Citrus Sinensis ID: 022827

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-
Protein Sequence
MATHVDMSLDDIIKSRKKSERERGQGRARRGRGRGRGPSGSVSGGRMTGAARRGPLSNARPSSYTIAKSFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNAEIPLQARVNVTGVNGRRKRTVVMTSGSGNAGGAAAINRGPGSQGRRGGLRRSSQGRGRGQGQGRGRGRGGGGGGGRGRGRGRGRGQGKKNPVDKSADDLDKELDNYHAEAMQI
Secondary Structure (PSIPRED)
ccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccccccccccEEEEccccccccHHHHHHHHHHcccccEEEEEccccccccEEEEEEEccHHHHHHHHHHHccccccccEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHHcHHHHHEEEEccccccccccEEEEccHHHHHHHHHHHcccccccccEEEEEEEccccccccccccccccccccccEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MATHVDMSLDDIIKSRKKSERERgqgrarrgrgrgrgpsgsvsggrmtgaarrgplsnarpssytIAKSFrrtrnfpwqhdlfEDSLRAAGISGIEVGTKLYvsnlhpgvtndDIRELFSEIGELKRYAIhfdkngrpsgsAEVVYARRSDAFAALKRYNnvlldgkpmkievvgtnaeiplqarvnvtgvngrrKRTVVMtsgsgnaggaaainrgpgsqgrrgglrrssqgrgrgqgqgrgrgrgggggggrgrgrgrgrgqgkknpvdksadDLDKELDNYHAEAMQI
Flexible Loop (DISEMBL)
mathvdmslddiiksrkkserergqgrarrgrgrgrgpsgsvsggrmtgaarrgplsnarpssYTIAKSFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAihfdkngrpsgSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVvgtnaeiplqarvnvtgvngrrKRTVVmtsgsgnaggaaainrgpgsqgrrgglrrssqgrgrgqgqgrgrgrgggggggrgrgrgrgrgqgkknpvdksaddldkELDNYHAEAMQI
Low Complexity Region (SEG)
MATHVDMSLDDIIKSRKKSErergqgrarrgrgrgrgpsgsvsggrMTGAARRGPLSNARPSSYTIAKSFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNAEIPLQARVNVTGVNGRRKRTVVMTsgsgnaggaaaINrgpgsqgrrgglrrssqgrgrgqgqgrgrgrgggggggrgrgrgrgrgqgKKNPVDKSADDLDKELDNYHAEAMQI
Disordered region (IsUnstruct)
*****************************************************************IAKSFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGR**GSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNAEIPLQARVNVTGVNGR*************************************************************************************************
Disordered Region (DISOPRED)
*ATHVDMSLD******************************************************************************************LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG*****************************************************************************************************LDKELDNYHAEAMQI
Disordered Region (DISEMBL)
MATHVDMSLDDIIKS***********************************ARRGPLSNARPSSYTIAKSFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNAEIPLQARVNVTGVNGRRKRTVVMTSGSGNAGGAAAINRG*******************************************************SADDLDKELDNYHAEAMQI
Disordered Region (DISPRO)
*******SL****************************************************************************S*RAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNAEIPLQARVNVTGVNGRRKRTVVMTSGSGNAGGAAAINRGPGS**R***************************************************DDLDKELDNYHAEAMQ*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MATHVDMSLDDIIKSRKKSERERGQGRARRGRGRGRGPSGSVSGGRMTGAARRGPLSNARPSSYTIAKSFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNAEIPLQARVNVTGVNGRRKRTVVMTSGSGNAGGAAAINRGPGSQGRRGGLRRSSQGRGRGQGQGRGRGRGGGGGGGRGRGRGRGRGQGKKNPVDKSADDLDKELDNYHAEAMQI
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	291	2.2.26 [Sep-21-2011]
Q9JJW6	218	RNA and export factor-bin	yes	no	0.525	0.701	0.414	4e-27
B5FXN8	254	THO complex subunit 4 OS=	yes	no	0.587	0.673	0.434	2e-25
Q58EA2	256	THO complex subunit 4-A O	N/A	no	0.405	0.460	0.442	1e-24
Q28FB9	260	THO complex subunit 4 OS=	yes	no	0.405	0.453	0.435	5e-24
Q6GLW1	256	THO complex subunit 4-B O	N/A	no	0.405	0.460	0.450	5e-23
O08583	255	THO complex subunit 4 OS=	no	no	0.570	0.650	0.393	3e-22
Q86V81	257	THO complex subunit 4 OS=	yes	no	0.371	0.420	0.437	1e-20
Q3T0I4	257	THO complex subunit 4 OS=	yes	no	0.371	0.420	0.437	2e-20
Q9BY77	421	Polymerase delta-interact	no	no	0.254	0.175	0.481	1e-13
Q8BG81	420	Polymerase delta-interact	no	no	0.254	0.176	0.481	1e-13

>sp|Q9JJW6|REFP2_MOUSE RNA and export factor-binding protein 2 OS=Mus musculus GN=Refbp2 PE=1 SV=1

 Score =  122 bits (305), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 75/181 (41%), Positives = 101/181 (55%), Gaps = 28/181 (15%)

Query: 1   MATHVDMSLDDIIKSRKKSERERGQGRARRGRGRGRGPSGSVSGGRMTGAARRGPLSNAR 60
           MA  +DMSLDDIIK        R Q R  RG G  R       GGR             R
Sbjct: 1   MADKMDMSLDDIIKL------NRNQRRVNRGGGPRRNRPAIARGGR------------NR 42

Query: 61  PSSYTIAKSFRRTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIREL 118
           P+ Y+      R +  P  WQHDLF+      G  G+E G KL VSNL  GV++ DI+EL
Sbjct: 43  PAPYS------RPKPLPDKWQHDLFDSG--CGGGEGVETGAKLLVSNLDFGVSDADIQEL 94

Query: 119 FSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNA 178
           F+E G LK+ A+ +D++GR  G+A+V + RR+DA  A+K+Y  V LDG+PM I++V +  
Sbjct: 95  FAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI 154

Query: 179 E 179
           +
Sbjct: 155 D 155

Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Integral part of the THO/TREX complex that is recruited to transcribed genes and travels with the RNA polymerase during elongation (By similarity). Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.
Mus musculus (taxid: 10090)

>sp|B5FXN8|THOC4_TAEGU THO complex subunit 4 OS=Taeniopygia guttata GN=ALYREF PE=2 SV=1

 Score =  116 bits (290), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 83/191 (43%), Positives = 112/191 (58%), Gaps = 20/191 (10%)

Query: 1   MATHVDMSLDDIIKSRKKSERERGQGRARRGRGRGRGPSGSVSGGRMTGAARRGPLSN-- 58
           MA  +DMSLDDIIK  +        GR  RGRG      G   GG   G A  GP+ N  
Sbjct: 1   MADKMDMSLDDIIKLNRSQRGASRGGRGGRGRGGTARGGGPGRGGVGGGRAGGGPVRNRP 60

Query: 59  --------ARPSSYTIAKSFRRTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNLHP 108
                    RP+ Y+      R +  P  WQHDLF DS   AG +G+E G KL VSNL  
Sbjct: 61  VMARGGGRNRPAPYS------RPKQLPEKWQHDLF-DSGFGAG-AGVETGGKLLVSNLDF 112

Query: 109 GVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKP 168
           GV++ DI+ELF+E G LK+ A+H+D++GR  G+A+V + R++DA  A+K+YN V LDG+P
Sbjct: 113 GVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRP 172

Query: 169 MKIEVVGTNAE 179
           M I++V +  +
Sbjct: 173 MNIQLVTSQID 183

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.

Taeniopygia guttata (taxid: 59729)

>sp|Q58EA2|THO4A_XENLA THO complex subunit 4-A OS=Xenopus laevis GN=alyref-a PE=2 SV=1

 Score =  114 bits (284), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 58/131 (44%), Positives = 87/131 (66%), Gaps = 13/131 (9%)

Query: 60  RPSSYTIAKSFRRTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRE 117
           RP+ Y+      R +  P  WQHDLF+    A   +G+E G KL VSNL  GV++ DI+E
Sbjct: 73  RPTPYS------RPKQLPDKWQHDLFDSGFGAG--AGMETGGKLLVSNLDFGVSDADIQE 124

Query: 118 LFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTN 177
           LF+E G LK+ A+H+D++GR  G+A+V + R++DA  A+K+YN V LDG+PM I++V + 
Sbjct: 125 LFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTSQ 184

Query: 178 AEI---PLQAR 185
            E    P+Q++
Sbjct: 185 IEAQRRPIQSQ 195

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.

Xenopus laevis (taxid: 8355)

>sp|Q28FB9|THOC4_XENTR THO complex subunit 4 OS=Xenopus tropicalis GN=alyref PE=2 SV=1

 Score =  112 bits (279), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 57/131 (43%), Positives = 86/131 (65%), Gaps = 13/131 (9%)

Query: 60  RPSSYTIAKSFRRTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRE 117
           RP+ Y+      R +  P  WQHDLF+        +G+E G KL VSNL  GV++ DI+E
Sbjct: 76  RPAPYS------RPKQLPDKWQHDLFDSGFGTG--AGMETGGKLLVSNLDFGVSDADIQE 127

Query: 118 LFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTN 177
           LF+E G LK+ A+H+D++GR  G+A+V + R++DA  A+K+YN V LDG+PM I++V + 
Sbjct: 128 LFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTSQ 187

Query: 178 AEI---PLQAR 185
            E    P+Q++
Sbjct: 188 IEAQRRPIQSQ 198

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.

Xenopus tropicalis (taxid: 8364)

>sp|Q6GLW1|THO4B_XENLA THO complex subunit 4-B OS=Xenopus laevis GN=alyref-b PE=2 SV=1

 Score =  108 bits (270), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 59/131 (45%), Positives = 87/131 (66%), Gaps = 13/131 (9%)

Query: 60  RPSSYTIAKSFRRTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRE 117
           RP+ Y+      R +  P  WQHDLF DS    G +G+E G KL VSNL  GV++ DI+E
Sbjct: 72  RPTPYS------RPKQLPDKWQHDLF-DSGFGTG-AGMETGGKLLVSNLDFGVSDADIQE 123

Query: 118 LFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTN 177
           LF+E G LK+ A+H+D++GR  G+A+V + R++DA  A+K+YN V LDG+ M I++V + 
Sbjct: 124 LFAEFGSLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRSMNIQLVTSQ 183

Query: 178 AEI---PLQAR 185
            E    P+Q++
Sbjct: 184 IEAQRRPIQSQ 194

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.

Xenopus laevis (taxid: 8355)

>sp|O08583|THOC4_MOUSE THO complex subunit 4 OS=Mus musculus GN=Alyref PE=1 SV=3

 Score =  105 bits (263), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 78/198 (39%), Positives = 107/198 (54%), Gaps = 32/198 (16%)

Query: 1   MATHVDMSLDDIIKSRKKSERERGQGRARRGRGRGRGPSGSVSGGRMTGAARR----GPL 56
           MA  +DMSLDDIIK  +     RG GR R   G   G  G+V       AAR     GP+
Sbjct: 1   MADKMDMSLDDIIKLNRSQRGGRGGGRGRGRAGSQGGRGGAVQA-----AARVNRGGGPM 55

Query: 57  SN-------------ARPSSYTIAKSFRRTRNFP--WQHDLFEDSLRAAGISGIEVGTKL 101
            N              RP+ Y+      R +  P  WQHDLF+             G KL
Sbjct: 56  RNRPAIARGAAGGGRNRPAPYS------RPKQLPDKWQHDLFDSGFGGGAGVE--TGGKL 107

Query: 102 YVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNN 161
            VSNL  GV++ DI+ELF+E G LK+ A+H+D++GR  G+A+V + R++DA  A+K+YN 
Sbjct: 108 LVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNG 167

Query: 162 VLLDGKPMKIEVVGTNAE 179
           V LDG+PM I++V +  +
Sbjct: 168 VPLDGRPMNIQLVTSQID 185

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Plays a role in mRNA processing and export. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. May function as scaffold that mediates interactions between proteins and/or RNA. Integral part of the THO/TREX complex that is recruited to transcribed genes and travels with the RNA polymerase during elongation. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.

Mus musculus (taxid: 10090)

>sp|Q86V81|THOC4_HUMAN THO complex subunit 4 OS=Homo sapiens GN=ALYREF PE=1 SV=3

 Score =  100 bits (249), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 49/112 (43%), Positives = 73/112 (65%), Gaps = 4/112 (3%)

Query: 70  FRRTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKR 127
           + R +  P  WQHDLF+             G KL VSNL  GV++ DI+ELF+E G LK+
Sbjct: 77  YSRPKQLPDKWQHDLFDSGFGGGAGVE--TGGKLLVSNLDFGVSDADIQELFAEFGTLKK 134

Query: 128 YAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNAE 179
            A+H+D++GR  G+A+V + R++DA  A+K+YN V LDG+PM I++V +  +
Sbjct: 135 AAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTSQID 186

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay. Directs mRNA derived from Herpes simplex virus intron-less genes to the NXF1-mediated export pathway.

Homo sapiens (taxid: 9606)

>sp|Q3T0I4|THOC4_BOVIN THO complex subunit 4 OS=Bos taurus GN=ALYREF PE=2 SV=1

 Score =  100 bits (248), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 49/112 (43%), Positives = 73/112 (65%), Gaps = 4/112 (3%)

Query: 70  FRRTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKR 127
           + R +  P  WQHDLF+             G KL VSNL  GV++ DI+ELF+E G LK+
Sbjct: 77  YSRPKQLPDKWQHDLFDSGFGGGAGVE--TGGKLLVSNLDFGVSDADIQELFAEFGTLKK 134

Query: 128 YAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNAE 179
            A+H+D++GR  G+A+V + R++DA  A+K+YN V LDG+PM I++V +  +
Sbjct: 135 AAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTSQID 186

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Integral part of the THO/TREX complex that is recruited to transcribed genes and travels with the RNA polymerase during elongation. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.

Bos taurus (taxid: 9913)

>sp|Q9BY77|PDIP3_HUMAN Polymerase delta-interacting protein 3 OS=Homo sapiens GN=POLDIP3 PE=1 SV=2

 Score = 77.0 bits (188), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 40/83 (48%), Positives = 52/83 (62%), Gaps = 9/83 (10%)

Query: 92  ISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRY-AIHFDKNGRPSGSAEVVYARRS 150
           +S +E GTK+ V+NLHP VT +DI ELF   G LKR   +H        G AEVV+ ++ 
Sbjct: 274 LSPLE-GTKMTVNNLHPRVTEEDIVELFCVCGALKRARLVH-------PGVAEVVFVKKD 325

Query: 151 DAFAALKRYNNVLLDGKPMKIEV 173
           DA  A K+YNN  LDG+PMK  +
Sbjct: 326 DAITAYKKYNNRCLDGQPMKCNL 348

Is involved in regulation of translation. Is preferentially associated with CBC-bound spliced mRNA-protein complexes during the pioneer round of mRNA translation. Contributes to enhanced translational efficiency of spliced over nonspliced mRNAs. Recruits activated ribosomal protein S6 kinase beta-1 I/RPS6KB1 to newly synthesized mRNA.

Homo sapiens (taxid: 9606)

>sp|Q8BG81|PDIP3_MOUSE Polymerase delta-interacting protein 3 OS=Mus musculus GN=Poldip3 PE=2 SV=1

 Score = 77.0 bits (188), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 40/83 (48%), Positives = 52/83 (62%), Gaps = 9/83 (10%)

Query: 92  ISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRY-AIHFDKNGRPSGSAEVVYARRS 150
           +S +E GTK+ V+NLHP VT +DI ELF   G LKR   +H        G AEVV+ ++ 
Sbjct: 274 LSPLE-GTKMTVNNLHPRVTEEDIVELFCVCGALKRARLVH-------PGVAEVVFVKKD 325

Query: 151 DAFAALKRYNNVLLDGKPMKIEV 173
           DA  A K+YNN  LDG+PMK  +
Sbjct: 326 DAITAYKKYNNRCLDGQPMKCNL 348

Is involved in regulation of translation. Is preferentially associated with CBC-bound spliced mRNA-protein complexes during the pioneer round of mRNA translation. Contributes to enhanced translational efficiency of spliced over nonspliced mRNAs. Recruits activated ribosomal protein S6 kinase beta-1 I/RPS6KB1 to newly synthesized mRNA.

