN  114 (173)
Q Consensus       105 ~v~~a~~~~~  114 (173)
                      +|+|++.+..
T Consensus       103 ~V~~a~~~~~  112 (127)
T 2a3j_A          103 VITFSETPQS  112 (127)
T ss_dssp             EEEECCCCCH
T ss_pred             EEEEccCcch
Confidence            9999987643

>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=99.82  E-value=1.4e-19  Score=121.17  Aligned_cols=80  Identities=15%  Similarity=0.174  Sum_probs=72.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhc--CCceeCCeEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM--NLFDLGGQYLRVG  107 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l--~g~~i~g~~l~v~  107 (173)
                      .+.++|||+|||+++++++|+++|++||.|..+.++++      ||||||+|.+.++|++|++.|  ++..+.|++|+|+
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            57899999999999999999999999999999998875      799999999999999999987  4678999999999


Q ss_pred             EeeCCCCC
Q psy2141         108 RAITPPNA  115 (173)
Q Consensus       108 ~a~~~~~~  115 (173)
                      +++.+...
T Consensus        87 ~a~~~~~~   94 (101)
T 2cq1_A           87 YSNHKELK   94 (101)
T ss_dssp             ECSCSSCC
T ss_pred             EcCcccCc
Confidence            99865444

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.82  E-value=7e-20  Score=125.91  Aligned_cols=82  Identities=13%  Similarity=0.171  Sum_probs=76.3

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCc---eeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGP---IKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLR  105 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~---v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~  105 (173)
                      ....++|||+|||+++++++|+++|+.||.   |..++|++++. |+++|||||+|.+.++|++|++ ||+..++|+.|+
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   91 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIE   91 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEE
Confidence            356789999999999999999999999999   89999999975 9999999999999999999998 999999999999


Q ss_pred             EEEeeCC
Q psy2141         106 VGRAITP  112 (173)
Q Consensus       106 v~~a~~~  112 (173)
                      |.++...
T Consensus        92 V~~a~~~   98 (118)
T 2db1_A           92 VFKSHRT   98 (118)
T ss_dssp             EEEECHH
T ss_pred             EEECCHH
Confidence            9998643

>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=99.82  E-value=2.3e-20  Score=133.24  Aligned_cols=80  Identities=19%  Similarity=0.411  Sum_probs=74.9

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ..+.++|||+|||+++++++|+++|++||.|..++++++     ++|||||+|.+.++|++|++.|||..+.|++|+|.+
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  144 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVEL  144 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            356899999999999999999999999999999999887     589999999999999999999999999999999999


Q ss_pred             eeCCC
Q psy2141         109 AITPP  113 (173)
Q Consensus       109 a~~~~  113 (173)
                      +++++
T Consensus       145 a~~~~  149 (150)
T 2i2y_A          145 SNGEK  149 (150)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98754

>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=99.82  E-value=2.1e-20  Score=134.59  Aligned_cols=99  Identities=19%  Similarity=0.400  Sum_probs=88.3

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY   81 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f   81 (173)
                      ++|+.|++.++..           ..+..+.++|||+|||.++++++|+++|++||.|..+.+..++.+|.++|||||+|
T Consensus        68 ~~g~~i~v~~~~~-----------~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f  136 (167)
T 2cjk_A           68 LDGKVIDPKRAIP-----------RDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY  136 (167)
T ss_dssp             ETTEECCCEECCC-----------HHHHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEE
T ss_pred             cCCeEcccccccc-----------hhhccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEE
Confidence            6788888887642           11223577999999999999999999999999999999999988999999999999


Q ss_pred             cCHHHHHHHHHhcCCceeCCeEEEEEEeeCC
Q psy2141          82 ETKQASNEAISSMNLFDLGGQYLRVGRAITP  112 (173)
Q Consensus        82 ~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~  112 (173)
                      .+.++|.+|++ +++..++|++|+|.++.++
T Consensus       137 ~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          137 DSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             SSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             CCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            99999999997 8999999999999999865

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=1.1e-19  Score=118.86  Aligned_cols=79  Identities=27%  Similarity=0.561  Sum_probs=73.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+.        +|||||+|.+.++|++|++.||+..+.|++|+|.++
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            468899999999999999999999999999999986        579999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      ++++...
T Consensus        78 ~~~~~~~   84 (90)
T 2dnq_A           78 KNKSKAS   84 (90)
T ss_dssp             SCCCCCC
T ss_pred             CCCCCCC
Confidence            8766554

>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=99.81  E-value=9.9e-20  Score=122.58  Aligned_cols=80  Identities=18%  Similarity=0.250  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCc--eeCCeEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLF--DLGGQYLRVG  107 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~--~i~g~~l~v~  107 (173)
                      .+.++|||+|||+++++++|+++|++||.|..+.++++      ||||||+|.+.++|++|++.|++.  .+.|++|+|.
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            46789999999999999999999999999999998765      799999999999999999988764  5999999999


Q ss_pred             EeeCCCCC
Q psy2141         108 RAITPPNA  115 (173)
Q Consensus       108 ~a~~~~~~  115 (173)
                      +++.+...
T Consensus        87 ~a~~~~~~   94 (104)
T 1wex_A           87 YSTSKRIT   94 (104)
T ss_dssp             ECSSSSCC
T ss_pred             EccCcccc
Confidence            99875544

>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=99.81  E-value=2.1e-19  Score=121.77  Aligned_cols=97  Identities=20%  Similarity=0.442  Sum_probs=80.6

Q ss_pred             CCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCC-CCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEE
Q psy2141           3 HFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPD-LTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY   81 (173)
Q Consensus         3 ~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~-~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f   81 (173)
                      .|+.|++..........        .....++|||+|||.+ +++++|+++|++||.|..+.+        ++|||||+|
T Consensus         6 ~g~~~~~~~s~~~~~~~--------~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f   69 (110)
T 1wf1_A            6 SGMSLKLQASNVTNKND--------PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQY   69 (110)
T ss_dssp             CSCCCCCCCCCSCCSCC--------CTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEEC
T ss_pred             CCcccccccCCCCCCCC--------CCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEE
Confidence            46777776554222111        1235689999999999 999999999999999999998        478999999


Q ss_pred             cCHHHHHHHHHhcCCceeCCeEEEEEEeeCCCCC
Q psy2141          82 ETKQASNEAISSMNLFDLGGQYLRVGRAITPPNA  115 (173)
Q Consensus        82 ~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~~~~  115 (173)
                      .+.++|++|++.||+..++|+.|+|.+++.++..
T Consensus        70 ~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~  103 (110)
T 1wf1_A           70 SNERHARAAVLGENGRVLAGQTLDINMAGEPKPD  103 (110)
T ss_dssp             SSSHHHHHHHHHHTTCEETTEECCEEESCCCCSC
T ss_pred             CCHHHHHHHHHHcCCCEECCeEEEEEECCCCCCC
Confidence            9999999999999999999999999999865443

>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=99.81  E-value=8.2e-20  Score=122.52  Aligned_cols=83  Identities=16%  Similarity=0.201  Sum_probs=75.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||+++++++|+++|++|| +..++|++++ +++++|||||+|.+.++|++|+ .+|+..++|+.|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFLN   89 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-ceEEEEEECC-CCCEeeEEEEEECCHHHHHHHH-HhCCCeECCcEEEEEEC
Confidence            4578999999999999999999999999 4599999997 8999999999999999999999 57999999999999998


Q ss_pred             eCCCCC
Q psy2141         110 ITPPNA  115 (173)
Q Consensus       110 ~~~~~~  115 (173)
                      .+....
T Consensus        90 ~~~~~~   95 (102)
T 1wez_A           90 STAGTS   95 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            765443

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.81  E-value=8.5e-20  Score=124.24  Aligned_cols=82  Identities=18%  Similarity=0.316  Sum_probs=72.7

Q ss_pred             hhCCCCeEEEcCCCCCCCHHHHHHHhhccC-ceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q psy2141          28 EAKLYNRIYVASIHPDLTEEDIKSVFEAFG-PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV  106 (173)
Q Consensus        28 ~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G-~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v  106 (173)
                      .....++|||+|||+++++++|+++|++|| .|..+.+..+    +++|||||+|.+.++|++|++.|||..++|+.|+|
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 LPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITV   99 (111)
T ss_dssp             -CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            345578999999999999999999999999 8999998643    47899999999999999999999999999999999


Q ss_pred             EEeeCCC
Q psy2141         107 GRAITPP  113 (173)
Q Consensus       107 ~~a~~~~  113 (173)
                      .++..++
T Consensus       100 ~~a~~~p  106 (111)
T 2jvr_A          100 ERDDNPP  106 (111)
T ss_dssp             EESCC--
T ss_pred             EECCCCC
Confidence            9987543

>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=99.81  E-value=5e-19  Score=119.65  Aligned_cols=80  Identities=20%  Similarity=0.346  Sum_probs=74.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC-----eEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG-----QYL  104 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g-----~~l  104 (173)
                      ...++|||+|||+++++++|+++|++||.|..+.++.+       |||||+|.+.++|++|++.||+..+.|     +.|
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            45789999999999999999999999999999999876       899999999999999999999999999     999


Q ss_pred             EEEEeeCCCCCC
Q psy2141         105 RVGRAITPPNAL  116 (173)
Q Consensus       105 ~v~~a~~~~~~~  116 (173)
                      +|+++.+++...
T Consensus        86 ~V~~a~~~~~~~   97 (108)
T 1x4c_A           86 RVKVDGPRSPSY   97 (108)
T ss_dssp             EEEESSCCSCCC
T ss_pred             EEEeCCCCCCCC
Confidence            999998765543

>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=99.81  E-value=4.7e-20  Score=140.52  Aligned_cols=81  Identities=17%  Similarity=0.238  Sum_probs=76.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccC--ceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFG--PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G--~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ..++|||+|||+++++++|+++|++||  .|..|+|++++.+++++|||||+|.+.++|++||+.||+..|.|+.|+|.+
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  999999999999999999999999999999999999999999999999999


Q ss_pred             eeC
Q psy2141         109 AIT  111 (173)
Q Consensus       109 a~~  111 (173)
                      +++
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            753

>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=99.81  E-value=1.5e-19  Score=121.41  Aligned_cols=82  Identities=12%  Similarity=0.245  Sum_probs=76.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeE-EEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKY-CKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~-~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      .+.++|||+|||+++++++|+++|++||.|.. +.|+++ .+|+++|||||+|.+.++|++|++. ++..++|+.|+|.+
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            46789999999999999999999999999987 889998 7999999999999999999999988 99999999999999


Q ss_pred             eeCCC
Q psy2141         109 AITPP  113 (173)
Q Consensus       109 a~~~~  113 (173)
                      +....
T Consensus        91 ~~~~~   95 (104)
T 1wg5_A           91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            86543

>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=99.81  E-value=8.7e-20  Score=125.48  Aligned_cols=81  Identities=22%  Similarity=0.226  Sum_probs=73.6

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCC--ceeCCeEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNL--FDLGGQYLRV  106 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g--~~i~g~~l~v  106 (173)
                      ..+.++|||+|||++++|++|+++|++||.|..++++++      ||||||+|.+.++|++|++.|++  ..+.|++|+|
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            356889999999999999999999999999999999876      79999999999999999999874  6899999999


Q ss_pred             EEeeCCCCC
Q psy2141         107 GRAITPPNA  115 (173)
Q Consensus       107 ~~a~~~~~~  115 (173)
                      .+++.+...
T Consensus       102 ~~a~~k~~~  110 (119)
T 2ad9_A          102 QFSNHKELK  110 (119)
T ss_dssp             EECSSSSCC
T ss_pred             EEccCCCCC
Confidence            999865444

>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=99.81  E-value=6e-20  Score=121.54  Aligned_cols=83  Identities=19%  Similarity=0.427  Sum_probs=76.0

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHH----HHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIK----SVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYL  104 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~----~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l  104 (173)
                      ..+.++|||+|||.++++++|+    ++|++||.|..+.+.+   +|.++|||||+|.+.++|++|++.|||..+.|++|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            4578999999999999999999    9999999999999874   57789999999999999999999999999999999


Q ss_pred             EEEEeeCCCC
Q psy2141         105 RVGRAITPPN  114 (173)
Q Consensus       105 ~v~~a~~~~~  114 (173)
                      +|.++++++.
T Consensus        82 ~v~~a~~~~~   91 (97)
T 1nu4_A           82 RIQYAKTDSD   91 (97)
T ss_dssp             EEEECSSCCT
T ss_pred             EEEEccCCCc
Confidence            9999987643

>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=99.81  E-value=1.6e-19  Score=133.17  Aligned_cols=109  Identities=16%  Similarity=0.352  Sum_probs=86.6

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY   81 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f   81 (173)
                      ++|+.|+|.++........     .....+.++|||+|||.++++++|+++|+.||.|..+.+++++.+|.++|||||+|
T Consensus        79 ~~g~~l~v~~~~~~~~~~~-----~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F  153 (196)
T 1l3k_A           79 VDGRVVEPKRAVSREDSQR-----PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF  153 (196)
T ss_dssp             ETTEECEEEECCC----------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEE
T ss_pred             ECCEEeeeecccCcccccc-----cccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEE
Confidence            6799999988764322111     12234578999999999999999999999999999999999988999999999999


Q ss_pred             cCHHHHHHHHHhcCCceeCCeEEEEEEeeCCCCCC
Q psy2141          82 ETKQASNEAISSMNLFDLGGQYLRVGRAITPPNAL  116 (173)
Q Consensus        82 ~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~~~~~  116 (173)
                      .+.++|.+|++. ++..++|+.|.|.++.++....
T Consensus       154 ~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~~  187 (196)
T 1l3k_A          154 DDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEMA  187 (196)
T ss_dssp             SSHHHHHHHHHC-SCCEETTEECEEEECC------
T ss_pred             CCHHHHHHHHHh-CCcEECCEEEEEEecCChhHhc
Confidence            999999999977 7999999999999998765554

>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=99.81  E-value=5.7e-20  Score=129.39  Aligned_cols=81  Identities=12%  Similarity=0.138  Sum_probs=75.9

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCc---eeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGP---IKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLR  105 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~---v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~  105 (173)
                      ....++|||+|||+++++++|+++|++||.   |..++|++++. |+++|||||+|.+.++|++|++ ||+..++|+.|+
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~  118 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIE  118 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEE
Confidence            356789999999999999999999999999   89999999976 9999999999999999999998 999999999999


Q ss_pred             EEEeeC
Q psy2141         106 VGRAIT  111 (173)
Q Consensus       106 v~~a~~  111 (173)
                      |.++.+
T Consensus       119 V~~a~~  124 (136)
T 2hgl_A          119 VFKSHR  124 (136)
T ss_dssp             EEECCH
T ss_pred             EEECCh
Confidence            999753

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.81  E-value=5.4e-21  Score=127.64  Aligned_cols=84  Identities=7%  Similarity=0.240  Sum_probs=76.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|.. .++.++.+|+++|||||+|.+.++|++|++ |||..+.|+.|+|.++
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            46789999999999999999999999999988 677777789999999999999999999998 9999999999999999


Q ss_pred             eCCCCC
Q psy2141         110 ITPPNA  115 (173)
Q Consensus       110 ~~~~~~  115 (173)
                      ++++..
T Consensus        93 ~~~~~~   98 (101)
T 1fj7_A           93 KGRDGT   98 (101)
T ss_dssp             SCCCCS
T ss_pred             CCCCCC
Confidence            875443

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.81  E-value=3.2e-20  Score=119.16  Aligned_cols=73  Identities=25%  Similarity=0.360  Sum_probs=67.9

Q ss_pred             CCeEEEcCCCCCC------CHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCe-EE
Q psy2141          32 YNRIYVASIHPDL------TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQ-YL  104 (173)
Q Consensus        32 ~~~l~V~nLp~~~------~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~-~l  104 (173)
                      .++|||+|||..+      ++++|+++|++||.|..+.+.  +.+|+++|||||+|.+.++|++|++.|||..++|+ +|
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            3789999999999      779999999999999999987  35899999999999999999999999999999999 88


Q ss_pred             EE
Q psy2141         105 RV  106 (173)
Q Consensus       105 ~v  106 (173)
                      +|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            76

>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=99.81  E-value=3.2e-20  Score=126.59  Aligned_cols=87  Identities=23%  Similarity=0.326  Sum_probs=74.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+..+..+++++|||||+|.+.++|++|++.|||..+.|++|+|.++
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            46799999999999999999999999999843322222237889999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      +++....
T Consensus       103 ~~~~~~~  109 (115)
T 2cpx_A          103 KNKKQRS  109 (115)
T ss_dssp             CCCSCCC
T ss_pred             cCCCCCC
Confidence            8766554

>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=99.81  E-value=6.3e-19  Score=118.06  Aligned_cols=81  Identities=25%  Similarity=0.425  Sum_probs=73.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.++        ++||||+|.+.++|++|++.||+..+.|++|+|.++
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            467899999999999999999999999999999986        459999999999999999999999999999999999


Q ss_pred             eCCCCCCCC
Q psy2141         110 ITPPNALHS  118 (173)
Q Consensus       110 ~~~~~~~~~  118 (173)
                      +++......
T Consensus        81 ~~~~~~~~~   89 (103)
T 2dgu_A           81 KPPDQKRKE   89 (103)
T ss_dssp             CCCCCCCCC
T ss_pred             CCCcccchh
Confidence            876655443

>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=99.80  E-value=3.6e-19  Score=118.23  Aligned_cols=79  Identities=18%  Similarity=0.403  Sum_probs=71.9

Q ss_pred             hhhCCCCeEEEcCCCC-CCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q psy2141          27 EEAKLYNRIYVASIHP-DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLR  105 (173)
Q Consensus        27 ~~~~~~~~l~V~nLp~-~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~  105 (173)
                      ....+.++|||+|||. ++++++|+++|++||.|..+.+.        +|||||+|.+.++|++|++.|||..++|++|+
T Consensus        17 ~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   88 (97)
T 2xnq_A           17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLI   88 (97)
T ss_dssp             --CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3446789999999998 99999999999999999999982        78999999999999999999999999999999


Q ss_pred             EEEeeCCC
Q psy2141         106 VGRAITPP  113 (173)
Q Consensus       106 v~~a~~~~  113 (173)
                      |+++++++
T Consensus        89 V~~a~~~~   96 (97)
T 2xnq_A           89 LEVSSSNA   96 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEecCCCC
Confidence            99987653

>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=99.80  E-value=3.4e-20  Score=117.10  Aligned_cols=75  Identities=21%  Similarity=0.517  Sum_probs=71.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        34 ~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      +|||+|||.++++++|+++|++||.|..+.+.+++.+|.++|||||+|.+.++|++|++. ++..+.|+.|+|+++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            599999999999999999999999999999999998999999999999999999999975 889999999999875

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.80  E-value=3e-19  Score=134.23  Aligned_cols=83  Identities=23%  Similarity=0.437  Sum_probs=78.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||++++|++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++|++.+++..+.|+.|++.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             eCC
Q psy2141         110 ITP  112 (173)
Q Consensus       110 ~~~  112 (173)
                      ...
T Consensus        93 ~~~   95 (213)
T 4f02_A           93 QRD   95 (213)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            644

>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=99.80  E-value=1.4e-19  Score=120.35  Aligned_cols=81  Identities=30%  Similarity=0.535  Sum_probs=74.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||..+++++|+++|++||.|..+.+.++      +|||||+|.+.++|++|++.|||..+.|++|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   86 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA   86 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEc
Confidence            46789999999999999999999999999999999865      789999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      +++....
T Consensus        87 ~~~~~~~   93 (99)
T 2cpj_A           87 CHSASLT   93 (99)
T ss_dssp             SCCSCCC
T ss_pred             CCCCCCC
Confidence            8765443

>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=99.80  E-value=2e-19  Score=116.15  Aligned_cols=75  Identities=28%  Similarity=0.440  Sum_probs=70.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhc-CCceeCCeEEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM-NLFDLGGQYLRVGR  108 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l-~g~~i~g~~l~v~~  108 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+++.++      +|||||+|.+.++|++|++.| ++..++|++|+|+|
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            46789999999999999999999999999999999874      799999999999999999999 99999999999999


Q ss_pred             ee
Q psy2141         109 AI  110 (173)
Q Consensus       109 a~  110 (173)
                      ++
T Consensus        84 ak   85 (85)
T 2ytc_A           84 GR   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.80  E-value=1.9e-19  Score=121.92  Aligned_cols=81  Identities=26%  Similarity=0.494  Sum_probs=72.8

Q ss_pred             hhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q psy2141          26 TEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLR  105 (173)
Q Consensus        26 ~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~  105 (173)
                      .....+.++|||+|||.++++++|+++|++||.|..+.+.        +|||||+|.+.++|++|++.|||..++|+.|+
T Consensus        25 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   96 (108)
T 2jvo_A           25 QEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLE   96 (108)
T ss_dssp             ---CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             cCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            3445678999999999999999999999999999999986        68999999999999999999999999999999


Q ss_pred             EEEeeCCCC
Q psy2141         106 VGRAITPPN  114 (173)
Q Consensus       106 v~~a~~~~~  114 (173)
                      |.++++++.
T Consensus        97 V~~a~~~~~  105 (108)
T 2jvo_A           97 VVYSKLPAK  105 (108)
T ss_dssp             EESCSCCC-
T ss_pred             EEEecCCCC
Confidence            999987654

>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=99.80  E-value=6.8e-20  Score=124.72  Aligned_cols=83  Identities=18%  Similarity=0.247  Sum_probs=74.0

Q ss_pred             hhCCCCeEEEcCCCCC-CCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCC--ceeCCeEE
Q psy2141          28 EAKLYNRIYVASIHPD-LTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNL--FDLGGQYL  104 (173)
Q Consensus        28 ~~~~~~~l~V~nLp~~-~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g--~~i~g~~l  104 (173)
                      ...+.++|||+|||++ +++++|+++|++||.|..+.+++.      ||||||+|.+.++|++|++.|++  ..+.|++|
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l   94 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   94 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            3567899999999998 999999999999999999999754      79999999999999999998864  56999999


Q ss_pred             EEEEeeCCCCCC
Q psy2141         105 RVGRAITPPNAL  116 (173)
Q Consensus       105 ~v~~a~~~~~~~  116 (173)
                      +|.+++.+....
T Consensus        95 ~V~~a~~~~~~~  106 (112)
T 1x4f_A           95 KVDLSEKYKKLV  106 (112)
T ss_dssp             EEEEECSCSSSS
T ss_pred             EEEECccccccc
Confidence            999998765544

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=5.9e-19  Score=115.79  Aligned_cols=80  Identities=23%  Similarity=0.493  Sum_probs=73.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+.+        +||||+|.+.++|++|++.||+..+.|+.|+|+++
T Consensus         8 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   79 (92)
T 2dgt_A            8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS   79 (92)
T ss_dssp             CSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            4678999999999999999999999999999999963        49999999999999999999999999999999999


Q ss_pred             eCCCCCCC
Q psy2141         110 ITPPNALH  117 (173)
Q Consensus       110 ~~~~~~~~  117 (173)
                      ++++....
T Consensus        80 ~~~~~~~~   87 (92)
T 2dgt_A           80 TSRLRTAS   87 (92)
T ss_dssp             SCCCSCCC
T ss_pred             cCCCCCCC
Confidence            87655543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=5e-19  Score=115.70  Aligned_cols=78  Identities=21%  Similarity=0.401  Sum_probs=72.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+++.+        +||||+|.+.++|++|++.|||..+.|++|+|.++
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 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS   78 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            5688999999999999999999999999999999963        49999999999999999999999999999999999


Q ss_pred             eCCCCC
Q psy2141         110 ITPPNA  115 (173)
Q Consensus       110 ~~~~~~  115 (173)
                      ++....
T Consensus        79 ~~~~~~   84 (90)
T 2dnp_A           79 TKGQKK   84 (90)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876443

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.80  E-value=3.3e-19  Score=118.93  Aligned_cols=76  Identities=29%  Similarity=0.429  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||.++++++|+++|++||.|..+++.+      ++|||||+|.+.++|++|++.|||..++|+.|+|.|+
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   98 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            4478999999999999999999999999999999974      4799999999999999999999999999999999998


Q ss_pred             eC
Q psy2141         110 IT  111 (173)
Q Consensus       110 ~~  111 (173)
                      ++
T Consensus        99 ~~  100 (101)
T 2la4_A           99 KE  100 (101)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.80  E-value=6.3e-20  Score=122.63  Aligned_cols=83  Identities=25%  Similarity=0.512  Sum_probs=76.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+++++++ +|+++|||||+|.+.++|++|++  ++..++|+.|.|.++
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            356899999999999999999999999999999999997 99999999999999999999998  999999999999999


Q ss_pred             eCCCCC
Q psy2141         110 ITPPNA  115 (173)
Q Consensus       110 ~~~~~~  115 (173)
                      .++...
T Consensus        84 ~~~~~~   89 (102)
T 2xs2_A           84 IRKQNL   89 (102)
T ss_dssp             EECC--
T ss_pred             CcCcch
Confidence            865443

>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=3.1e-19  Score=128.39  Aligned_cols=97  Identities=23%  Similarity=0.366  Sum_probs=87.1