Mus musculus (taxid: 10090)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	291
224069282	274	predicted protein [Populus trichocarpa]	0.903	0.959	0.636	1e-84
356537904	298	PREDICTED: uncharacterized protein LOC10	0.962	0.939	0.626	1e-81
356569696	298	PREDICTED: THO complex subunit 4-like [G	0.955	0.932	0.612	9e-81
449456227	286	PREDICTED: THO complex subunit 4-like [C	0.975	0.993	0.611	2e-80
255582255	268	RNA and export factor binding protein, p	0.914	0.992	0.601	7e-80
225453197	269	PREDICTED: THO complex subunit 4 [Vitis	0.910	0.985	0.648	9e-78
147860765	348	hypothetical protein VITISV_029873 [Viti	0.941	0.787	0.605	5e-75
224077330	264	predicted protein [Populus trichocarpa]	0.876	0.965	0.577	3e-71
357460875	291	THO complex subunit [Medicago truncatula	0.945	0.945	0.577	1e-70
449532026	368	PREDICTED: THO complex subunit 4-like, p	0.676	0.535	0.678	3e-66

>gi|224069282|ref|XP_002302945.1| predicted protein [Populus trichocarpa] gi|222844671|gb|EEE82218.1| predicted protein [Populus trichocarpa]

 Score =  318 bits (816), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 191/300 (63%), Positives = 223/300 (74%), Gaps = 37/300 (12%)

Query: 1   MATHVDMSLDDIIKSRKKSERERGQGRARRGRGRGRGPSGSVSGGRMTGAARRGPLS-NA 59
           MA  VDMSLDDIIK  K  ER RG+GRA RGRGRGRGP  S + GRM+GA RRGPLS N 
Sbjct: 1   MAATVDMSLDDIIK--KNRERGRGRGRASRGRGRGRGPVRSFNNGRMSGAVRRGPLSVNT 58

Query: 60  RPSSYTIAKSF-------RRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTN 112
            PS Y+IAK+        RR R+ PWQHDL EDS+RAAGI+G+EVGTKLYVSNL  GVTN
Sbjct: 59  WPSKYSIAKASSKLWMPSRRVRSLPWQHDLLEDSIRAAGITGVEVGTKLYVSNLDYGVTN 118

Query: 113 DDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE 172
           +DIRELF+E+G+LKRYA+H+DK+GR SGSAEV+Y RRSDAFAALK+YNNVLLDGKPMKIE
Sbjct: 119 EDIRELFAEVGDLKRYAVHYDKDGRSSGSAEVMYTRRSDAFAALKKYNNVLLDGKPMKIE 178

Query: 173 VVGTNAEIPLQARVNVTGVNGRRKRTVVMTSGSGNAGGAAAINRGPGSQGRRGG--LRRS 230
           +VG N  +P+ AR+NVTG NG++KRTVV T                  Q RRGG  LR  
Sbjct: 179 IVGPNPVVPISARMNVTGANGKKKRTVVTT------------------QSRRGGGDLRNG 220

Query: 231 SQGRGRGQGQGRGRGRGGGGGGGRGRGRGRGRGQGKKNPVDKSADDLDKELDNYHAEAMQ 290
           ++  GRGQ  GRGR        GRG+  GRGRG+GKK PV+KS D+LDKEL++YHAEAMQ
Sbjct: 221 TRN-GRGQAPGRGR------APGRGQAPGRGRGRGKKQPVEKSVDELDKELESYHAEAMQ 273

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356537904|ref|XP_003537446.1| PREDICTED: uncharacterized protein LOC100820344 [Glycine max]

 Score =  309 bits (791), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 193/308 (62%), Positives = 220/308 (71%), Gaps = 28/308 (9%)

Query: 1   MATHVDMSLDDIIKSRKKSERERG----------------QGRARRGRGRGRGPSGSVSG 44
           MA+ +DMSLDD IK+R  +                      GR   G    R  +G+ +G
Sbjct: 1   MASSLDMSLDDRIKNRSNNRGRGRGGRGRAHSGRGPSGTLNGRRMVGAVNSRRMAGAGNG 60

Query: 45  GRMTGAARRGPLS-NARPSSYTIAKSFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYV 103
           GR TGA RRGPL  N RPSSY IAKS RR R FPWQHDLFEDSLRAAGI G+EVGTKLYV
Sbjct: 61  GRTTGAVRRGPLMVNTRPSSYAIAKSIRRARPFPWQHDLFEDSLRAAGIQGVEVGTKLYV 120

Query: 104 SNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVL 163
           SNL  GVTN+DIRELFSE+GELKR+A+H+DKNG PSGSAEVVY RRSDAFAALKRYNNVL
Sbjct: 121 SNLDHGVTNEDIRELFSELGELKRFAVHYDKNGHPSGSAEVVYTRRSDAFAALKRYNNVL 180

Query: 164 LDGKPMKIEVVGTNAEIPLQARVNVTGVNGRRKRTVVMTSGSGNAGGAAAINRGPGSQGR 223
           LDGKPMKIE+VG+N+E+P+ ARVNVTGVNGRRKRTVVMTS  G AGG  A+         
Sbjct: 181 LDGKPMKIEIVGSNSELPISARVNVTGVNGRRKRTVVMTSRGGQAGGGPAM--------- 231

Query: 224 RGGLRRSSQGRGRGQGQGRGRGRGGGGGGGRGRGRGRGRGQGKKNPVDKSADDLDKELDN 283
               R +  GR  G   G GRG  GG G GRGRG   GRG+G+K+ V+KSA++LDKEL+ 
Sbjct: 232 --PTRGAGWGRRGGPRSGSGRGGAGGRGRGRGRGGAGGRGRGRKDAVEKSAEELDKELET 289

Query: 284 YHAEAMQI 291
           YHAEAM I
Sbjct: 290 YHAEAMNI 297

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356569696|ref|XP_003553032.1| PREDICTED: THO complex subunit 4-like [Glycine max]

 Score =  306 bits (783), Expect = 9e-81,   Method: Compositional matrix adjust.
 Identities = 190/310 (61%), Positives = 215/310 (69%), Gaps = 32/310 (10%)

Query: 1   MATHVDMSLDDIIKSRKKSERERGQGRARRGRGRGRGPSGSVSGGRM------------- 47
           MA+ +DMSLDD IK+R    R RG             PSG+++GGRM             
Sbjct: 1   MASSLDMSLDDRIKNRSNRGRGRGGRGRAHSGRG---PSGALNGGRMAGAVSSRRMAGAS 57

Query: 48  -----TGAARRGPLS-NARPSSYTIAKSFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKL 101
                TGA RRGPL  N RPSSY IAKS RR R FPWQHDLFEDSLRAAGI G+EVGTKL
Sbjct: 58  NGGRTTGAVRRGPLMVNTRPSSYAIAKSIRRARPFPWQHDLFEDSLRAAGIQGVEVGTKL 117

Query: 102 YVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNN 161
           YVSNL  GVTN+DIRELFSE+GELKR+A+H+DKNG PSGSAEVVY RRSDAFAALKRYNN
Sbjct: 118 YVSNLDHGVTNEDIRELFSELGELKRFAVHYDKNGHPSGSAEVVYTRRSDAFAALKRYNN 177

Query: 162 VLLDGKPMKIEVVGTNAEIPLQARVNVTGVNGRRKRTVVMTSGSGNAGGAAAINRGPGSQ 221
           VLLDGKPMKIE+VG+N+E+P+ ARVNVTGVNGRRKRTVVMT   G AGG      GP   
Sbjct: 178 VLLDGKPMKIEIVGSNSELPISARVNVTGVNGRRKRTVVMTPRGGQAGG------GPTMP 231

Query: 222 GRRGGLRRSSQGRGRGQGQGRGRGRGGGGGGGRGRGRGRGRGQGKKNPVDKSADDLDKEL 281
            R          RG  +      G GG G G   RG G GRG+G+K+ V+KSA++LDKEL
Sbjct: 232 NR----GAGRGRRGGPRSGSGRGGGGGRGRGRGSRGGGGGRGRGRKDAVEKSAEELDKEL 287

Query: 282 DNYHAEAMQI 291
           + YHAEAM I
Sbjct: 288 ETYHAEAMNI 297

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449456227|ref|XP_004145851.1| PREDICTED: THO complex subunit 4-like [Cucumis sativus]

 Score =  305 bits (780), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 178/291 (61%), Positives = 215/291 (73%), Gaps = 7/291 (2%)

Query: 1   MATHVDMSLDDIIKSRKKSERERGQGRARRGRGRGRGPSGSVSGGRMTGAARRGPL-SNA 59
           M T +DMSL+D+IK   K+ RE+ + R R  RGRG G S +   G + G+ RRGPL  NA
Sbjct: 1   MTTPLDMSLEDVIK---KNNREKLRARGRARRGRGAGGSFNGGRGVVIGSVRRGPLGINA 57

Query: 60  RPSSYTIAKSFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELF 119
           R S+Y+I K   R +N  WQHDLFEDSLRA+GISGI++GTKLYVSNL  GVT +DI+ELF
Sbjct: 58  RASAYSIRKPPHRMKNVQWQHDLFEDSLRASGISGIQIGTKLYVSNLDYGVTKEDIKELF 117

Query: 120 SEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNAE 179
           SEIG++KR+AIH+DKNGRPSGSAEVVY RRSDAFAALKRYNNVLLDGKPMKIE++G NAE
Sbjct: 118 SEIGDVKRFAIHYDKNGRPSGSAEVVYTRRSDAFAALKRYNNVLLDGKPMKIEMLGDNAE 177

Query: 180 IPLQARVNVTGVNGRRKRTVVMTSGSGNAGGAAAINRGPGSQGRRGGLRRSSQGRGRGQG 239
           +P+ AR+NVTG NGR +RTVV+TS SG    +  +N  PG    RGGL R+++GRGRG  
Sbjct: 178 MPVSARINVTGTNGRNRRTVVLTSESGRNATSNVVNSFPGP-SHRGGL-RNARGRGRGAW 235

Query: 240 QGRGRGRGGGGGGGRGRGRGRGRGQGKKNPVDKSADDLDKELDNYHAEAMQ 290
                  GG GGG             KK PV+KS+D+LDKEL+NYHAEAMQ
Sbjct: 236 SRGVGLGGGSGGGRGRGRGRGRGQGRKK-PVEKSSDELDKELENYHAEAMQ 285

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255582255|ref|XP_002531919.1| RNA and export factor binding protein, putative [Ricinus communis] gi|223528429|gb|EEF30463.1| RNA and export factor binding protein, putative [Ricinus communis]

 Score =  303 bits (775), Expect = 7e-80,   Method: Compositional matrix adjust.
 Identities = 175/291 (60%), Positives = 201/291 (69%), Gaps = 25/291 (8%)

Query: 1   MATHVDMSLDDIIKSRKKSERERGQGRARRGRGRGRGPSGSVSGGRMTGAARRGPLS-NA 59
           M+T VDMSLDDIIK  ++  R       R          GS SGGRMTGA R+GPLS NA
Sbjct: 1   MSTSVDMSLDDIIKKNRERGRGGRGRARRGRGR-----GGSFSGGRMTGAGRKGPLSVNA 55

Query: 60  RPSSYTIAKSFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELF 119
           RPS ++IAK  RR RN PWQHDL EDS+RAAGI+G+EVGTKLYVSNL  GV+N+DIRELF
Sbjct: 56  RPSQFSIAKPNRRIRNLPWQHDLLEDSIRAAGITGVEVGTKLYVSNLEYGVSNEDIRELF 115

Query: 120 SEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNAE 179
           +EIG+LKRYA+H+DKNGR +GSAEVVY RRS+AFAALK+YNNVLLDGKPMKIE+VG   E
Sbjct: 116 AEIGDLKRYAVHYDKNGRSTGSAEVVYTRRSEAFAALKKYNNVLLDGKPMKIEIVGVTGE 175

Query: 180 IPLQARVNVTGVNGRRKRTVVMTSGSGNAGGAAAINRGPGSQGRRGGLRRSSQGRGRGQG 239
            P+ ARVNVTG+NGRRKRTVVMT G G   G A  NRG G + R G              
Sbjct: 176 APISARVNVTGINGRRKRTVVMTPGPGRGRGFAPSNRGAGQRSRGGLRNLGRGRGRGRGR 235

Query: 240 QGRGRGRGGGGGGGRGRGRGRGRGQGKKNPVDKSADDLDKELDNYHAEAMQ 290
            G                     G+GKK P++KSAD+LDKELD YHAEAMQ
Sbjct: 236 GG-------------------HGGRGKKQPLEKSADELDKELDTYHAEAMQ 267

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225453197|ref|XP_002276497.1| PREDICTED: THO complex subunit 4 [Vitis vinifera] gi|296087136|emb|CBI33510.3| unnamed protein product [Vitis vinifera]

 Score =  296 bits (757), Expect = 9e-78,   Method: Compositional matrix adjust.
 Identities = 190/293 (64%), Positives = 222/293 (75%), Gaps = 28/293 (9%)

Query: 1   MATHVDMSLDDIIKSRKKSERERGQGRARRGRGRGRGPSGSVSGGRMTGAA-RRGPL-SN 58
           MAT +DMSLDDIIK R  SER RG+GRARRGRG      GS +GGRM+G   RRGPL  N
Sbjct: 1   MATSLDMSLDDIIK-RSNSERVRGRGRARRGRGPI---GGSFNGGRMSGIPPRRGPLRVN 56

Query: 59  ARPSSYTIAKSFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIREL 118
           ARPSSY IAKS RRT+  PWQHDLFEDSLRAAG+ G+E GTKLY+SNL  GVTN+DIREL
Sbjct: 57  ARPSSYAIAKSSRRTK-IPWQHDLFEDSLRAAGLPGLEAGTKLYISNLDYGVTNEDIREL 115

Query: 119 FSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNA 178
           FSEIG++KRYA+H++KNGRPSGSAEVVY RRSDAFAA+KRYNNVLLDGKPMKIE++G+++
Sbjct: 116 FSEIGDIKRYAVHYEKNGRPSGSAEVVYTRRSDAFAAVKRYNNVLLDGKPMKIEIIGSDS 175

Query: 179 EIPLQARVNVT-GVNGRRKRTVVMTSGSGNAGGAAAINRGPGSQGRRGGLRRSSQGRGRG 237
           ++P+ ARVNV  GVNG+R+RTVVMT G G+A G+ AIN                    R 
Sbjct: 176 DMPVSARVNVIGGVNGKRRRTVVMTPGVGHARGSTAIN--------------------RS 215

Query: 238 QGQGRGRGRGGGGGGGRGRGRGRGRGQGKKNPVDKSADDLDKELDNYHAEAMQ 290
             +    G   G G GR   RGRGRG+G+K PV+KSA +LDKELDNYHAEAM 
Sbjct: 216 SSRRGRGGLSNGRGRGRAGSRGRGRGRGRKQPVEKSAVELDKELDNYHAEAMH 268

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147860765|emb|CAN80452.1| hypothetical protein VITISV_029873 [Vitis vinifera]

 Score =  286 bits (733), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 195/322 (60%), Positives = 231/322 (71%), Gaps = 48/322 (14%)

Query: 1   MATHVDMSLDDIIKSRKKSERERGQGRARRGRGRGRGPSGSVSGGRMTGAA-RRGPLSNA 59
           MAT +DMSLDDIIK R  SER RG+GRARRGRG      GS +GGRM+G   RRGPL   
Sbjct: 42  MATSLDMSLDDIIK-RSNSERVRGRGRARRGRGPI---GGSFNGGRMSGIPPRRGPL--- 94

Query: 60  RPSSYTIAKSFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELF 119
                   +S RRT+  PWQHDLFEDSLRAAG+ G+E GTKLY+SNL  GVTN+DIRELF
Sbjct: 95  --------RSSRRTK-IPWQHDLFEDSLRAAGLPGLEAGTKLYISNLDYGVTNEDIRELF 145

Query: 120 SEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNAE 179
           SEIG++KRYA+H++KNGRPSGSAEVVY RRSDAFAA+KRYNNVLLDGKPMKIE++G++++
Sbjct: 146 SEIGDIKRYAVHYEKNGRPSGSAEVVYTRRSDAFAAVKRYNNVLLDGKPMKIEIIGSDSD 205

Query: 180 IPLQARVNVT-GVNGRRKRTVVMTSGSGNAGGAAAINRGP--------GSQG-------- 222
           +P+ ARVNV  GVNG+R+RTVVMT G G+A G+ AINR           SQG        
Sbjct: 206 MPVSARVNVIGGVNGKRRRTVVMTPGVGHARGSTAINRSSREACGNLKVSQGLAWVHVIS 265

Query: 223 ----------RRGGLRRSSQGRGRG-QGQGRGRGRGG---GGGGGRGRGRGRGRGQGKKN 268
                     + GGLRR ++G G G +     RGRGG   G G GR   RGRGRG+G+K 
Sbjct: 266 STLEDKGRNLKEGGLRRGAEGVGCGRRPMASRRGRGGLSNGRGRGRAGSRGRGRGRGRKQ 325

Query: 269 PVDKSADDLDKELDNYHAEAMQ 290
           PV+KSA +LDKELDNYHAEAM 
Sbjct: 326 PVEKSAVELDKELDNYHAEAMH 347

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224077330|ref|XP_002305214.1| predicted protein [Populus trichocarpa] gi|222848178|gb|EEE85725.1| predicted protein [Populus trichocarpa]

 Score =  274 bits (700), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 172/298 (57%), Positives = 205/298 (68%), Gaps = 43/298 (14%)

Query: 1   MATHVDMSLDDIIKSRKKSERERGQGRARRGRGRGRGPSGSVSGGRMTGAARRGPLS-NA 59
           MAT VDMSLDDIIK  ++  R RG+    R RG GR      + GRM+GA RRGPLS NA
Sbjct: 1   MATTVDMSLDDIIKKNRERGRGRGRASRGRDRGPGRF----FNNGRMSGAVRRGPLSVNA 56

Query: 60  RPSSYTIAKSF-------RRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTN 112
           RP  Y+IAK+        RR R+ PWQHDL EDS+RAAGI+G+EVGTKLYVSNL  GVTN
Sbjct: 57  RPPKYSIAKASSKLWMPSRRIRSLPWQHDLLEDSIRAAGITGLEVGTKLYVSNLDYGVTN 116

Query: 113 DDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE 172
           +DIRELF+EIG+LKR+A+H+DKNGR +GSAEV+Y RRSDAF+ALK+YNNVLLDG+PMKIE
Sbjct: 117 EDIRELFAEIGDLKRFAVHYDKNGRSTGSAEVMYTRRSDAFSALKKYNNVLLDGRPMKIE 176

Query: 173 VVGTNAEIPLQARVNVTGVNGRRKRTVVMTSGSGNAGGAAAINRGPGSQGRRGGLRRSSQ 232
           +VG N E+P+ ARVNVTG NG++KRTVVM                             S+
Sbjct: 177 IVGANPEVPISARVNVTGANGKKKRTVVMI---------------------------QSR 209

Query: 233 GRGRGQGQGRGRGRGGGGGGGRGRGRGRGRGQGKKNPVDKSADDLDKELDNYHAEAMQ 290
             G G   G   GRG G   G+GRGRGRG+ Q  +  VD    DLDKEL++YHAEAMQ
Sbjct: 210 RGGGGPRNGMRNGRGRGRAQGQGRGRGRGKKQPAEKSVD----DLDKELESYHAEAMQ 263

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357460875|ref|XP_003600719.1| THO complex subunit [Medicago truncatula] gi|355489767|gb|AES70970.1| THO complex subunit [Medicago truncatula]

 Score =  272 bits (696), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 176/305 (57%), Positives = 207/305 (67%), Gaps = 30/305 (9%)

Query: 1   MATHVDMSLDDIIKSRKKSERERGQGRA----RRGRGRGRGPSGSVSGGRM-----TGAA 51
           MA+ +D+SLDD IKSR    R RG+G+A      G   G   +G+V+G R      TGA 
Sbjct: 1   MASSLDISLDDRIKSRSNRGRGRGRGKALSGRGSGTLGGGRRTGAVNGRRTSNGGRTGAV 60

Query: 52  RRGPLS-NARPSSYTIAKSFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGV 110
           RRGPL+ N R SSY IAKS RR +   WQ DLFEDSLRAAGI G+E  TKLYVSNL  GV
Sbjct: 61  RRGPLNVNTRASSYAIAKSIRRPKTLAWQSDLFEDSLRAAGIQGVEADTKLYVSNLDRGV 120

Query: 111 TNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMK 170
           TN+DIRELFSE+GELKRYA+H+DKNG P+GSAEVVY RRSDAFAALKRYNNVLLDGKPMK
Sbjct: 121 TNEDIRELFSELGELKRYAVHYDKNGHPTGSAEVVYNRRSDAFAALKRYNNVLLDGKPMK 180

Query: 171 IEVVGTNAEIPLQARV-----NVTGVNGRRKRTVVMTSGSGNAGGAAAINRGPGSQGRRG 225
           IE+VGTN+ +P+ ARV     NV+ +NG+RKRTVVMT   G  GG A +N          
Sbjct: 181 IEIVGTNSALPVTARVNVSSMNVSAMNGQRKRTVVMTPRGGRGGGPAMLN---------- 230

Query: 226 GLRRSSQGRGRGQGQGRGRGRGGGGGGGRGRGRGRGRGQGKKNPVDKSADDLDKELDNYH 285
                       +G  RG      G G    GRG GRG+G+K+ V+KSA+ LDKEL+ YH
Sbjct: 231 -----RGAGWGRRGGSRGGSGSMRGRGRGRPGRGGGRGRGRKDGVEKSAEQLDKELETYH 285

Query: 286 AEAMQ 290
           AEAMQ
Sbjct: 286 AEAMQ 290

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449532026|ref|XP_004172985.1| PREDICTED: THO complex subunit 4-like, partial [Cucumis sativus]

 Score =  257 bits (657), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 139/205 (67%), Positives = 167/205 (81%), Gaps = 8/205 (3%)

Query: 1   MATHVDMSLDDIIKSRKKSERERGQGRARRGRGRGRGPSGSVSGGR--MTGAARRGPL-S 57
           M T +DMSL+D+IK   K+ RE+ + R R  RGRG    GS +GGR  + G+ RRGPL  
Sbjct: 1   MTTPLDMSLEDVIK---KNNREKLRARGRARRGRGA--GGSFNGGRGVVIGSVRRGPLGI 55

Query: 58  NARPSSYTIAKSFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRE 117
           NAR S+Y+I K   R +N  WQHDLFEDSLRA+GISGI++GTKLYVSNL  GVT +DI+E
Sbjct: 56  NARASAYSIRKPPHRMKNVQWQHDLFEDSLRASGISGIQIGTKLYVSNLDYGVTKEDIKE 115

Query: 118 LFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTN 177
           LFSEIG++KR+AIH+DKNGRPSGSAEVVY RRSDAFAALKRYNNVLLDGKPMKIE++G N
Sbjct: 116 LFSEIGDVKRFAIHYDKNGRPSGSAEVVYTRRSDAFAALKRYNNVLLDGKPMKIEMLGDN 175

Query: 178 AEIPLQARVNVTGVNGRRKRTVVMT 202
           AE+P+ AR+NVTG NGR +RTVV+T
Sbjct: 176 AEMPVSARINVTGTNGRNRRTVVLT 200

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	291
TAIR|locus:2151779	288	ALY4 "ALWAYS EARLY 4" [Arabido	0.525	0.531	0.715	5.4e-63
TAIR|locus:2205293	295	AT1G66260 [Arabidopsis thalian	0.680	0.671	0.540	1.1e-60
TAIR|locus:2181763	292	AT5G02530 [Arabidopsis thalian	0.608	0.606	0.448	5.1e-39
ZFIN|ZDB-GENE-070928-29	280	alyref "Aly/REF export factor"	0.470	0.489	0.401	2.2e-31
MGI|MGI:1913144	218	Alyref2 "Aly/REF export factor	0.498	0.665	0.414	3.8e-30
UNIPROTKB|E1C2L5	258	THOC4 "Uncharacterized protein	0.621	0.701	0.395	1.8e-29
MGI|MGI:1341044	255	Alyref "Aly/REF export factor"	0.615	0.701	0.374	5.2e-28
UNIPROTKB|Q3T0I4	257	ALYREF "THO complex subunit 4"	0.652	0.739	0.358	6.6e-28
UNIPROTKB|F1PL92	257	ALYREF "Uncharacterized protei	0.652	0.739	0.358	6.6e-28
UNIPROTKB|E9PB61	264	ALYREF "THO complex subunit 4"	0.652	0.719	0.358	6.6e-28

TAIR|locus:2151779 ALY4 "ALWAYS EARLY 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 572 (206.4 bits), Expect = 5.4e-63, Sum P(2) = 5.4e-63
 Identities = 113/158 (71%), Positives = 134/158 (84%)

Query:    49 GAARRGPLS-NARPSSYTIAKSFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLH 107
             G ARRGPL+ NARPSS+TI K  RR R+ PWQ  LFED LRAAG SG+EVGT+L+V+NL 
Sbjct:    42 GPARRGPLAVNARPSSFTINKPVRRVRSLPWQSGLFEDGLRAAGASGVEVGTRLHVTNLD 101

Query:   108 PGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGK 167
              GVTN+DIRELFSEIGE++RYAIH+DKNGRPSG+AEVVY RRSDAF ALK+YNNVLLDG+
Sbjct:   102 QGVTNEDIRELFSEIGEVERYAIHYDKNGRPSGTAEVVYPRRSDAFQALKKYNNVLLDGR 161

Query:   168 PMKIEVVGTN--AEIPLQARVNV--TGVNGRRKRTVVM 201
             PM++E++G N  +E PL  RVNV  TG+NGR KRTVV+
Sbjct:   162 PMRLEILGGNNSSEAPLSGRVNVNVTGLNGRLKRTVVI 199

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0008150 "biological_process" evidence=ND

GO:0005730 "nucleolus" evidence=IDA

TAIR|locus:2205293 AT1G66260 [Arabidopsis thaliana (taxid:3702)]

 Score = 543 (196.2 bits), Expect = 1.1e-60, Sum P(2) = 1.1e-60
 Identities = 113/209 (54%), Positives = 148/209 (70%)

Query:     1 MATHVDMSLDDIIKSRKKSEXXXXXXXXXXXXXXXXXXXXXXXXXXMTGA-----ARRGP 55
             M+  ++M+LD+I+K + KSE                          + G       RRGP
Sbjct:     1 MSDALNMTLDEIVK-KSKSERSAAARSGGKGVSRKSGRGRGGPNGVVGGGRGGGPVRRGP 59

Query:    56 LS-NARPSS-YTIAKSFRRTRNFPWQH--DLFEDSLRAAGISGIEVGTKLYVSNLHPGVT 111
             L+ N RPSS ++I K  RR R+ PWQ+  DL+E++LRA G+SG+EVGT +Y++NL  GVT
Sbjct:    60 LAVNTRPSSSFSINKLARRKRSLPWQNQNDLYEETLRAVGVSGVEVGTTVYITNLDQGVT 119

Query:   112 NDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI 171
             N+DIREL++EIGELKRYAIH+DKNGRPSGSAEVVY RRSDA  A+++YNNVLLDG+PMK+
Sbjct:   120 NEDIRELYAEIGELKRYAIHYDKNGRPSGSAEVVYMRRSDAIQAMRKYNNVLLDGRPMKL 179

Query:   172 EVVGTNAE-IPLQARVNVTGVNGRRKRTV 199
             E++G N E  P+ ARVNVTG+NGR KR+V
Sbjct:   180 EILGGNTESAPVAARVNVTGLNGRMKRSV 208

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2181763 AT5G02530 [Arabidopsis thaliana (taxid:3702)]

 Score = 363 (132.8 bits), Expect = 5.1e-39, Sum P(2) = 5.1e-39
 Identities = 87/194 (44%), Positives = 115/194 (59%)

Query:     1 MATHVDMSLDDIIKSRKKSEXXXXXXXXXXXXXXXXXXXXXXXXXXMTGAARR-GPLSNA 59
             M+  +DMSLDDIIKS +K                             +G +RR      A
Sbjct:     1 MSGGLDMSLDDIIKSNRKPTGSRGRGGIGGGNNTGGRGGSGSN----SGPSRRFANRVGA 56

Query:    60 RPSSYTIAKSFRRTRNFPWQHDLF--EDSLRAA----------GISGIEVGTKLYVSNLH 107
             R + Y+     ++  +  WQ+D+F  + S+ AA          G S IE GTKLY+SNL 
Sbjct:    57 RTAPYSRPIQQQQAHDAMWQNDVFATDASVAAAFGHHQTAVVGGGSSIETGTKLYISNLD 116

Query:   108 PGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGK 167
              GV+N+DI+ELFSE+G+LKRY IH+D++GR  G+AEVV++RR DA AA+KRYNNV LDGK
Sbjct:   117 YGVSNEDIKELFSEVGDLKRYGIHYDRSGRSKGTAEVVFSRRGDALAAVKRYNNVQLDGK 176

Query:   168 PMKIEVVGTNAEIP 181
              MKIE+VGTN   P
Sbjct:   177 LMKIEIVGTNLSAP 190

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

ZFIN|ZDB-GENE-070928-29 alyref "Aly/REF export factor" [Danio rerio (taxid:7955)]

 Score = 272 (100.8 bits), Expect = 2.2e-31, Sum P(3) = 2.2e-31
 Identities = 61/152 (40%), Positives = 95/152 (62%)

Query:    54 GPLSNARPSSYTIAKS--FRRTRNFP--WQHDLFEDSLRA---------AGISGIEVGTK 100
             GP+ N +  S   ++   + R +  P  WQHDLF++   +          G +G+E G K
Sbjct:    67 GPMRNRQNLSRGRSRPTPYSRPKQLPDKWQHDLFDNGYSSNAGGGGGGGGGGAGVETGGK 126

Query:   101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
             L VSNL  GV++ DI+ELF+E G LK+ A+H+D++GR  G+A+V + R++DA  A+K+YN
Sbjct:   127 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 186

Query:   161 NVLLDGKPMKIEVVGTNAEIPLQARVNVTGVN 192
              V LDG+PM I++V   ++I  Q R  + G+N
Sbjct:   187 GVPLDGRPMNIQLV--TSQIDAQRRTPMQGLN 216

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

MGI|MGI:1913144 Alyref2 "Aly/REF export factor 2" [Mus musculus (taxid:10090)]

 Score = 263 (97.6 bits), Expect = 3.8e-30, Sum P(3) = 3.8e-30
 Identities = 63/152 (41%), Positives = 90/152 (59%)

Query:    49 GAARRGPLSNARPSSYTIAKSFRRTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNL 106
             G  RR   + AR      A  + R +  P  WQHDLF+      G  G+E G KL VSNL
Sbjct:    26 GGPRRNRPAIARGGRNRPAP-YSRPKPLPDKWQHDLFDSG--CGGGEGVETGAKLLVSNL 82

Query:   107 HPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDG 166
               GV++ DI+ELF+E G LK+ A+ +D++GR  G+A+V + RR+DA  A+K+Y  V LDG
Sbjct:    83 DFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDG 142

Query:   167 KPMKIEVVGTNAEIPLQARVNVTGVNGRRKRT 198
             +PM I++V +  +I  Q R   +G  G   R+
Sbjct:   143 RPMDIQLVAS--QIDPQRRPAQSGNRGGMTRS 172

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0003723 "RNA binding" evidence=IDA

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0008380 "RNA splicing" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

UNIPROTKB|E1C2L5 THOC4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 299 (110.3 bits), Expect = 1.8e-29, Sum P(2) = 1.8e-29
 Identities = 76/192 (39%), Positives = 105/192 (54%)

Query:     1 MATHVDMSLDDIIKSRKKSEXXXXXXXXXXXXXXXXXXXXXXXXXXM-TGAARRGPLSN- 58
             MA  +DMSLDDIIK  +                             +  G A  GP+ N 
Sbjct:     1 MADKMDMSLDDIIKLNRSQRGGGRGGGRGGRGRGGVTRGGGPGRGGVGAGRAGGGPVRNR 60

Query:    59 ---ARPSSYTIAKSFRRTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTND 113
                AR         + R +  P  WQHDLF DS   AG +G+E G KL VSNL  GV++ 
Sbjct:    61 PVMARGGGRNRPAPYSRPKQLPEKWQHDLF-DSGFGAG-AGVETGGKLLVSNLDFGVSDA 118

Query:   114 DIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV 173
             DI+ELF+E G LK+ A+H+D++GR  G+A+V + R++DA  A+K+YN V LDG+PM I++
Sbjct:   119 DIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 178

Query:   174 VGTNAEIPLQAR 185
             V   ++I  Q R
Sbjct:   179 V--TSQIDTQRR 188

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000346 "transcription export complex" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IEA

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

MGI|MGI:1341044 Alyref "Aly/REF export factor" [Mus musculus (taxid:10090)]

 Score = 285 (105.4 bits), Expect = 5.2e-28, Sum P(2) = 5.2e-28
 Identities = 73/195 (37%), Positives = 101/195 (51%)

Query:     1 MATHVDMSLDDIIKSRKKSEXXXXXXXXXXXXXXXXXXXXXXXXXXMTGAARRGPLSNAR 60
             MA  +DMSLDDIIK  +                                    GP+ N R
Sbjct:     1 MADKMDMSLDDIIKLNRSQRGGRGGGRGRGRAGSQGGRGGAVQAAARVNRGG-GPMRN-R 58

Query:    61 PSSYTIAKSFRRTRNFP----------WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGV 110
             P+    A    R R  P          WQHDLF+      G +G+E G KL VSNL  GV
Sbjct:    59 PAIARGAAGGGRNRPAPYSRPKQLPDKWQHDLFDSGF--GGGAGVETGGKLLVSNLDFGV 116

Query:   111 TNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMK 170
             ++ DI+ELF+E G LK+ A+H+D++GR  G+A+V + R++DA  A+K+YN V LDG+PM 
Sbjct:   117 SDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMN 176

Query:   171 IEVVGTNAEIPLQAR 185
             I++V   ++I  Q R
Sbjct:   177 IQLV--TSQIDTQRR 189

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000346 "transcription export complex" evidence=ISO

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0003723 "RNA binding" evidence=IDA

GO:0005634 "nucleus" evidence=TAS

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

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

GO:0006810 "transport" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=ISO

GO:0051028 "mRNA transport" evidence=IEA

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

UNIPROTKB|Q3T0I4 ALYREF "THO complex subunit 4" [Bos taurus (taxid:9913)]