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY   81 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f   81 (173)
                      ++|+.|+|.++....           ...+.++|||+|||..+++++|+++|++||.|..+.+.+++.+|+++|+|||+|
T Consensus        70 ~~g~~l~v~~~~~~~-----------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f  138 (168)
T 1b7f_A           70 VRNKRLKVSYARPGG-----------ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRY  138 (168)
T ss_dssp             ETTEECEEEECCCCS-----------STTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEE
T ss_pred             eCCcEEEEEecCCCc-----------ccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEE
Confidence            578999998875321           124578999999999999999999999999999999999988999999999999


Q ss_pred             cCHHHHHHHHHhcCCceeCC--eEEEEEEe
Q psy2141          82 ETKQASNEAISSMNLFDLGG--QYLRVGRA  109 (173)
Q Consensus        82 ~~~~~a~~a~~~l~g~~i~g--~~l~v~~a  109 (173)
                      .+.++|.+|++.|||..+.|  ++|+|++|
T Consensus       139 ~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          139 NKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             SSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            99999999999999999988  99999985

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.80  E-value=2.2e-19  Score=119.80  Aligned_cols=79  Identities=18%  Similarity=0.442  Sum_probs=73.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCC
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITP  112 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~  112 (173)
                      ++|||+|||.++++++|+++|++||.|..+.+.++     ++|||||+|.+.++|++|++.|||..+.|+.|+|.+++++
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            58999999999999999999999999999999887     6899999999999999999999999999999999999877


Q ss_pred             CCCC
Q psy2141         113 PNAL  116 (173)
Q Consensus       113 ~~~~  116 (173)
                      +...
T Consensus        76 ~~~~   79 (101)
T 2hvz_A           76 PRRS   79 (101)
T ss_dssp             CCSS
T ss_pred             CCcc
Confidence            6543

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.80  E-value=1.2e-19  Score=136.39  Aligned_cols=100  Identities=26%  Similarity=0.422  Sum_probs=86.1

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY   81 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f   81 (173)
                      ++||.|++.++....         .......++|||+|||..+++++|+++|++||.|..++|++++  +.++|||||+|
T Consensus        82 ~~g~~i~~~~~~~~~---------~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f  150 (213)
T 4f02_A           82 IKGKPVRIMWSQRDP---------SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHF  150 (213)
T ss_dssp             ETTEECEEEECCCCT---------HHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEE
T ss_pred             cCCcccccccccccc---------cccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEe
Confidence            568888887765211         1122356899999999999999999999999999999999984  45799999999


Q ss_pred             cCHHHHHHHHHhcCCceeCCeEEEEEEeeCC
Q psy2141          82 ETKQASNEAISSMNLFDLGGQYLRVGRAITP  112 (173)
Q Consensus        82 ~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~  112 (173)
                      .+.++|++|++.|||..|+|++|+|.+++++
T Consensus       151 ~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          151 ETQEAAERAIEKMNGMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             SSHHHHHHHHHHHTTCEETTEECEEEECCCH
T ss_pred             CCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            9999999999999999999999999998764

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.80  E-value=1.4e-19  Score=119.56  Aligned_cols=81  Identities=16%  Similarity=0.306  Sum_probs=73.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||..+++++|+++|++||.|..+     ..++.++|||||+|.+.++|++|++.|+|..+.|++|+|.++
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            467899999999999999999999999988777     247889999999999999999999999999999999999999


Q ss_pred             eCCCCC
Q psy2141         110 ITPPNA  115 (173)
Q Consensus       110 ~~~~~~  115 (173)
                      .++...
T Consensus        89 ~~~~~~   94 (96)
T 1fjc_A           89 GEKGGT   94 (96)
T ss_dssp             SSSCCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.80  E-value=2.8e-19  Score=129.81  Aligned_cols=98  Identities=14%  Similarity=0.276  Sum_probs=85.1

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY   81 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f   81 (173)
                      ++|++|+|.++......         ...+.++|||+|||..+++++|+++|++||.|..+     ..++.++|||||+|
T Consensus        78 ~~g~~l~v~~~~~~~~~---------~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f  143 (175)
T 1fje_B           78 VFGNEIKLEKPKGRDSK---------KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEF  143 (175)
T ss_dssp             ETTEEEEEECCCCSSCS---------TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEEC
T ss_pred             eCCeEEEEecCCCcccc---------ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEE
Confidence            67999999988643211         12357899999999999999999999999988776     35788999999999


Q ss_pred             cCHHHHHHHHHhcCCceeCCeEEEEEEeeCCC
Q psy2141          82 ETKQASNEAISSMNLFDLGGQYLRVGRAITPP  113 (173)
Q Consensus        82 ~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~~  113 (173)
                      .+.++|.+|++.|||..++|++|+|+|+.+++
T Consensus       144 ~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k~  175 (175)
T 1fje_B          144 KSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG  175 (175)
T ss_dssp             SSHHHHHHHHHHHTEEEETTEEEEEEECSSCC
T ss_pred             CCHHHHHHHHHHhCCCEECCeEEEEEecCCCC
Confidence            99999999999999999999999999998754

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=8.8e-19  Score=116.47  Aligned_cols=80  Identities=21%  Similarity=0.323  Sum_probs=72.9

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhcc--CceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAF--GPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV  106 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~--G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v  106 (173)
                      ..+.++|||+|||.++++++|+++|++|  |.|..+++.        +|||||+|.+.++|++|++.|||..+.|++|+|
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            3568999999999999999999999999  999998874        679999999999999999999999999999999


Q ss_pred             EEeeCCCCCC
Q psy2141         107 GRAITPPNAL  116 (173)
Q Consensus       107 ~~a~~~~~~~  116 (173)
                      .+++++....
T Consensus        84 ~~a~~~~~~~   93 (99)
T 2cpd_A           84 TLAKPVDKDS   93 (99)
T ss_dssp             ECCCCCCCCC
T ss_pred             EECCCCCCCC
Confidence            9998765543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=1.7e-19  Score=119.58  Aligned_cols=81  Identities=25%  Similarity=0.402  Sum_probs=72.8

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ....++|||+|||.++++++|+++|++||.|. +.++.+    +++|||||+|.+.++|++|++.|||..+.|++|+|.+
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   90 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVAL   90 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34578999999999999999999999999997 666543    5789999999999999999999999999999999999


Q ss_pred             eeCCCC
Q psy2141         109 AITPPN  114 (173)
Q Consensus       109 a~~~~~  114 (173)
                      +++++.
T Consensus        91 a~~~~~   96 (97)
T 2e5j_A           91 ARQQRD   96 (97)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            987643

>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=99.79  E-value=5.7e-20  Score=127.24  Aligned_cols=81  Identities=11%  Similarity=0.231  Sum_probs=74.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||+++++++|+++|+.||.|..+.++.+..+|+++|||||+|.+.++|++|++ ||+..++|+.|.|.++
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            457899999999999999999999999999886666666799999999999999999999999 9999999999999998


Q ss_pred             eC
Q psy2141         110 IT  111 (173)
Q Consensus       110 ~~  111 (173)
                      ..
T Consensus       102 ~~  103 (124)
T 1wel_A          102 TK  103 (124)
T ss_dssp             CH
T ss_pred             CH
Confidence            64

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.79  E-value=4.1e-20  Score=124.88  Aligned_cols=81  Identities=17%  Similarity=0.171  Sum_probs=75.9

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCc---eeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGP---IKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLR  105 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~---v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~  105 (173)
                      ....++|||+|||+++++++|+++|+.||.   |..+.+++++. |+++|||||+|.+.++|++|++ +|+..++|+.|+
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            356889999999999999999999999998   89999999976 9999999999999999999998 999999999999


Q ss_pred             EEEeeC
Q psy2141         106 VGRAIT  111 (173)
Q Consensus       106 v~~a~~  111 (173)
                      |.++.+
T Consensus        86 V~~a~~   91 (107)
T 2lmi_A           86 VYEINN   91 (107)
T ss_dssp             CEECCH
T ss_pred             EEECCH
Confidence            999764

>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=99.79  E-value=3.1e-19  Score=121.71  Aligned_cols=81  Identities=19%  Similarity=0.420  Sum_probs=74.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||..+++++|+++|++||.|..+.++++   +.++|||||+|.+.++|++|++.|||..++|+.|+|.++
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   456999999999999999999999999999999999998


Q ss_pred             eCCC
Q psy2141         110 ITPP  113 (173)
Q Consensus       110 ~~~~  113 (173)
                      .+..
T Consensus        83 ~~~~   86 (115)
T 3lqv_A           83 NANR   86 (115)
T ss_dssp             CHHH
T ss_pred             cCCh
Confidence            7543

>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=99.79  E-value=9.1e-19  Score=125.59  Aligned_cols=84  Identities=25%  Similarity=0.479  Sum_probs=79.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      +.++|||+|||.++++++|+++|+.||.|..+++++++.+|+++|||||+|.+.++|++|++.|+|..+.|++|+|.++.
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            35899999999999999999999999999999999998899999999999999999999999999999999999999987


Q ss_pred             CCCC
Q psy2141         111 TPPN  114 (173)
Q Consensus       111 ~~~~  114 (173)
                      +...
T Consensus        81 ~~~~   84 (167)
T 1fxl_A           81 PSSA   84 (167)
T ss_dssp             CCCG
T ss_pred             CCcc
Confidence            6543

>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=99.79  E-value=6.9e-19  Score=126.57  Aligned_cols=85  Identities=22%  Similarity=0.450  Sum_probs=80.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      +.++|||+|||.++++++|+++|++||.|..+++++++.+|+++|||||+|.+.++|++|++.|+|..+.|++|+|.++.
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            56899999999999999999999999999999999998899999999999999999999999999999999999999988


Q ss_pred             CCCCC
Q psy2141         111 TPPNA  115 (173)
Q Consensus       111 ~~~~~  115 (173)
                      +....
T Consensus        82 ~~~~~   86 (168)
T 1b7f_A           82 PGGES   86 (168)
T ss_dssp             CCSST
T ss_pred             CCccc
Confidence            65443

>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=99.79  E-value=6.9e-19  Score=126.22  Aligned_cols=97  Identities=19%  Similarity=0.342  Sum_probs=85.7

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY   81 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f   81 (173)
                      ++|+.|+|.++....           ...+.++|||+|||..+++++|+++|++||.|..+++..++.+|.++|||||+|
T Consensus        69 ~~g~~l~v~~~~~~~-----------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f  137 (167)
T 1fxl_A           69 LQTKTIKVSYARPSS-----------ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRF  137 (167)
T ss_dssp             ETTEECEEEECCCCC-----------GGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEE
T ss_pred             cCCceEEEEecCCCc-----------ccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEe
Confidence            578889988765211           124578999999999999999999999999999999999988999999999999


Q ss_pred             cCHHHHHHHHHhcCCceeCCeE--EEEEEe
Q psy2141          82 ETKQASNEAISSMNLFDLGGQY--LRVGRA  109 (173)
Q Consensus        82 ~~~~~a~~a~~~l~g~~i~g~~--l~v~~a  109 (173)
                      .+.++|.+|++.|||..+.|+.  |+|+||
T Consensus       138 ~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          138 DKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             SSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            9999999999999999999965  888875

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.79  E-value=3.6e-19  Score=117.81  Aligned_cols=80  Identities=18%  Similarity=0.359  Sum_probs=71.8

Q ss_pred             hCCCCeEEEcCCCC-CCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q psy2141          29 AKLYNRIYVASIHP-DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG  107 (173)
Q Consensus        29 ~~~~~~l~V~nLp~-~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~  107 (173)
                      ..+.++|||+|||. .+++++|+++|++||.|..+.+.        +|||||+|.+.++|++|++.|||..+.|++|+|.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   78 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45789999999998 99999999999999999999983        6899999999999999999999999999999999


Q ss_pred             EeeCCCCCC
Q psy2141         108 RAITPPNAL  116 (173)
Q Consensus       108 ~a~~~~~~~  116 (173)
                      ++++.+...
T Consensus        79 ~a~~~~~~~   87 (96)
T 2kvi_A           79 VSSSNARPQ   87 (96)
T ss_dssp             EEECCCC--
T ss_pred             EcCcCCCCC
Confidence            998765543

>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=99.78  E-value=3.5e-19  Score=121.14  Aligned_cols=77  Identities=13%  Similarity=0.142  Sum_probs=71.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      +..++|||+|||.++++++|+++|++||.|..|.+..      ++|||||+|.+.++|++|++.|||..+.|++|+|.|+
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   81 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            3468999999999999999999999999999999875      4789999999999999999999999999999999999


Q ss_pred             eCC
Q psy2141         110 ITP  112 (173)
Q Consensus       110 ~~~  112 (173)
                      ...
T Consensus        82 ~~~   84 (111)
T 1whx_A           82 PIG   84 (111)
T ss_dssp             ETT
T ss_pred             CCC
Confidence            864

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=1.3e-18  Score=118.10  Aligned_cols=77  Identities=19%  Similarity=0.299  Sum_probs=72.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeC
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAIT  111 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~  111 (173)
                      .++|||+|||+++++++|+++|+.| .|..+.|++++ +|+++|||||+|.+.++|++|+ .+|+..++|+.|.|..+..
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 4999999999999999999999 6899999999999988754

>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=99.78  E-value=7.8e-19  Score=119.68  Aligned_cols=82  Identities=16%  Similarity=0.181  Sum_probs=73.5

Q ss_pred             hCCCCeEEE--cCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCcee-----CC
Q psy2141          29 AKLYNRIYV--ASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDL-----GG  101 (173)
Q Consensus        29 ~~~~~~l~V--~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i-----~g  101 (173)
                      ..+.++|||  |||++++++++|+++|++||.|..+.+..+      ||||||+|.+.++|++|++.|||.++     .|
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCC
Confidence            456889999  779999999999999999999999988643      79999999999999999999999998     68


Q ss_pred             eEEEEEEeeCCCCCC
Q psy2141         102 QYLRVGRAITPPNAL  116 (173)
Q Consensus       102 ~~l~v~~a~~~~~~~  116 (173)
                      ++|.|.+++..+...
T Consensus        96 ~~l~v~~a~~~p~~~  110 (114)
T 2cq2_A           96 ITLYLNFVEKVQWSG  110 (114)
T ss_dssp             EECEEEEESCCCCSS
T ss_pred             cEEEEEecccCcccC
Confidence            999999998665544

>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=99.78  E-value=7e-19  Score=115.60  Aligned_cols=80  Identities=20%  Similarity=0.414  Sum_probs=71.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCc-eeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCC-ceeCCeEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGP-IKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNL-FDLGGQYLRVG  107 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~-v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g-~~i~g~~l~v~  107 (173)
                      .+.++|||+|||.++++++|+++|++||. |..+.+.       ++|||||+|.+.++|++|++.||| ..++|++|+|.
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            46789999999999999999999999999 6666552       479999999999999999999999 99999999999


Q ss_pred             EeeCCCCCC
Q psy2141         108 RAITPPNAL  116 (173)
Q Consensus       108 ~a~~~~~~~  116 (173)
                      +++++....
T Consensus        79 ~a~~~~~~~   87 (93)
T 2cqh_A           79 YSVSKKLRS   87 (93)
T ss_dssp             ECCCCCCCC
T ss_pred             EccCccccC
Confidence            998765543

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.78  E-value=7.5e-19  Score=121.22  Aligned_cols=78  Identities=15%  Similarity=0.122  Sum_probs=71.6

Q ss_pred             CeEEEcCC----CCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcC----HHH----HHHHHH--hcCCce
Q psy2141          33 NRIYVASI----HPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYET----KQA----SNEAIS--SMNLFD   98 (173)
Q Consensus        33 ~~l~V~nL----p~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~----~~~----a~~a~~--~l~g~~   98 (173)
                      .+|||+||    |+.+++.+|+.+|+.||.|.++.++.|+.||.++|||||+|.+    .++    |.+|+.  .|+|..
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    9999999999999999999999999999999999999999996    333    788988  789999


Q ss_pred             eCCeEEEEEEee
Q psy2141          99 LGGQYLRVGRAI  110 (173)
Q Consensus        99 i~g~~l~v~~a~  110 (173)
                      |+|++|+|.+.+
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            999999999865

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=1.7e-18  Score=114.07  Aligned_cols=80  Identities=19%  Similarity=0.299  Sum_probs=70.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||.++++++|+++|++||.|..|  +.++.+++   ||||+|.+.++|++|++ |||..++|+.|+|+++
T Consensus         6 ~~~~~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            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            356899999999999999999999999999987  55555555   99999999999999999 9999999999999988


Q ss_pred             eCCCCC
Q psy2141         110 ITPPNA  115 (173)
Q Consensus       110 ~~~~~~  115 (173)
                      .++...
T Consensus        80 ~~~~~~   85 (94)
T 2e5g_A           80 EQKEFQ   85 (94)
T ss_dssp             CCSCCC
T ss_pred             CcCCCC
Confidence            655443

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.77  E-value=8.5e-19  Score=128.62  Aligned_cols=82  Identities=16%  Similarity=0.320  Sum_probs=78.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||..+++++|+++|++||.|..|.+..++ ++.++|||||+|.+.++|++|++.|||..+.|++|+|.++
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            456899999999999999999999999999999999997 9999999999999999999999999999999999999998


Q ss_pred             eCC
Q psy2141         110 ITP  112 (173)
Q Consensus       110 ~~~  112 (173)
                      ...
T Consensus       165 ~~~  167 (177)
T 2f3j_A          165 ASQ  167 (177)
T ss_dssp             SSG
T ss_pred             cCC
Confidence            754

>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=99.77  E-value=1.7e-19  Score=127.65  Aligned_cols=85  Identities=24%  Similarity=0.301  Sum_probs=73.5

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEE--EccC---CCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCK--LQQG---SSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQY  103 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~--i~~~---~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~  103 (173)
                      ..+.++|||+|||+.+++++|+++|++||.|..+.  ++.+   ..+|+++|||||+|.+.++|.+|++.|||..+.|++
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            35678999999999999999999999999987641  1111   247889999999999999999999999999999999


Q ss_pred             EEEEEeeCCC
Q psy2141         104 LRVGRAITPP  113 (173)
Q Consensus       104 l~v~~a~~~~  113 (173)
                      |+|.++++..
T Consensus       122 l~V~~a~~~~  131 (143)
T 3egn_A          122 MVVQFARSAR  131 (143)
T ss_dssp             CEEEECCCSC
T ss_pred             EEEEECCCCC
Confidence            9999997643

>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=99.77  E-value=1.4e-18  Score=136.02  Aligned_cols=107  Identities=19%  Similarity=0.278  Sum_probs=87.7

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCC-CCHHHHHHHhhccCceeEEEEccCCC-CCCcceEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPD-LTEEDIKSVFEAFGPIKYCKLQQGSS-PHRHKGYGFI   79 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~-~~e~~L~~~F~~~G~v~~~~i~~~~~-~g~~~g~afv   79 (173)
                      ++|+.|+|.++........    ......+.++|||+|||.. +++++|+++|++||.|..++++++.. +|.++|||||
T Consensus       184 ~~g~~l~v~~a~~~~~~~~----~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV  259 (292)
T 2ghp_A          184 IEGYTLVTKVSNPLEKSKR----TDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFM  259 (292)
T ss_dssp             ETTEECEEEECCCC-------------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEE
T ss_pred             eCCcEEEEEECCCCccccc----ccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEE
Confidence            6789999987653221111    1123456799999999999 99999999999999999999999865 5999999999


Q ss_pred             EEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCCC
Q psy2141          80 EYETKQASNEAISSMNLFDLGGQYLRVGRAITPP  113 (173)
Q Consensus        80 ~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~~  113 (173)
                      +|.+.++|.+|+ .|||..++|++|+|.|+.+++
T Consensus       260 ~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k~  292 (292)
T 2ghp_A          260 VFENKDSAERAL-QMNRSLLGNREISVSLADKKP  292 (292)
T ss_dssp             EESSHHHHHHHG-GGTTEEETTEEEEEEECCCCC
T ss_pred             EeCCHHHHHHHH-HhcCCEECCcEEEEEEecCCC
Confidence            999999999999 999999999999999998764

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.5e-18  Score=120.17  Aligned_cols=80  Identities=16%  Similarity=0.208  Sum_probs=73.7

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCce----eEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPI----KYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYL  104 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v----~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l  104 (173)
                      ....++|||+|||+++++++|+++|++||.|    ..|.|+++ .+|+++|||||+|.+.++|++|++. |+..++|+.|
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i   97 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYI   97 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEE
Confidence            3567899999999999999999999999875    68999998 4899999999999999999999986 9999999999


Q ss_pred             EEEEee
Q psy2141         105 RVGRAI  110 (173)
Q Consensus       105 ~v~~a~  110 (173)
                      .|..+.
T Consensus        98 ~V~~a~  103 (123)
T 2dha_A           98 ELFRST  103 (123)
T ss_dssp             CCEEEC
T ss_pred             EEEECC
Confidence            998875

>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=99.77  E-value=3.7e-18  Score=123.14  Aligned_cols=79  Identities=15%  Similarity=0.161  Sum_probs=71.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC--eEEEEEEe
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG--QYLRVGRA  109 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g--~~l~v~~a  109 (173)
                      ..+|||+||++.+++++|+++|++||.|.++.+..+    .++|||||+|.+.++|++|++.|||..|.|  ++|+|+|+
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~A  121 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            457899999999999999999999999999998654    257999999999999999999999999965  99999999


Q ss_pred             eCCCC
Q psy2141         110 ITPPN  114 (173)
Q Consensus       110 ~~~~~  114 (173)
                      +++..
T Consensus       122 k~~~l  126 (164)
T 1sjr_A          122 KLTSL  126 (164)
T ss_dssp             SSSSC
T ss_pred             cCCcc
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=99.76  E-value=2e-18  Score=112.43  Aligned_cols=76  Identities=20%  Similarity=0.367  Sum_probs=70.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||+++++++|+++|++| .|..+++.      +++|||||+|.+.++|++|++.|||..++|++|+|+++
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   75 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEc
Confidence            357899999999999999999999999 99999884      46899999999999999999999999999999999998


Q ss_pred             eCC
Q psy2141         110 ITP  112 (173)
Q Consensus       110 ~~~  112 (173)
                      ...
T Consensus        76 ~~~   78 (88)
T 1wg1_A           76 PTD   78 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.76  E-value=2.3e-18  Score=134.26  Aligned_cols=104  Identities=22%  Similarity=0.318  Sum_probs=90.4

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCC-CHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDL-TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIE   80 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~-~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~   80 (173)
                      ++|+.|+|.++....        ......+.++|||+|||..+ ++++|+++|+.||.|..+++..++ +|+++|+|||+
T Consensus       162 ~~g~~i~v~~a~~~~--------~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~  232 (284)
T 3smz_A          162 LGPRTLYVHWTDAGQ--------LTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLE  232 (284)
T ss_dssp             ETTEECEEEECCGGG--------CCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEE
T ss_pred             eCCcEEEEEECCCCC--------CCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEE
Confidence            688999998875321        11223568899999999995 999999999999999999999985 89999999999


Q ss_pred             EcCHHHHHHHHHhcCCceeCCeEEEEEEeeCCCC
Q psy2141          81 YETKQASNEAISSMNLFDLGGQYLRVGRAITPPN  114 (173)
Q Consensus        81 f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~~~  114 (173)
                      |.+.++|.+|++.|||..++|++|+|.++.++..
T Consensus       233 f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          233 YETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             CSSHHHHHHHHHHHTTCEETTEECEEEECCSSSC
T ss_pred             eCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCc
Confidence            9999999999999999999999999999976543

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=1.5e-18  Score=114.52  Aligned_cols=79  Identities=20%  Similarity=0.365  Sum_probs=72.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEE-EEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYC-KLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~-~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ...++|||+|||+++++++|+++|++||.|..+ .++.++.++    .|||+|.+.++|++|++.|||..++|++|+|.+
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 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            357899999999999999999999999999999 588876443    399999999999999999999999999999999


Q ss_pred             eeCC
Q psy2141         109 AITP  112 (173)
Q Consensus       109 a~~~  112 (173)
                      +.++
T Consensus        89 a~~~   92 (96)
T 2e44_A           89 IPDE   92 (96)
T ss_dssp             CCCC
T ss_pred             cCcc
Confidence            9876

>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=99.76  E-value=3.1e-19  Score=126.04  Aligned_cols=83  Identities=17%  Similarity=0.213  Sum_probs=75.3

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ....++|||+|||+++++++|+++|++|| |..|.|++++. |+++|||||+|.+.++|++|+ .+|+..++|+.|+|.+
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~  119 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFL  119 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEE
Confidence            35678999999999999999999999999 77999999975 999999999999999999999 8899999999999999


Q ss_pred             eeCCCC
Q psy2141         109 AITPPN  114 (173)
Q Consensus       109 a~~~~~  114 (173)
                      +.+...
T Consensus       120 a~~~~~  125 (139)
T 2hgn_A          120 NSTTGA  125 (139)
T ss_dssp             CCCSCC
T ss_pred             CCCCCC
Confidence            876544

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=5.6e-18  Score=112.19  Aligned_cols=79  Identities=23%  Similarity=0.363  Sum_probs=71.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+||  ++++++|+++|++||.|..+.+.      +++|||||+|.+.++|++|++.|||..+.|++|+|.++
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a   84 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   84 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECC
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            46789999996  89999999999999999999984      35899999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      ++++...
T Consensus        85 ~~~~~~~   91 (97)
T 1x5p_A           85 RKQPMLD   91 (97)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            8765543

>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=99.76  E-value=3.4e-18  Score=141.36  Aligned_cols=84  Identities=25%  Similarity=0.452  Sum_probs=79.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      +.++|||+|||..+++++|+.+|++||.|..|.|+.++.+|+++|||||+|.+.++|++||+.|||..|.|+.|.|.++.
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~  180 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  180 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            45799999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             CCCC
Q psy2141         111 TPPN  114 (173)
Q Consensus       111 ~~~~  114 (173)
                      +...
T Consensus       181 ~~~~  184 (437)
T 3pgw_S          181 GRTV  184 (437)
T ss_pred             CCCC
Confidence            6543

>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=99.76  E-value=3.5e-18  Score=125.91  Aligned_cols=83  Identities=20%  Similarity=0.545  Sum_probs=77.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|+.||.|..+.+++++.+|.++|||||+|.+.++|++|++. ++..+.|+.|.|.++
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~   89 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRA   89 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecc
Confidence            4578999999999999999999999999999999999998999999999999999999999977 899999999999998


Q ss_pred             eCCC
Q psy2141         110 ITPP  113 (173)
Q Consensus       110 ~~~~  113 (173)
                      ....
T Consensus        90 ~~~~   93 (196)
T 1l3k_A           90 VSRE   93 (196)
T ss_dssp             CC--
T ss_pred             cCcc
Confidence            7653

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.76  E-value=7.7e-18  Score=117.24  Aligned_cols=81  Identities=15%  Similarity=0.195  Sum_probs=72.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceE-EEEEEcCHHHHHHHHHhcCCceeCC--eEEEEE
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGY-GFIEYETKQASNEAISSMNLFDLGG--QYLRVG  107 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~-afv~f~~~~~a~~a~~~l~g~~i~g--~~l~v~  107 (173)
                      +--.|||+||++.+++++|+++|++||.|.++.+..+     .+|| |||+|.+.++|++|++.|||..|.|  ++|+|+
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~  101 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  101 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEE
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEE
Confidence            3457889999999999999999999999999988764     3688 9999999999999999999999988  999999


Q ss_pred             EeeCCCCCC
Q psy2141         108 RAITPPNAL  116 (173)
Q Consensus       108 ~a~~~~~~~  116 (173)
                      |+++..-..
T Consensus       102 ~ak~~~l~v  110 (130)
T 3zzy_A          102 FSKLTSLNV  110 (130)
T ss_dssp             ECSCSSCCC
T ss_pred             ecCCCceeE
Confidence            998764433

>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=99.76  E-value=5.1e-18  Score=110.95  Aligned_cols=77  Identities=14%  Similarity=0.344  Sum_probs=63.3

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCce--eCCeEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFD--LGGQYLRV  106 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~--i~g~~l~v  106 (173)
                      ..+..+|||+|||+++++++|+++|++||.|.+++++++     ++|||||+|.+.++|++    |++..  +.|++|.|
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v   78 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHI   78 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEE
Confidence            357899999999999999999999999999999999875     69999999999999984    45544  56999999


Q ss_pred             EEeeCCCC
Q psy2141         107 GRAITPPN  114 (173)
Q Consensus       107 ~~a~~~~~  114 (173)
                      .++.++..
T Consensus        79 ~~a~~k~~   86 (89)
T 3d2w_A           79 SNAEPKHN   86 (89)
T ss_dssp             EECC----
T ss_pred             EEcCCCCc
Confidence            99987644

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=7.3e-18  Score=114.98  Aligned_cols=76  Identities=20%  Similarity=0.460  Sum_probs=66.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCC---CCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSP---HRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV  106 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~---g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v  106 (173)
                      ...++|||+|||+++++++|+++|++||.|. +.++.++.+   |+++|||||+|.+.++|++|++.|+  .++|+.+.+
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            4679999999999999999999999999999 888888777   7999999999999999999999983  355555555


Q ss_pred             EE
Q psy2141         107 GR  108 (173)
Q Consensus       107 ~~  108 (173)
                      ..
T Consensus        83 ~~   84 (114)
T 2dnl_A           83 VS   84 (114)
T ss_dssp             EC
T ss_pred             cc
Confidence            43

>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=99.75  E-value=1.4e-18  Score=120.68  Aligned_cols=80  Identities=15%  Similarity=0.260  Sum_probs=72.7

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCcee--EEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIK--YCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV  106 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~--~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v  106 (173)
                      ..+.++|||+|||+++++++|+++|++| .|.  .|+|++++. |+++|||||+|.+.++|++|++. ++..++|+.|+|
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V  115 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-HKERIGHRYIEV  115 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEE
Confidence            3467899999999999999999999999 576  899999976 99999999999999999999975 779999999999


Q ss_pred             EEeeC
Q psy2141         107 GRAIT  111 (173)
Q Consensus       107 ~~a~~  111 (173)
                      .++..
T Consensus       116 ~~a~~  120 (126)
T 2hgm_A          116 FKSSQ  120 (126)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            88754

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.75  E-value=8.3e-18  Score=120.42  Aligned_cols=81  Identities=22%  Similarity=0.442  Sum_probs=75.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCC
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITP  112 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~  112 (173)
                      ++|||+|||.++++++|+++|++||.|..+++.+++ +++++|||||+|.+.++|++|++.|+|..+.|+.|+|.++.+.
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            689999999999999999999999999999999996 5789999999999999999999999999999999999998765


Q ss_pred             CC
Q psy2141         113 PN  114 (173)
Q Consensus       113 ~~  114 (173)
                      ..
T Consensus        80 ~~   81 (166)
T 3md3_A           80 QQ   81 (166)
T ss_dssp             CC
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=99.75  E-value=2.8e-18  Score=112.23  Aligned_cols=79  Identities=10%  Similarity=0.141  Sum_probs=69.6

Q ss_pred             CCCCe-EEEcCCCCCCCHHH----HHHHhhcc-CceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeE
Q psy2141          30 KLYNR-IYVASIHPDLTEED----IKSVFEAF-GPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQY  103 (173)
Q Consensus        30 ~~~~~-l~V~nLp~~~~e~~----L~~~F~~~-G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~  103 (173)
                      .+..+ |||+|||+.+++++    |+++|++| |+|.++       ++   |+|||+|.+.++|++|++.|+|..+.|++
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~   75 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNR   75 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSC
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCce
Confidence            34566 99999999999987    56899999 599998       33   99999999999999999999999999999


Q ss_pred             EEEEEeeCCCCCCCC
Q psy2141         104 LRVGRAITPPNALHS  118 (173)
Q Consensus       104 l~v~~a~~~~~~~~~  118 (173)
                      |+|++++..++....
T Consensus        76 i~v~~A~~~sd~~~~   90 (96)
T 2diu_A           76 IIVSFTPKNRELCET   90 (96)
T ss_dssp             CEEESSCCSCCCCCC
T ss_pred             EEEEecCCCcceeEe
Confidence            999999987766543

>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=99.75  E-value=7.3e-18  Score=126.30  Aligned_cols=77  Identities=19%  Similarity=0.259  Sum_probs=72.4

Q ss_pred             CCCeEEEcCCC-CCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          31 LYNRIYVASIH-PDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        31 ~~~~l~V~nLp-~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      +.++|||+||| +.+++++|+++|++||.|.++++++++     +|||||+|.+.++|++|++.|||..+.|++|+|.++
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 899999999999999999999998763     799999999999999999999999999999999998


Q ss_pred             eCC
Q psy2141         110 ITP  112 (173)
Q Consensus       110 ~~~  112 (173)
                      +..
T Consensus        78 ~~~   80 (205)
T 3tyt_A           78 KQP   80 (205)
T ss_dssp             SCS
T ss_pred             cCC
Confidence            754

>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=99.74  E-value=1e-17  Score=130.56  Aligned_cols=96  Identities=25%  Similarity=0.332  Sum_probs=87.6

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY   81 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f   81 (173)
                      ++|+.|+|.+..                 +.++|||+|||..+++++|+++|+.||.|..+.+++++.+|.++|||||+|
T Consensus        82 ~~g~~i~v~~~~-----------------~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f  144 (284)
T 3smz_A           82 LRERELSVQLQP-----------------TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEY  144 (284)
T ss_dssp             ETTEECEEEECC-----------------CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEE
T ss_pred             eCCeEEEEEecC-----------------CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEE
Confidence            567788887642                 458999999999999999999999999999999999988999999999999


Q ss_pred             cCHHHHHHHHHhcCCceeCCeEEEEEEeeCCCC
Q psy2141          82 ETKQASNEAISSMNLFDLGGQYLRVGRAITPPN  114 (173)
Q Consensus        82 ~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~~~  114 (173)
                      .+.++|.+|++.|+|..++|++|.|.++.+...
T Consensus       145 ~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~  177 (284)
T 3smz_A          145 MKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQL  177 (284)
T ss_dssp             SSHHHHHHHHHHHTTCEETTEECEEEECCGGGC
T ss_pred             CCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCC
Confidence            999999999999999999999999999976543

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.74  E-value=4.1e-18  Score=127.30  Aligned_cols=85  Identities=38%  Similarity=0.663  Sum_probs=76.4

Q ss_pred             hhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q psy2141          28 EAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG  107 (173)
Q Consensus        28 ~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~  107 (173)
                      ...+.++|||+|||.++++++|+++|+.||.|..+++++++.+|+++|||||+|.+.++|++|++.|++..+.|+.|+|.
T Consensus        24 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~  103 (216)
T 2qfj_A           24 ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVG  103 (216)
T ss_dssp             HHHHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEE
T ss_pred             ccCcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEe
Confidence            34567999999999999999999999999999999999998899999999999999999999999999999999999998


Q ss_pred             EeeCC
Q psy2141         108 RAITP  112 (173)
Q Consensus       108 ~a~~~  112 (173)
                      ++...
T Consensus       104 ~~~~~  108 (216)
T 2qfj_A          104 RPSNI  108 (216)
T ss_dssp             CCSCC
T ss_pred             cCCCc
Confidence            86543

>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=99.74  E-value=6.3e-18  Score=115.54  Aligned_cols=77  Identities=19%  Similarity=0.320  Sum_probs=67.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeE-----E
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQY-----L  104 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~-----l  104 (173)
                      ...++|||+|||+++++++|+++|++||.|..+.++.+       |||||+|.+.++|++|++.|||..|+|+.     |
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i   86 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   86 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEE
Confidence            35689999999999999999999999999999999765       89999999999999999999999999988     7


Q ss_pred             EEEEeeCCC
Q psy2141         105 RVGRAITPP  113 (173)
Q Consensus       105 ~v~~a~~~~  113 (173)
                      +|..+.+..
T Consensus        87 ~v~~~~~~~   95 (115)
T 3beg_B           87 RVKVDGPRS   95 (115)
T ss_dssp             EEEECC---
T ss_pred             EeccCCCCC
Confidence            777766543

>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=99.74  E-value=7.2e-18  Score=109.17  Aligned_cols=72  Identities=28%  Similarity=0.527  Sum_probs=67.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhcc----C-------ceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCce
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAF----G-------PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFD   98 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~----G-------~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~   98 (173)
                      .+.++|||+|||.++++++|+++|++|    |       .|..+.+.++      +|||||+|.+.++|++|+ .|||..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~   76 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGII   76 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCE
Confidence            457899999999999999999999999    8       8999998765      799999999999999999 999999


Q ss_pred             eCCeEEEEEE
Q psy2141          99 LGGQYLRVGR  108 (173)
Q Consensus        99 i~g~~l~v~~  108 (173)
                      +.|+.|+|++
T Consensus        77 ~~g~~l~V~r   86 (87)
T 2hzc_A           77 FQGQSLKIRR   86 (87)
T ss_dssp             ETTEECEEEC
T ss_pred             ECCeEEEEeC
Confidence            9999999975

>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=99.73  E-value=9.5e-18  Score=124.61  Aligned_cols=81  Identities=15%  Similarity=0.188  Sum_probs=74.0

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ....++|||+|||+++++++|+++|++||.|..+++.+++ +|.++|||||+|.+.++|++|+..++ ..++|++|.|.+
T Consensus       106 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~  183 (193)
T 2voo_A          106 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILF  183 (193)
T ss_dssp             HHHHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEE
T ss_pred             ccccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEE
Confidence            3457899999999999999999999999999999999985 69999999999999999999997765 599999999998


Q ss_pred             eeC
Q psy2141         109 AIT  111 (173)
Q Consensus       109 a~~  111 (173)
                      ++.
T Consensus       184 ~~~  186 (193)
T 2voo_A          184 KDD  186 (193)
T ss_dssp             TTT
T ss_pred             hHH
Confidence            764

>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=99.73  E-value=9.4e-18  Score=109.12  Aligned_cols=80  Identities=14%  Similarity=0.314  Sum_probs=68.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..++++++     ++|||||+|.+.++|++++..  ...+.|++|+|.++
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a   75 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEec
Confidence            35799999999999999999999999999999999865     689999999999999765322  34568999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      .++....
T Consensus        76 ~~~~~~~   82 (88)
T 1wf0_A           76 EPKHNSN   82 (88)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            8765544

>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=99.73  E-value=1.5e-17  Score=120.18  Aligned_cols=79  Identities=24%  Similarity=0.448  Sum_probs=73.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeC---CeEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLG---GQYLRV  106 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~---g~~l~v  106 (173)
                      .+.++|||+|||..+++++|+++|++||.|..+.+.+++ +|+++|||||+|.+.++|.+|++.|||..+.   +++|+|
T Consensus        93 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V  171 (175)
T 3nmr_A           93 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV  171 (175)
T ss_dssp             GGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEE
T ss_pred             CCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEE
Confidence            357899999999999999999999999999999999995 6999999999999999999999999998776   399999


Q ss_pred             EEe
Q psy2141         107 GRA  109 (173)
Q Consensus       107 ~~a  109 (173)
                      +|+
T Consensus       172 ~~a  174 (175)
T 3nmr_A          172 KFA  174 (175)
T ss_dssp             EEC
T ss_pred             Eec
Confidence            987

>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=99.73  E-value=2e-17  Score=128.69  Aligned_cols=76  Identities=14%  Similarity=0.320  Sum_probs=71.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeC-CeEEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLG-GQYLRVGR  108 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~-g~~l~v~~  108 (173)
                      .+.++|||+|||..+++++|+++|++||.|..++++.++     +|||||+|.+.++|.+|++.|||..+. |+.|+|+|
T Consensus       205 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~  279 (282)
T 3pgw_A          205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISF  279 (282)
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEE
Confidence            357889999999999999999999999999999998764     689999999999999999999999999 99999999


Q ss_pred             ee
Q psy2141         109 AI  110 (173)
Q Consensus       109 a~  110 (173)
                      ++
T Consensus       280 ak  281 (282)
T 3pgw_A          280 AK  281 (282)
T ss_pred             ec
Confidence            86

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.72  E-value=3.5e-17  Score=113.24  Aligned_cols=76  Identities=14%  Similarity=0.183  Sum_probs=68.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceE-EEEEEcCHHHHHHHHHhcCCceeCC--eEEEEEEee
Q psy2141          34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGY-GFIEYETKQASNEAISSMNLFDLGG--QYLRVGRAI  110 (173)
Q Consensus        34 ~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~-afv~f~~~~~a~~a~~~l~g~~i~g--~~l~v~~a~  110 (173)
                      .|||+||++.+++++|+++|++||.|.++.+...      .|| |||+|.+.++|++|++.|||..|.|  ++|+|.+++
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak  100 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR  100 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCS
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEec
Confidence            4789999999999999999999999999998652      276 9999999999999999999999987  699999998


Q ss_pred             CCCCC
Q psy2141         111 TPPNA  115 (173)
Q Consensus       111 ~~~~~  115 (173)
                      ++.-.
T Consensus       101 ~~~l~  105 (124)
T 2e5i_A          101 PTRLN  105 (124)
T ss_dssp             CSCCC
T ss_pred             CCcce
Confidence            76533

>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=99.72  E-value=4.4e-17  Score=123.63  Aligned_cols=78  Identities=24%  Similarity=0.379  Sum_probs=72.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccC-ceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeC-CeEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFG-PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLG-GQYLRVG  107 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G-~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~-g~~l~v~  107 (173)
                      .+.++|||+|||..+++++|+++|++|| .|..++++.+     .+|+|||+|.+.++|.+|++.|||..++ |++|+|.
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~  223 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  223 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEE
Confidence            4578999999999999999999999999 9999999664     3789999999999999999999999999 9999999


Q ss_pred             EeeCC
Q psy2141         108 RAITP  112 (173)
Q Consensus       108 ~a~~~  112 (173)
                      |++++
T Consensus       224 ~a~~~  228 (229)
T 2adc_A          224 FSKST  228 (229)
T ss_dssp             ECSSC
T ss_pred             EecCC
Confidence            98764

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.72  E-value=8.3e-17  Score=108.37  Aligned_cols=82  Identities=15%  Similarity=0.178  Sum_probs=73.3

Q ss_pred             CCCCeEEEcCCCC-----CCCHHHHHHHhhccCceeEEEEccCCCC-CCcceEEEEEEcCHHHHHHHHHhcCCceeCCeE
Q psy2141          30 KLYNRIYVASIHP-----DLTEEDIKSVFEAFGPIKYCKLQQGSSP-HRHKGYGFIEYETKQASNEAISSMNLFDLGGQY  103 (173)
Q Consensus        30 ~~~~~l~V~nLp~-----~~~e~~L~~~F~~~G~v~~~~i~~~~~~-g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~  103 (173)
                      .++++|+|.||..     +-++++|++.|++||.|.++.+.+++.+ ++++||+||+|.+.++|.+|++.|||..++|+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            5789999999963     2368999999999999999999998644 688999999999999999999999999999999


Q ss_pred             EEEEEeeC
Q psy2141         104 LRVGRAIT  111 (173)
Q Consensus       104 l~v~~a~~  111 (173)
                      |.|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999864

>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=99.72  E-value=4.4e-17  Score=126.82  Aligned_cols=84  Identities=20%  Similarity=0.437  Sum_probs=76.9

Q ss_pred             hhCCCCeEEEcCCCCCCCHHHHH----HHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeE
Q psy2141          28 EAKLYNRIYVASIHPDLTEEDIK----SVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQY  103 (173)
Q Consensus        28 ~~~~~~~l~V~nLp~~~~e~~L~----~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~  103 (173)
                      +..+.++|||+|||.++++++|+    ++|++||.|..|++.+   +++++|||||+|.+.++|++|++.|||..+.|+.
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            34678999999999999999976    8999999999999876   6789999999999999999999999999999999


Q ss_pred             EEEEEeeCCCC
Q psy2141         104 LRVGRAITPPN  114 (173)
Q Consensus       104 l~v~~a~~~~~  114 (173)
                      |+|.+++....
T Consensus        82 l~v~~a~~~~~   92 (282)
T 3pgw_A           82 MRIQYAKTDSD   92 (282)
T ss_pred             EEEEEeccCcc
Confidence            99999976553

>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=99.71  E-value=1.7e-17  Score=119.23  Aligned_cols=79  Identities=22%  Similarity=0.508  Sum_probs=73.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      +.++|||+|||.++++++|+++|++||.|..+++++++.+|+++|||||+|.+.++|++|++.  +..+.|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            468999999999999999999999999999999999998999999999999999999999985  578999999998875


Q ss_pred             C
Q psy2141         111 T  111 (173)
Q Consensus       111 ~  111 (173)
                      +
T Consensus        80 ~   80 (167)
T 2cjk_A           80 P   80 (167)
T ss_dssp             C
T ss_pred             c
Confidence            4

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.71  E-value=2.6e-17  Score=121.78  Aligned_cols=78  Identities=24%  Similarity=0.379  Sum_probs=72.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccC-ceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeC-CeEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFG-PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLG-GQYLRVG  107 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G-~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~-g~~l~v~  107 (173)
                      .+.++|||+|||..+++++|+++|++|| .|..++++.+     .+|+|||+|.+.++|.+|++.|||..++ |++|+|.
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  192 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  192 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEE
Confidence            4578999999999999999999999999 9999999765     2799999999999999999999999999 9999999


Q ss_pred             EeeCC
Q psy2141         108 RAITP  112 (173)
Q Consensus       108 ~a~~~  112 (173)
                      |++++
T Consensus       193 ~a~~~  197 (198)
T 1qm9_A          193 FSKST  197 (198)
T ss_dssp             EECCC
T ss_pred             eeccc
Confidence            98764

>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=99.71  E-value=3e-17  Score=118.53  Aligned_cols=84  Identities=19%  Similarity=0.349  Sum_probs=75.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCC--CcceEEEEEEcCHHHHHHHHHhcCCceeC---CeEEE
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPH--RHKGYGFIEYETKQASNEAISSMNLFDLG---GQYLR  105 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g--~~~g~afv~f~~~~~a~~a~~~l~g~~i~---g~~l~  105 (173)
                      +.++|||+|||.++++++|+++|++||.|..+++++++.++  +++|||||+|.+.++|++|++.|++..+.   ++.+.
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            46899999999999999999999999999999999998776  89999999999999999999999998876   57888


Q ss_pred             EEEeeCCCC
Q psy2141         106 VGRAITPPN  114 (173)
Q Consensus       106 v~~a~~~~~  114 (173)
                      +.++.....
T Consensus        82 ~~~~~~~~~   90 (175)
T 3nmr_A           82 MKPADSEKN   90 (175)
T ss_dssp             EEECGGGCC
T ss_pred             Ecccccccc
Confidence            888765443

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.70  E-value=2.2e-17  Score=126.18  Aligned_cols=82  Identities=27%  Similarity=0.377  Sum_probs=71.5

Q ss_pred             hCCCCeEEEcCCCCCC---------CHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCcee
Q psy2141          29 AKLYNRIYVASIHPDL---------TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDL   99 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~---------~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i   99 (173)
                      ....++||||||+..+         +|++|+++|++||.|..|+++.+      +|||||+|.+.++|+.|++.|+|..+
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            4568999999999998         79999999999999999999864      89999999999999999999999999


Q ss_pred             ------------CCeEEEEEEeeCCCCCC
Q psy2141         100 ------------GGQYLRVGRAITPPNAL  116 (173)
Q Consensus       100 ------------~g~~l~v~~a~~~~~~~  116 (173)
                                  .|+.|.|+|++..+...
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~pnp~  233 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDPDPA  233 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC------
T ss_pred             eccccccccccCCCCEEEEEEccCCCCHH
Confidence                        89999999998765543

>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=99.70  E-value=4e-17  Score=122.29  Aligned_cols=78  Identities=15%  Similarity=0.265  Sum_probs=70.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCce--eEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCe----E
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPI--KYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQ----Y  103 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v--~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~----~  103 (173)
                      .+.++|||+|||+++++++|+++|++||.|  ..+++..++  +.++|+|||+|.+.++|.+|+..|||..+.|+    +
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p  198 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP  198 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcc
Confidence            356799999999999999999999999999  899998874  55679999999999999999999999999886    6


Q ss_pred             EEEEEe
Q psy2141         104 LRVGRA  109 (173)
Q Consensus       104 l~v~~a  109 (173)
                      +.|+++
T Consensus       199 ~~vk~~  204 (205)
T 3tyt_A          199 YTLKLC  204 (205)
T ss_dssp             EECEEE
T ss_pred             eEEEec
Confidence            777765

>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=99.68  E-value=9.8e-17  Score=125.41  Aligned_cols=83  Identities=11%  Similarity=0.225  Sum_probs=71.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccC-ceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFG-PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G-~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      +.++|||+|||..+++++|+++|+.|| .|..+.++.++ .|.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++
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 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            478999999999999999999999999 99999999986 4889999999999999999999999999999999999998


Q ss_pred             eCCCC
Q psy2141         110 ITPPN  114 (173)
Q Consensus       110 ~~~~~  114 (173)
                      .+...
T Consensus       195 ~~~~~  199 (292)
T 2ghp_A          195 NPLEK  199 (292)
T ss_dssp             CCC--
T ss_pred             CCCcc
Confidence            76543

>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=99.68  E-value=1.3e-16  Score=123.35  Aligned_cols=93  Identities=17%  Similarity=0.226  Sum_probs=82.6

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEE
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY   81 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f   81 (173)
                      |+|+.|+|.++.                 +.++|||+|||..+++++|+++|+.||.|..+.++.+ .+|+++|||||+|
T Consensus        83 i~g~~l~v~~a~-----------------~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f  144 (261)
T 3sde_A           83 LKSRPLRIRFAT-----------------HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEF  144 (261)
T ss_dssp             ETTEECEEEECC-----------------CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEE
T ss_pred             ECCceeEeeecc-----------------cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEe
Confidence            567888888764                 4679999999999999999999999999999999999 5899999999999


Q ss_pred             cCHHHHHHHHHhcCC-ceeC---CeEEEEEEeeCC
Q psy2141          82 ETKQASNEAISSMNL-FDLG---GQYLRVGRAITP  112 (173)
Q Consensus        82 ~~~~~a~~a~~~l~g-~~i~---g~~l~v~~a~~~  112 (173)
                      .+.++|.+|++.||+ ..+.   +++|.|.++...
T Consensus       145 ~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~  179 (261)
T 3sde_A          145 AAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQF  179 (261)
T ss_dssp             SSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCE
T ss_pred             CCHHHHHHHHHHhcCCeEEecCCCceEEEeecccc
Confidence            999999999999954 4444   899999998754

>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=99.67  E-value=2.1e-16  Score=119.87  Aligned_cols=79  Identities=16%  Similarity=0.297  Sum_probs=74.3