 Score = 284 (105.0 bits), Expect = 6.6e-28, Sum P(2) = 6.6e-28
 Identities = 75/209 (35%), Positives = 107/209 (51%)

Query:     1 MATHVDMSLDDIIKSRKKSEXXXXXXXXXXXXXXXXXXXXXXXXXXMTGAARRGPLSNAR 60
             MA  +DMSLDDIIK  +                                    GP+ N R
Sbjct:     1 MADKMDMSLDDIIKLNRSQRGGRGGGRGRGRAGSQGGRGGGAQAAARVNRGG-GPIRN-R 58

Query:    61 PSSYTIAKS---------FRRTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPG 109
             P+    A           + R +  P  WQHDLF+      G +G+E G KL VSNL  G
Sbjct:    59 PAIARGAAGGGGRNRPAPYSRPKQLPDKWQHDLFDSGF--GGGAGVETGGKLLVSNLDFG 116

Query:   110 VTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPM 169
             V++ DI+ELF+E G LK+ A+H+D++GR  G+A+V + R++DA  A+K+YN V LDG+PM
Sbjct:   117 VSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPM 176

Query:   170 KIEVVGTNAEI---PLQARVNVTGVNGRR 195
              I++V +  +    P Q+ VN  G+   R
Sbjct:   177 NIQLVTSQIDTQRRPAQS-VNRGGMTRNR 204

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IEA

GO:0000346 "transcription export complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1PL92 ALYREF "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 284 (105.0 bits), Expect = 6.6e-28, Sum P(2) = 6.6e-28
 Identities = 75/209 (35%), Positives = 107/209 (51%)

Query:     1 MATHVDMSLDDIIKSRKKSEXXXXXXXXXXXXXXXXXXXXXXXXXXMTGAARRGPLSNAR 60
             MA  +DMSLDDIIK  +                                    GP+ N R
Sbjct:     1 MADKMDMSLDDIIKLNRSQRGGRGGGRGRGRAGSQGGRGGGAQAAARVSRGG-GPIRN-R 58

Query:    61 PSSYTIAKS---------FRRTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPG 109
             P+    A           + R +  P  WQHDLF+      G +G+E G KL VSNL  G
Sbjct:    59 PALARGAAGGGGRNRPAPYSRPKQLPDKWQHDLFDSGF--GGGAGVETGGKLLVSNLDFG 116

Query:   110 VTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPM 169
             V++ DI+ELF+E G LK+ A+H+D++GR  G+A+V + R++DA  A+K+YN V LDG+PM
Sbjct:   117 VSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPM 176

Query:   170 KIEVVGTNAEI---PLQARVNVTGVNGRR 195
              I++V +  +    P Q+ VN  G+   R
Sbjct:   177 NIQLVTSQIDTQRRPAQS-VNRGGMTRNR 204

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E9PB61 ALYREF "THO complex subunit 4" [Homo sapiens (taxid:9606)]

 Score = 284 (105.0 bits), Expect = 6.6e-28, Sum P(2) = 6.6e-28
 Identities = 75/209 (35%), Positives = 107/209 (51%)

Query:     1 MATHVDMSLDDIIKSRKKSEXXXXXXXXXXXXXXXXXXXXXXXXXXMTGAARRGPLSNAR 60
             MA  +DMSLDDIIK  +                                    GP+ N R
Sbjct:     8 MADKMDMSLDDIIKLNRSQRGGRGGGRGRGRAGSQGGRGGGAQAAARVNRGG-GPIRN-R 65

Query:    61 PSSYTIAKS---------FRRTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPG 109
             P+    A           + R +  P  WQHDLF+      G +G+E G KL VSNL  G
Sbjct:    66 PAIARGAAGGGGRNRPAPYSRPKQLPDKWQHDLFDSGF--GGGAGVETGGKLLVSNLDFG 123

Query:   110 VTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPM 169
             V++ DI+ELF+E G LK+ A+H+D++GR  G+A+V + R++DA  A+K+YN V LDG+PM
Sbjct:   124 VSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPM 183

Query:   170 KIEVVGTNAEI---PLQARVNVTGVNGRR 195
              I++V +  +    P Q+ VN  G+   R
Sbjct:   184 NIQLVTSQIDAQRRPAQS-VNRGGMTRNR 211

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	fgenesh4_pg.C_LG_II002243	hypothetical protein (274 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	HCP902	histone deacetylase complex protein (120 aa)						•			0.800
	HCP901	histone deacetylase complex protein (114 aa)						•			0.800
	HCP903	histone deacetylase complex protein (114 aa)						•			0.800
	estExt_fgenesh4_pm.C_400112	hypothetical protein (697 aa)						•			0.800
	estExt_fgenesh4_pg.C_LG_VI1784	SubName- Full=Putative uncharacterized protein; (428 aa)						•			0.800
	eugene3.01470005	hypothetical protein (187 aa)			•			•			0.547
	gw1.XVIII.2163.1	hypothetical protein (198 aa)			•			•			0.541
	gw1.XII.145.1	hypothetical protein (286 aa)			•			•			0.504
	gw1.XV.140.1	hypothetical protein (219 aa)			•			•			0.487
	gw1.XIX.900.1	hypothetical protein (179 aa)			•			•			0.463

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	291
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	1e-39
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	9e-31
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	7e-24
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	5e-18
smart00360	73	smart00360, RRM, RNA recognition motif	4e-16
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-14
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	3e-12
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	6e-12
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	2e-11
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-11
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	9e-11
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-10
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	6e-10
pfam05918	543	pfam05918, API5, Apoptosis inhibitory protein 5 (A	1e-09
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	2e-09
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	2e-09
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	7e-09
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	8e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-08
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-08
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	2e-08
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	2e-08
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	4e-08
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	4e-08
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	6e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-08
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	8e-08
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	8e-08
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	9e-08
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	1e-07
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-07
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-07
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-07
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	3e-07
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	3e-07
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	4e-07
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	5e-07
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	5e-07
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	6e-07
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	7e-07
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	7e-07
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	9e-07
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-06
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	2e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-06
cd12281	92	cd12281, RRM1_TatSF1_like, RNA recognition motif 1	3e-06
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	3e-06
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	6e-06
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	8e-06
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	8e-06
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-05
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-05
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	1e-05
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-05
cd12589	80	cd12589, RRM2_PSP1, RNA recognition motif 2 in ver	2e-05
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	2e-05
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-05
cd12590	80	cd12590, RRM2_PSF, RNA recognition motif 2 in vert	2e-05
cd12259	76	cd12259, RRM_SRSF11_SREK1, RNA recognition motif i	2e-05
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	3e-05
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	4e-05
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	4e-05
cd12438	98	cd12438, RRM_CNOT4, RNA recognition motif in Eukar	4e-05
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	4e-05
pfam13865	76	pfam13865, FoP_duplication, C-terminal duplication	4e-05
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	4e-05
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	4e-05
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	5e-05
cd12268	68	cd12268, RRM_Vip1, RNA recognition motif in fissio	5e-05
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	5e-05
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	6e-05
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	7e-05
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	8e-05
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	8e-05
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	8e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	9e-05
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	1e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	1e-04
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-04
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	1e-04
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	1e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-04
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	2e-04
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	2e-04
PTZ00070	257	PTZ00070, PTZ00070, 40S ribosomal protein S2; Prov	2e-04
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	2e-04
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-04
cd12591	80	cd12591, RRM2_p54nrb, RNA recognition motif 2 in v	2e-04
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	3e-04
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	3e-04
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	3e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-04
cd12506	75	cd12506, RRM3_hnRNPH_CRSF1_like, RNA recognition m	3e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	3e-04
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	3e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-04
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	4e-04
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	5e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	5e-04
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	6e-04
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	6e-04
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	7e-04
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	7e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	9e-04
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	9e-04
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	9e-04
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	0.001
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	0.001
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	0.002
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	0.002
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	0.002
cd12511	73	cd12511, RRM2_RBM12_like, RNA recognition motif 2	0.002
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	0.002
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	0.002
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	0.002
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	0.002
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	0.003
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	0.003
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	0.003
cd12568	72	cd12568, RRM3_MRD1, RNA recognition motif 3 in yea	0.003
cd12733	75	cd12733, RRM3_GRSF1, RNA recognition motif 3 in G-	0.003
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	0.004
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	0.004
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	0.004
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	0.004
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	0.004
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	0.004
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	0.004

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

 Score =  132 bits (335), Expect = 1e-39
 Identities = 44/74 (59%), Positives = 61/74 (82%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           TKL VSNL  GV++DDI+ELF+E G LK+ A+H+D++GR  G+A+VV+ RR+DA  A+K+
Sbjct: 1   TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQ 60

Query: 159 YNNVLLDGKPMKIE 172
           YN V LDG+PMKI+
Sbjct: 61  YNGVPLDGRPMKIQ 74

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

 Score =  109 bits (276), Expect = 9e-31
 Identities = 38/75 (50%), Positives = 59/75 (78%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           T+L VSNLH  VT +D+ ELF  +GE+K+  I++D++GR  G+A+VV+ +R DA  A+K+
Sbjct: 1   TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQ 60

Query: 159 YNNVLLDGKPMKIEV 173
           +N VLLDG+PM++E+
Sbjct: 61  FNGVLLDGQPMQVEL 75

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

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

 Score = 91.6 bits (228), Expect = 7e-24
 Identities = 43/74 (58%), Positives = 50/74 (67%), Gaps = 6/74 (8%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           T+L VSNLHP VT DDI ELFS IG LKR  +      RP G AEVVY R+ DA  A+ +
Sbjct: 1   TRLVVSNLHPSVTEDDIVELFSAIGALKRARLV-----RP-GVAEVVYVRKDDALTAIDK 54

Query: 159 YNNVLLDGKPMKIE 172
           YNN  LDG+PMK +
Sbjct: 55  YNNRELDGQPMKCK 68

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

 Score = 76.2 bits (188), Expect = 5e-18
 Identities = 30/72 (41%), Positives = 43/72 (59%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           L+V NL P  T +D+RELFS+ GE++   I  DK+G+  G A V +    DA  AL+  N
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 161 NVLLDGKPMKIE 172
              LDG+ +K+ 
Sbjct: 61  GKELDGRKLKVS 72

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

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

 Score = 71.1 bits (175), Expect = 4e-16
 Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN-GRPSGSAEVVYARRSDAFAALKR 158
            L+V NL P  T +++RELFS+ G+++   +  DK  G+  G A V +    DA  AL+ 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 159 YNNVLLDGKPMKI 171
            N   LDG+P+K+
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 66.5 bits (163), Expect = 2e-14
 Identities = 25/70 (35%), Positives = 39/70 (55%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           L+V NL P  T +D+++LFS+ G ++   I  D+ GR  G A V +    DA  AL+  N
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 161 NVLLDGKPMK 170
              L G+ ++
Sbjct: 61  GKELGGRELR 70

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

>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 60.8 bits (148), Expect = 3e-12
 Identities = 28/80 (35%), Positives = 38/80 (47%), Gaps = 8/80 (10%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYA--------IHFDKNGRPSGSAEVVYARRSDA 152
           +Y+S L   VT D + ELF  IG +KR          I+ DK   P G A V Y   S A
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60

Query: 153 FAALKRYNNVLLDGKPMKIE 172
            AA++ +N     G  +K+ 
Sbjct: 61  QAAIEWFNGYEFRGNKIKVS 80

This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15. . Length = 81

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

 Score = 59.5 bits (145), Expect = 6e-12
 Identities = 31/68 (45%), Positives = 44/68 (64%), Gaps = 1/68 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           LYV NL P VT +D+RE FS  G+++   +  +K+ RP G A V +A   DA AALK+ N
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLN 59

Query: 161 NVLLDGKP 168
            ++LDG+ 
Sbjct: 60  GLVLDGRT 67

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

>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins

 Score = 58.6 bits (142), Expect = 2e-11
 Identities = 31/77 (40%), Positives = 46/77 (59%), Gaps = 2/77 (2%)

Query: 100 KLYVSNLHPGVTNDDIRELF-SEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           K+ VSNL   VT   IRE F S+IG +KR  + +++ G+ +G A + + R  DA  A  +
Sbjct: 1   KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDK 60

Query: 159 YNNVLLDGK-PMKIEVV 174
           +N  + DG   MK+EVV
Sbjct: 61  FNGRIDDGNRKMKVEVV 77

This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p. . Length = 77

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

 Score = 58.5 bits (142), Expect = 2e-11
 Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           LYV NL   VT D + ELFS+IG +K   +  +    P    E  Y     A AAL+  N
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVE--YYDHRSAAAALQTMN 58

Query: 161 NVLLDGKPMKI 171
             L+ G+ +K+
Sbjct: 59  GRLILGQEIKV 69

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

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

 Score = 61.1 bits (147), Expect = 9e-11
 Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALK 157
             L+V NL   VT +D+RELF + G +KR  +  D+  G+  G A V +     A  A++
Sbjct: 116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIE 175

Query: 158 RYNNVLLDGKPMKIE 172
             N   L+G+P++++
Sbjct: 176 ELNGKELEGRPLRVQ 190

Length = 306

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

 Score = 56.5 bits (137), Expect = 1e-10
 Identities = 27/72 (37%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRY 159
           LYV NLH  +T DD+R +F   GE++   +  D   GR  G   + +A   DA  AL++ 
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 160 NNVLLDGKPMKI 171
           N   L G+P+K+
Sbjct: 61  NGFELAGRPIKV 72

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

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

 Score = 54.5 bits (132), Expect = 6e-10
 Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPS-GSAEVVYARRSDAFAALKRY 159
           L+V NL    T++ + E FSE+G +KR  +  DK  +   G   V +A   DA  AL+  
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 160 NNVLLDGKPMKIEV 173
                 G+ + +E 
Sbjct: 62  KKTKFGGRKIHVEF 75

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|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5)

 Score = 58.5 bits (141), Expect = 1e-09
 Identities = 40/176 (22%), Positives = 61/176 (34%), Gaps = 29/176 (16%)

Query: 95  IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFA 154
           +E  TK  +  L  G++        ++  E K                E +  +      
Sbjct: 386 VEDLTKATMKKLTQGMSEHSKAMSTAKTDEEK----------------EELKTKEQLTTT 429

Query: 155 ALKRYNNVLLDGKPMKIEVVGTNAEIPLQARVNVTGVNGRRKRTVVMTSGSGNAGGAAAI 214
            L+  NN+L   K +         ++ +     V   N  +    +   G   A G    
Sbjct: 430 GLRTCNNILAMTKDLFHSPPIFKHDLAIVLSWIVPKNN--KLGKPITFGGKRPANGKG-- 485

Query: 215 NRGPGSQGRRGGLRR---------SSQGRGRGQGQGRGRGRGGGGGGGRGRGRGRG 261
           N  P  + R    ++          S+      G+GR RGRG GGGGGRGRG  RG
Sbjct: 486 NNVPAKKSRPSNDQKQYVNKSGEGISKVGQSYGGRGRTRGRGRGGGGGRGRGYNRG 541

This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterized by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in human chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors. Length = 543

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

 Score = 52.9 bits (128), Expect = 2e-09
 Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGR-PSGSAEVVYARRSDAFAALKRY 159
           LYV NL    T + I ELFS  G++KR  +  D+  + P G   V Y  R DA  A+K  
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 160 NNVLLDGKPMKIE 172
           N   LD + ++++
Sbjct: 61  NGTKLDDRIIRVD 73

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

 Score = 52.5 bits (127), Expect = 2e-09
 Identities = 26/72 (36%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN-GRPSGSAEVVYARRSDAFAALKRY 159
           LYV +LHP VT   + E+FS  G +    +  D    R  G A V +   +DA  AL   
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 160 NNVLLDGKPMKI 171
           N  ++ GKP++I
Sbjct: 62  NFDVIKGKPIRI 73

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

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

 Score = 51.1 bits (123), Expect = 7e-09
 Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 21/80 (26%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGE------LKRYA-IHFDKNGRPSGSAEVVYARRSDA 152
           KL+V NL    T++++R LF + G       +K Y  +H ++                DA
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVTECDVVKNYGFVHMEEE--------------EDA 46

Query: 153 FAALKRYNNVLLDGKPMKIE 172
             A+K  N     GK + +E
Sbjct: 47  EDAIKALNGYEFMGKRINVE 66

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

 Score = 51.2 bits (123), Expect = 8e-09
 Identities = 23/72 (31%), Positives = 37/72 (51%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           L+V NL   VT + + ELF + G L+   I  D NG+P   A V +        A++  N
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLN 63

Query: 161 NVLLDGKPMKIE 172
            + L G+ ++I+
Sbjct: 64  GIRLFGRELRIK 75

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

>gnl|CDD|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 = 50.4 bits (121), Expect = 2e-08
 Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 1/69 (1%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKR 158
           +L+V NL    T +++RELF   GE+    +  DK   R  G A V +     A  A   
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 159 YNNVLLDGK 167
            +  +  G+
Sbjct: 61  LDGSIFQGR 69

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

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

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           ++VSNL   V  D++R+LFS+ GE+    +  +  G+  G A V +        ALK  +
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKL-D 60