Q ss_pred             hCCCCeEEEcCCCC-CCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q psy2141          29 AKLYNRIYVASIHP-DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG  107 (173)
Q Consensus        29 ~~~~~~l~V~nLp~-~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~  107 (173)
                      ..+.++|||+|||. ++++++|+++|++||.|..+++.+++     +|||||+|.+.++|++|++.|+|..+.|+.|+|.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~  105 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRIT  105 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            35689999999999 99999999999999999999999885     7899999999999999999999999999999999


Q ss_pred             EeeCC
Q psy2141         108 RAITP  112 (173)
Q Consensus       108 ~a~~~  112 (173)
                      +++..
T Consensus       106 ~a~~~  110 (229)
T 2adc_A          106 LSKHQ  110 (229)
T ss_dssp             CCSCC
T ss_pred             EecCc
Confidence            98765

>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=99.65  E-value=3.9e-17  Score=118.39  Aligned_cols=84  Identities=7%  Similarity=0.244  Sum_probs=73.6

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ..+.++|||+|||.++++++|+++|+.||.+.. .++.+..+|.++|||||+|.+.++|++|+ .|||..+.|++|+|.+
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-LAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK   87 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEec
Confidence            356899999999999999999999999998766 34445567889999999999999999999 5999999999999999


Q ss_pred             eeCCCC
Q psy2141         109 AITPPN  114 (173)
Q Consensus       109 a~~~~~  114 (173)
                      +.+...
T Consensus        88 ~~~~~~   93 (175)
T 1fje_B           88 PKGRDS   93 (175)
T ss_dssp             CCCSSC
T ss_pred             CCCccc
Confidence            876543

>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=3.1e-16  Score=115.91  Aligned_cols=78  Identities=17%  Similarity=0.296  Sum_probs=73.0

Q ss_pred             CCCeEEEcCCCC-CCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          31 LYNRIYVASIHP-DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        31 ~~~~l~V~nLp~-~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ..++|||+|||. ++++++|+++|++||.|..+++++++     +|||||+|.+.++|++|++.|||..+.|++|+|.++
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            358999999999 99999999999999999999999875     789999999999999999999999999999999998


Q ss_pred             eCCC
Q psy2141         110 ITPP  113 (173)
Q Consensus       110 ~~~~  113 (173)
                      ....
T Consensus        77 ~~~~   80 (198)
T 1qm9_A           77 KHQN   80 (198)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            7653

>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=99.63  E-value=2.7e-15  Score=101.84  Aligned_cols=82  Identities=12%  Similarity=0.212  Sum_probs=70.6

Q ss_pred             CCCCeEEEcCCCCCCC-----------HHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCce
Q psy2141          30 KLYNRIYVASIHPDLT-----------EEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFD   98 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~-----------e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~   98 (173)
                      .+.++|+|.||.....           +++|+++|++||.|..+.| .++   .++|||||+|.+.++|++|++.|||..
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~~   88 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGRW   88 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCCE
Confidence            4689999999954332           5799999999999999966 553   379999999999999999999999999


Q ss_pred             eCCeEEEEEEeeCCCCC
Q psy2141          99 LGGQYLRVGRAITPPNA  115 (173)
Q Consensus        99 i~g~~l~v~~a~~~~~~  115 (173)
                      ++|++|+|.++.+....
T Consensus        89 ~~gr~l~v~~a~~~~~~  105 (112)
T 2dit_A           89 FGGRQITAQAWDGTTDY  105 (112)
T ss_dssp             ETTEECEEEECCSCCCS
T ss_pred             ECCcEEEEEEeCCCCCc
Confidence            99999999999875543

>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=99.63  E-value=1.3e-15  Score=117.62  Aligned_cols=76  Identities=28%  Similarity=0.461  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+.++      +|||||+|.+.++|.+|+..|+|..+.|+.|+|.++
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a   93 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA   93 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeec
Confidence            45689999999999999999999999999999999654      799999999999999999999999999999999998


Q ss_pred             eC
Q psy2141         110 IT  111 (173)
Q Consensus       110 ~~  111 (173)
                      .+
T Consensus        94 ~~   95 (261)
T 3sde_A           94 TH   95 (261)
T ss_dssp             CC
T ss_pred             cc
Confidence            65

>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=99.62  E-value=2.3e-15  Score=101.26  Aligned_cols=82  Identities=11%  Similarity=0.161  Sum_probs=71.3

Q ss_pred             CCCCeEEEcCC--CCCCC--------HHHHHHHhhccCceeEEEEccCCCC--CCcceEEEEEEcCHHHHHHHHHhcCCc
Q psy2141          30 KLYNRIYVASI--HPDLT--------EEDIKSVFEAFGPIKYCKLQQGSSP--HRHKGYGFIEYETKQASNEAISSMNLF   97 (173)
Q Consensus        30 ~~~~~l~V~nL--p~~~~--------e~~L~~~F~~~G~v~~~~i~~~~~~--g~~~g~afv~f~~~~~a~~a~~~l~g~   97 (173)
                      .+++.|.+.|+  |.++.        +++|++.|++||.|.++.|.+++.+  ++++|++||+|.+.++|.+|++.|||.
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            46788999998  33443        3689999999999999999998654  467999999999999999999999999


Q ss_pred             eeCCeEEEEEEeeC
Q psy2141          98 DLGGQYLRVGRAIT  111 (173)
Q Consensus        98 ~i~g~~l~v~~a~~  111 (173)
                      .++||.|+|.+...
T Consensus        83 ~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           83 KFANRVVVTKYCDP   96 (105)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EeCCCEEEEEEeCH
Confidence            99999999999753

>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=99.61  E-value=2.7e-15  Score=108.14  Aligned_cols=75  Identities=27%  Similarity=0.490  Sum_probs=67.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcc----C-------ceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCcee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAF----G-------PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDL   99 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~----G-------~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i   99 (173)
                      +.++|||+|||.++++++|+++|++|    |       .|..+.+.+      ++|||||+|.+.++|++|+ .|||..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            56899999999999999999999999    6       777777654      3799999999999999999 8999999


Q ss_pred             CCeEEEEEEeeCC
Q psy2141         100 GGQYLRVGRAITP  112 (173)
Q Consensus       100 ~g~~l~v~~a~~~  112 (173)
                      .|++|+|.++...
T Consensus        76 ~g~~i~v~~~~~~   88 (172)
T 2g4b_A           76 QGQSLKIRRPHDY   88 (172)
T ss_dssp             TTEECEEECCSSC
T ss_pred             cCceeeecCCccc
Confidence            9999999987654

>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=99.59  E-value=6.7e-16  Score=103.71  Aligned_cols=72  Identities=10%  Similarity=0.280  Sum_probs=63.7

Q ss_pred             EcCCCCCCCHHHHHHHh------------hccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEE
Q psy2141          37 VASIHPDLTEEDIKSVF------------EAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYL  104 (173)
Q Consensus        37 V~nLp~~~~e~~L~~~F------------~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l  104 (173)
                      +.+|++.+++++|++.|            ++||.|.++.+.+++ +++++|||||+|.+.++|.+|++.|||..++|++|
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            56677777777776666            999999999999985 57899999999999999999999999999999999


Q ss_pred             EEEEe
Q psy2141         105 RVGRA  109 (173)
Q Consensus       105 ~v~~a  109 (173)
                      +|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99985

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.58  E-value=6.1e-15  Score=108.54  Aligned_cols=75  Identities=25%  Similarity=0.506  Sum_probs=66.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcc----C-------ceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCcee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAF----G-------PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDL   99 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~----G-------~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i   99 (173)
                      ..++|||+|||.++++++|+++|++|    |       .|..+.+.      +++|||||+|.+.++|++|+ .|||..+
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~------~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE------TTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec------CCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            57899999999999999999999999    5       56666653      45899999999999999999 8999999


Q ss_pred             CCeEEEEEEeeCC
Q psy2141         100 GGQYLRVGRAITP  112 (173)
Q Consensus       100 ~g~~l~v~~a~~~  112 (173)
                      .|++|+|.++...
T Consensus        76 ~g~~i~v~~~~~~   88 (198)
T 2yh0_A           76 QGQSLKIRRPHDY   88 (198)
T ss_dssp             TTEEEEEECCCCC
T ss_pred             cCceEEEeCCCCC
Confidence            9999999998764

>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=99.57  E-value=9.1e-15  Score=100.31  Aligned_cols=82  Identities=13%  Similarity=0.144  Sum_probs=71.8

Q ss_pred             CCCCeEEEcCCCC--CC---CHHHHHHHhhccCceeEEEEccCCC----CCCcceEEEEEEcCHHHHHHHHHhcCCceeC
Q psy2141          30 KLYNRIYVASIHP--DL---TEEDIKSVFEAFGPIKYCKLQQGSS----PHRHKGYGFIEYETKQASNEAISSMNLFDLG  100 (173)
Q Consensus        30 ~~~~~l~V~nLp~--~~---~e~~L~~~F~~~G~v~~~~i~~~~~----~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~  100 (173)
                      .++++|++.|+-.  ++   .+++|++.|++||.|.++.|.+++.    +++++|++||+|.+.++|.+|++.|||..++
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            4789999999942  22   3689999999999999999998854    4567899999999999999999999999999


Q ss_pred             CeEEEEEEeeC
Q psy2141         101 GQYLRVGRAIT  111 (173)
Q Consensus       101 g~~l~v~~a~~  111 (173)
                      |+.|+|.+...
T Consensus        98 GR~i~v~~~~~  108 (118)
T 3ue2_A           98 GRKVVAEVYDQ  108 (118)
T ss_dssp             TEECEEEEECH
T ss_pred             CcEEEEEEcCh
Confidence            99999999753

>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=99.52  E-value=2.5e-14  Score=114.50  Aligned_cols=76  Identities=21%  Similarity=0.291  Sum_probs=66.2

Q ss_pred             hCCCCeEEEcC--CCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeC---Ce-
Q psy2141          29 AKLYNRIYVAS--IHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLG---GQ-  102 (173)
Q Consensus        29 ~~~~~~l~V~n--Lp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~---g~-  102 (173)
                      ..++++|||||  |+..++|++|+++|++||.|..+.+..      +||||||+|.+.++|++|++.|||.++.   |+ 
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            46789999999  578999999999999999999988754      4799999999999999999999998883   44 


Q ss_pred             -EEEEEEee
Q psy2141         103 -YLRVGRAI  110 (173)
Q Consensus       103 -~l~v~~a~  110 (173)
                       .|.+.+..
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             57778764

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.52  E-value=6.1e-14  Score=93.43  Aligned_cols=68  Identities=15%  Similarity=0.239  Sum_probs=59.4

Q ss_pred             CCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCCCCCC
Q psy2141          42 PDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNAL  116 (173)
Q Consensus        42 ~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~~~~~  116 (173)
                      ..+++++|+++|++||.|..|.|+     ++++|||||+|.+.++|++|++.+++  +.|++|+|.|+++++...
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~~~   94 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQDA   94 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCCCC
Confidence            468999999999999999999987     35799999999999999999998655  679999999998765443

>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=99.43  E-value=1e-12  Score=89.42  Aligned_cols=78  Identities=10%  Similarity=0.133  Sum_probs=66.1

Q ss_pred             CCCCeEEEcCCCCCCC----------HHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCcee
Q psy2141          30 KLYNRIYVASIHPDLT----------EEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDL   99 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~----------e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i   99 (173)
                      .+++.|.+.|+=..-.          +++|++.|++||.|.++.+.++.    .+|++||+|.+.++|.+|++.|||..+
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f   80 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            3577888888843211          25789999999999999997663    589999999999999999999999999


Q ss_pred             CCeEEEEEEeeC
Q psy2141         100 GGQYLRVGRAIT  111 (173)
Q Consensus       100 ~g~~l~v~~a~~  111 (173)
                      +|+.|+|.+...
T Consensus        81 ~GR~i~v~~~~~   92 (114)
T 3s6e_A           81 AGKMITAAYVPL   92 (114)
T ss_dssp             TTEECEEEEECH
T ss_pred             CCEEEEEEEEcH
Confidence            999999999853

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.31  E-value=1.4e-11  Score=79.80  Aligned_cols=73  Identities=10%  Similarity=0.208  Sum_probs=63.6

Q ss_pred             CCCCeEEEcCCC----CCCCH----HHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2141          30 KLYNRIYVASIH----PDLTE----EDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG  101 (173)
Q Consensus        30 ~~~~~l~V~nLp----~~~~e----~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g  101 (173)
                      ++..||+|..++    .++..    .+|.+.|++||.|..+++..++        +||+|.+.++|.+|++ |||..+.|
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~G   75 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLN   75 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETT
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCC
Confidence            567889998876    23434    5799999999999999999873        8999999999999998 99999999


Q ss_pred             eEEEEEEeeC
Q psy2141         102 QYLRVGRAIT  111 (173)
Q Consensus       102 ~~l~v~~a~~  111 (173)
                      +.|+|+.+.+
T Consensus        76 r~LkV~lkt~   85 (91)
T 2dnr_A           76 RTITIALKSP   85 (91)
T ss_dssp             EEEEEEECCC
T ss_pred             eEEEEEeCCC
Confidence            9999999875

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.23  E-value=5.4e-11  Score=81.44  Aligned_cols=75  Identities=17%  Similarity=0.230  Sum_probs=66.3

Q ss_pred             hCCCCeEEEcCCCCC-CCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcC-HHHHHHHHHhcC--CceeCCeEE
Q psy2141          29 AKLYNRIYVASIHPD-LTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYET-KQASNEAISSMN--LFDLGGQYL  104 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~-~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~-~~~a~~a~~~l~--g~~i~g~~l  104 (173)
                      ..+.+.|||+||+.+ +++++|+++|++||.|..|.+.++.      -.|||.|.+ .++|..|++.|+  +..|.|..+
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 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA------KEGIILFKEKAKEALGKAKDANNGNLQLRNKEV   88 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC------SEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC------CEEEEEECCChHHHHHHHHHhhcCCcEEeCcEE
Confidence            357899999999999 9999999999999999999998884      259999999 899999999995  678888887


Q ss_pred             EEEEe
Q psy2141         105 RVGRA  109 (173)
Q Consensus       105 ~v~~a  109 (173)
                      ++...
T Consensus        89 ~~evL   93 (121)
T 1owx_A           89 TWEVL   93 (121)
T ss_dssp             EEEEC
T ss_pred             EEEEC
Confidence            77653

>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=99.13  E-value=1.3e-10  Score=75.65  Aligned_cols=74  Identities=11%  Similarity=0.298  Sum_probs=63.6

Q ss_pred             hhCCCCeEEEcCCCCC-----CCH----HHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCce
Q psy2141          28 EAKLYNRIYVASIHPD-----LTE----EDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFD   98 (173)
Q Consensus        28 ~~~~~~~l~V~nLp~~-----~~e----~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~   98 (173)
                      ..++..||+|..++..     +..    .+|.+.|+.||.|..+++..++        +||+|.+.++|.+|++ |||..
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~   81 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMK   81 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSE
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCee
Confidence            3467899999888742     322    4689999999999999999883        9999999999999998 99999


Q ss_pred             eCCeEEEEEEee
Q psy2141          99 LGGQYLRVGRAI  110 (173)
Q Consensus        99 i~g~~l~v~~a~  110 (173)
                      ++|+.|+|++..
T Consensus        82 v~Gr~L~V~~k~   93 (95)
T 1ufw_A           82 VKGRAVKISGPS   93 (95)
T ss_dssp             ETTEEEEEECCC
T ss_pred             eCCeEEEEeccC
Confidence            999999998854

>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=99.09  E-value=2.4e-10  Score=85.88  Aligned_cols=67  Identities=15%  Similarity=0.126  Sum_probs=60.1

Q ss_pred             CCHHHHHHHhhccCceeEEEEccC----CCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          44 LTEEDIKSVFEAFGPIKYCKLQQG----SSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        44 ~~e~~L~~~F~~~G~v~~~~i~~~----~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      -.+++|++.|++||.|..+.+.++    +.+++++|++||+|.+.++|.+|++.|||..++||.|.+.+..
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            346789999999999999999854    3455899999999999999999999999999999999999965

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.84  E-value=2.4e-08  Score=66.33  Aligned_cols=72  Identities=14%  Similarity=0.147  Sum_probs=67.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcc-----CceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAF-----GPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLR  105 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~-----G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~  105 (173)
                      ..++|-+-|||..+++..++.+.+++     |.+..+.+..|.      +-|+|+|.+...|.+|.-.|+|.++.|++|+
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            47889999999999999999999999     999999998883      6799999999999999999999999999999


Q ss_pred             EEE
Q psy2141         106 VGR  108 (173)
Q Consensus       106 v~~  108 (173)
                      |.-
T Consensus        94 ~gT   96 (117)
T 2l9w_A           94 SGT   96 (117)
T ss_dssp             EEC
T ss_pred             ecC
Confidence            864

>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=98.07  E-value=2.4e-05  Score=51.53  Aligned_cols=77  Identities=12%  Similarity=0.106  Sum_probs=64.4

Q ss_pred             CCCeEEEcCCCCCC-CH----HHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q psy2141          31 LYNRIYVASIHPDL-TE----EDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLR  105 (173)
Q Consensus        31 ~~~~l~V~nLp~~~-~e----~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~  105 (173)
                      -.++|+|.||+.++ ..    +.++++|..|+++.....++.-      .-..|.|.+.++|.+|-..||+..++|+.++
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            46789999998754 22    4679999999999888777652      2468999999999999999999999999999


Q ss_pred             EEEeeCCC
Q psy2141         106 VGRAITPP  113 (173)
Q Consensus       106 v~~a~~~~  113 (173)
                      |-++.+.+
T Consensus        78 ~YFgq~~~   85 (104)
T 1wey_A           78 LYFAQTLH   85 (104)
T ss_dssp             EECCCCSS
T ss_pred             EEecCCCC
Confidence            99988543

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.69  E-value=0.0015  Score=42.90  Aligned_cols=72  Identities=17%  Similarity=0.200  Sum_probs=59.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhc-----cCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEA-----FGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLR  105 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~-----~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~  105 (173)
                      ..++|.|.|||..+.++.|.-+|+.     -|.|..++...        +-|+|+|.+...+++.++. ..+.+.+.+|.
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--------CGGVLTFREPADAERVLAQ-ADHELHGAQLS   77 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBCE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEEE
Confidence            4678999999999999999999987     25888887632        5789999999999999854 45788899999


Q ss_pred             EEEeeC
Q psy2141         106 VGRAIT  111 (173)
Q Consensus       106 v~~a~~  111 (173)
                      |....+
T Consensus        78 V~P~~~   83 (104)
T 2dhx_A           78 LRPAPP   83 (104)
T ss_dssp             EEECCC
T ss_pred             EEcCCC
Confidence            966443

>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=97.59  E-value=0.00046  Score=44.46  Aligned_cols=69  Identities=9%  Similarity=0.212  Sum_probs=57.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCC--cceEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHR--HKGYGFIEYETKQASNEAISSMNLFDLGG  101 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~--~~g~afv~f~~~~~a~~a~~~l~g~~i~g  101 (173)
                      ++|.|.+||+.++|+++.+.++....+.....+..+.+.+  .-.-|+|.|.+.+++..-.+.++|..+.+
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            5789999999999999999999988877776666543332  34568999999999999999999987754

>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=97.20  E-value=0.0011  Score=43.03  Aligned_cols=54  Identities=15%  Similarity=0.231  Sum_probs=44.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhc
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM   94 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l   94 (173)
                      .+.+++ ..|.++...||.++|+.|| -..|+.+-|       --|||.|.+.+.|..|+..+
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fg-gv~I~WidD-------TsAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDD-------TSAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTC-SCCCEEEET-------TEEEEECSCHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccC-CEEEEEEcC-------CeEEEEecCHHHHHHHHHhc
Confidence            456677 9999999999999999998 344555555       27999999999999999876

>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=97.06  E-value=0.0029  Score=42.63  Aligned_cols=71  Identities=17%  Similarity=0.153  Sum_probs=56.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC-eEEEEEEe
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG-QYLRVGRA  109 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g-~~l~v~~a  109 (173)
                      ..+.|.|-+.|... -..+...|++||.|.+....      ....+-.|.|.+..+|++|+.. ||..++| -.|-|...
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~------~~~NWihI~Y~s~~~A~rAL~k-NG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALSK-DGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHTT-TTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC------CCCCeEEEEeCCHHHHHHHHHh-CCeEecCCEEEEEEEC
Confidence            46788899999884 56677799999999988762      1357999999999999999955 9999986 45566554

>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=96.90  E-value=0.0016  Score=42.32  Aligned_cols=54  Identities=15%  Similarity=0.254  Sum_probs=45.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcC
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMN   95 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~   95 (173)
                      +.++| +.|.++...+|.++|+.|| -..|+.+-|       --|||.|.+.+.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidD-------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDD-------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEET-------TEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcC-------CeEEEEecCHHHHHHHHHhcc
Confidence            45666 9999999999999999998 455666655       279999999999999998764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.81  E-value=0.0047  Score=40.09  Aligned_cols=70  Identities=9%  Similarity=0.137  Sum_probs=50.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCC--cceEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHR--HKGYGFIEYETKQASNEAISSMNLFDLGG  101 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~--~~g~afv~f~~~~~a~~a~~~l~g~~i~g  101 (173)
                      .-+|.|++||+.+||+++.+.++..-.+.....+..+.+.+  .-.-|+|.|.+.++...-.+..+|..+.+
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            45799999999999999888887654443333333222221  22458999999999999999999977644

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.30  E-value=0.0025  Score=52.70  Aligned_cols=58  Identities=14%  Similarity=0.263  Sum_probs=43.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHh
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS   93 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~   93 (173)
                      ...++|+|. .|...++.+|.++|++||+|..+.+-.++     .-|+.|+|.+.+++..++..
T Consensus        51 qa~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           51 QAQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HHHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHSS
T ss_pred             HhcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHhc
Confidence            347899997 79999999999999999999998776553     47999999999998877643

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.23  E-value=0.0082  Score=41.04  Aligned_cols=78  Identities=18%  Similarity=0.196  Sum_probs=54.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeE-EEEccCC------------CCC-CcceEEEEEEcCHHHHHHHHHhcCC
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKY-CKLQQGS------------SPH-RHKGYGFIEYETKQASNEAISSMNL   96 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~-~~i~~~~------------~~g-~~~g~afv~f~~~~~a~~a~~~l~g   96 (173)
                      ....|.|-+.|.... ..+.+.|++||.|.+ ....++.            ... ....+-.|.|.+..+|.+|+.. ||
T Consensus         6 ~e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~-NG   83 (132)
T 3p3d_A            6 GELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE-NG   83 (132)
T ss_dssp             --CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT-TT
T ss_pred             CceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh-CC
Confidence            345677778887654 566679999999876 2222110            001 1356889999999999999955 99


Q ss_pred             ceeCCeEEEEEEee
Q psy2141          97 FDLGGQYLRVGRAI  110 (173)
Q Consensus        97 ~~i~g~~l~v~~a~  110 (173)
                      ..++|..|-|....
T Consensus        84 ~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           84 AVFNGVLLGVIPYT   97 (132)
T ss_dssp             CEETTEECEEEECC
T ss_pred             eEeCcEEEEEEECC
Confidence            99999877776653

>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=96.10  E-value=0.00078  Score=44.89  Aligned_cols=44  Identities=23%  Similarity=0.338  Sum_probs=11.4

Q ss_pred             CCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCCCCCCHHH
Q psy2141           2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEED   48 (173)
Q Consensus         2 l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~~e~~   48 (173)
                      |+||+|+|.+........   ..........++|||+|||+++|++.
T Consensus        70 ~~g~~i~V~~a~~~~~~~---~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           70 LNDRKVFVGRFKSRKERE---AELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             ETTEECEEEESSCCCC-------------------------------
T ss_pred             ECCEEEEEEECCCccccc---cccccccCCCCceEeCCCCCCccccc
Confidence            689999998765432211   12222334567899999999998864

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=96.10  E-value=0.0044  Score=43.25  Aligned_cols=35  Identities=14%  Similarity=0.003  Sum_probs=28.5

Q ss_pred             EEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCc
Q psy2141          61 YCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLF   97 (173)
Q Consensus        61 ~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~   97 (173)
                      .+++.++.  ++++|||||+|.+.++|++|++.+++.
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhccc
Confidence            45666664  368999999999999999999887753

>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=95.43  E-value=0.004  Score=43.20  Aligned_cols=41  Identities=15%  Similarity=0.054  Sum_probs=36.9

Q ss_pred             CCCcceEEEEEEcCHHHHHHHHHhc-CCceeCCeEEEEEEeeC
Q psy2141          70 PHRHKGYGFIEYETKQASNEAISSM-NLFDLGGQYLRVGRAIT  111 (173)
Q Consensus        70 ~g~~~g~afv~f~~~~~a~~a~~~l-~g~~i~g~~l~v~~a~~  111 (173)
                      ....+|+++++|.+.++|++|++.| ||..++| .+.++++..
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            3567999999999999999999999 9999999 999988754

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=88.96  E-value=1.2  Score=37.11  Aligned_cols=56  Identities=14%  Similarity=0.234  Sum_probs=45.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCC
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNL   96 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g   96 (173)
                      ...++|+ .|..+...+|.++|+.||. ..++.+-+       ..+||.|.+.+.|..+++.+..
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widd-------t~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDD-------TSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSS-------SEEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcC-------CeEEEEECCHHHHHHHHHHHHh
Confidence            3467776 8889999999999999994 45555444       3799999999999999998853

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=86.19  E-value=0.14  Score=32.51  Aligned_cols=40  Identities=15%  Similarity=0.206  Sum_probs=23.7

Q ss_pred             CCCCcccccCCCCCCCCCcchhhhhhhhhCCCCeEEEcCCC
Q psy2141           1 MQHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIH   41 (173)
Q Consensus         1 ~l~gr~i~v~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp   41 (173)
                      .++|+.|+|.++...+.....- ..........+||||||+
T Consensus        61 ~~~g~~l~V~~a~~~~~~~~~~-~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           61 VICGSRVRVELSTGMPRRSRFD-RPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CSSSCCCEEEESSSCCCSSCCC-SCCCSCCCCSCCCSCCCC
T ss_pred             eECCcEEEEEEccCCCCcccCC-CCCccccCCCceecCCCC
Confidence            3789999998776543222111 111111337789999997

---

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	173
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-16
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-16
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-16
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-15
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-15
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-15
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-15
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-15
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-15
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-15
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	6e-15
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	7e-15
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-14
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-14
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-14
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-14
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-14
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-14
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	4e-14
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-14
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	7e-14
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	8e-14
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	9e-14
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	9e-14
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-13
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-13
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-13
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-13
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-13
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-13
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-13
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-13
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-13
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	5e-13
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	6e-13
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	8e-13
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	9e-13
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-12
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-12
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-12
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-12
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-10
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	4e-12
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	4e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	5e-12
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-11
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-11
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	5e-11
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-10
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-10
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-10
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	4e-10
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	5e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	8e-10
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:) 8e-10
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-09
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-09
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-09
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	6e-09
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	9e-09
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-08
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	2e-08
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	3e-08
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	6e-08
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	7e-08
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	8e-08
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	2e-07
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	3e-07
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	4e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	6e-07
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	1e-06
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-06
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-06
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	3e-06
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	6e-06
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	7e-06
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	1e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-05
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	4e-05
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	3e-04
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-04

>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 = 68.8 bits (168), Expect = 1e-16
 Identities = 19/75 (25%), Positives = 38/75 (50%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +YV  +HPD+TE  +   F   GPI   ++ +     R  GY ++ ++    +  A+ +M
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 95  NLFDLGGQYLRVGRA 109
           N   + G+ +R+  +
Sbjct: 63  NFDVIKGKPVRIMWS 77

>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 = 68.1 bits (166), Expect = 3e-16
 Identities = 18/74 (24%), Positives = 32/74 (43%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             +YV ++    TEE I  +F   G IK   +          G+ F+EY ++  +  A+ 
Sbjct: 8   CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

Query: 93  SMNLFDLGGQYLRV 106
            +N   L  + +R 
Sbjct: 68  YINGTRLDDRIIRT 81

>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 = 67.3 bits (164), Expect = 4e-16
 Identities = 20/78 (25%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            +YV ++   +T++ + ++F  +G I    + +     R +G  F+ Y  ++ + EAIS+
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 94  MN--LFDLGGQYLRVGRA 109
           +N  + + G Q L V  A
Sbjct: 68  LNNVIPEGGSQPLSVRLA 85

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.6 bits (162), Expect = 1e-15
 Identities = 23/77 (29%), Positives = 43/77 (55%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           +++++  +   L ++ +K +  +FGP+K   L + S+    KGY F EY     +++AI+
Sbjct: 2   HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

Query: 93  SMNLFDLGGQYLRVGRA 109
            +N   LG + L V RA
Sbjct: 62  GLNGMQLGDKKLLVQRA 78

>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 = 65.8 bits (160), Expect = 1e-15
 Identities = 13/76 (17%), Positives = 37/76 (48%), Gaps = 1/76 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++++  +    T+E ++  F  FG +K C + +     R +G+GF+ +  +   ++ + +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-A 60

Query: 94  MNLFDLGGQYLRVGRA 109
            +  +L  + +    A
Sbjct: 61  QSRHELDSKTIDPKVA 76

>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 = 66.0 bits (161), Expect = 2e-15
 Identities = 20/102 (19%), Positives = 49/102 (48%), Gaps = 14/102 (13%)

Query: 26  TEEAKLYNRIYVASIHPDLT-EEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETK 84
           T+   + +R+++ +++  +  + D++++F  +G I  C +        HKG+ F++Y  +
Sbjct: 9   TDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNE 60

Query: 85  QASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPST 126
           + +  A++  +   + GQ L +  A  P           PS+
Sbjct: 61  RNARAAVAGEDGRMIAGQVLDINLAAEPKV-----NRSGPSS 97

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.9 bits (160), Expect = 3e-15
 Identities = 15/84 (17%), Positives = 44/84 (52%), Gaps = 1/84 (1%)

Query: 27  EEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQA 86
            E + + ++++  +  + TEE +++ +E +G +  C + +  +  R +G+GF+ + +   
Sbjct: 15  REKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAE 74

Query: 87  SNEAISSMNLFDLGGQYLRVGRAI 110
            + A+ +     + G+ +   RA+
Sbjct: 75  VDAAM-AARPHSIDGRVVEPKRAV 97

>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 = 66.2 bits (161), Expect = 3e-15
 Identities = 15/77 (19%), Positives = 36/77 (46%), Gaps = 3/77 (3%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             +Y+ ++   +T E++  +F  +GPI+  ++         +G  ++ YE    +  A  
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACD 64

Query: 93  SMNLFDLGGQYLRVGRA 109
            ++ F++  +YL V   
Sbjct: 65  HLSGFNVCNRYLVVLYY 81

>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 = 65.3 bits (159), Expect = 3e-15
 Identities = 21/79 (26%), Positives = 46/79 (58%), Gaps = 2/79 (2%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL-QQGSSPHRHKGYGFIEYETKQASNEAI 91
           ++I V +I     + +I+ +F  FG +K  +L ++ +    H+G+GF+++ TKQ + +A 
Sbjct: 9   SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 68

Query: 92  SSM-NLFDLGGQYLRVGRA 109
           +++ +   L G+ L +  A
Sbjct: 69  NALCHSTHLYGRRLVLEWA 87

>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 = 65.4 bits (159), Expect = 3e-15
 Identities = 20/77 (25%), Positives = 43/77 (55%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             +YV  +   ++E  +  +F   GP+    + +     +H+GYGF+E+ +++ ++ AI 
Sbjct: 10  ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 69

Query: 93  SMNLFDLGGQYLRVGRA 109
            M++  L G+ +RV +A
Sbjct: 70  IMDMIKLYGKPIRVNKA 86

>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 = 64.6 bits (157), Expect = 6e-15
 Identities = 20/95 (21%), Positives = 42/95 (44%), Gaps = 7/95 (7%)

Query: 22  IDEITEEAKLYN-RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIE 80
            +++  ++   N  +Y   I   LT++ ++  F  FG I   ++         KGY F+ 
Sbjct: 7   FEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRV------FPEKGYSFVR 60

Query: 81  YETKQASNEAISSMNLFDLGGQYLRVGRAITPPNA 115
           + T +++  AI S+N   + G  ++       P+ 
Sbjct: 61  FSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDM 95

>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 = 64.0 bits (155), Expect = 7e-15
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 1/81 (1%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYC-KLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           I++ ++ P++ E+ +   F AFG I    K+ +       KGY FI + +  AS+ AI +
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 94  MNLFDLGGQYLRVGRAITPPN 114
           MN   L  + + V  A    +
Sbjct: 61  MNGQYLCNRPITVSYAFKKDS 81

>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 = 64.0 bits (155), Expect = 1e-14
 Identities = 21/91 (23%), Positives = 44/91 (48%), Gaps = 2/91 (2%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            R++V ++    +EED++ +F A+GP+        S   + KG+ F+ +   + + +A +
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 93  SMNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
            ++     G+ L V  +     A  S  GP+
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEA--SQSGPS 97

>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 = 63.8 bits (155), Expect = 1e-14
 Identities = 15/77 (19%), Positives = 35/77 (45%), Gaps = 2/77 (2%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           + + V  +    TE+D+K  F  FG +   ++++       KG+GF+ +   +   + +S
Sbjct: 9   SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

Query: 93  SMNLFDLGGQYLRVGRA 109
             ++ D  G++      
Sbjct: 69  QRHMID--GRWCDCKLP 83

>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 = 63.1 bits (153), Expect = 2e-14
 Identities = 19/76 (25%), Positives = 39/76 (51%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            + V  +  D+T+ ++ ++F A GPI  C++ +        GY F+++ ++  S  AI  
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 94  MNLFDLGGQYLRVGRA 109
           +N   +  + L+V  A
Sbjct: 64  LNGITVRNKRLKVSYA 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 = 63.1 bits (153), Expect = 2e-14
 Identities = 18/85 (21%), Positives = 47/85 (55%), Gaps = 1/85 (1%)

Query: 27  EEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQA 86
           +E +   ++++  +  + T+E ++S FE +G +  C + +  +  R +G+GF+ Y T + 
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 87  SNEAISSMNLFDLGGQYLRVGRAIT 111
            + A+++     + G+ +   RA++
Sbjct: 61  VDAAMNARP-HKVDGRVVEPKRAVS 84

>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 = 62.6 bits (152), Expect = 2e-14
 Identities = 14/76 (18%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++ V+++   +++ DI+ +F  FG +K   +    S         + +E K  + +A+  
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLG-TADVHFERKADALKAMKQ 60

Query: 94  MNLFDLGGQYLRVGRA 109
            N   L G+ + +   
Sbjct: 61  YNGVPLDGRPMNIQLV 76

>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 = 62.7 bits (152), Expect = 3e-14
 Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 3/78 (3%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIK---YCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
           +++ +++   TEE +K VF   G IK     K +  +      G+GF+EY+  + + +A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 92  SSMNLFDLGGQYLRVGRA 109
             +    + G  L V  +
Sbjct: 61  KQLQGHTVDGHKLEVRIS 78

>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 = 62.7 bits (152), Expect = 4e-14
 Identities = 16/95 (16%), Positives = 38/95 (40%), Gaps = 1/95 (1%)

Query: 22  IDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEY 81
           +D ++ E +    ++   +   +   D++  F A G ++  ++    +  R KG  ++E+
Sbjct: 8   VDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 67

Query: 82  ETKQASNEAISSMNLFDLGGQYLRVGRAITPPNAL 116
              Q+       +    L G  + V  +    N L
Sbjct: 68  CEIQSV-PLAIGLTGQRLLGVPIIVQASQAEKNRL 101

>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 = 61.2 bits (148), Expect = 7e-14
 Identities = 17/76 (22%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           ++++  +  D T++D+K  F  FG +  C L+      R +G+GF+ ++  ++ ++ +  
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-D 59

Query: 94  MNLFDLGGQYLRVGRA 109
                L G+ +   RA
Sbjct: 60  QKEHKLNGKVIDPKRA 75

>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 = 61.6 bits (149), Expect = 7e-14
 Identities = 15/73 (20%), Positives = 35/73 (47%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            +YV+ +   +T+++++ +F  +G I   ++         +G GFI ++ +  + EAI  
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 94  MNLFDLGGQYLRV 106
           +N     G    +
Sbjct: 68  LNGQKPSGATEPI 80

>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 = 61.3 bits (148), Expect = 8e-14
 Identities = 20/74 (27%), Positives = 34/74 (45%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             + V  +    TE D++ VF  +GPI    +       R +G+ F+ +E    + EA  
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 93  SMNLFDLGGQYLRV 106
             N  +L G+ +RV
Sbjct: 70  RANGMELDGRRIRV 83

>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 = 61.7 bits (149), Expect = 9e-14
 Identities = 19/82 (23%), Positives = 42/82 (51%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            +++V  +  D  E+ ++ VF  +G I    + +     R +G+GF+ +E    + +A+ 
Sbjct: 6   GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 65

Query: 93  SMNLFDLGGQYLRVGRAITPPN 114
           +MN   + G+ +RV +A    +
Sbjct: 66  AMNGKSVDGRQIRVDQAGKSSD 87

>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 = 61.2 bits (148), Expect = 9e-14
 Identities = 15/79 (18%), Positives = 39/79 (49%), Gaps = 7/79 (8%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           N++Y+ ++ P +T +D++ +F         ++          GY F++Y  +  +  AI 
Sbjct: 2   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV------LLKSGYAFVDYPDQNWAIRAIE 55

Query: 93  SMN-LFDLGGQYLRVGRAI 110
           +++   +L G+ + V  ++
Sbjct: 56  TLSGKVELHGKIMEVDYSV 74

>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 = 60.7 bits (147), Expect = 1e-13
 Identities = 16/76 (21%), Positives = 37/76 (48%), Gaps = 1/76 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           +I+V  + PD  EE I+  F  FG ++  +L   +  ++ +G+ FI ++ ++   + +  
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 94  MNLFDLGGQYLRVGRA 109
               ++G     +  A
Sbjct: 61  KY-HNVGLSKCEIKVA 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.5 bits (146), Expect = 1e-13
 Identities = 18/76 (23%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           +I+V  +  + T ED+K  FE FG +    L    + +RH+G+GF+ +E++    +    
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-E 59

Query: 94  MNLFDLGGQYLRVGRA 109
           ++  ++  + +   +A
Sbjct: 60  IHFHEINNKMVECKKA 75

>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 = 60.8 bits (147), Expect = 2e-13
 Identities = 23/82 (28%), Positives = 43/82 (52%), Gaps = 2/82 (2%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             +YV ++  D+TE  I  +F   GP K CK+    + +    Y F+E+   + +  A++
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALA 66

Query: 93  SMNLFDLGGQYLRVGRAITPPN 114
           +MN   + G+ ++V  A TP +
Sbjct: 67  AMNGRKILGKEVKVNWATTPSS 88

>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 = 60.4 bits (146), Expect = 2e-13
 Identities = 25/82 (30%), Positives = 44/82 (53%), Gaps = 6/82 (7%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           +R++V ++ PD+TEE+++ +FE +G             H+ KG+GFI  ET+  +  A  
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYGKAGEVF------IHKDKGFGFIRLETRTLAEIAKV 62

Query: 93  SMNLFDLGGQYLRVGRAITPPN 114
            ++   L G+ LRV  A    +
Sbjct: 63  ELDNMPLRGKQLRVRFACHSAS 84

>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 = 60.9 bits (147), Expect = 2e-13
 Identities = 15/80 (18%), Positives = 30/80 (37%), Gaps = 4/80 (5%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYC--KLQQGSSPHRHKGYGFIEYETKQASNEAI 91
           R+++  I      E+I                    +   +++G+ F+EYE+ +A+  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 92  SSMNL--FDLGGQYLRVGRA 109
             +      L G  + V  A
Sbjct: 63  RKLMPGRIQLWGHQIAVDWA 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 = 60.1 bits (145), Expect = 2e-13
 Identities = 21/76 (27%), Positives = 43/76 (56%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            + V  +  ++T+E+ +S+F + G I+ CKL +     +  GYGF+ Y   + + +AI++
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 94  MNLFDLGGQYLRVGRA 109
           +N   L  + ++V  A
Sbjct: 64  LNGLRLQTKTIKVSYA 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 = 60.4 bits (146), Expect = 2e-13
 Identities = 20/77 (25%), Positives = 41/77 (53%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             +YV  +  ++ ++ + + F  FG I   ++       +H+G+ F+E+E  + +  AI 
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

Query: 93  SMNLFDLGGQYLRVGRA 109
           +MN  +L G+ +RV  A
Sbjct: 66  NMNESELFGRTIRVNLA 82

>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 = 59.7 bits (144), Expect = 3e-13
 Identities = 14/77 (18%), Positives = 35/77 (45%), Gaps = 1/77 (1%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           +I+V  I  D  E  ++  FE +G I+  ++       + +G+ F+ ++   + ++ +  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-I 62

Query: 94  MNLFDLGGQYLRVGRAI 110
                + G    V +A+
Sbjct: 63  QKYHTVNGHNCEVRKAL 79

>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 = 60.1 bits (145), Expect = 3e-13
 Identities = 21/82 (25%), Positives = 37/82 (45%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             I V ++  D  E D++ +F  FG I    L +  +  + KG+ FI +  ++ +  AI+
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 93  SMNLFDLGGQYLRVGRAITPPN 114
            ++ F      L V  A    N
Sbjct: 69  GVSGFGYDHLILNVEWAKPSTN 90

>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 = 59.3 bits (143), Expect = 5e-13
 Identities = 23/79 (29%), Positives = 39/79 (49%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             ++V SIH +  E++I+  F  +G IK   L         KGY  +EYET + +  A  
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 93  SMNLFDLGGQYLRVGRAIT 111
           ++N  ++ GQ ++V     
Sbjct: 68  ALNGAEIMGQTIQVDWCFV 86

>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 = 59.3 bits (143), Expect = 6e-13
 Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 2/79 (2%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             I++ ++   +  + +   F AFG I  CK+      +  KGYGF+ +ET++A+  AI 
Sbjct: 9   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIE 66

Query: 93  SMNLFDLGGQYLRVGRAIT 111
            MN   L  + + VGR  +
Sbjct: 67  KMNGMLLNDRKVFVGRFKS 85

>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 = 59.4 bits (143), Expect = 8e-13
 Identities = 20/89 (22%), Positives = 34/89 (38%), Gaps = 8/89 (8%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS--------SPHRHKGYGFIEYETK 84
           + IYV  ++  +T +D+   F+  G +K  K                + KG   + YE  
Sbjct: 9   SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 68

Query: 85  QASNEAISSMNLFDLGGQYLRVGRAITPP 113
             +  A+   +  D  G  L+V  A   P
Sbjct: 69  PTAKAAVEWFDGKDFQGSKLKVSLARKKP 97

>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 = 58.9 bits (142), Expect = 9e-13
 Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 3/77 (3%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            RIYV ++ PD+  +DI+ VF  +G I+        +      + F+E+E  + + +A+ 
Sbjct: 15  CRIYVGNLPPDIRTKDIEDVFYKYGAIRDI---DLKNRRGGPPFAFVEFEDPRDAEDAVY 71

Query: 93  SMNLFDLGGQYLRVGRA 109
             + +D  G  LRV   
Sbjct: 72  GRDGYDYDGYRLRVEFP 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 = 58.5 bits (141), Expect = 1e-12
 Identities = 15/84 (17%), Positives = 38/84 (45%), Gaps = 1/84 (1%)

Query: 33  NRIYVASIHPDLTEEDIK-SVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
           + IY+ +++  + ++++K S+   F           S   + +G  F+ ++   ++  A+
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63

Query: 92  SSMNLFDLGGQYLRVGRAITPPNA 115
            SM  F    + +R+  A T  + 
Sbjct: 64  RSMQGFPFYDKPMRIQYAKTDSDI 87

>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 = 58.2 bits (140), Expect = 1e-12
 Identities = 18/81 (22%), Positives = 36/81 (44%), Gaps = 6/81 (7%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPH-----RHKGYGFIEYETKQASN 88
           R+YV +I   +TEE +   F A   +       G+        + K + F+E+ +   + 
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 89  EAISSMNLFDLGGQYLRVGRA 109
           +A+ + +     GQ L++ R 
Sbjct: 63  QAM-AFDGIIFQGQSLKIRRP 82

>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 = 58.6 bits (141), Expect = 1e-12
 Identities = 25/81 (30%), Positives = 44/81 (54%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            ++V +I  + TEE +K +F   GP+   +L       + KGYGF EY+ ++ +  A+ +
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 94  MNLFDLGGQYLRVGRAITPPN 114
           +N  +  G+ LRV  A +  N
Sbjct: 70  LNGREFSGRALRVDNAASEKN 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 = 57.8 bits (139), Expect = 2e-12
 Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            R++V++I     + D++ +F  FG I   ++    +    KG+GF+ +E    ++ A  
Sbjct: 12  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF--NERGSKGFGFVTFENSADADRARE 69

Query: 93  SMNLFDLGGQYLRVGRA 109
            ++   + G+ + V  A
Sbjct: 70  KLHGTVVEGRKIEVNNA 86

>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 = 59.2 bits (142), Expect = 4e-12
 Identities = 14/82 (17%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 32  YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
             +I+V  I  D  E  ++  FE +G I+  ++       + +G+ F+ ++   + ++ +
Sbjct: 97  VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156

Query: 92  SSMNLFDLGGQYLRVGRAITPP 113
                  + G    V +A++  
Sbjct: 157 -IQKYHTVNGHNCEVRKALSKQ 177

>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 = 54.2 bits (129), Expect = 3e-10
 Identities = 14/62 (22%), Positives = 36/62 (58%)

Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
          ++++  +  + T+E ++S FE +G +  C + +  +  R +G+GF+ Y T +  + A+++
Sbjct: 8  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 94 MN 95
            
Sbjct: 68 RP 69

>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 = 57.4 bits (138), Expect = 4e-12
 Identities = 18/83 (21%), Positives = 34/83 (40%), Gaps = 1/83 (1%)

Query: 32  YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
           + +I+V  +    T+  ++  FE FG I+   +       + +GYGF+    + A+  A 
Sbjct: 10  FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 69

Query: 92  SSMNLFDLGGQYLRVGRAITPPN 114
              N   + G+   V  A     
Sbjct: 70  KDPN-PIIDGRKANVNLAYLGAK 91

>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 = 56.7 bits (136), Expect = 4e-12
 Identities = 8/76 (10%), Positives = 30/76 (39%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            +++ +  P  T+ +I+ + +    +           +  + + +I+  +K+ +   +  
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 94  MNLFDLGGQYLRVGRA 109
           +N   + G  L    +
Sbjct: 63  LNGLKIEGYTLVTKVS 78

>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 = 57.0 bits (137), Expect = 5e-12
 Identities = 17/92 (18%), Positives = 37/92 (40%), Gaps = 9/92 (9%)

Query: 23  DEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYE 82
           ++     K    +YV ++    +EE I+  F    P    ++       + + Y F+ + 
Sbjct: 2   EDTMSSVK---ILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFS 52

Query: 83  TKQASNEAISSMNLFDLGGQYLRVGRAITPPN 114
            ++ + EA+ ++N   L G  + V  A     
Sbjct: 53  NREDAVEAMKALNGKVLDGSPIEVTLAKPVDK 84

>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 = 56.2 bits (135), Expect = 1e-11
 Identities = 18/77 (23%), Positives = 38/77 (49%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             +++  +  +  ++D+  +F  FG +   K+      +  K +GF+ Y+   ++  AI 
Sbjct: 19  ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 78

Query: 93  SMNLFDLGGQYLRVGRA 109
           SMN F +G + L+V   
Sbjct: 79  SMNGFQIGMKRLKVQLK 95

>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 = 55.4 bits (133), Expect = 2e-11
 Identities = 15/91 (16%), Positives = 35/91 (38%), Gaps = 10/91 (10%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           + ++V     D+TE++++  F  +G +          P   + + F+ +   Q +     
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVF-----IPKPFRAFAFVTFADDQIAQSLC- 59

Query: 93  SMNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
                 + G  + +  A    N   S+ GP+
Sbjct: 60  -GEDLIIKGISVHISNAEPKHN---SNSGPS 86

>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 = 53.9 bits (129), Expect = 5e-11
 Identities = 10/74 (13%), Positives = 31/74 (41%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             I V ++   ++ ++I   F  +  I      + +      G   + +E++  +  A+ 
Sbjct: 10  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 69

Query: 93  SMNLFDLGGQYLRV 106
            +N   +G + +++
Sbjct: 70  DLNDRPIGSRKVKL 83

>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 = 52.9 bits (126), Expect = 2e-10
 Identities = 12/80 (15%), Positives = 28/80 (35%), Gaps = 6/80 (7%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGP------IKYCKLQQGSSPHRHKGYGFIEYETKQA 86
           N ++V  +   L + ++    E FG       +        +         ++ Y   + 
Sbjct: 9   NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 87  SNEAISSMNLFDLGGQYLRV 106
           +  AI  +N   + G+ L+ 
Sbjct: 69  ALRAIQCVNNVVVDGRTLKA 88

>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 = 52.9 bits (126), Expect = 2e-10
 Identities = 20/77 (25%), Positives = 38/77 (49%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             +Y+ ++ P +TE D+ S+F  F   K   +Q      R +G  FI +  K+ + +A+ 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 93  SMNLFDLGGQYLRVGRA 109
            +N + L G+ L +   
Sbjct: 79  LVNGYKLYGKILVIEFG 95

>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 = 52.4 bits (125), Expect = 3e-10
 Identities = 12/84 (14%), Positives = 39/84 (46%), Gaps = 5/84 (5%)

Query: 26  TEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQ 85
           +++ +    +   ++  ++TE+++K VFE    I+           + KG  +IE++++ 
Sbjct: 10  SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEA 64

Query: 86  ASNEAISSMNLFDLGGQYLRVGRA 109
            + + +      ++ G+ + +   
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYYT 88

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 53.0 bits (126), Expect = 4e-10
 Identities = 26/111 (23%), Positives = 57/111 (51%), Gaps = 3/111 (2%)

Query: 2   QHFPHVQVGRPSNMPQAQS---VIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGP 58
           Q+ P+ Q  +   + Q Q       ++  E  +   + V  I   + E  ++ +FE +GP
Sbjct: 9   QYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGP 68

Query: 59  IKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA 109
           I+  K+       + +GYGF+++++  ++ +AI+ +N F++  + L+V  A
Sbjct: 69  IESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA 119