Query: 161 NVLLDGKPM 169
             L+ G+PM
Sbjct: 61  RELIKGRPM 69

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

 Score = 50.0 bits (120), Expect = 2e-08
 Identities = 22/74 (29%), Positives = 37/74 (50%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           ++L V NL  G+  D +R+LF   G +    + + K+G+      V Y    +A  ALK 
Sbjct: 1   SRLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKH 60

Query: 159 YNNVLLDGKPMKIE 172
           +NN  +D   + +E
Sbjct: 61  FNNSFIDTSKITVE 74

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

 Score = 50.0 bits (120), Expect = 2e-08
 Identities = 23/58 (39%), Positives = 36/58 (62%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           L V NL P V+N+ + + FS+ GE++R  +  D  GR +G   V ++R+  A AA+KR
Sbjct: 2   LRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKR 59

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

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

 Score = 49.2 bits (118), Expect = 4e-08
 Identities = 30/81 (37%), Positives = 38/81 (46%), Gaps = 23/81 (28%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKR------YA-IHFDKNGRPSGSAEVVYARRSDAF 153
           LYV NL    T + +RELFSE GE++R      YA +HF                R DA 
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKDYAFVHF--------------EERDDAV 49

Query: 154 AALKRYNNVLLDGKPMKIEVV 174
            A++  N   L+G P  IEV 
Sbjct: 50  KAMEEMNGKELEGSP--IEVS 68

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

 Score = 49.3 bits (118), Expect = 4e-08
 Identities = 21/74 (28%), Positives = 40/74 (54%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY 159
           KL+VS L   VT +++ +LF + G +K   +  +++G+P G A V Y   S A  A+ + 
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 160 NNVLLDGKPMKIEV 173
           +   +  K + + +
Sbjct: 64  DGTEIKEKTISVAI 77

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

 Score = 48.7 bits (116), Expect = 6e-08
 Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALK 157
           T LYV+NL   +T D++R++F   G + +  +  DK  G P G A V Y +R +A AA+ 
Sbjct: 1   TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 158 RYNNVLLDGKPMKIEV 173
             N  +  G  M + V
Sbjct: 61  SLNGTIPPGSTMPLSV 76

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

 Score = 52.9 bits (127), Expect = 7e-08
 Identities = 40/162 (24%), Positives = 62/162 (38%), Gaps = 19/162 (11%)

Query: 98  GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALK 157
           G  LYV NL   VT++ +RELFSE GE+    +  D+ G   G   V ++   +A  A+ 
Sbjct: 285 GVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVT 344

Query: 158 RYNNVLLDGKPMKIEVVGTNAE--IPLQARVNVTGVNGRRKRTVVMTSGSGNAGGAAAIN 215
             +  +L GKP+ + +     +    LQ +        R+     +  GS          
Sbjct: 345 EMHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQLQPRMRQ-----LPMGSPM-------- 391

Query: 216 RGPGSQGRR--GGLRRSSQGRGRGQGQGRGRGRGGGGGGGRG 255
              G+ G+    G     Q  G+  G  R        G G  
Sbjct: 392 --GGAMGQPPYYGQGPQQQFNGQPLGWPRMSMMPTPMGPGGP 431

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

 Score = 48.5 bits (116), Expect = 8e-08
 Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           ++V  L P VT +++ E FS  G++    +    N   +  A + + R   A  A++  N
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNA-FAFIKFEREQAAARAVESEN 64

Query: 161 NVLLDGKPMKIE 172
           + +L  K M ++
Sbjct: 65  HSMLKNKTMHVQ 76

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

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

 Score = 48.5 bits (116), Expect = 8e-08
 Identities = 27/71 (38%), Positives = 43/71 (60%), Gaps = 1/71 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPS-GSAEVVYARRSDAFAALKRY 159
           +YVSNL   +TN+D+ ++FS+ G++ +  I  DK  R S G A +++  R DA   +K  
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 160 NNVLLDGKPMK 170
           NN  L G+ +K
Sbjct: 64  NNKELFGRTLK 74

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

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

 Score = 48.4 bits (116), Expect = 9e-08
 Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 2/70 (2%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN-GRPSGSAEVVYARRSDAFAALK 157
           TK++V  L    T+D +R+ FS+ GE++   +  D+  G+  G   V +  +  A  A K
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 158 RYNNVLLDGK 167
              N ++DG+
Sbjct: 61  D-PNPIIDGR 69

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|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 = 48.1 bits (115), Expect = 1e-07
 Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 7/74 (9%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRY-AIHFDKNGRPSGSAEVVYARRSDAFAALK 157
           T L++ +L   VT +D++ LF E GE++    I       P G A V    R DA  AL+
Sbjct: 3   TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP------PRGCAYVCMETRQDAHRALQ 56

Query: 158 RYNNVLLDGKPMKI 171
           +  NV L GK +K+
Sbjct: 57  KLRNVKLAGKKIKV 70

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

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

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 6/78 (7%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN-GRPSGSAEVVYARRSDAFAALKRY 159
           +++ NL    T ++++ELFS+ GE+K   I  DK  G   G+A V +  +  A   L+  
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 160 NN-----VLLDGKPMKIE 172
           +N     + LDG+ + + 
Sbjct: 63  DNAEDSGLSLDGRRLIVT 80

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

 Score = 47.5 bits (114), Expect = 2e-07
 Identities = 24/68 (35%), Positives = 35/68 (51%), Gaps = 6/68 (8%)

Query: 103 VSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN-GRPSGSAEVVYARRSDAFAALK---- 157
           V+NL      DD+RELF   G + R  +  DK  G+  G A V +  R DA  A++    
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

Query: 158 -RYNNVLL 164
             Y+N++L
Sbjct: 64  FGYDNLIL 71

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

 Score = 47.5 bits (113), Expect = 2e-07
 Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALKRY 159
           L+V NL   VT +D+ + FS++  +K   +  D + G   G   V +A   DA  AL + 
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 160 NNVLLDGKPMKIEV 173
            N  L G+ +++++
Sbjct: 62  KNKKLHGRILRLDI 75

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|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 50.5 bits (121), Expect = 3e-07
 Identities = 26/56 (46%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 215 NRGPGSQGRRGGLRRSSQGRGRGQGQGRGRGRGGGGGGGRGRGRGRGRGQGKKNPV 270
             G G  G RGG     +G G G+G GRG GRG G GGG G   G G G   K  V
Sbjct: 5   GFGGGRGGGRGGGGGGGRGGG-GRGGGRGGGRGRGRGGGGGGRGGGGGGGPGKVIV 59

Length = 293

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

 Score = 46.4 bits (111), Expect = 3e-07
 Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 4/59 (6%)

Query: 115 IRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV 173
           + +LFS  G +++  I   K     G A V ++    A  A++  N VL  G+P++++ 
Sbjct: 1   LYKLFSPFGNVEK--IKLLKKKP--GFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

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

>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 46.4 bits (111), Expect = 4e-07
 Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 3/65 (4%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHF--DKNGRPSGSAEVVYARRSDAFAALKR 158
           + +  L    T +DIR+ FS +  +    IH   D +GRP+G A V +A   DA  AL++
Sbjct: 2   VRLRGLPFSATEEDIRDFFSGLD-IPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRK 60

Query: 159 YNNVL 163
           +NN +
Sbjct: 61  HNNKM 65

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 46.5 bits (111), Expect = 5e-07
 Identities = 22/72 (30%), Positives = 36/72 (50%)

Query: 98  GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALK 157
           G  LYV NL   + ++ +RE FS  G +    +  D+ GR  G   V ++   +A  A+ 
Sbjct: 1   GVNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVT 60

Query: 158 RYNNVLLDGKPM 169
             N  ++ GKP+
Sbjct: 61  EMNGRIIGGKPL 72

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

 Score = 46.5 bits (111), Expect = 5e-07
 Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 102 YVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNN 161
           YV NL P  T D + E FS+ GE+K Y        +P+  A V +A ++    ALK  N 
Sbjct: 8   YVGNLDPTTTADQLLEFFSQAGEVK-YVRMAGDETQPTRYAFVEFAEQTSVINALK-LNG 65

Query: 162 VLLDGKPMKIE 172
            +  G+P+K+ 
Sbjct: 66  AMFGGRPLKVN 76

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

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

 Score = 45.8 bits (109), Expect = 6e-07
 Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           L+V NL      DD+ E F E GE+    I  D +GR  G   V +A    A  AL++  
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEKSG 61

Query: 161 NVLLDGKPMKIEV 173
              L G+ +++++
Sbjct: 62  E-ELLGREIRVDL 73

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

 Score = 45.7 bits (109), Expect = 7e-07
 Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 11/80 (13%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGEL-------KRYAIHFDKNGRPSGSAEVVYARRSDA 152
           ++YV NL   +  DD+R +FS+ GE+       K+       N    G A V +   S A
Sbjct: 2   EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNN---GFAFVTFKDASSA 58

Query: 153 FAALKRYNNVLLDGKPMKIE 172
             AL+  N   L G+ + + 
Sbjct: 59  ENALQ-LNGTELGGRKISVS 77

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

 Score = 46.1 bits (110), Expect = 7e-07
 Identities = 19/72 (26%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRY 159
           ++V+ +H     +D+ + F+E GE+K   ++ D+  G   G A + Y  + +A AA++  
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 160 NNVLLDGKPMKI 171
           N   L G+ + +
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|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 45.3 bits (108), Expect = 9e-07
 Identities = 22/71 (30%), Positives = 40/71 (56%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           ++V NL   VT  D+++LF E G + R  +  D +GR  G   V++    DA  A++ +N
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 161 NVLLDGKPMKI 171
              L+G+ +++
Sbjct: 61  GYDLEGRELEV 71

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

>gnl|CDD|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 = 45.3 bits (108), Expect = 1e-06
 Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 98  GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPS-GSAEVVYARRSDAFAAL 156
           G KL+VS L    T  ++  LFS+ G ++   +  D     S G   V +    DA AA+
Sbjct: 1   GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAI 60

Query: 157 KRYNNVLLDGKPMKIE 172
           +  N   L+G+ +K+E
Sbjct: 61  RDLNGKELEGRVIKVE 76

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

>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRY 159
           +YV NL   VT + + ELF + G +    I  D+      G   V +    DA  A+K  
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 160 NNVLLDGKPMKI 171
           N + L GKP+++
Sbjct: 61  NMIKLYGKPIRV 72

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 44.1 bits (104), Expect = 2e-06
 Identities = 25/72 (34%), Positives = 38/72 (52%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           L+V NL P VT + I ELF + G + +  I  DK+G+P   A V +        A+   N
Sbjct: 4   LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLN 63

Query: 161 NVLLDGKPMKIE 172
            + L G+P+ I+
Sbjct: 64  GIKLYGRPLNIQ 75

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

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

 Score = 47.9 bits (114), Expect = 3e-06
 Identities = 28/77 (36%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           T LYV NL P V  D +RELF++ GE+   A+  D +GR  G A V + +  DA  A++ 
Sbjct: 179 TNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEE 238

Query: 159 YNNVLLDG--KPMKIEV 173
            N   +    +  K+ V
Sbjct: 239 MNGKKIGLAKEGKKLYV 255

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|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 44.4 bits (106), Expect = 3e-06
 Identities = 24/88 (27%), Positives = 38/88 (43%), Gaps = 19/88 (21%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIG--------ELKRYAIHFDKNGRPSGSAEVVYARRS 150
           T +YVS L   +T ++  E+FS+ G           +  ++ D+NG   G A   Y +  
Sbjct: 2   TNVYVSGLPLDITVEEFVEVFSKCGIIKEDPETGKPKIKLYRDENGNLKGDALCCYLKEE 61

Query: 151 DAFAALKRYNNVLLD------GKPMKIE 172
               A++     LLD      G  MK+E
Sbjct: 62  SVELAIQ-----LLDGTEIGRGYKMKVE 84

This subfamily corresponds to the RRM1 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well. . Length = 92

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

 Score = 44.1 bits (105), Expect = 3e-06
 Identities = 24/78 (30%), Positives = 34/78 (43%), Gaps = 5/78 (6%)

Query: 100 KLYVSNLHPGVTNDDIRELFS---EIGELKRYAIHFD--KNGRPSGSAEVVYARRSDAFA 154
           +LYV NL   VT +D+  +F    +    ++          GR  G A V +     A  
Sbjct: 3   RLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATK 62

Query: 155 ALKRYNNVLLDGKPMKIE 172
           AL   N  +L GKPM I+
Sbjct: 63  ALNLVNGYVLKGKPMVIQ 80

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

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 46.6 bits (111), Expect = 6e-06
 Identities = 24/55 (43%), Positives = 24/55 (43%)

Query: 215 NRGPGSQGRRGGLRRSSQGRGRGQGQGRGRGRGGGGGGGRGRGRGRGRGQGKKNP 269
             G G  G RGG R    G GRG G   G   GG G G  G G GRG G G    
Sbjct: 1   GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPG 55

Length = 293

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

 Score = 42.8 bits (101), Expect = 8e-06
 Identities = 27/74 (36%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN-GRPSGSAEVVYARRSDAFAALK 157
           T L V+ L   +T D+IR LFS IGE++   +  DK  G+  G   V Y    DA  A+ 
Sbjct: 2   TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN 61

Query: 158 RYNNVLLDGKPMKI 171
             N + L  K +K+
Sbjct: 62  TLNGLRLQNKTIKV 75

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

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

 Score = 42.9 bits (102), Expect = 8e-06
 Identities = 18/71 (25%), Positives = 35/71 (49%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           T +YV NL   + ++ ++ELF + G++    +  D  G+  G   V +     A  A++ 
Sbjct: 2   TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEE 61

Query: 159 YNNVLLDGKPM 169
            N   ++GK +
Sbjct: 62  LNGKEVNGKKL 72

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

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

 Score = 42.5 bits (101), Expect = 1e-05
 Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 2/69 (2%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN-GRPSGSAEVVYARRSDAFAALKR 158
           KL+V  L    T +D+R LF E G ++   I  DK+ G+  G A V ++ R +A  A++ 
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 159 YNN-VLLDG 166
            +  V + G
Sbjct: 61  LHGKVTMPG 69

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN-GRPSGSAEVVYARRSDAFAALKR 158
            LYV NL   VT +D+++LF + GE+    +  D+  GR  G   V      +A AA+++
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 159 YNNVLLDGKPMKI 171
            N     G+ + +
Sbjct: 61  LNGTDFGGRTLTV 73

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

>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 27/82 (32%), Positives = 39/82 (47%), Gaps = 9/82 (10%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYA--------IHFDK-NGRPSGSAEVVYARRSD 151
           ++VSNL P  T  D+ E F  IG +K           ++ DK  G P G A V Y     
Sbjct: 1   VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 152 AFAALKRYNNVLLDGKPMKIEV 173
           A AA++ +NN    G  +K+ +
Sbjct: 61  ASAAIEWFNNKDFMGNTIKVSL 82

This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

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

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRY 159
           L+V  L   V  D ++E+FS  G +K   +  D+    P G A V +    DA  A+K  
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 160 NNVLLDGKPMKIE 172
           +   +DG+ + +E
Sbjct: 61  DGGQIDGQEVTVE 73

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

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

 Score = 41.9 bits (98), Expect = 2e-05
 Identities = 22/58 (37%), Positives = 34/58 (58%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           L V NL P V+N+ + + FS+ G ++R  +  D  GRP+G   V +A +  A  AL+R
Sbjct: 2   LTVKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKALER 59

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

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 18/75 (24%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSE-IGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALK 157
           ++L V NL   +T  +++E FS+  GE+    +   ++G+    A + Y    +A  A  
Sbjct: 1   SRLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKD 60

Query: 158 RYNNVLLDGKPMKIE 172
            +NN  ++   + +E
Sbjct: 61  YFNNTYINTSKISVE 75

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

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

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN-GRPSGSAEVVYARRSDAFAALKRY 159
           L+V NL      D I E F E GE+    +  D + GRP G   V ++ +  A AAL   
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 160 NNVLLDGKPMKIE 172
               L G+P++++
Sbjct: 61  GGTDLLGRPVRLD 73

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

 Score = 42.0 bits (98), Expect = 2e-05
 Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 2/75 (2%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           L V NL P V+N+ + E FS+ G ++R  +  D  GR +G   V +A +  A  A +R  
Sbjct: 2   LSVRNLSPYVSNELLEEAFSQFGPVERAVVIVDDRGRSTGKGIVEFASKPAARKAFERCT 61

Query: 161 N--VLLDGKPMKIEV 173
               LL   P  + V
Sbjct: 62  EGVFLLTTTPRPVIV 76

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

>gnl|CDD|240705 cd12259, RRM_SRSF11_SREK1, RNA recognition motif in serine/arginine-rich splicing factor 11 (SRSF11), splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 21/66 (31%), Positives = 28/66 (42%), Gaps = 3/66 (4%)

Query: 103 VSNLHPGVTNDDIRELFSEIG---ELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY 159
           V+N+ P  T + +R LF  +G   EL+ Y    D     S    V Y    D   AL   
Sbjct: 4   VTNVSPQATEEQMRTLFGFLGKIEELRLYPSDDDLAPVLSKVCFVKYEDPEDVGVALHLT 63