>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 = 51.6 bits (123), Expect = 5e-10
 Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 8/81 (9%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           N +YV     D+T   ++  F  FG I              +   F+ YE  +++++A++
Sbjct: 6   NTLYVYGE--DMTPTLLRGAFSPFGNIIDLS------MDPPRNCAFVTYEKMESADQAVA 57

Query: 93  SMNLFDLGGQYLRVGRAITPP 113
            +N   +    L+V  A   P
Sbjct: 58  ELNGTQVESVQLKVNIARKQP 78

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 8e-10
 Identities = 12/78 (15%), Positives = 31/78 (39%), Gaps = 6/78 (7%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
           RI V ++   +T + +  +F  FG +             ++    ++Y    ++  A  S
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFT----KNNQFQALLQYADPVSAQHAKLS 64

Query: 94  MNLFDL--GGQYLRVGRA 109
           ++  ++      LR+  +
Sbjct: 65  LDGQNIYNACCTLRIDFS 82

>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 = 51.6 bits (123), Expect = 8e-10
 Identities = 11/95 (11%), Positives = 37/95 (38%), Gaps = 2/95 (2%)

Query: 13  SNMPQAQSVIDEITEEAKL-YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPH 71
            N+ +      +  +  +   + + +   + +  EE    + E +G ++   +      H
Sbjct: 7   LNIYRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDH 66

Query: 72  RHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV 106
              G  ++++  ++ + +A+  +N     GQ +  
Sbjct: 67  -LVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA 100

>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 = 50.9 bits (121), Expect = 1e-09
 Identities = 12/100 (12%), Positives = 32/100 (32%), Gaps = 11/100 (11%)

Query: 33  NRIYVASIHPDLTEE-----DIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQAS 87
           + +     + D+  E       +S+F  +      +        +      I +    ++
Sbjct: 6   SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQY------FKSFKRVRINFSNPLSA 59

Query: 88  NEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTS 127
            +A   ++  +  G+ +++  A T          P P  S
Sbjct: 60  ADARLRLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKS 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 = 50.9 bits (121), Expect = 1e-09
 Identities = 25/94 (26%), Positives = 43/94 (45%), Gaps = 6/94 (6%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
              ++ ++  D+TEE IK  F           ++ S+P R KG+G+ E+E   +   +  
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSL-LSAL 74

Query: 93  SMNLFDLGGQYLRVGRAITPPNALHSSKGPAPST 126
           S+N   LG + +RV  A    +     K   PS+
Sbjct: 75  SLNEESLGNKRIRVDVADQAQD-----KDSGPSS 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 = 49.8 bits (118), Expect = 1e-09
 Identities = 15/71 (21%), Positives = 40/71 (56%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +Y+  + P  T++D+  + + +G I   K     + ++ KGYGF+++++  A+ +A++++
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 95  NLFDLGGQYLR 105
               +  Q  +
Sbjct: 61  KASGVQAQMAK 71

>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 = 49.0 bits (116), Expect = 6e-09
 Identities = 21/89 (23%), Positives = 44/89 (49%), Gaps = 6/89 (6%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             +++ ++  D  EE +  V + FG +KY ++         KG  F ++ T++A+ + ++
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 68

Query: 93  SMNL------FDLGGQYLRVGRAITPPNA 115
           + +L        L G+ L+V  A+T   A
Sbjct: 69  AASLEAEGGGLKLDGRQLKVDLAVTRDEA 97

>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 = 48.4 bits (115), Expect = 9e-09
 Identities = 17/102 (16%), Positives = 35/102 (34%), Gaps = 21/102 (20%)

Query: 12  PSNMPQAQSVI-------DEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL 64
           PS M   + VI        +  ++  + N I           ED++     FG I+   L
Sbjct: 2   PSRMRHERVVIIKNMFHPMDFEDDPLVLNEI----------REDLRVECSKFGQIRKLLL 51

Query: 65  QQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV 106
                     G   + +   + ++  I +++    GG+ +  
Sbjct: 52  FDR----HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 89

>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 = 47.4 bits (112), Expect = 2e-08
 Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 3/83 (3%)

Query: 33  NRIYVASIHPDLTEED-IKSVFEAFG-PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEA 90
             I + ++  +L +E+ ++  FE FG   K            +    F+ +E K ++  A
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 91  ISSMNLFDLGGQYLRVGRAITPP 113
           +  MN   LG + + V  A   P
Sbjct: 65  LQ-MNRSLLGNREISVSLADKKP 86

>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 = 47.2 bits (111), Expect = 2e-08
 Identities = 15/96 (15%), Positives = 31/96 (32%), Gaps = 10/96 (10%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           NR+ V+ + P  + +D+K      G + Y             G G +E+  K+    A+ 
Sbjct: 1   NRVVVSGLPPSGSWQDLKDHMREAGDVCYA-------DVYRDGTGVVEFVRKEDMTYAVR 53

Query: 93  SMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSH 128
            ++                  +     + P+   S 
Sbjct: 54  KLDNTKFRSHEGETAYIRVKVDG---PRSPSYGRSR 86

>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 = 47.0 bits (111), Expect = 3e-08
 Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 8/85 (9%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            R++V  + P+ +   +   F+ FG I+           +   + +I+YE+  A+  A +
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTID------HVKGDSFAYIQYESLDAAQAACA 71

Query: 93  SMNLFDLGGQY--LRVGRAITPPNA 115
            M  F LGG    LRV  A + P++
Sbjct: 72  KMRGFPLGGPDRRLRVDFAKSGPSS 96

>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 = 46.3 bits (109), Expect = 6e-08
 Identities = 14/97 (14%), Positives = 39/97 (40%), Gaps = 6/97 (6%)

Query: 33  NRIYVASIHPD-LTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
           + + V++++P+ +T + +  +F  +G ++  K+         K    ++      +  A+
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKIL-----FNKKENALVQMADGNQAQLAM 57

Query: 92  SSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSH 128
           S +N   L G+ +R+  +      L          + 
Sbjct: 58  SHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTK 94

>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 = 45.9 bits (108), Expect = 7e-08
 Identities = 17/91 (18%), Positives = 35/91 (38%), Gaps = 10/91 (10%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
           + I V ++  D   +++  + + +               R+K   F+     + +  AI 
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLKYCY-------VDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 93  SMNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
             + +   G+ L V     P +AL  S GP+
Sbjct: 59  MFHQYSFRGKDLIVQLQ--PTDALLCS-GPS 86

>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 = 45.9 bits (108), Expect = 8e-08
 Identities = 16/93 (17%), Positives = 30/93 (32%), Gaps = 12/93 (12%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
            R+ V+ + P  + +D+K      G + Y          +  G G +EY  K+    A+ 
Sbjct: 16  FRVLVSGLPPSGSWQDLKDHMREAGDVCYA-------DVQKDGMGMVEYLRKEDMEYALR 68

Query: 93  SMNLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
            ++                 P      +   PS
Sbjct: 69  KLDDTKFRSHEGETSYIRVYPE-----RSSGPS 96

>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 = 44.5 bits (104), Expect = 2e-07
 Identities = 12/75 (16%), Positives = 29/75 (38%), Gaps = 3/75 (4%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           + V ++     +  +   F+  GPI +  +    S  ++  +  IE+     +  AI+  
Sbjct: 3   VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVAD--SLKKNFRFARIEFARYDGALAAITKT 60

Query: 95  NLFDLGGQYLRVGRA 109
           +   +G   + V   
Sbjct: 61  H-KVVGQNEIIVSHL 74

>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 = 3e-07
 Identities = 11/77 (14%), Positives = 30/77 (38%), Gaps = 1/77 (1%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             +Y++++   + E++++++ + FG +   +     S    +G GF   E+ +     I 
Sbjct: 19  TNLYISNLPLSMDEQELENMLKPFGQVISTR-ILRDSSGTSRGVGFARMESTEKCEAVIG 77

Query: 93  SMNLFDLGGQYLRVGRA 109
             N   +          
Sbjct: 78  HFNGKFIKTPPGVSAPT 94

>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 = 44.1 bits (103), Expect = 4e-07
 Identities = 11/91 (12%), Positives = 32/91 (35%), Gaps = 2/91 (2%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
            ++ +I   +T+ D+    E     +        +  +  G   ++++ +  + ++   +
Sbjct: 11  AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE-RL 69

Query: 95  NLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
           +   L G+   V    T  +     K P   
Sbjct: 70  HRKKLNGREAFVHVV-TLEDMREIEKNPPAQ 99

>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 = 43.2 bits (101), Expect = 6e-07
 Identities = 16/78 (20%), Positives = 39/78 (50%), Gaps = 5/78 (6%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             +++++I P ++EED+K +F + G +            + +    I+  + + + +A+ 
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALI 66

Query: 93  SMNLFDLG-GQYLRVGRA 109
            ++  DLG   +LRV  +
Sbjct: 67  DLHNHDLGENHHLRVSFS 84

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.4 bits (99), Expect = 1e-06
 Identities = 12/73 (16%), Positives = 29/73 (39%), Gaps = 2/73 (2%)

Query: 34  RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
            +Y+     D T +DIK   E  G +   +  + +     KG  F+ +++ +++ + +  
Sbjct: 8   SVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDSIESAKKFV-E 65

Query: 94  MNLFDLGGQYLRV 106
                     L +
Sbjct: 66  TPGQKYKETDLLI 78

>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 = 42.4 bits (99), Expect = 2e-06
 Identities = 12/76 (15%), Positives = 24/76 (31%), Gaps = 11/76 (14%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +    +   ++   +  V E  G +             +K Y F  Y T + S  A  ++
Sbjct: 23  VANGGLGNGVSRNQLLPVLEKCGLVDALL------MPPNKPYSFARYRTTEESKRAYVTL 76

Query: 95  NLFDLGGQYLRVGRAI 110
           N     G+ +      
Sbjct: 77  N-----GKEVVDDLGQ 87

>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 = 42.0 bits (98), Expect = 2e-06
 Identities = 14/92 (15%), Positives = 35/92 (38%), Gaps = 8/92 (8%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           +++  +    TE DI + F    P++                  +E+ T + +  A++  
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTG--EADVEFATHEDAVAAMA-K 74

Query: 95  NLFDLGGQYLRVGRAITPPNALHSSKGPAPST 126
           +  ++  +Y+ +    T       + G  PS+
Sbjct: 75  DKANMQHRYVELFLNSTAG-----TSGSGPSS 101

>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 = 41.9 bits (97), Expect = 3e-06
 Identities = 6/77 (7%), Positives = 35/77 (45%), Gaps = 2/77 (2%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             +++ +++P+ +  ++K             +    +   ++ +G++++E+ +   +A+ 
Sbjct: 14  FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT-GTNRKFGYVDFESAEDLEKAL- 71

Query: 93  SMNLFDLGGQYLRVGRA 109
            +    + G  +++ + 
Sbjct: 72  ELTGLKVFGNEIKLEKP 88

>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 = 40.8 bits (95), Expect = 6e-06
 Identities = 12/83 (14%), Positives = 25/83 (30%), Gaps = 9/83 (10%)

Query: 35  IYVASIHPD-LTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS- 92
           +++            +  + E FG I                  FIE  T + +  A+  
Sbjct: 11  VHIMDFQRGKNLRYQLLQLVEPFGVISNHL------ILNKINEAFIEMATTEDAQAAVDY 64

Query: 93  -SMNLFDLGGQYLRVGRAITPPN 114
            +     + G+ +RV  +     
Sbjct: 65  YTTTPALVFGKPVRVHLSQKYKR 87

>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 = 40.3 bits (94), Expect = 7e-06
 Identities = 12/77 (15%), Positives = 23/77 (29%), Gaps = 9/77 (11%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           + V           +   F  +G I                +  I Y++K  + +A+ S 
Sbjct: 7   VTVFGFPQASASYILL-QFAQYGNILKHV------MSNTGNWMHIRYQSKLQARKAL-SK 58

Query: 95  NLFDLGGQY-LRVGRAI 110
           +    G    + V   I
Sbjct: 59  DGRIFGESIMIGVKPCI 75

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.6 bits (94), Expect = 1e-05
 Identities = 15/83 (18%), Positives = 26/83 (31%), Gaps = 7/83 (8%)

Query: 27  EEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETK-Q 85
           EE       +   +      ED+  +F   G IK+          R    G I ++ K +
Sbjct: 6   EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDF------VRGAKEGIILFKEKAK 59

Query: 86  ASNEAISSMNLFDLGGQYLRVGR 108
            +       N  +L  +   V  
Sbjct: 60  EALGKAKDANNGNLQLRNKEVTW 82

>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 = 39.6 bits (92), Expect = 2e-05
 Identities = 11/83 (13%), Positives = 27/83 (32%), Gaps = 6/83 (7%)

Query: 30  KLYNRIYVASIHPDL----TEEDIKSVFEAFGPIKYCKL--QQGSSPHRHKGYGFIEYET 83
            L N +    +  D       ED++     +G +K  ++            G  F+E+ +
Sbjct: 8   CLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTS 67

Query: 84  KQASNEAISSMNLFDLGGQYLRV 106
                +A+  +       + +  
Sbjct: 68  VFDCQKAMQGLTGRKFANRVVVT 90

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.0 bits (90), Expect = 3e-05
 Identities = 14/79 (17%), Positives = 28/79 (35%), Gaps = 8/79 (10%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             ++V  +   + E D+    E FG I Y  +         K    +E+E   ++ E ++
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMM------MPFKRQALVEFENIDSAKECVT 69

Query: 93  SMNL--FDLGGQYLRVGRA 109
                   + GQ      +
Sbjct: 70  FAADVPVYIAGQQAFFNYS 88

>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 = 38.8 bits (89), Expect = 4e-05
 Identities = 13/108 (12%), Positives = 29/108 (26%), Gaps = 8/108 (7%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             I   ++       +I+  F  FG +                   +E+     + +A  
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVL------LPEGGITAIVEFLEPLEARKAFR 64

Query: 93  SMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHMPTAAAVAAAAA 140
            +         L +  A  P     ++     S    P   A +  ++
Sbjct: 65  HLAYSKFHHVPLYLEWA--PIGVFGAAPQKKDSQHEQPAEKAESGPSS 110

>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 = 38.0 bits (87), Expect = 4e-05
 Identities = 14/82 (17%), Positives = 32/82 (39%), Gaps = 9/82 (10%)

Query: 35  IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
           I +  +  D+T +++  +   +               ++KG  F+     + +  AI++ 
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKYCFV-------DKYKGTAFVTLLNGEQAEAAINTF 53

Query: 95  NLFDLGGQYLRVGRAITPPNAL 116
           +   L  + L V     P +AL
Sbjct: 54  HQSRLRERELSVQLQ--PTDAL 73

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.0 bits (82), Expect = 3e-04
 Identities = 11/76 (14%), Positives = 32/76 (42%), Gaps = 8/76 (10%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             +++  +  ++TE ++ ++   FG +            + K   F+E  T++A+   ++
Sbjct: 9   RVLHIRKLPGEVTETEVIALGLPFGKVTNIL------MLKGKNQAFLELATEEAAITMVN 62

Query: 93  SMNL--FDLGGQYLRV 106
             +     L  Q + +
Sbjct: 63  YYSAVTPHLRNQPIYI 78

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.0 bits (82), Expect = 4e-04
 Identities = 9/77 (11%), Positives = 32/77 (41%), Gaps = 1/77 (1%)

Query: 33  NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
             + +  +    ++E+I   F     +            R  G  F+++ +++ + +A+ 
Sbjct: 16  GFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL- 74

Query: 93  SMNLFDLGGQYLRVGRA 109
             +   +G +Y+ + ++
Sbjct: 75  KKHKERIGHRYIEIFKS 91

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	173
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.91
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.91
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.91
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.91
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.91
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.9
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.9
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.9
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.9
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.9
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.9
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.9
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.89
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.89
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.89
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.89
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.89
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.89
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.89
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.89
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.89
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.89
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.88
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.88
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.88
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.88
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.88
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.87
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.87
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.87
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.87
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.87
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.87
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.87
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.87
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.86
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.86
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.85
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.85
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.85
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.85
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.85
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.84
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.84
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.83
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.83
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.83
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.83
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.83
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.83
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.83
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.83
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.83
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.82
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.82
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.82
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.82
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.81
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.81
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.81
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.81
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.8
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.79
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.79
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.79
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.79
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.79
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.78
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.78
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.78
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.77
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.76
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.76
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.75
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.75
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.74
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.71
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	99.66
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.64
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.6
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.59
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.54
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.53
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.45
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.73
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.6
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.49
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.44

>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=99.91  E-value=1.5e-24  Score=141.84  Aligned_cols=86  Identities=23%  Similarity=0.468  Sum_probs=81.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|.++++++++.+|.++|||||+|.+.++|++|++.|||..++|++|+|+++
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCCCCC
Q psy2141         110 ITPPNA  115 (173)
Q Consensus       110 ~~~~~~  115 (173)
                      +++...
T Consensus        87 ~~~~~n   92 (93)
T d1x5ua1          87 SAHNKN   92 (93)
T ss_dssp             TTTSCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.91  E-value=1.6e-24  Score=138.39  Aligned_cols=80  Identities=24%  Similarity=0.491  Sum_probs=77.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeC
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAIT  111 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~  111 (173)
                      .++|||+|||.++++++|+++|++||.|..+++.+++.+|+++|||||+|.+.++|++|++.|||..++|++|+|+|++|
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            57899999999999999999999999999999999989999999999999999999999999999999999999999875

>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=99.91  E-value=7.4e-24  Score=138.54  Aligned_cols=84  Identities=23%  Similarity=0.281  Sum_probs=80.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||.++++++|+++|++||+|.++.+++++.++.++|||||+|.+.++|+.|++.|||..++|++|+|+|+
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            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             eCCC
Q psy2141         110 ITPP  113 (173)
Q Consensus       110 ~~~~  113 (173)
                      ....
T Consensus        85 ~~~~   88 (93)
T d1h2vz_          85 AGFK   88 (93)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7543

>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=99.91  E-value=2.8e-24  Score=139.42  Aligned_cols=84  Identities=24%  Similarity=0.443  Sum_probs=79.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||+++++++|+++|++||+|.++.+++++.+|+++|||||+|.+.++|++|++.|||..++|++|+|+++
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a   82 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   82 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCCC
Q psy2141         110 ITPP  113 (173)
Q Consensus       110 ~~~~  113 (173)
                      +++.
T Consensus        83 ~p~~   86 (89)
T d2cqba1          83 KPMR   86 (89)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

>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=99.91  E-value=3.3e-24  Score=139.40  Aligned_cols=84  Identities=24%  Similarity=0.407  Sum_probs=80.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|++|++.|||..++|++|+|+|+
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            45679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCCC
Q psy2141         110 ITPP  113 (173)
Q Consensus       110 ~~~~  113 (173)
                      +++.
T Consensus        86 kp~~   89 (90)
T d2cq0a1          86 KPST   89 (90)
T ss_dssp             SCCC
T ss_pred             eCCC
Confidence            8754

>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=99.90  E-value=7.8e-24  Score=135.16  Aligned_cols=80  Identities=26%  Similarity=0.510  Sum_probs=76.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeC
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAIT  111 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~  111 (173)
                      .++|||+|||.++++++|+++|++||.|..+++++++.+|+++|||||+|.+.++|++|++.|||..++|++|+|+|++|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            35799999999999999999999999999999999989999999999999999999999999999999999999999875

>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=99.90  E-value=7.3e-24  Score=137.19  Aligned_cols=82  Identities=28%  Similarity=0.417  Sum_probs=78.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      ..++|||+|||.++++++|+++|++||.|.++++++++.+|+++|||||+|.+.++|++|++.|||..++|++|+|+|+.
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            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CC
Q psy2141         111 TP  112 (173)
Q Consensus       111 ~~  112 (173)
                      ++
T Consensus        86 ~k   87 (88)
T d1rk8a_          86 VK   87 (88)
T ss_dssp             EC
T ss_pred             CC
Confidence            65

>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=99.90  E-value=8.8e-24  Score=134.43  Aligned_cols=77  Identities=25%  Similarity=0.496  Sum_probs=75.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        34 ~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      +|||+|||+++++++|+++|++||.|.+++|++++.+|+++|||||+|.+.++|..|++.|||..+.|++|+|.|++
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            69999999999999999999999999999999999999999999999999999999999999999999999999985

>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=99.90  E-value=2e-23  Score=137.97  Aligned_cols=86  Identities=21%  Similarity=0.353  Sum_probs=81.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      ..++|||+|||+++++++|+++|++||.|..+++++++.+++++|||||+|.+.++|++|++.||+..++|++|+|.++.
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~   86 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST   86 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCCC
Q psy2141         111 TPPNAL  116 (173)
Q Consensus       111 ~~~~~~  116 (173)
                      ++....
T Consensus        87 ~~~~~~   92 (99)
T d1whwa_          87 IKKEAS   92 (99)
T ss_dssp             CCSTTC
T ss_pred             CCCccC
Confidence            765443

>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=99.90  E-value=2.5e-23  Score=145.49  Aligned_cols=86  Identities=23%  Similarity=0.513  Sum_probs=80.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||+++++++|+++|++||.|.++++++++.+|+++|||||+|.+.++|++|++.|||..|+|++|+|+++
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            44678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCCCCC
Q psy2141         110 ITPPNA  115 (173)
Q Consensus       110 ~~~~~~  115 (173)
                      +.....
T Consensus       120 ~~~~~~  125 (139)
T d1u6fa1         120 ASGHQR  125 (139)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            765443

>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=99.90  E-value=6.3e-24  Score=136.64  Aligned_cols=82  Identities=28%  Similarity=0.545  Sum_probs=78.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCC
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITP  112 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~  112 (173)
                      .+|||+|||.++++++|+++|++||+|..+++++|+.+|+++|||||+|.+.++|+.|++.|||..++|++|+|.++.+.
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            47999999999999999999999999999999999999999999999999999999999999999999999999999765


Q ss_pred             CC
Q psy2141         113 PN  114 (173)
Q Consensus       113 ~~  114 (173)
                      ..
T Consensus        82 ~~   83 (85)
T d2u2fa_          82 AK   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.90  E-value=1.1e-23  Score=139.95  Aligned_cols=85  Identities=21%  Similarity=0.405  Sum_probs=80.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ++.++|||+|||+++++++|+++|+.||.|..+++++++.+|.++|||||+|.+.++|++|++.|||..++|++|+|+|+
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            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCCCC
Q psy2141         110 ITPPN  114 (173)
Q Consensus       110 ~~~~~  114 (173)
                      +++.+
T Consensus        96 ~~k~~  100 (102)
T d2cpza1          96 RSKND  100 (102)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            87654

>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=99.89  E-value=3.7e-23  Score=134.35  Aligned_cols=85  Identities=27%  Similarity=0.471  Sum_probs=77.6

Q ss_pred             hhCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q psy2141          28 EAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG  107 (173)
Q Consensus        28 ~~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~  107 (173)
                      +..+.++|||+|||.++++++|+++|+.||+|..+++.+++.++  +|||||+|.+.++|++|++.|||..+.|+.|+|.
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~   81 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   81 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999986544  7899999999999999999999999999999999


Q ss_pred             EeeCCCC
Q psy2141         108 RAITPPN  114 (173)
Q Consensus       108 ~a~~~~~  114 (173)
                      |+++++.
T Consensus        82 ~a~~~~~   88 (90)
T d2cqia1          82 WATTPSS   88 (90)
T ss_dssp             ECCCTTC
T ss_pred             EcCCCCC
Confidence            9986543

>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=99.89  E-value=6.5e-23  Score=136.38  Aligned_cols=83  Identities=22%  Similarity=0.412  Sum_probs=77.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      ..++|||+|||+.+++++|+++|++||.|.++++++++.+|+++|||||+|.+.++|++|++.+++ .++|++|+|+++.
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            457899999999999999999999999999999999999999999999999999999999999876 7999999999987


Q ss_pred             CCCC
Q psy2141         111 TPPN  114 (173)
Q Consensus       111 ~~~~  114 (173)
                      ....
T Consensus        88 ~~~~   91 (103)
T d2cqda1          88 LGAK   91 (103)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            6543

>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=99.89  E-value=2.7e-23  Score=134.92  Aligned_cols=86  Identities=22%  Similarity=0.469  Sum_probs=80.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||+++++++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|++|++.|||..++|++|+|+++
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            35688999999999999999999999999999999999899999999999999999999999999999999999999999


Q ss_pred             eCCCCC
Q psy2141         110 ITPPNA  115 (173)
Q Consensus       110 ~~~~~~  115 (173)
                      .++...
T Consensus        83 ~~~~~~   88 (90)
T d1x5sa1          83 GKSSDN   88 (90)
T ss_dssp             ECCCCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.89  E-value=3.6e-23  Score=133.03  Aligned_cols=79  Identities=22%  Similarity=0.421  Sum_probs=75.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC--eEEEEEE
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG--QYLRVGR  108 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g--~~l~v~~  108 (173)
                      ..++|||+|||.++++++|+++|++||+|.++++++++.+|+++|||||+|.+.++|++|++.|||..+.|  ++|+|+|
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            46789999999999999999999999999999999999899999999999999999999999999999997  5699988


Q ss_pred             e
Q psy2141         109 A  109 (173)
Q Consensus       109 a  109 (173)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.89  E-value=3.2e-23  Score=133.22  Aligned_cols=80  Identities=25%  Similarity=0.443  Sum_probs=75.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC--eEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG--QYLRVG  107 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g--~~l~v~  107 (173)
                      ...++|||+|||.++++++|+++|++||.|..+++++++.+|+++|||||+|.+.++|++|++.|||..+.|  ++|+|+
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            356789999999999999999999999999999999999999999999999999999999999999999976  889999


Q ss_pred             Ee
Q psy2141         108 RA  109 (173)
Q Consensus       108 ~a  109 (173)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>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=99.89  E-value=2.7e-23  Score=133.03  Aligned_cols=77  Identities=26%  Similarity=0.446  Sum_probs=74.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRV  106 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v  106 (173)
                      .+.++|||+|||..+++++|+++|++||.|.++++++++.+|+++|||||+|.+.++|++|++.|||..++|++|+|
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            35679999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.89  E-value=5e-23  Score=133.72  Aligned_cols=83  Identities=17%  Similarity=0.349  Sum_probs=76.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||+++++++|+++|++||.|..++|++|+.+|+++|||||+|.+.++|++|++.  ...++|+.|.|+++
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeC
Confidence            4678999999999999999999999999999999999999999999999999999999999985  45899999999999


Q ss_pred             eCCCC
Q psy2141         110 ITPPN  114 (173)
Q Consensus       110 ~~~~~  114 (173)
                      .++..
T Consensus        84 ~~k~~   88 (90)
T d2cqga1          84 NSKQS   88 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            87543

>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=99.89  E-value=2.8e-23  Score=132.32  Aligned_cols=80  Identities=10%  Similarity=0.241  Sum_probs=70.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeC
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAIT  111 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~  111 (173)
                      .++|||+|||+++++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|++.|||..++|++|+|++++|
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            37999999999999999999999999999998888888999999999999999999999999999999999999999875

>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=99.89  E-value=9.8e-24  Score=139.93  Aligned_cols=83  Identities=17%  Similarity=0.295  Sum_probs=77.4

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ....++|||+|||+++++++|+++|+.||.|.++++++++.+|+++|||||+|.+.++|++|++ |||..++|+.|+|++
T Consensus        15 ~~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~   93 (101)
T d2cq4a1          15 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQA   93 (101)
T ss_dssp             HHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEE
Confidence            3446899999999999999999999999999999999999999999999999999999999995 999999999999999


Q ss_pred             eeCC
Q psy2141         109 AITP  112 (173)
Q Consensus       109 a~~~  112 (173)
                      +.++
T Consensus        94 a~~~   97 (101)
T d2cq4a1          94 SQAE   97 (101)
T ss_dssp             HHHH
T ss_pred             CCCC
Confidence            7643

>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=99.89  E-value=4.7e-23  Score=132.18  Aligned_cols=79  Identities=22%  Similarity=0.559  Sum_probs=75.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      ..++|||+|||+++++++|+++|++||.|..+++++|+.+|+++|||||+|.+.++|++|++ +++..++|+.|+|+.|.
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            45799999999999999999999999999999999999999999999999999999999996 58899999999999875

>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=99.88  E-value=6.5e-23  Score=134.23  Aligned_cols=84  Identities=25%  Similarity=0.461  Sum_probs=78.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCC-CCCCcceEEEEEEcCHHHHHHHHHhc-CCceeCCeEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS-SPHRHKGYGFIEYETKQASNEAISSM-NLFDLGGQYLRVG  107 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~-~~g~~~g~afv~f~~~~~a~~a~~~l-~g~~i~g~~l~v~  107 (173)
                      ...++|||+|||.++++++|+++|++||.|..+++++++ .+|+++|||||+|.+.++|++|++.| ||..+.|++|+|+
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            457889999999999999999999999999999998875 47999999999999999999999998 8999999999999


Q ss_pred             EeeCCC
Q psy2141         108 RAITPP  113 (173)
Q Consensus       108 ~a~~~~  113 (173)
                      |+....
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998654

>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=99.88  E-value=7.4e-23  Score=130.90  Aligned_cols=79  Identities=29%  Similarity=0.481  Sum_probs=74.7

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCceeEE-EEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCCC
Q psy2141          35 IYVASIHPDLTEEDIKSVFEAFGPIKYC-KLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPP  113 (173)
Q Consensus        35 l~V~nLp~~~~e~~L~~~F~~~G~v~~~-~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~~  113 (173)
                      |||+|||+++++++|+++|++||.|..+ ++++++.+|+++|||||+|.+.++|++|++.|+|..++|++|+|+++.++.
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            7999999999999999999999999764 789999999999999999999999999999999999999999999998654

>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=99.88  E-value=1.9e-23  Score=131.87  Aligned_cols=76  Identities=17%  Similarity=0.470  Sum_probs=73.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      |+|||+|||+++++++|+++|++||.|.++++++|+.+|+++|||||+|.+.++|++|++ +++..++|+.|+|+.|
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            689999999999999999999999999999999999999999999999999999999996 6999999999999876

>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=99.88  E-value=1.8e-22  Score=127.70  Aligned_cols=76  Identities=20%  Similarity=0.378  Sum_probs=73.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        34 ~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      +|||+|||+++++++|+++|++||.|..+++.+++ +|+++|||||+|.+.++|++|++.|||..++|++|+|+++.
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            69999999999999999999999999999999995 89999999999999999999999999999999999999975

>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=99.88  E-value=1.1e-22  Score=135.16  Aligned_cols=82  Identities=17%  Similarity=0.544  Sum_probs=77.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeC
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAIT  111 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~  111 (173)
                      .++|||+|||+++++++|+++|++||.|..+.|.+++.++.++|||||+|.+.++|++|++ +++..|+|+.|.|+++.+
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            5799999999999999999999999999999999999999999999999999999999995 699999999999999887


Q ss_pred             CCC
Q psy2141         112 PPN  114 (173)
Q Consensus       112 ~~~  114 (173)
                      +.+
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            654

>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=99.87  E-value=6e-23  Score=136.73  Aligned_cols=82  Identities=29%  Similarity=0.540  Sum_probs=78.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      +.++|||+|||.++++++|+++|++||.|..+++++++.+|+++|||||+|.+.++|++|++.|||..+.|++|+|+++.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             CC
Q psy2141         111 TP  112 (173)
Q Consensus       111 ~~  112 (173)
                      +.
T Consensus        87 ~~   88 (104)
T d1p1ta_          87 SE   88 (104)
T ss_dssp             CT
T ss_pred             CC
Confidence            54

>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=99.87  E-value=4.9e-22  Score=129.70  Aligned_cols=83  Identities=20%  Similarity=0.364  Sum_probs=76.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||+++++++|+++|++||.|..++++.++  +.++|||||+|.+.++|.+|++.|||..++|++|+|+++
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            457899999999999999999999999999999999985  346899999999999999999999999999999999999


Q ss_pred             eCCCC
Q psy2141         110 ITPPN  114 (173)
Q Consensus       110 ~~~~~  114 (173)
                      +++..
T Consensus        87 ~~r~~   91 (93)
T d2cq3a1          87 TARVM   91 (93)
T ss_dssp             CSSCC
T ss_pred             CcCCC
Confidence            87643

>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=99.87  E-value=1.7e-22  Score=129.73  Aligned_cols=78  Identities=24%  Similarity=0.515  Sum_probs=72.6

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCC---CcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeC
Q psy2141          35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPH---RHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAIT  111 (173)
Q Consensus        35 l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g---~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~  111 (173)
                      |||+|||+++++++|+++|++||.|..+++++++.++   .++|||||+|.+.++|++|++.|||..++|++|+|++++.
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            7999999999999999999999999999999886655   4689999999999999999999999999999999999864


Q ss_pred             C
Q psy2141         112 P  112 (173)
Q Consensus       112 ~  112 (173)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.87  E-value=2.4e-22  Score=130.13  Aligned_cols=82  Identities=29%  Similarity=0.519  Sum_probs=76.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      ...+|||+|||.++++++|+++|++||.|..++++.++  +.++|||||+|.+.++|++|++.|||..++|++|+|.+++
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 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   84 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            45689999999999999999999999999999999985  4478999999999999999999999999999999999998


Q ss_pred             CCCC
Q psy2141         111 TPPN  114 (173)
Q Consensus       111 ~~~~  114 (173)
                      ++++
T Consensus        85 ~~~~   88 (89)
T d1cvja2          85 SRKE   88 (89)
T ss_dssp             CTTT
T ss_pred             CCCC
Confidence            7654

>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=99.87  E-value=1.2e-22  Score=127.58  Aligned_cols=75  Identities=23%  Similarity=0.554  Sum_probs=71.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        34 ~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      +|||+|||++++|++|+++|++||.|..+.+.+++.+++++|||||+|.+.++|++|++ +++..++|+.|.|+.|
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            58999999999999999999999999999999999999999999999999999999997 6999999999998754

>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=99.87  E-value=3.7e-22  Score=131.30  Aligned_cols=85  Identities=22%  Similarity=0.442  Sum_probs=78.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcC------CceeCCeE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMN------LFDLGGQY  103 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~------g~~i~g~~  103 (173)
                      ...++|||+|||+++++++|+++|++||.|..+.+..++.+++++|||||+|.+.++|.+|++.|+      |..+.|++
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            457899999999999999999999999999999999999999999999999999999999999886      67899999


Q ss_pred             EEEEEeeCCCC
Q psy2141         104 LRVGRAITPPN  114 (173)
Q Consensus       104 l~v~~a~~~~~  114 (173)
                      |+|+++.++++
T Consensus        86 l~v~~a~~k~~   96 (98)
T d1x4ha1          86 LKVDLAVTRDE   96 (98)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEECCCCCc
Confidence            99999987644

>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=99.87  E-value=2.7e-22  Score=129.17  Aligned_cols=82  Identities=24%  Similarity=0.390  Sum_probs=71.9

Q ss_pred             CCCeEEEcCCCCCCC-HHHHHHHhhccCceeEEEEccC-CCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          31 LYNRIYVASIHPDLT-EEDIKSVFEAFGPIKYCKLQQG-SSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~-e~~L~~~F~~~G~v~~~~i~~~-~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ..++|||+|||.+++ +++|+++|++||.|..+++..+ +.+++++|||||+|.+.++|++|++ |||..++|+.|+|++
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            468999999999875 6679999999999999998764 5789999999999999999999995 999999999999999


Q ss_pred             eeCCC
Q psy2141         109 AITPP  113 (173)
Q Consensus       109 a~~~~  113 (173)
                      ++++|
T Consensus        82 a~~kP   86 (86)
T d2ghpa3          82 ADKKP   86 (86)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98764

>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=99.87  E-value=6.2e-22  Score=125.33  Aligned_cols=77  Identities=18%  Similarity=0.501  Sum_probs=73.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .++|||||||+++++++|+++|++||.|..+.+..++.+++++|||||+|.+.+++++|+ .++|..|+|++|+|++|
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 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH-HCSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHH-HhCCCEECCEEEEEEEC
Confidence            478999999999999999999999999999999999999999999999999999999999 47999999999999876

>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=99.87  E-value=4.8e-22  Score=131.49  Aligned_cols=86  Identities=22%  Similarity=0.344  Sum_probs=78.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCcee--------EEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIK--------YCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG  101 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~--------~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g  101 (173)
                      ...++|||+|||..+++++|+++|+.||.|.        .+.+.+++.+|+++|||||+|.+.++|.+|++.|||..|+|
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            4678999999999999999999999999874        57788888899999999999999999999999999999999


Q ss_pred             eEEEEEEeeCCCCC
Q psy2141         102 QYLRVGRAITPPNA  115 (173)
Q Consensus       102 ~~l~v~~a~~~~~~  115 (173)
                      ++|+|+++++++..
T Consensus        86 r~i~V~~a~~~~p~   99 (101)
T d2cpea1          86 SKLKVSLARKKPPM   99 (101)
T ss_dssp             EECEEECSSCCCCS
T ss_pred             EEEEEEEcCCCCCC
Confidence            99999999875443

>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=99.86  E-value=1e-21  Score=128.87  Aligned_cols=80  Identities=24%  Similarity=0.446  Sum_probs=74.2

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ..+.++|||+|||.++++++|+++|++||.|.++++..+      +|||||+|.+.++|++|++.|||..++|++|+|.|
T Consensus        15 ~~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~   88 (96)
T d1x4ga1          15 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   88 (96)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345679999999999999999999999999999999877      68999999999999999999999999999999999


Q ss_pred             eeCCCC
Q psy2141         109 AITPPN  114 (173)
Q Consensus       109 a~~~~~  114 (173)
                      +++.+.
T Consensus        89 ak~~p~   94 (96)
T d1x4ga1          89 GKESPD   94 (96)
T ss_dssp             CCCCCS
T ss_pred             cCCCCC
Confidence            987653

>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=99.86  E-value=2.8e-22  Score=125.78  Aligned_cols=75  Identities=21%  Similarity=0.517  Sum_probs=70.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        34 ~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      +|||||||+++++++|+++|++||+|..+++++++.+++++|||||+|.+.++|++|++. ++..++|+.|.|+.|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCCEECCEEeEEEEC
Confidence            599999999999999999999999999999999999999999999999999999999965 778899999998864

>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=99.85  E-value=7.4e-22  Score=123.69  Aligned_cols=75  Identities=24%  Similarity=0.584  Sum_probs=72.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        34 ~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      +|||+|||.+++|++|+++|++||.+..+.+.+++.++.++|||||+|.+.++|++|++ +||..++|++|+|++|
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            59999999999999999999999999999999999999999999999999999999996 8999999999999875

>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=99.85  E-value=1.7e-22  Score=133.91  Aligned_cols=85  Identities=24%  Similarity=0.344  Sum_probs=80.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+.+..+..+|+++|||||+|.+.++|++|++.|||..|.|++|+|+|+
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            46789999999999999999999999999999998888788999999999999999999999999999999999999999


Q ss_pred             eCCCC
Q psy2141         110 ITPPN  114 (173)
Q Consensus       110 ~~~~~  114 (173)
                      +++.+
T Consensus        96 k~k~~  100 (102)
T d2cpxa1          96 KNKKQ  100 (102)
T ss_dssp             CCCSC
T ss_pred             CCccc
Confidence            87654

>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=99.85  E-value=4.5e-21  Score=125.54  Aligned_cols=80  Identities=28%  Similarity=0.495  Sum_probs=73.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+.++|||+|||+++++++|+++|++||.|..+.+..+   +.++|||||+|.+.++|+.|++.|||..+.|++|+|+|+
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 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            45789999999999999999999999999999988654   456899999999999999999999999999999999998


Q ss_pred             eCC
Q psy2141         110 ITP  112 (173)
Q Consensus       110 ~~~  112 (173)
                      ++.
T Consensus        89 ~~~   91 (95)
T d1x4aa1          89 RSG   91 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            754

>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=99.85  E-value=4.2e-21  Score=129.59  Aligned_cols=79  Identities=19%  Similarity=0.411  Sum_probs=73.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||..+++++|+++|++||.|..|++..+   +.++|||||+|.+.++|..|++.|||..+.|++|+|.++
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            35789999999999999999999999999999999764   567999999999999999999999999999999999998


Q ss_pred             eC
Q psy2141         110 IT  111 (173)
Q Consensus       110 ~~  111 (173)
                      ..
T Consensus        82 ~~   83 (114)
T d2f9da1          82 NA   83 (114)
T ss_dssp             CH
T ss_pred             CC
Confidence            64

>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=99.85  E-value=2.5e-21  Score=123.69  Aligned_cols=77  Identities=17%  Similarity=0.295  Sum_probs=71.2

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeC-CeEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLG-GQYLRVG  107 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~-g~~l~v~  107 (173)
                      .+|.++|||+|||.++++++|+++|+.||.|..+++++++     +|||||+|.+.++|.+|++.|||..+. |++|+|+
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~   79 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKIT   79 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEE
Confidence            4578999999999999999999999999999999998763     789999999999999999999999885 6899999


Q ss_pred             Eee
Q psy2141         108 RAI  110 (173)
Q Consensus       108 ~a~  110 (173)
                      |++
T Consensus        80 ~ak   82 (83)
T d2b0ga1          80 FAK   82 (83)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            986

>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=99.84  E-value=8e-21  Score=121.88  Aligned_cols=78  Identities=15%  Similarity=0.181  Sum_probs=73.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      ..++|||+|||.++++++|+++|+.||+|..+++.+++ +|+++|||||+|.+.++|++|++ +++..+.|+.|.|.+..
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            46899999999999999999999999999999998885 89999999999999999999995 69999999999999864

>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=99.84  E-value=3.2e-22  Score=130.09  Aligned_cols=81  Identities=7%  Similarity=0.260  Sum_probs=74.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ....+|||+|||+++++++|+++|+.||.|..++++.+ .+|+++|||||+|.+.++|++|++ |||..++|++|+|+++
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            34668999999999999999999999999999988765 589999999999999999999996 8999999999999998


Q ss_pred             eCC
Q psy2141         110 ITP  112 (173)
Q Consensus       110 ~~~  112 (173)
                      +.+
T Consensus        89 k~k   91 (91)
T d1fjeb1          89 KGR   91 (91)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            753

>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=99.83  E-value=1.5e-20  Score=120.77  Aligned_cols=79  Identities=20%  Similarity=0.315  Sum_probs=71.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||.++++++|+++|++||.+..+.+..      ++|||||+|.+.++|.+|+..|||..|+|+.|+|+|+
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~a   79 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA   79 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            3468999999999999999999999999998887743      4799999999999999999999999999999999999


Q ss_pred             eCCCC
Q psy2141         110 ITPPN  114 (173)
Q Consensus       110 ~~~~~  114 (173)
                      +|+..
T Consensus        80 kP~~~   84 (86)
T d2cpda1          80 KPVDK   84 (86)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            87654

>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=99.83  E-value=1.7e-20  Score=124.62  Aligned_cols=85  Identities=28%  Similarity=0.440  Sum_probs=74.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCC-CCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS-SPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~-~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      .+.++|||+|||+++++++|+++|+.|| +..+.++.++ .+++++|||||+|.+.++|++|+ .||+..|+|+.|+|++
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-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEE
Confidence            3578999999999999999999999999 7777777764 47889999999999999998777 5999999999999999


Q ss_pred             eeCCCCCC
Q psy2141         109 AITPPNAL  116 (173)
Q Consensus       109 a~~~~~~~  116 (173)
                      +.++....
T Consensus        91 a~~~~~~~   98 (104)
T d1wi8a_          91 ADQAQDKD   98 (104)
T ss_dssp             CCCCCCCC
T ss_pred             CCCCCCCC
Confidence            98765543

>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=99.83  E-value=1.8e-21  Score=128.85  Aligned_cols=80  Identities=14%  Similarity=0.266  Sum_probs=74.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||.++++++|+++|++||.|..+.+..+ .++.++|||||+|.+.++|.+|++.|||..|.|+++.|.++
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            45689999999999999999999999999999999988 48899999999999999999999999999999998888665


Q ss_pred             e
Q psy2141         110 I  110 (173)
Q Consensus       110 ~  110 (173)
                      +
T Consensus        95 ~   95 (101)
T d1x5oa1          95 E   95 (101)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.83  E-value=1e-20  Score=124.05  Aligned_cols=84  Identities=18%  Similarity=0.283  Sum_probs=74.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCc-eeEEEEccCC-CCCCcceEEEEEEcCHHHHHHHHHhcCC--ceeCCeEEEEE
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGP-IKYCKLQQGS-SPHRHKGYGFIEYETKQASNEAISSMNL--FDLGGQYLRVG  107 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~-v~~~~i~~~~-~~g~~~g~afv~f~~~~~a~~a~~~l~g--~~i~g~~l~v~  107 (173)
                      .++|||+|||.++++++|+++|++||. |..+.++++. .+++++|||||+|.+.++|.+|++.|++  ..++|++|+|+
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            368999999999999999999999996 8999999875 4688999999999999999999999965  55679999999


Q ss_pred             EeeCCCCC
Q psy2141         108 RAITPPNA  115 (173)
Q Consensus       108 ~a~~~~~~  115 (173)
                      |++++...
T Consensus        81 ~A~p~~~~   88 (96)
T d2disa1          81 WAEPEIDV   88 (96)
T ss_dssp             ESCSSCST
T ss_pred             EcCCCCCC
Confidence            99875544

>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=99.83  E-value=6.8e-21  Score=122.48  Aligned_cols=76  Identities=32%  Similarity=0.576  Sum_probs=71.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      ..++|||+|||.++++++|+++|++||.|.++++.++      +|||||+|.+.++|++|++.|||..+.|++|+|+|+.
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            4568999999999999999999999999999999876      6899999999999999999999999999999999987


Q ss_pred             CC
Q psy2141         111 TP  112 (173)
Q Consensus       111 ~~  112 (173)
                      ..
T Consensus        81 ~~   82 (86)
T d2cpja1          81 HS   82 (86)
T ss_dssp             CC
T ss_pred             Cc
Confidence            64

>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=99.83  E-value=7.4e-21  Score=123.04  Aligned_cols=76  Identities=18%  Similarity=0.358  Sum_probs=69.8

Q ss_pred             CCeEEEcCCCCCCCHHHH---HHHhhccCceeEEEEccCCCCCCc---ceEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q psy2141          32 YNRIYVASIHPDLTEEDI---KSVFEAFGPIKYCKLQQGSSPHRH---KGYGFIEYETKQASNEAISSMNLFDLGGQYLR  105 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L---~~~F~~~G~v~~~~i~~~~~~g~~---~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~  105 (173)
                      .++|||+|||+++++++|   +++|++||.|..+.+.+++.++.+   +|||||+|.+.++|.+|++.|||..++|++|+
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   678999999999999998766654   48999999999999999999999999999999


Q ss_pred             EE
Q psy2141         106 VG  107 (173)
Q Consensus       106 v~  107 (173)
                      |+
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            85

>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=99.83  E-value=1e-20  Score=124.07  Aligned_cols=80  Identities=15%  Similarity=0.291  Sum_probs=73.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ++.++|||+|||.++++++|+++|++||.|..+..     +++++|||||+|.+.++|++|++.|||..++|++|+|.|+
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a   88 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45789999999999999999999999999877653     6778999999999999999999999999999999999999


Q ss_pred             eCCCC
Q psy2141         110 ITPPN  114 (173)
Q Consensus       110 ~~~~~  114 (173)
                      .++..
T Consensus        89 ~~k~~   93 (96)
T d1fjca_          89 GEKGG   93 (96)
T ss_dssp             SSSCC
T ss_pred             CCCCC
Confidence            87654

>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=99.83  E-value=7.2e-21  Score=123.59  Aligned_cols=82  Identities=20%  Similarity=0.425  Sum_probs=73.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHH----HhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKS----VFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLR  105 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~----~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~  105 (173)
                      +|+++|||+|||+++++++|++    +|++||.|..|++..   +++++|||||+|.+.++|.+|++.|||..++|++|+
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            3679999999999999998864    689999999998754   467899999999999999999999999999999999


Q ss_pred             EEEeeCCCC
Q psy2141         106 VGRAITPPN  114 (173)
Q Consensus       106 v~~a~~~~~  114 (173)
                      |.|++++++
T Consensus        78 v~~ak~~~~   86 (91)
T d1nu4a_          78 IQYAKTDSD   86 (91)
T ss_dssp             EEECSSCCT
T ss_pred             EEEeCCCch
Confidence            999987643

>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=99.83  E-value=1.2e-20  Score=119.39  Aligned_cols=76  Identities=22%  Similarity=0.392  Sum_probs=70.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|++  +++++|+++|++||.|.++++.++      +|||||+|.+.++|.+|++.|||..++|++|+|.|+
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            457899999996  899999999999999999999765      689999999999999999999999999999999999


Q ss_pred             eCCC
Q psy2141         110 ITPP  113 (173)
Q Consensus       110 ~~~~  113 (173)
                      +++|
T Consensus        75 ~~~P   78 (79)
T d2bz2a1          75 RKQP   78 (79)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            8654

>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=99.82  E-value=7.1e-21  Score=120.77  Aligned_cols=76  Identities=20%  Similarity=0.428  Sum_probs=68.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCc-eeCCeEEEEEEeeC
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLF-DLGGQYLRVGRAIT  111 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~-~i~g~~l~v~~a~~  111 (173)
                      ++|||+|||.++++++|+++|++||.|..+.+..      ++|||||+|.+.++|++|++.|||. .++|++|+|+|+.+
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            5799999999999999999999999988776654      4799999999999999999999995 69999999999987


Q ss_pred             CCC
Q psy2141         112 PPN  114 (173)
Q Consensus       112 ~~~  114 (173)
                      +..
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            654

>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=99.82  E-value=2.1e-20  Score=120.59  Aligned_cols=79  Identities=19%  Similarity=0.271  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCcee-CCeEEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDL-GGQYLRVGR  108 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i-~g~~l~v~~  108 (173)
                      .|+++|||+|||.++++++|+++|++||.|..+.+..+    +++|||||+|.+.++|.+|+..|||..+ +|++|+|+|
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 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            46789999999999999999999999999988877554    3578999999999999999999999988 589999999


Q ss_pred             eeCC
Q psy2141         109 AITP  112 (173)
Q Consensus       109 a~~~  112 (173)
                      +++.
T Consensus        84 sk~~   87 (88)
T d2adca2          84 SKST   87 (88)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            8753

>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=99.82  E-value=2.5e-20  Score=122.61  Aligned_cols=77  Identities=22%  Similarity=0.553  Sum_probs=69.5

Q ss_pred             CCCCeEEEcCCC-CCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          30 KLYNRIYVASIH-PDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        30 ~~~~~l~V~nLp-~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ...++|||+||| ..+++++|+++|++||.|..+++        ++|||||+|.+.++|++|++.|||..+.|++|+|++
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            346789999997 56889999999999999999998        379999999999999999999999999999999999