Query: 160 NNVLLD 165
           N V +D
Sbjct: 64  NTVFID 69

This subfamily corresponds to the RRM domain of SRSF11 (SRp54 or p54), SREK1 ( SFRS12 or SRrp86) and similar proteins, a group of proteins containing regions rich in serine-arginine dipeptides (SR protein family). These are involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SR proteins have been identified as crucial regulators of alternative splicing. Different SR proteins display different substrate specificity, have distinct functions in alternative splicing of different pre-mRNAs, and can even negatively regulate splicing. All SR family members are characterized by the presence of one or two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and the C-terminal regions rich in serine and arginine dipeptides (SR domains). The RRM domain is responsible for RNA binding and specificity in both alternative and constitutive splicing. In contrast, SR domains are thought to be protein-protein interaction domains that are often interchangeable. . Length = 76

>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 41.3 bits (97), Expect = 3e-05
 Identities = 28/72 (38%), Positives = 36/72 (50%), Gaps = 4/72 (5%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           L V NL P V+NDD+ ++F   GE+K   I    N R     E    R   A AALK  N
Sbjct: 4   LVVFNLDPSVSNDDLHQIFGAYGEIKE--IRETPNKRHHKFIEFYDVR--SAEAALKALN 59

Query: 161 NVLLDGKPMKIE 172
              + GK +K+E
Sbjct: 60  RSEIAGKRIKLE 71

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|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 44.0 bits (104), Expect = 4e-05
 Identities = 25/56 (44%), Positives = 27/56 (48%)

Query: 206 GNAGGAAAINRGPGSQGRRGGLRRSSQGRGRGQGQGRGRGRGGGGGGGRGRGRGRG 261
           G  GG      G    G  GG     +G GRG G+GRGRG GGGG GG G G    
Sbjct: 1   GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPGK 56

Length = 293

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 41.0 bits (97), Expect = 4e-05
 Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 6/76 (7%)

Query: 101 LYVSNLHPGVTNDDIR----ELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
           LY++NL+  +  D+++     LFS+ G +    I   K  +  G A VV+     A  AL
Sbjct: 2   LYINNLNEKIKKDELKRSLYALFSQFGPV--LDIVASKTLKMRGQAFVVFKDVESATNAL 59

Query: 157 KRYNNVLLDGKPMKIE 172
           +         KPM+I+
Sbjct: 60  RALQGFPFYDKPMRIQ 75

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins

 Score = 41.4 bits (98), Expect = 4e-05
 Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 7/76 (9%)

Query: 102 YVSNLHPGVTNDDI---RELFSEIGELKRYAI----HFDKNGRPSGSAEVVYARRSDAFA 154
           YV  L P + ++++    E F + G++K+  I     ++ +  PS SA V Y+R+ DA  
Sbjct: 9   YVVGLPPRLADEEVLKKPEYFGQYGKIKKIVINRNTSYNGSQGPSASAYVTYSRKEDALR 68

Query: 155 ALKRYNNVLLDGKPMK 170
            ++  +   LDG+ +K
Sbjct: 69  CIQAVDGFYLDGRLLK 84

This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T. Length = 98

>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 41.1 bits (96), Expect = 4e-05
 Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 1/76 (1%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALK 157
             LYVS L   +T  ++ +LFS+ G +    I  D+  G   G   + + +R +A  A+K
Sbjct: 1   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 158 RYNNVLLDGKPMKIEV 173
             N    +G    I V
Sbjct: 61  GLNGQKPEGASEPITV 76

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|222425 pfam13865, FoP_duplication, C-terminal duplication domain of Friend of PRMT1

 Score = 40.9 bits (96), Expect = 4e-05
 Identities = 24/54 (44%), Positives = 30/54 (55%), Gaps = 1/54 (1%)

Query: 232 QGRGRGQGQGRGRGRGGGGGGGRGRGRGRGRGQG-KKNPVDKSADDLDKELDNY 284
            G  +G   G+ R RG G   GR RGRG  +G+G    P  K+ +DLD ELD Y
Sbjct: 1   SGGRKGSRGGKFRPRGRGARRGRRRGRGGRKGKGGAAKPKPKTREDLDAELDQY 54

Fop, or Friend of Prmt1, proteins are conserved from fungi and plants to vertebrates. There is little that is actually conserved except for this C-terminal LDXXLDAYM region where X is any amino acid). The Fop proteins themselves are nuclear proteins localised to regions with low levels of DAPI, with a punctate/speckle-like distribution. Fop is a chromatin-associated protein and it colocalises with facultative heterochromatin. It is is critical for oestrogen-dependent gene activation. Length = 76

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

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 22/69 (31%), Positives = 35/69 (50%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY 159
           +L V NL    T  D+++LFS  G +    I    +G+  G A V +  ++DA  A+K  
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGV 60

Query: 160 NNVLLDGKP 168
           N   + G+P
Sbjct: 61  NGKKIKGRP 69

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

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 4/77 (5%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHF----DKNGRPSGSAEVVYARRSDAFA 154
           T LYV NL+P VT + + + F   G L    I +    ++  R      V +  R+DA  
Sbjct: 2   TNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAER 61

Query: 155 ALKRYNNVLLDGKPMKI 171
           AL   +   + G  +K+
Sbjct: 62  ALDELDGKDVMGYELKL 78

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

 Score = 40.4 bits (95), Expect = 5e-05
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 2/71 (2%)

Query: 102 YVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN-GRPSGSAEVVYARRSDAFAALKRYN 160
           +V N+  G T ++++E F   G + R  I  DK  G+P G A + +  +S    AL   N
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-LN 61

Query: 161 NVLLDGKPMKI 171
                G+ +K+
Sbjct: 62  ESEFRGRQIKV 72

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

>gnl|CDD|240714 cd12268, RRM_Vip1, RNA recognition motif in fission yeast protein Vip1 and similar proteins

 Score = 40.2 bits (94), Expect = 5e-05
 Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 4/71 (5%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           +YVSN+ P  T   I + FS  G++         N   S +A + + + S A  AL   +
Sbjct: 1   VYVSNISPKTTEKQISDFFSFCGKISNL---DLTNDGESQTATITFEKPSAAKTAL-LLD 56

Query: 161 NVLLDGKPMKI 171
           N LL GK +++
Sbjct: 57  NALLGGKVIQV 67

This subfamily corresponds to Vip1, an RNA-binding protein encoded by gene vip1 from fission yeast Schizosaccharomyces pombe. Its biological role remains unclear. Vip1 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 68

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 40.6 bits (95), Expect = 5e-05
 Identities = 24/62 (38%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELK--RYAIHFDKNGRPSGSAEVVYARRS-DAFAA 155
           TK+ V NL    T  D+R LFS  G+LK  R    FD++ R     E   A+ + +A  A
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNA 60

Query: 156 LK 157
           LK
Sbjct: 61  LK 62

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

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

 Score = 40.3 bits (95), Expect = 6e-05
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNG----RPSGSAEVVYARRSDAFAA 155
           +L++ NL   +T   + +LFS+ G++K++   F K+G    +P G   V +  + +A  A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 156 LKRYNNVLLDGK 167
           LK  N     GK
Sbjct: 61  LKSLNGKTALGK 72

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

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

 Score = 40.1 bits (94), Expect = 7e-05
 Identities = 26/72 (36%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALKR 158
           +L+V NL      DD+ +LFS+ GEL    +  D K+G+  G A V++    DA  A K 
Sbjct: 4   RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 159 YNNVLLDGKPMK 170
                LDGK  +
Sbjct: 64  -----LDGKVFQ 70

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

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

 Score = 40.1 bits (94), Expect = 8e-05
 Identities = 20/71 (28%), Positives = 37/71 (52%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           ++V+NL   V    ++E+F   G++ R  I  DK G+  G   V +    +A  A+  +N
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60

Query: 161 NVLLDGKPMKI 171
             +L  +PM++
Sbjct: 61  GQMLFDRPMRV 71

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

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

 Score = 39.7 bits (93), Expect = 8e-05
 Identities = 17/70 (24%), Positives = 27/70 (38%), Gaps = 7/70 (10%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY 159
           +LYV    P  +   IRE+FS  G +K   +           A V +     A  A    
Sbjct: 1   RLYVRPFPPDTSESAIREIFSPYGAVKEVKMIS-------NFAFVEFESLESAIRAKDSV 53

Query: 160 NNVLLDGKPM 169
           +  +L+  P+
Sbjct: 54  HGKVLNNNPL 63

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

>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 40.0 bits (94), Expect = 8e-05
 Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAI-HFDKNGRPSGSAEVVYARRSDAFAALKRY 159
           +YV  L    T++ ++ +FS+ G +   ++  +   G   G A + +    +A  A K  
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 160 NN 161
           NN
Sbjct: 62  NN 63

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

 Score = 39.5 bits (93), Expect = 9e-05
 Identities = 20/72 (27%), Positives = 31/72 (43%), Gaps = 1/72 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALKRY 159
           LYV  L   V    +   F   G++K   I  D +  +  G A V +    DA AA+   
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 160 NNVLLDGKPMKI 171
           N   L G+ +++
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|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 42.4 bits (100), Expect = 1e-04
 Identities = 27/56 (48%), Positives = 29/56 (51%), Gaps = 2/56 (3%)

Query: 204 GSGNAGGAAAINRGPGSQGRRGGLRRSSQGRGRGQGQGRGRGRGGGGGGGRGRGRG 259
           G G  GG      G G  GR GG R    GRG G+G+GRG G GG GGGG G    
Sbjct: 3   GGGFGGGRGGGRGGGGGGGRGGGGRGG--GRGGGRGRGRGGGGGGRGGGGGGGPGK 56

Length = 293

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 10/76 (13%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAE--------VVYARRS 150
           T L+V NL+   T + +++ F + G ++  ++   K   P G  +        V +  + 
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVR--SVTIAKKKDPKGPGKLLSMGYGFVEFKSKE 58

Query: 151 DAFAALKRYNNVLLDG 166
            A  ALKR    +LDG
Sbjct: 59  AAQKALKRLQGTVLDG 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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 1/75 (1%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKR 158
            L+V NL   V ++ ++  F + G +    +  D+  GR  G   V +    DA  A++ 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 159 YNNVLLDGKPMKIEV 173
            +   LDG+P+ ++ 
Sbjct: 61  MDGKELDGRPINVDF 75

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

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDA-FAALK 157
           T LYV  L   VT  D+R+ F + GE++   +   +       A V +  R  A  AA +
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQ-----CAFVTFTTREAAEKAAER 56

Query: 158 RYNNVLLDGKPMKI 171
            +N ++++G+ +K+
Sbjct: 57  LFNKLIINGRRLKL 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|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 39.1 bits (92), Expect = 1e-04
 Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 2/67 (2%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           LYV NL   ++++++ +LF + G +++  I   K  R  G+A VVY    DA  A    +
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETR--GTAFVVYEDIYDAKNACDHLS 62

Query: 161 NVLLDGK 167
              +  +
Sbjct: 63  GFNVANR 69

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

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

 Score = 42.6 bits (100), Expect = 1e-04
 Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN-GRPSGSAEVVYARRSDAFAALKR 158
           KLYV NLH  +T  ++R++F   G+++   +H D   GR  G   + +    +A  AL+ 
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEV 247

Query: 159 YNNVLLDGKPMKI 171
            N   L G+P+K+
Sbjct: 248 MNGFELAGRPIKV 260

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

>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 22/73 (30%), Positives = 40/73 (54%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           ++V+NL   V    ++E+FS  G +KR  I  DK+G+  G   V + +  +A  A+  +N
Sbjct: 3   IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMFN 62

Query: 161 NVLLDGKPMKIEV 173
              L  +PM +++
Sbjct: 63  GQFLFDRPMHVKM 75

This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 2/61 (3%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           +YV  +    T  ++R+ F   GE++   +HF  +G   G   V Y    DAF A++  N
Sbjct: 5   IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGF--VTYRYACDAFRAIEHGN 62

Query: 161 N 161
           +
Sbjct: 63  D 63

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|240255 PTZ00070, PTZ00070, 40S ribosomal protein S2; Provisional

 Score = 41.6 bits (98), Expect = 2e-04
 Identities = 22/37 (59%), Positives = 24/37 (64%), Gaps = 2/37 (5%)

Query: 238 QGQGRGRGRGGGGGGGRGRGRGRGRGQGKKN--PVDK 272
            G+GRG GR G GG GRGRGRGRG    +K   PV K
Sbjct: 6   GGEGRGFGRRGRGGRGRGRGRGRGGEGEEKEWVPVTK 42

Length = 257

>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 12/72 (16%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGS-AEVVYARRSDAFAAL- 156
           T + V NL  G T +++RELF + G L R  +       PS + A V +   SDA  A  
Sbjct: 1   TVILVKNLPFGTTEEELRELFEKFGSLGRLLL------PPSRTIALVEFLEPSDARKAFK 54

Query: 157 ----KRYNNVLL 164
               KR+ +V L
Sbjct: 55  SLAYKRFKHVPL 66

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 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 homologues 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. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>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 = 38.4 bits (90), Expect = 2e-04
 Identities = 22/74 (29%), Positives = 38/74 (51%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           TKL V N+    T  ++RELFS  G++K   +    +G   G A V +  + +A  A++ 
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60

Query: 159 YNNVLLDGKPMKIE 172
             +  L G+ + +E
Sbjct: 61  LKSTHLYGRHLVLE 74

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

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 22/58 (37%), Positives = 32/58 (55%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           L V NL   V+N+ + E FS  G+++R  +  D  GRP+G   V +A +  A  AL R
Sbjct: 2   LTVKNLPQFVSNELLEEAFSMFGQVERAVVIVDDRGRPTGKGIVEFAGKPSARKALDR 59

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

>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 12/74 (16%)

Query: 103 VSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNV 162
           V NL    T + IR+ F + GE++   I   + G     A + +    +A AAL +    
Sbjct: 5   VKNLPKDTTENKIRQFFKDCGEIREVKIVESEGGL---VAVIEFETEDEALAALTK---- 57

Query: 163 LLDGKPM---KIEV 173
             D K +   +I V
Sbjct: 58  --DHKRLGGNEISV 69

This subfamily corresponds to the RRM1 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 71

>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 38.1 bits (88), Expect = 3e-04
 Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 7/74 (9%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           TKL+V N+    TN ++R  F E G +    I  D        A V   R  DA  A++ 
Sbjct: 1   TKLHVGNISSSCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRG 53

Query: 159 YNNVLLDGKPMKIE 172
            +N    GK M ++
Sbjct: 54  LDNTEFQGKRMHVQ 67

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|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 = 38.4 bits (90), Expect = 3e-04
 Identities = 16/72 (22%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 102 YVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN-GRPSGSAEVVYARRSDAFAALKRYN 160
           +V N+    T + + E+FSE+G +  + +  D++ G+P G     +     A +A++  N
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 161 NVLLDGKPMKIE 172
               +G+ ++++
Sbjct: 62  GYEFNGRALRVD 73

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

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

 Score = 41.5 bits (97), Expect = 3e-04
 Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 96  EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFA 154
           E  T L V+ L   +T ++IR LF+ IGE++   +  DK  G+  G   V Y R  DA  
Sbjct: 1   ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEK 60

Query: 155 ALKRYNNVLLDGKPMKI 171
           A+   N + L  K +K+
Sbjct: 61  AVNSLNGLRLQNKTIKV 77

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|240950 cd12506, RRM3_hnRNPH_CRSF1_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein hnRNP H protein family, G-rich sequence factor 1 (GRSF-1) and similar proteins

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 1/48 (2%)

Query: 111 TNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           T +DI E FS +  +    I ++ +GR +G A+V +A   DA AA+ +
Sbjct: 13  TENDIFEFFSPLNPV-NVRIEYNADGRATGEADVEFATHEDAVAAMSK 59

This subfamily corresponds to the RRM3 of hnRNP H proteins and GRSF-1. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. These proteins have similar RNA binding affinities and specifically recognize the sequence GGGA. They can either stimulate or repress splicing upon binding to a GGG motif. hnRNP H binds to the RNA substrate in the presence or absence of these proteins, whereas hnRNP F binds to the nuclear mRNA only in the presence of cap-binding proteins. hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. hnRNP H3 may be involved in the splicing arrest induced by heat shock. Most family members contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. For instance, members in this family can regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. The family also includes a cytoplasmic poly(A)+ mRNA binding protein, GRSF-1, which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 also contains three potential RRMs responsible for the RNA binding, and two auxiliary domains (an acidic alpha-helical domain and an N-terminal alanine-rich region) that may play a role in protein-protein interactions and provide binding specificity. . Length = 75

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

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 17/72 (23%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY 159
           +L+V NL   +T ++ +ELFS+ GE+    ++ +K     G   +    R++A  A    
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEK-----GFGFIRLDTRTNAEKAKAEL 57

Query: 160 NNVLLDGKPMKI 171
           + ++  G+ +++
Sbjct: 58  DGIMRKGRQLRV 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|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 38.3 bits (89), Expect = 3e-04
 Identities = 19/58 (32%), Positives = 31/58 (53%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALK 157
           KL+V  L      +D+R +F+  G ++   +  D+NG+  G A V +A R  A  A+K
Sbjct: 3   KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIK 60

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

 Score = 41.3 bits (97), Expect = 4e-04
 Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPS-GSAEVVYARRSDAFAALKRY 159
           LYV +L P VT   + +LF   G +    +  D   R S G   V +   +DA  AL+  
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 160 NNVLLDGKPMKI 171
           N   L GKP++I
Sbjct: 63  NFKRLGGKPIRI 74

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

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

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALKRY 159
           L+V  L+P  T++D+  +FS  G++K   +  D K G     A + +  + D   A  + 
Sbjct: 6   LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKM 65

Query: 160 NNVLLD 165
           +NVL+D
Sbjct: 66  DNVLID 71

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|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 37.7 bits (87), Expect = 5e-04
 Identities = 22/75 (29%), Positives = 41/75 (54%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           + ++V+NL   V    ++E+FS  G + R  I  DK+G+  G   V + +  +A  A+  
Sbjct: 1   STVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISM 60

Query: 159 YNNVLLDGKPMKIEV 173
           +N  LL  +PM +++
Sbjct: 61  FNGQLLFDRPMHVKM 75

This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 40.8 bits (95), Expect = 5e-04
 Identities = 42/148 (28%), Positives = 62/148 (41%), Gaps = 16/148 (10%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALK 157
           T LYV+NL   +T+D +  +F + G++ +  I  DK  G P G A V + +R +A  A+ 
Sbjct: 194 TNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAIS 253

Query: 158 RYNNVLLDGKPMKIEVVGTNAEIPLQARVNVTGVNGRRKRTVVMTS-GSGNAGGAAAINR 216
             NNV+ +G              PL  R  +   +G+ K    M+  G GN G     N 
Sbjct: 254 ALNNVIPEG-----------GSQPLTVR--LAEEHGKAKAHHYMSQMGHGNMGNMGHGNM 300

Query: 217 GPGSQGRRGGLRRSSQGRGRGQGQGRGR 244
           G  + G            G      RGR
Sbjct: 301 G-MAGGSGMNPPNPPAFMGMNNMVHRGR 327

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|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 37.3 bits (87), Expect = 6e-04
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKR 158
           KL+V NL   V + +++E FS+ G++K   + FDK  G   G   V ++ R D      +
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSR-DGLENALQ 59

Query: 159 YNNVLLDGKPMKI 171
               +L+G  +++
Sbjct: 60  KQKHILEGNKLQV 72

This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities. . Length = 73

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

 Score = 37.5 bits (87), Expect = 6e-04
 Identities = 22/60 (36%), Positives = 31/60 (51%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           LYV NL P VT D ++++F   G ++   I  DKN +      V Y +  DA  AL+  N
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 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|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 40.1 bits (94), Expect = 7e-04
 Identities = 26/56 (46%), Positives = 29/56 (51%), Gaps = 1/56 (1%)

Query: 201 MTSGSGNAGGAAAINRGPGSQGRRGGLRRSSQGRGRGQGQGRGRGRGGGGGGGRGR 256
           M  G G   G      G G +G  G       GRGRG+G G G GRGGGGGGG G+
Sbjct: 2   MGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGG-GRGGGGGGGPGK 56

Length = 293

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

 Score = 37.2 bits (86), Expect = 7e-04
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 6/73 (8%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN-GRPSGSAEVVYARRSDAFAALKRY 159
           L V+NL    + D ++E+F      K  +I   +N GRP G A V +    DA  AL   
Sbjct: 4   LVVNNLSYSASEDSLQEVFE-----KATSIRIPQNNGRPKGYAFVEFESAEDAKEALNSC 58

Query: 160 NNVLLDGKPMKIE 172
           NN  ++G+ +++E
Sbjct: 59  NNTEIEGRSIRLE 71

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

 Score = 37.2 bits (87), Expect = 9e-04
 Identities = 22/74 (29%), Positives = 27/74 (36%), Gaps = 2/74 (2%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKR- 158
           L+V  L P VT  D+ E FS  G +    I   K  G   G A +            K  
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 159 YNNVLLDGKPMKIE 172
            N     G  +KIE
Sbjct: 62  LNGTKWKGSVLKIE 75

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

 Score = 37.3 bits (86), Expect = 9e-04
 Identities = 22/63 (34%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 111 TNDDIRELFSEIGELKRYAIHFDKNGRPS-GSAEVVYARRSDAFAALKRYNNVLLDGKPM 169
           T  D+RE+FS+ G +   +I +D+  R S G A V +    DA  A +R N + LDG+ +
Sbjct: 22  TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 81

Query: 170 KIE 172
           +++
Sbjct: 82  RVD 84

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|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 = 9e-04
 Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 6/75 (8%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIH---FDKNGRPSGSAEVVYARRSDAFAALK 157
           +YV  +    T D+IR  FS  GE++   +    F   GR  G A + +     A  AL 
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIE--ELDLMTFPDTGRFRGIAFITFKTEEAAKRALA 58

Query: 158 RYNNVLLDGKPMKIE 172
             +   + G+ +K+E
Sbjct: 59  -LDGEDMGGRFLKVE 72

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

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

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 24/75 (32%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALK 157
           T LYV N+      DD+R LF + G +    I  D    RP G A V +    DA  AL 
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60

Query: 158 RYNNVLLDGKPMKIE 172
             +     G+ ++I+
Sbjct: 61  YLDRTRFLGREIEIQ 75

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|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional

 Score = 39.8 bits (93), Expect = 0.001
 Identities = 20/51 (39%), Positives = 21/51 (41%), Gaps = 1/51 (1%)

Query: 219 GSQGRRGGLRRSSQGRGRGQGQGRGRGRGGGGGGGRGRGRGRGRGQGKKNP 269
           G Q R GG R    GRG+ QGQ R RG GG             R  G   P
Sbjct: 390 GRQQRGGGGRGQGGGRGQQQGQPR-RGEGGAKSASAKPAEKPSRRLGDAKP 439

Length = 456

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPS-GSAEVVYARRSDAFAALKRY 159
           L V NL    T DD+R +F + GE+    I  D+  R S G A V +  + DA  A+   
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 160 NNVLLDGKPMKI 171
           +   LDG+ +++
Sbjct: 61  DGKELDGRELRV 72

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

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

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 22/71 (30%), Positives = 34/71 (47%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           L+V NL   V  + + ELF + G L +  I  DK G+P     V +        A+   N
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLN 63

Query: 161 NVLLDGKPMKI 171
            + L G+P+K+
Sbjct: 64  GIRLYGRPIKV 74

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

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

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
            K+ +SN+ P V  +D+  L S  G +K       K+   + +  V Y     A  A+ +
Sbjct: 1   RKIQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSE--TATVNVTYESPEQAQQAVNK 58

Query: 159 YNNVLLDGKPMKIE 172
            N    +G  +K+ 
Sbjct: 59  LNGHEYEGSKLKVS 72

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|240955 cd12511, RRM2_RBM12_like, RNA recognition motif 2 in RNA-binding protein RBM12, RBM12B and similar proteins

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 5/60 (8%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHF--DKNGRPSGSAEVVYARRSDAFAALKR 158
           +++  L       D++E F     L    + F    NGR +G+A V +A   DA  ALKR
Sbjct: 2   VFLHGLPYTADEHDVKEFFHG---LDVEDVIFLKRHNGRNNGNAIVKFATFQDAKEALKR 58

This subfamily corresponds to the RRM2 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B shows high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear. . Length = 73

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

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 111 TNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPM 169
           T  D+RE+FS  G L    + +D + GR  G A V + R  D+  A++  N + LDG+ +
Sbjct: 12  TERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRI 71

Query: 170 KIE 172
           +++
Sbjct: 72  RVD 74

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|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           +++ V NL   VT D +RE F   GE+    +   ++G+      V +    DA  A+K 
Sbjct: 1   SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKY 60

Query: 159 YNNVLLDGKPMKIEV 173
           +N   +D    KI V
Sbjct: 61  FNKTFID--TSKISV 73

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 10/29 (34%), Positives = 21/29 (72%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKR 127
            ++YV+++HP ++ DDI+ +F   G++K 
Sbjct: 1   NRIYVASVHPDLSEDDIKSVFEAFGKIKS 29

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

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 26/74 (35%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALK 157
           T L V+ L   +T D++R LFS IGE++   +  DK  G   G   V Y    DA  A+ 
Sbjct: 2   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAIN 61

Query: 158 RYNNVLLDGKPMKI 171
             N + L  K +K+
Sbjct: 62  TLNGLRLQSKTIKV 75

This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional

 Score = 38.3 bits (89), Expect = 0.003
 Identities = 12/59 (20%), Positives = 22/59 (37%)

Query: 216 RGPGSQGRRGGLRRSSQGRGRGQGQGRGRGRGGGGGGGRGRGRGRGRGQGKKNPVDKSA 274
           RG G +G+ GG  +      RG+G  +           R  G  +  G+ ++    +  
Sbjct: 394 RGGGGRGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPAGEQQRRRRPRKP 452

Length = 456

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

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALKRY 159
           L V  L    T  D+RE+FS  G +++  + +D K GR  G   V +    DA  A +R 
Sbjct: 2   LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61

Query: 160 NNVLLDGKPMKIEVVGT 176
           N + +DG+ ++++   T
Sbjct: 62  NGMEIDGRRIRVDYSIT 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|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 22/74 (29%), Positives = 32/74 (43%), Gaps = 1/74 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPS-GSAEVVYARRSDAFAALKRY 159
           LYVS L   +T  ++  LFS  G +    I  D     S G   + + +R +A  A+K  
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 160 NNVLLDGKPMKIEV 173
           N  +  G    I V
Sbjct: 63  NGTIPPGATEPITV 76

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|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 7/61 (11%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVV-YARRSDAFAALK 157
           T + V N   G T +++R+LF   G+L R  +       P+G+  +V +A    A  A K
Sbjct: 1   TTILVKNFPYGTTAEELRDLFEPHGKLTRVLM------PPAGTIAIVEFANPQQARLAFK 54

Query: 158 R 158
            
Sbjct: 55  A 55

This subgroup corresponds to the RRM3 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 = 72

>gnl|CDD|241177 cd12733, RRM3_GRSF1, RNA recognition motif 3 in G-rich sequence factor 1 (GRSF-1) and similar proteins

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           +++  L    +  DI   F+ + +  R  I +  +GR +G A+V +    DA AA+ +
Sbjct: 3   VHMRGLPFQASGQDIVNFFAPL-KPTRILIEYSSDGRATGEADVHFESHDDAVAAMAK 59

This subgroup corresponds to the RRM3 of G-rich sequence factor 1 (GRSF-1), a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic alpha-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity. . Length = 75

>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 9/77 (11%)

Query: 98  GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVV--YARRSDAFAA 155
           GT L V NL   +++ ++R LFS+ GE+K       +      S + V  Y  R  A AA
Sbjct: 2   GT-LLVFNLDSPISDQELRSLFSQFGEVKDI-----RETPLRPSQKFVEFYDIR-AAEAA 54

Query: 156 LKRYNNVLLDGKPMKIE 172
           L   N     G  +K++
Sbjct: 55  LDALNGRPFLGGRLKVK 71

This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score = 35.8 bits (82), Expect = 0.004
 Identities = 21/84 (25%), Positives = 44/84 (52%), Gaps = 6/84 (7%)

Query: 101 LYVSNLHPGVTNDDIRE----LFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
           +Y++NL+  +  D++++    +FS  G++    I   ++ +  G A V++   S A  AL
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 63

Query: 157 KRYNNVLLDGKPMKIEVVGTNAEI 180
           +         KPM+I+   T+++I
Sbjct: 64  RSMQGFPFYDKPMRIQYAKTDSDI 87

This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 89

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

 Score = 35.2 bits (82), Expect = 0.004
 Identities = 22/74 (29%), Positives = 31/74 (41%), Gaps = 16/74 (21%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGE--------LKRYAIHFDKNGRPSGSAEVVYARRSDA 152
           L+V+N  P     DIR+LF + GE        L+     F+K  R      V +     A
Sbjct: 3   LWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLR-----FNKTRR---FCYVQFTSPESA 54

Query: 153 FAALKRYNNVLLDG 166
            AA+   N  L +G
Sbjct: 55  AAAVALLNGKLGEG 68

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

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

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 1/67 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALKRY 159
           L+V  L    T + +RE+FS  G+++R  +  D   G   G A V Y    DA  A +  
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 160 NNVLLDG 166
           + +++DG
Sbjct: 66  HKLVIDG 72

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

 Score = 35.0 bits (81), Expect = 0.004
 Identities = 17/72 (23%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALKRY 159
           ++V +L P +  + +R  F+  GE+    +  D + G+  G   V + ++ DA  A++  
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 160 NNVLLDGKPMKI 171
           N   L G+ ++ 
Sbjct: 62  NGQWLGGRAIRT 73

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

>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 38.1 bits (88), Expect = 0.004
 Identities = 42/197 (21%), Positives = 60/197 (30%), Gaps = 16/197 (8%)

Query: 101 LYVSNLHPGVTNDDIRELFSEI--GELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           LYV NL    T + I + FSE   G+++R     D        A V +  R DA  A+  
Sbjct: 236 LYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD-------YAFVHFEDREDAVKAMDE 288

Query: 159 YNNVLLDGKPMKIEVVGTNAEIPLQARVNVTGVNGRRKRTVVMTSGSGNAGGAAAINRGP 218
            N   L+G  +++  +    +     R         ++R     S       A+      
Sbjct: 289 LNGKELEGSEIEV-TLAKPVDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYE 347

Query: 219 G------SQGRRGGLRRSSQGRGRGQGQGRGRGRGGGGGGGRGRGRGRGRGQGKKNPVDK 272
                          R     RGRG+G    R  GG G    G     G   G  +   K
Sbjct: 348 DYYYHPPYAPSLHFPRMPGPIRGRGRGGAPSRAAGGRGYPPYGYEAYYGDYYGYHDYRGK 407

Query: 273 SADDLDKELDNYHAEAM 289
             D             M
Sbjct: 408 YEDKYYGYDPGMELTPM 424

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 6/68 (8%)

Query: 112 NDDIRELF-----SEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALKRYNNVLLD 165
           ND+I E F      + GE++   I+F  K  +  G A VV+     A   +++ N   + 
Sbjct: 11  NDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKLNQTSVM 70

Query: 166 GKPMKIEV 173
           GK +K+ +
Sbjct: 71  GKIIKVFL 78

This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo. . Length = 93

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	291
KOG0533	243	consensus RRM motif-containing protein [RNA proces	99.97
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.85
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.77
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.71
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.71
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.7
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.7
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.69
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.69
KOG0122	270	consensus Translation initiation factor 3, subunit	99.68
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.65
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.65
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.63
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.62
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.61
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.6
PLN03120	260	nucleic acid binding protein; Provisional	99.59
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.57
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.56
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.55
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.55
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.55
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.54
smart00362	72	RRM_2 RNA recognition motif.	99.54
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.53
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.53
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.52
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.52
PLN03213	759	repressor of silencing 3; Provisional	99.51
PLN03121	243	nucleic acid binding protein; Provisional	99.51
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.5
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.49
smart00360	71	RRM RNA recognition motif.	99.49
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.48
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.48
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.47
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.47
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.47
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.46
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.45
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.44
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.44
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.43
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.42
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.41
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.39
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.38
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.38
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.37
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.36
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.36
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.32
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.31
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.31
smart00361	70	RRM_1 RNA recognition motif.	99.3
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.27
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.25
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.24
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.23
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.2
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.2
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.19
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.19
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.15
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.12
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.1
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.08
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.07
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.05
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.05
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.04
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.02
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.0
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.99
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.93
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.93
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.93
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.92
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.87
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.85
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.84
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.74
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.65
PF13865	74	FoP_duplication: C-terminal duplication domain of	98.62
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.62
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.57
KOG0226	290	consensus RNA-binding proteins [General function p	98.56
KOG0151	877	consensus Predicted splicing regulator, contains R	98.54
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.43
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.43
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.39
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.39
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.36
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.27
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.22
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.21
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.21
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.19
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.18
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.14
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.01
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.93
KOG4210	285	consensus Nuclear localization sequence binding pr	97.88
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.86
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.85
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.82
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.79
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.73
KOG2314	698	consensus Translation initiation factor 3, subunit	97.73
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.72
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.59
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.54
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.51
PF07078	316	FYTT: Forty-two-three protein; InterPro: IPR009782	97.48
KOG3152	278	consensus TBP-binding protein, activator of basal	97.48
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.47
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.29
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.24
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.23
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.13
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.02
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.95
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.9
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	96.86
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.84
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.84
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.78
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.77
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.51
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.41
KOG2068	327	consensus MOT2 transcription factor [Transcription	96.17
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.06
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	96.0
KOG2591	684	consensus c-Mpl binding protein, contains La domai	95.97
KOG2135	526	consensus Proteins containing the RNA recognition	95.94
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	95.48
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.39
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.33
PF13865	74	FoP_duplication: C-terminal duplication domain of	95.32
KOG4660	549	consensus Protein Mei2, essential for commitment t	95.04
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	94.81
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	94.71
KOG2318	650	consensus Uncharacterized conserved protein [Funct	94.32
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.08
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	93.86
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	93.7
KOG4210	285	consensus Nuclear localization sequence binding pr	93.34
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	93.03
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	92.59
KOG3973	465	consensus Uncharacterized conserved glycine-rich p	91.91
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	91.37
KOG4019	193	consensus Calcineurin-mediated signaling pathway i	87.84
PF03468	116	XS: XS domain; InterPro: IPR005380 The XS (rice ge	84.39
KOG4483	528	consensus Uncharacterized conserved protein [Funct	84.16
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	83.62
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	82.99