Q ss_pred             eeCCCC
Q psy2141         109 AITPPN  114 (173)
Q Consensus       109 a~~~~~  114 (173)
                      ++++..
T Consensus        85 a~~~~~   90 (98)
T d1wf2a_          85 AAEPKV   90 (98)
T ss_dssp             TTSCCC
T ss_pred             CCCCCC
Confidence            976433

>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=99.82  E-value=4e-21  Score=119.49  Aligned_cols=71  Identities=21%  Similarity=0.555  Sum_probs=68.5

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q psy2141          35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLR  105 (173)
Q Consensus        35 l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~  105 (173)
                      |||+|||.++++++|+++|++||.|..+++.+++.++.++|+|||+|.+.++|++|++.|||..++|+.|+
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            79999999999999999999999999999999999999999999999999999999999999999998764

>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=99.82  E-value=2.1e-20  Score=125.47  Aligned_cols=78  Identities=13%  Similarity=0.132  Sum_probs=71.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      +..++|||+|||.++++++|+++|++||.|..|.|..      ++|||||+|.+.++|++|++.|||..+.|++|.|+|+
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a   81 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEEC
Confidence            4567999999999999999999999999999998843      4799999999999999999999999999999999999


Q ss_pred             eCCC
Q psy2141         110 ITPP  113 (173)
Q Consensus       110 ~~~~  113 (173)
                      ....
T Consensus        82 ~~~~   85 (111)
T d1whxa_          82 PIGV   85 (111)
T ss_dssp             ETTT
T ss_pred             CCCc
Confidence            7654

>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=99.81  E-value=3.6e-20  Score=123.89  Aligned_cols=76  Identities=17%  Similarity=0.327  Sum_probs=70.6

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          32 YNRIYVASIHP-DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        32 ~~~l~V~nLp~-~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      .++|||+|||+ .+++++|+++|+.||.|..+.+++++     +|||||+|.+.++|.+|++.|||..+.|+.|+|++++
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            57899999965 59999999999999999999999874     7999999999999999999999999999999999987


Q ss_pred             CC
Q psy2141         111 TP  112 (173)
Q Consensus       111 ~~  112 (173)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.81  E-value=6.1e-20  Score=120.51  Aligned_cols=79  Identities=29%  Similarity=0.551  Sum_probs=72.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCC--eEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGG--QYLRVG  107 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g--~~l~v~  107 (173)
                      .+.++|||+|||.++++++|+++|++||.|..+++.++      ++||||+|.+.++|++|++.||+..|.|  ++|+|+
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            46789999999999999999999999999999999765      6899999999999999999999999986  589999


Q ss_pred             EeeCCCC
Q psy2141         108 RAITPPN  114 (173)
Q Consensus       108 ~a~~~~~  114 (173)
                      |+++.+.
T Consensus        89 ~ak~~~~   95 (97)
T d1whya_          89 FAKSGPS   95 (97)
T ss_dssp             ECCCCCC
T ss_pred             eCCCCCC
Confidence            9986543

>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=99.81  E-value=3.5e-20  Score=119.55  Aligned_cols=80  Identities=14%  Similarity=0.316  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||++++|++|+++|++||.|..+++..+     ++|||||+|.+.++|++|+.  ++..|+|++|+|+++
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 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec-----cCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC
Confidence            35789999999999999999999999999999987543     58999999999999999984  788999999999999


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      .++....
T Consensus        76 ~~k~~~~   82 (88)
T d1wf0a_          76 EPKHNSN   82 (88)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            8765443

>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=99.81  E-value=2.9e-20  Score=119.36  Aligned_cols=78  Identities=14%  Similarity=0.190  Sum_probs=70.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEE-EEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYC-KLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~-~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...+|||+|||+++++++|+++|+.||.+... .+..+ .+++++|+|||+|.+.++|++|++.||+..++|++|+|.++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~-~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeC-CCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45679999999999999999999999998764 45554 68999999999999999999999999999999999999874

>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=99.80  E-value=1e-19  Score=117.33  Aligned_cols=76  Identities=20%  Similarity=0.369  Sum_probs=66.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      ..++|||+|||.++++++|+++|++|| +..+.+      +.++|||||+|.+.++|++|++.||+..++|++|+|++++
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            467899999999999999999999999 333433      3458999999999999999999999999999999999986


Q ss_pred             CCC
Q psy2141         111 TPP  113 (173)
Q Consensus       111 ~~~  113 (173)
                      ...
T Consensus        77 ~~~   79 (88)
T d1wg1a_          77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.79  E-value=2.6e-19  Score=112.06  Aligned_cols=74  Identities=15%  Similarity=0.246  Sum_probs=67.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ++|||+|||+++++++|+++|+.||.|..+++..++.  ..++||||+|.+.++|++|+ .+|+..++|++|.|..+
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--KNFRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            4899999999999999999999999999999999863  34679999999999999999 58999999999999864

>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=99.79  E-value=3e-19  Score=118.54  Aligned_cols=85  Identities=11%  Similarity=0.177  Sum_probs=75.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      .+..+|||+|||+++++++|+++|+.+|.+....++.+..+++++|+|||+|.+.++|++|++ +|+..|+|+.|+|.++
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            456789999999999999999999999999886666666789999999999999999999995 8999999999999999


Q ss_pred             eCCCCC
Q psy2141         110 ITPPNA  115 (173)
Q Consensus       110 ~~~~~~  115 (173)
                      .+....
T Consensus        92 ~~~~~~   97 (104)
T d1wg5a_          92 SRAEVR   97 (104)
T ss_dssp             CTTTSC
T ss_pred             CHHHhc
Confidence            766433

>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=99.79  E-value=3.1e-19  Score=115.02  Aligned_cols=78  Identities=15%  Similarity=0.197  Sum_probs=71.3

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhc--CCceeCCeEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM--NLFDLGGQYLRV  106 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l--~g~~i~g~~l~v  106 (173)
                      ..|+++|||+|||.++++++|+++|++||.|..+++..+      +++|||+|.+.++|++|++.+  ++..+.|++|+|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            468999999999999999999999999999999998865      589999999999999999865  568899999999


Q ss_pred             EEeeCC
Q psy2141         107 GRAITP  112 (173)
Q Consensus       107 ~~a~~~  112 (173)
                      .|++.+
T Consensus        79 ~~sk~~   84 (88)
T d2cq1a1          79 QYSNHK   84 (88)
T ss_dssp             EECSCS
T ss_pred             EECCCC
Confidence            998754

>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=99.79  E-value=1.8e-19  Score=119.30  Aligned_cols=84  Identities=15%  Similarity=0.181  Sum_probs=74.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ....+|||+|||+++++++|+++|..|| +..+.++++. +++.+|||||+|.+.++|++|++ ||+..|+||.|+|.++
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s   89 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            4567999999999999999999999997 5577787774 78999999999999999999985 8999999999999998


Q ss_pred             eCCCCCC
Q psy2141         110 ITPPNAL  116 (173)
Q Consensus       110 ~~~~~~~  116 (173)
                      .+.+...
T Consensus        90 ~~~~~~~   96 (102)
T d1weza_          90 STAGTSG   96 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            8765443

>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=99.79  E-value=4.6e-19  Score=110.88  Aligned_cols=71  Identities=21%  Similarity=0.412  Sum_probs=64.3

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCC
Q psy2141          35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITP  112 (173)
Q Consensus        35 l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~  112 (173)
                      |||+|||.++++++|+++|++|| +..+.+      ++++|||||+|.+.++|++|++.|||..+.|++|+|++++..
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 555554      345899999999999999999999999999999999998654

>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=99.79  E-value=6.4e-19  Score=116.95  Aligned_cols=81  Identities=17%  Similarity=0.237  Sum_probs=72.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhc--CCceeCCeEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM--NLFDLGGQYLRVG  107 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l--~g~~i~g~~l~v~  107 (173)
                      .+.++|||+|||..++|++|+++|++||.|..+.+.++      +|+|||+|.+.++|++|++.|  ++..+.|++|+|.
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            57889999999999999999999999999999999765      689999999999999999988  5567889999999


Q ss_pred             EeeCCCCCC
Q psy2141         108 RAITPPNAL  116 (173)
Q Consensus       108 ~a~~~~~~~  116 (173)
                      |++.+....
T Consensus        87 ~s~~~~~~~   95 (104)
T d1wexa_          87 YSTSKRITR   95 (104)
T ss_dssp             ECSSSSCCC
T ss_pred             EcCCCccCC
Confidence            997654443

>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=99.78  E-value=2.4e-19  Score=117.81  Aligned_cols=81  Identities=19%  Similarity=0.281  Sum_probs=73.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||+++++++|+++|++||.|..+.+.+       +|||||+|.+.++|++|++.|||..+.|+.|+|.+.
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            3567899999999999999999999999999999864       489999999999999999999999999999999999


Q ss_pred             eCCCCCCC
Q psy2141         110 ITPPNALH  117 (173)
Q Consensus       110 ~~~~~~~~  117 (173)
                      +..+....
T Consensus        86 ~~~~~~~~   93 (98)
T d1wg4a_          86 RVYPERSS   93 (98)
T ss_dssp             EEECCCSS
T ss_pred             ecCCCCCC
Confidence            87665443

>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=99.78  E-value=5.7e-20  Score=118.29  Aligned_cols=74  Identities=18%  Similarity=0.281  Sum_probs=67.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeCC
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITP  112 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~~  112 (173)
                      ++|||+|||+++++++|+++|++||.|..+++..+       |||||+|.+.++|++|++.|||..+.|+.|+|.+++..
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            46999999999999999999999999999998654       79999999999999999999999999999998887654


Q ss_pred             C
Q psy2141         113 P  113 (173)
Q Consensus       113 ~  113 (173)
                      +
T Consensus        74 ~   74 (87)
T d3begb1          74 V   74 (87)
T ss_dssp             E
T ss_pred             c
Confidence            3

>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=99.78  E-value=2.2e-19  Score=119.99  Aligned_cols=81  Identities=15%  Similarity=0.160  Sum_probs=72.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCcee--CCeEEEEE
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDL--GGQYLRVG  107 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i--~g~~l~v~  107 (173)
                      .+..+|||+|||+.+++++|+++|++||.|..+.+.+++    ++|+|||+|.+.++|++|++.|||..+  .+++|+|.
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            356789999999999999999999999999999998764    589999999999999999999999998  47889999


Q ss_pred             EeeCCCC
Q psy2141         108 RAITPPN  114 (173)
Q Consensus       108 ~a~~~~~  114 (173)
                      ++++...
T Consensus        81 ~s~~~~~   87 (108)
T d2adba1          81 FSKLTSL   87 (108)
T ss_dssp             ECSSCSC
T ss_pred             ecCCccc
Confidence            9876543

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=4e-19  Score=117.70  Aligned_cols=81  Identities=10%  Similarity=0.067  Sum_probs=71.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ....+|||+|||+++++++|+++|..||.+..+.++....+|+++|+|||+|.+.++|++|++ ||+..|+|+.|.|.++
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            345789999999999999999999999998775444444699999999999999999999996 8999999999999887


Q ss_pred             eC
Q psy2141         110 IT  111 (173)
Q Consensus       110 ~~  111 (173)
                      ..
T Consensus        85 ~~   86 (103)
T d2cpya1          85 TL   86 (103)
T ss_dssp             CH
T ss_pred             CH
Confidence            53

>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=99.76  E-value=4.7e-19  Score=116.63  Aligned_cols=79  Identities=19%  Similarity=0.258  Sum_probs=71.2

Q ss_pred             hCCCCeEEEcCCCCC-CCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHH--hcCCceeCCeEEE
Q psy2141          29 AKLYNRIYVASIHPD-LTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS--SMNLFDLGGQYLR  105 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~-~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~--~l~g~~i~g~~l~  105 (173)
                      ..+.++|||+|||.+ +++++|+++|++||.|..+.+.++      +|+|||+|.+.++|.+|++  .+++..++|++|+
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~   88 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   88 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEE
Confidence            356789999999985 899999999999999999999876      6899999999999999998  4688899999999


Q ss_pred             EEEeeCCC
Q psy2141         106 VGRAITPP  113 (173)
Q Consensus       106 v~~a~~~~  113 (173)
                      |.+++.++
T Consensus        89 V~~s~~~~   96 (99)
T d1x4fa1          89 VDLSEKYK   96 (99)
T ss_dssp             EEEECSCS
T ss_pred             EEEcCCcc
Confidence            99997654

>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=99.76  E-value=2.9e-18  Score=123.94  Aligned_cols=83  Identities=17%  Similarity=0.463  Sum_probs=77.7

Q ss_pred             hCCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEE
Q psy2141          29 AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGR  108 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~  108 (173)
                      ....++|||+|||..+++++|+++|+.||.|..+.+..++.+|+++|||||+|.+.++|.+|++ +++..+.|++|+|.+
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~  172 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRK  172 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEE
T ss_pred             ccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEe
Confidence            4567899999999999999999999999999999999999899999999999999999999996 788999999999999


Q ss_pred             eeCC
Q psy2141         109 AITP  112 (173)
Q Consensus       109 a~~~  112 (173)
                      +.++
T Consensus       173 A~~k  176 (183)
T d1u1qa_         173 ALSK  176 (183)
T ss_dssp             CCCH
T ss_pred             cCCc
Confidence            8654

>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=99.75  E-value=2.5e-18  Score=110.90  Aligned_cols=78  Identities=15%  Similarity=0.131  Sum_probs=70.5

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhc--CCceeCCeEEEE
Q psy2141          30 KLYNRIYVASIHPD-LTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM--NLFDLGGQYLRV  106 (173)
Q Consensus        30 ~~~~~l~V~nLp~~-~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l--~g~~i~g~~l~v  106 (173)
                      ++.++|||+|||.. +++++|.++|++||.|..+.+..+      +++|||+|.+.++|..|++.|  ++..+.|++|+|
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            57899999999986 889999999999999999999876      579999999999999999966  678899999999


Q ss_pred             EEeeCCC
Q psy2141         107 GRAITPP  113 (173)
Q Consensus       107 ~~a~~~~  113 (173)
                      +|++..+
T Consensus        80 ~~s~~~~   86 (89)
T d1x4da1          80 HLSQKYK   86 (89)
T ss_dssp             EEECCCT
T ss_pred             EECCCcc
Confidence            9997543

>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=99.75  E-value=1.8e-18  Score=114.77  Aligned_cols=83  Identities=11%  Similarity=0.078  Sum_probs=72.3

Q ss_pred             CCCCeEEEcCCCCCC-CH----HHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEE
Q psy2141          30 KLYNRIYVASIHPDL-TE----EDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYL  104 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~-~e----~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l  104 (173)
                      ...++|||+||+.++ ++    ++|+++|+.||.|.++++++.      +++|||+|.+.++|.+|++.|||..++|++|
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            357899999999875 33    569999999999999999764      6899999999999999999999999999999


Q ss_pred             EEEEeeCCCCCCCC
Q psy2141         105 RVGRAITPPNALHS  118 (173)
Q Consensus       105 ~v~~a~~~~~~~~~  118 (173)
                      +|.|+++.......
T Consensus        77 ~v~~a~~~~~~~~~   90 (104)
T d1weya_          77 KLYFAQTLHIGSSH   90 (104)
T ss_dssp             EEECCCCSSCCSCC
T ss_pred             EEeecccCCCCCcc
Confidence            99999876554433

>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=99.74  E-value=9.8e-19  Score=117.55  Aligned_cols=80  Identities=11%  Similarity=0.233  Sum_probs=71.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          30 KLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        30 ~~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ...++|||+|||+++++++|+++|+.||.+..+.++.+..+|.++|+|||+|.+.++|++|++ ||+..|+|+.|.|..+
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEc
Confidence            457799999999999999999999999998775555555789999999999999999999995 8999999999999876


Q ss_pred             e
Q psy2141         110 I  110 (173)
Q Consensus       110 ~  110 (173)
                      .
T Consensus        95 ~   95 (112)
T d1wela1          95 T   95 (112)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.71  E-value=7e-20  Score=118.54  Aligned_cols=77  Identities=22%  Similarity=0.375  Sum_probs=67.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEcc-----CCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQ-----GSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG  107 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~-----~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~  107 (173)
                      ++|||+|||.+++|++|+++|++||.+..+.+..     +..+++++|||||+|.+.++|++|++ |||..+.|++|+|+
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            6899999999999999999999999887665542     34577889999999999999999985 99999999999997


Q ss_pred             Eee
Q psy2141         108 RAI  110 (173)
Q Consensus       108 ~a~  110 (173)
                      +++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>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=99.66  E-value=6.6e-18  Score=111.96  Aligned_cols=76  Identities=12%  Similarity=0.202  Sum_probs=71.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEe
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA  109 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a  109 (173)
                      ..++|++++.+++|++|+++|++||.|.+|+|.++ .+++++|+|||+|.+.++|.+|++.|||+.++|++|+|++.
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            35788899889999999999999999999999887 58999999999999999999999999999999999999884

>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=99.64  E-value=3.5e-16  Score=102.97  Aligned_cols=67  Identities=19%  Similarity=0.287  Sum_probs=60.5

Q ss_pred             hhCCCCeEEEcC--CCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeC
Q psy2141          28 EAKLYNRIYVAS--IHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLG  100 (173)
Q Consensus        28 ~~~~~~~l~V~n--Lp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~  100 (173)
                      ...+.++|||+|  ||.++++++|+++|++||.|..+.+..+      ++||||+|.+.++|.+|++.|||+.+.
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            346788999955  9999999999999999999999998776      679999999999999999999998873

>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=99.60  E-value=1.1e-15  Score=110.05  Aligned_cols=81  Identities=21%  Similarity=0.560  Sum_probs=73.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEeeC
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAIT  111 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~~  111 (173)
                      .++|||+|||+++++++|+++|++||.|..+.++++..++.++|||||+|.+.++|++|+.. ++..++++.+.+.+...
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhhhh
Confidence            47999999999999999999999999999999999999999999999999999999999965 56778888888877654


Q ss_pred             CC
Q psy2141         112 PP  113 (173)
Q Consensus       112 ~~  113 (173)
                      ..
T Consensus        85 ~~   86 (183)
T d1u1qa_          85 RE   86 (183)
T ss_dssp             TT
T ss_pred             cc
Confidence            43

>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=99.59  E-value=1.2e-15  Score=102.36  Aligned_cols=74  Identities=18%  Similarity=0.236  Sum_probs=65.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCH-HHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETK-QASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~-~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      ...+||||||..+|+++|+++|++||+|..|.++++      +|||||.|.+. ++|..|+..|++..+.++.+.|.+..
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            445699999999999999999999999999999865      79999999985 78999999999999888877777765


Q ss_pred             C
Q psy2141         111 T  111 (173)
Q Consensus       111 ~  111 (173)
                      .
T Consensus        85 ~   85 (113)
T d1owxa_          85 L   85 (113)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.54  E-value=1.6e-14  Score=94.55  Aligned_cols=80  Identities=14%  Similarity=0.226  Sum_probs=68.9

Q ss_pred             CCCCeEEEcCC--CCCCC---------HHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCce
Q psy2141          30 KLYNRIYVASI--HPDLT---------EEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFD   98 (173)
Q Consensus        30 ~~~~~l~V~nL--p~~~~---------e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~   98 (173)
                      ...++|+|.||  |.++.         +++|++.|++||.|..+.+..+    ..+|++||+|.+.++|.+|+..|||..
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            46889999999  54321         2679999999999999998665    367999999999999999999999999


Q ss_pred             eCCeEEEEEEeeCCC
Q psy2141          99 LGGQYLRVGRAITPP  113 (173)
Q Consensus        99 i~g~~l~v~~a~~~~  113 (173)
                      ++|++|+|.+..++.
T Consensus        82 ~~gr~i~v~~~~g~~   96 (99)
T d2dita1          82 FGGRQITAQAWDGTT   96 (99)
T ss_dssp             ETTEECEEEECCSCC
T ss_pred             ECCEEEEEEEeCCcC
Confidence            999999999987654

>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=99.53  E-value=8.7e-15  Score=92.29  Aligned_cols=72  Identities=17%  Similarity=0.176  Sum_probs=61.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeE-EEEEEee
Q psy2141          32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQY-LRVGRAI  110 (173)
Q Consensus        32 ~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~-l~v~~a~  110 (173)
                      .+.|+|+++|++.+++.| +.|++||.|.++++.++      +||+||+|.+.++|++|++ +||..++|+. |.|..+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~------~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC------CCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            467999999999886655 57999999999987543      7999999999999999995 8999999985 4677764


Q ss_pred             C
Q psy2141         111 T  111 (173)
Q Consensus       111 ~  111 (173)
                      .
T Consensus        76 ~   76 (81)
T d1wwha1          76 D   76 (81)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=5.3e-14  Score=92.74  Aligned_cols=81  Identities=11%  Similarity=0.163  Sum_probs=69.1

Q ss_pred             CCCCeEEEcCC--CCCCC--------HHHHHHHhhccCceeEEEEccCCCC--CCcceEEEEEEcCHHHHHHHHHhcCCc
Q psy2141          30 KLYNRIYVASI--HPDLT--------EEDIKSVFEAFGPIKYCKLQQGSSP--HRHKGYGFIEYETKQASNEAISSMNLF   97 (173)
Q Consensus        30 ~~~~~l~V~nL--p~~~~--------e~~L~~~F~~~G~v~~~~i~~~~~~--g~~~g~afv~f~~~~~a~~a~~~l~g~   97 (173)
                      .|++.|.+.||  |.++.        .++|++.|++||.|.++.|.++..+  ....|++||+|.+.++|.+|++.|||.
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            47889999999  54433        2568999999999999999886544  335689999999999999999999999


Q ss_pred             eeCCeEEEEEEee
Q psy2141          98 DLGGQYLRVGRAI  110 (173)
Q Consensus        98 ~i~g~~l~v~~a~  110 (173)
                      .++||+|.+.+..
T Consensus        82 ~f~gR~v~v~f~~   94 (104)
T d1o0pa_          82 KFANRVVVTKYCD   94 (104)
T ss_dssp             CSSSSCCEEEEEC
T ss_pred             EECCeEEEEEEcC
Confidence            9999999999975

>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=97.73  E-value=0.00016  Score=42.45  Aligned_cols=61  Identities=18%  Similarity=0.289  Sum_probs=52.1

Q ss_pred             HHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEEee
Q psy2141          47 EDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAI  110 (173)
Q Consensus        47 ~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i~g~~l~v~~a~  110 (173)
                      +.|...|.++|.|..+.+... ..|.  -.|-|...+..+|.-++..|+...|++++|.|.++.
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 QLLQEAFARHGKVKSVELSPH-TDYQ--LKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSC-CSTT--CCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEec-cCCc--EEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            346668889999999998776 2343  479999999999999999999999999999999864

>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=97.60  E-value=0.00015  Score=45.14  Aligned_cols=69  Identities=9%  Similarity=0.212  Sum_probs=57.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCC--cceEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2141          33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHR--HKGYGFIEYETKQASNEAISSMNLFDLGG  101 (173)
Q Consensus        33 ~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~--~~g~afv~f~~~~~a~~a~~~l~g~~i~g  101 (173)
                      ++|.|++||+.++|+++.+.++..|.+........+.+-+  .-.-|+|.|.+.++.....+..+|+.+.+
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            5789999999999999999999999888877766654433  23568999999999999999999987643

>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=97.49  E-value=0.00018  Score=44.43  Aligned_cols=72  Identities=14%  Similarity=0.359  Sum_probs=56.9

Q ss_pred             hCCCCeEEEcCCCCCC------CH---HHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcCCcee
Q psy2141          29 AKLYNRIYVASIHPDL------TE---EDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDL   99 (173)
Q Consensus        29 ~~~~~~l~V~nLp~~~------~e---~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~g~~i   99 (173)
                      .++.-||.|.=.....      .|   .+|.+.|..||.|.-++++.+        --.|+|.+-++|.+|+ .++|.++
T Consensus        12 GPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al-~l~g~~v   82 (95)
T d1ufwa_          12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVL-DVDGMKV   82 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHH-HGGGSEE
T ss_pred             CCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHh-ccCCeEE
Confidence            3567777774443222      22   468889999999999999876        4799999999999999 6699999


Q ss_pred             CCeEEEEEEe
Q psy2141         100 GGQYLRVGRA  109 (173)
Q Consensus       100 ~g~~l~v~~a  109 (173)
                      .|+.|+|...
T Consensus        83 ~G~~l~It~~   92 (95)
T d1ufwa_          83 KGRAVKISGP   92 (95)
T ss_dssp             TTEEEEEECC
T ss_pred             cceEEEEecC
Confidence            9999998754

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.44  E-value=0.078  Score=32.72  Aligned_cols=57  Identities=14%  Similarity=0.301  Sum_probs=45.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCceeEEEEccCCCCCCcceEEEEEEcCHHHHHHHHHhcC
Q psy2141          31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMN   95 (173)
Q Consensus        31 ~~~~l~V~nLp~~~~e~~L~~~F~~~G~v~~~~i~~~~~~g~~~g~afv~f~~~~~a~~a~~~l~   95 (173)
                      ...-||.-..|..+...+|.++|+.||.|.---| -|       --|||...+.++++.++..+.
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-dd-------TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DD-------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ET-------TEEEEECSCHHHHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cC-------ceEEEEecCHHHHHHHHHHhc
Confidence            3456888899999999999999999997754433 22       269999999999999887654