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=99.97  E-value=2.5e-30  Score=226.12  Aligned_cols=159  Identities=44%  Similarity=0.698  Sum_probs=114.8

Q ss_pred             CCCcCCCChHHHHHhcccCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCC-CCCCCccccccccccCCCCCC
Q 022827            1 MATHVDMSLDDIIKSRKKSERERGQGRARRGRGRGRGPSGSVSGGRMTGAARRG-PLS-NARPSSYTIAKSFRRTRNFPW   78 (291)
Q Consensus         1 m~~~ld~sLddii~~~~~~~~~~~~~~~~rg~gr~rg~~~~~~~~~g~g~~r~~-~~~-~~R~~~~~~~~~~~~~~~~~~   78 (291)
                      |++.|||||||||+++++.  +  +-+..++..++.++     ..++.+|.|+. ... ..+.           ..+..|
T Consensus         1 ms~~ld~sLd~iI~~~r~r--~--G~g~~r~~~r~~gg-----~~~~~~psR~~g~~r~~~~~-----------~~~~~w   60 (243)
T KOG0533|consen    1 MSDSLDMSLDDIIKSNRKR--G--GVGGKRGIKRRSGG-----QNRGRGPSRRTGKPRAQTRG-----------GIDGKW   60 (243)
T ss_pred             CcchhhhhHHHHHHhcccc--C--CcCccccccccccC-----CccCCCCccccCcccccccC-----------CCCCcc
Confidence            8999999999999999661  1  11111111111111     02223344441 100 1111           047889


Q ss_pred             Cc--hhhhhhhhhcCC-CCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHH
Q 022827           79 QH--DLFEDSLRAAGI-SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAA  155 (291)
Q Consensus        79 ~~--d~~~~~~~~~~~-~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~A  155 (291)
                      +|  ++|......... ......++|+|.|||+.|+++||++||.+|++++.+.|+++++|.+.|+|-|+|...++|++|
T Consensus        61 ~~~~~v~~~~~~~~~~~~~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~a  140 (243)
T KOG0533|consen   61 QHDRDVFRSAKRLGAVGINETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERA  140 (243)
T ss_pred             cchHHHHhcccccccccccCCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHH
Confidence            99  666655432111 133345899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhCCceeCCeeeEEEEecCCCC
Q 022827          156 LKRYNNVLLDGKPMKIEVVGTNAE  179 (291)
Q Consensus       156 i~~lng~~l~g~~i~V~~a~~~~~  179 (291)
                      |+.||++.|+|++|+|+++.+...
T Consensus       141 vk~~~gv~ldG~~mk~~~i~~~~~  164 (243)
T KOG0533|consen  141 VKKYNGVALDGRPMKIEIISSPSQ  164 (243)
T ss_pred             HHHhcCcccCCceeeeEEecCccc
Confidence            999999999999999999876654

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

Probab=99.85  E-value=1.9e-20  Score=153.58  Aligned_cols=83  Identities=22%  Similarity=0.430  Sum_probs=78.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ..+++|||.|||+++||++|+++|++||+|++|.|+.|+ ++++++||||+|.+.++|++||+.||++.|++++|+|+++
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a  111 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPA  111 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeC
Confidence            467899999999999999999999999999999999998 8999999999999999999999999999999999999998


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      ..++
T Consensus       112 ~~~~  115 (144)
T PLN03134        112 NDRP  115 (144)
T ss_pred             CcCC
Confidence            7554

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.77  E-value=9.2e-18  Score=156.14  Aligned_cols=82  Identities=32%  Similarity=0.583  Sum_probs=75.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCC--eeeEEEE
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDG--KPMKIEV  173 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g--~~i~V~~  173 (291)
                      ..++|||.|||+.+||++|+++|++||+|+.|.|+.++ ++++++||||+|.+.++|++||+.||++.|.+  ++|+|.+
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            46789999999999999999999999999999999998 99999999999999999999999999999876  6888888


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +....
T Consensus       272 a~~~~  276 (346)
T TIGR01659       272 AEEHG  276 (346)
T ss_pred             CCccc
Confidence            77543

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).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.71  E-value=8e-17  Score=150.18  Aligned_cols=82  Identities=21%  Similarity=0.297  Sum_probs=78.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      .+.+|||.|||+++++++|+++|++||.|.+|.|++|. ++.++|||||+|.+.++|.+||+.||+..|+|+.|+|.|+.
T Consensus       268 ~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~  347 (352)
T TIGR01661       268 AGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKT  347 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcc
Confidence            34579999999999999999999999999999999999 99999999999999999999999999999999999999988


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      .+.
T Consensus       348 ~~~  350 (352)
T TIGR01661       348 NKA  350 (352)
T ss_pred             CCC
Confidence            764

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.71  E-value=5e-17  Score=151.23  Aligned_cols=84  Identities=26%  Similarity=0.369  Sum_probs=79.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      .....++|||.|||+++||++|+++|++||+|++|+|+.|+ ++++++||||+|.++++|++||+.||+++|.+++|+|.
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            34577899999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             EecCC
Q 022827          173 VVGTN  177 (291)
Q Consensus       173 ~a~~~  177 (291)
                      ++.+.
T Consensus       183 ~a~p~  187 (346)
T TIGR01659       183 YARPG  187 (346)
T ss_pred             ccccc
Confidence            88653

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

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

Probab=99.70  E-value=3e-17  Score=128.18  Aligned_cols=80  Identities=33%  Similarity=0.504  Sum_probs=76.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ..+++|||+||++.|+|+.|.+||+.||+|+.|.+-.|+ +..+.|||||+|.+.++|+.||+-++++.|+.++|.|.|.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            478999999999999999999999999999999999999 8899999999999999999999999999999999999985


Q ss_pred             c
Q 022827          175 G  175 (291)
Q Consensus       175 ~  175 (291)
                      .
T Consensus       114 ~  114 (153)
T KOG0121|consen  114 A  114 (153)
T ss_pred             c
Confidence            4

>PF00076 RRM_1: RNA recognition motif

Probab=99.70  E-value=1.3e-16  Score=113.65  Aligned_cols=70  Identities=31%  Similarity=0.613  Sum_probs=67.4

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeE
Q 022827          101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMK  170 (291)
Q Consensus       101 l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~  170 (291)
                      |||+|||+++|+++|+++|++||.|..+.|..+.++.++++|||+|.+.++|++|++.||+..+.++.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            7999999999999999999999999999999988888999999999999999999999999999999885

(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 ....

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

Probab=99.69  E-value=1.7e-16  Score=131.28  Aligned_cols=77  Identities=22%  Similarity=0.352  Sum_probs=69.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ...++|||+|||.++.|.||++||.+||.|..|.|...+  ....||||+|+++.+|+.||..-++..++++.|.|+++
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~--g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP--GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC--CCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            357899999999999999999999999999999886543  23569999999999999999999999999999999974

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.69  E-value=1.4e-16  Score=148.54  Aligned_cols=82  Identities=32%  Similarity=0.464  Sum_probs=78.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      +.++|||+|||+.++|++|+++|++||+|.+|.|+.++ +++++|||||+|.+.++|++||+.||+..|.++.|+|+++.
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            56899999999999999999999999999999999998 89999999999999999999999999999999999999987


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      +..
T Consensus        82 ~~~   84 (352)
T TIGR01661        82 PSS   84 (352)
T ss_pred             ccc
Confidence            554

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

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

Probab=99.68  E-value=1.6e-16  Score=136.61  Aligned_cols=81  Identities=28%  Similarity=0.386  Sum_probs=78.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ..++|.|.||+.+++|+||++||..||.|..|.|..|+ ||.++|||||+|.+.++|++||+.||++-++.-.|+|+|++
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            56799999999999999999999999999999999999 99999999999999999999999999999999999999998


Q ss_pred             CC
Q 022827          176 TN  177 (291)
Q Consensus       176 ~~  177 (291)
                      +.
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            75

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

Probab=99.65  E-value=7.3e-16  Score=135.88  Aligned_cols=101  Identities=26%  Similarity=0.377  Sum_probs=95.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      .++-+||||.-|+++++|..|+..|+.||+|+.|.|+.|+ |++++|||||+|+++.+.++|.+..++.+|+++.|.|.+
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            4677899999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             ecCCCCCccccccCCCCCCCCc
Q 022827          174 VGTNAEIPLQARVNVTGVNGRR  195 (291)
Q Consensus       174 a~~~~~~~~~~r~~~~g~~g~~  195 (291)
                      -.....+-+.+|....|.++..
T Consensus       178 ERgRTvkgW~PRRLGGGLGg~r  199 (335)
T KOG0113|consen  178 ERGRTVKGWLPRRLGGGLGGRR  199 (335)
T ss_pred             cccccccccccccccCCcCCcc
Confidence            9999988898988877777665

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

Probab=99.65  E-value=4.5e-16  Score=127.77  Aligned_cols=78  Identities=24%  Similarity=0.334  Sum_probs=73.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      -.++|||+||+..+++.||+.+|..||+|..|.|..++    .|||||||+++.+|+.|+..|++..|+|..|.|+++..
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC----CCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            46899999999999999999999999999999998764    89999999999999999999999999999999999886


Q ss_pred             CC
Q 022827          177 NA  178 (291)
Q Consensus       177 ~~  178 (291)
                      .+
T Consensus        85 ~~   86 (195)
T KOG0107|consen   85 RP   86 (195)
T ss_pred             Cc
Confidence            65

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

Probab=99.63  E-value=4.5e-16  Score=130.85  Aligned_cols=87  Identities=26%  Similarity=0.382  Sum_probs=81.9

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeE
Q 022827           92 ISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMK  170 (291)
Q Consensus        92 ~~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~  170 (291)
                      ++.++.-++|.|-||.+-|+.++|..+|++||.|-+|.|..|+ |..++|||||.|....+|+.|+++|++.+|+|+.|.
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelr   86 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELR   86 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceee
Confidence            4566777899999999999999999999999999999999999 999999999999999999999999999999999999


Q ss_pred             EEEecCCC
Q 022827          171 IEVVGTNA  178 (291)
Q Consensus       171 V~~a~~~~  178 (291)
                      |++|.-..
T Consensus        87 Vq~arygr   94 (256)
T KOG4207|consen   87 VQMARYGR   94 (256)
T ss_pred             ehhhhcCC
Confidence            99987544

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

Probab=99.62  E-value=9.2e-15  Score=143.26  Aligned_cols=77  Identities=27%  Similarity=0.357  Sum_probs=71.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhc--CCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEI--GELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~--G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ...++|||.||++++|+++|+++|++|  |+|++|.++       ++||||+|.+.++|++||+.||+.+|+++.|+|++
T Consensus       231 ~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~-------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~  303 (578)
T TIGR01648       231 AKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI-------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTL  303 (578)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee-------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            456799999999999999999999999  999999887       45999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 022827          174 VGTNAE  179 (291)
Q Consensus       174 a~~~~~  179 (291)
                      +++...
T Consensus       304 Akp~~~  309 (578)
T TIGR01648       304 AKPVDK  309 (578)
T ss_pred             ccCCCc
Confidence            987653

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.

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.61  E-value=4.3e-15  Score=106.36  Aligned_cols=70  Identities=33%  Similarity=0.596  Sum_probs=65.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeE
Q 022827          101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMK  170 (291)
Q Consensus       101 l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~  170 (291)
                      |||+|||+.+++++|.++|+.||.|..|.+..++++.++++|||+|.++++|++|++.+++..|+|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            7999999999999999999999999999999998888899999999999999999999999999999874

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 ....

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

Probab=99.60  E-value=2.2e-15  Score=118.74  Aligned_cols=87  Identities=25%  Similarity=0.388  Sum_probs=80.3

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeE
Q 022827           92 ISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMK  170 (291)
Q Consensus        92 ~~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~  170 (291)
                      |...-.+-.|||.++++.+||++|.+.|..||+|+.|.+..|+ ||..+|||+|+|++.++|++||+.+|+..|.+++|.
T Consensus        66 PqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~  145 (170)
T KOG0130|consen   66 PQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVS  145 (170)
T ss_pred             CccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCcee
Confidence            3334456799999999999999999999999999999999999 999999999999999999999999999999999999


Q ss_pred             EEEecCCC
Q 022827          171 IEVVGTNA  178 (291)
Q Consensus       171 V~~a~~~~  178 (291)
                      |.|+-...
T Consensus       146 VDw~Fv~g  153 (170)
T KOG0130|consen  146 VDWCFVKG  153 (170)
T ss_pred             EEEEEecC
Confidence            99986553

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.59  E-value=1.1e-14  Score=128.48  Aligned_cols=78  Identities=22%  Similarity=0.233  Sum_probs=71.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      ..++|||+|||+.+||++|+++|+.||+|.+|.|+.+..  +++||||+|.++++|+.|| .||+..|.++.|.|.++..
T Consensus         3 ~~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~--~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          3 QVRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE--RSQIAYVTFKDPQGAETAL-LLSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC--CCCEEEEEeCcHHHHHHHH-HhcCCeeCCceEEEEeccC
Confidence            357999999999999999999999999999999998863  4689999999999999999 5999999999999999764


Q ss_pred             C
Q 022827          177 N  177 (291)
Q Consensus       177 ~  177 (291)
                      -
T Consensus        80 ~   80 (260)
T PLN03120         80 Y   80 (260)
T ss_pred             C
Confidence            4

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

Probab=99.57  E-value=4.3e-15  Score=127.36  Aligned_cols=80  Identities=25%  Similarity=0.385  Sum_probs=73.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ..-++|||++|+|+++.++|+++|++||+|+++.|+.|+ ++++|||+||+|.+.++|.+|++. .+-.|+|++..+.|+
T Consensus        10 T~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA   88 (247)
T KOG0149|consen   10 TTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLA   88 (247)
T ss_pred             ceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchh
Confidence            355799999999999999999999999999999999999 999999999999999999999954 567899999888886


Q ss_pred             cC
Q 022827          175 GT  176 (291)
Q Consensus       175 ~~  176 (291)
                      .-
T Consensus        89 ~l   90 (247)
T KOG0149|consen   89 SL   90 (247)
T ss_pred             hh
Confidence            53

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

Probab=99.56  E-value=2.2e-14  Score=141.04  Aligned_cols=83  Identities=19%  Similarity=0.346  Sum_probs=78.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ..++|||.||++++++++|+++|+.||.|++|.|..++ ++.++|||||+|.+.++|.+||+.||+..|+|+.|+|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            45799999999999999999999999999999999998 78899999999999999999999999999999999999988


Q ss_pred             CCCC
Q 022827          176 TNAE  179 (291)
Q Consensus       176 ~~~~  179 (291)
                      +.+.
T Consensus       283 ~pP~  286 (612)
T TIGR01645       283 TPPD  286 (612)
T ss_pred             CCcc
Confidence            6553

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.

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

Probab=99.55  E-value=1.8e-14  Score=141.67  Aligned_cols=81  Identities=26%  Similarity=0.447  Sum_probs=76.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ....++|||+||++++++++|+++|++||+|++|.|+.|+ +++++|||||+|.+.++|++||+.||+..|.|+.|+|.+
T Consensus       104 ~~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~r  183 (612)
T TIGR01645       104 LAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  183 (612)
T ss_pred             hcCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecc
Confidence            3467899999999999999999999999999999999998 999999999999999999999999999999999999986


Q ss_pred             ec
Q 022827          174 VG  175 (291)
Q Consensus       174 a~  175 (291)
                      ..
T Consensus       184 p~  185 (612)
T TIGR01645       184 PS  185 (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.

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

Probab=99.55  E-value=2.3e-14  Score=141.92  Aligned_cols=80  Identities=30%  Similarity=0.438  Sum_probs=75.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecCC
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTN  177 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~~  177 (291)
                      .+|||+|||+++||++|+++|++||+|.+|+|+.|. +++++|||||+|.+.++|++||+.||...|.+++|+|.|+...
T Consensus         1 ~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         1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRD   80 (562)
T ss_pred             CeEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccccc
Confidence            379999999999999999999999999999999999 7999999999999999999999999999999999999998654


Q ss_pred             C
Q 022827          178 A  178 (291)
Q Consensus       178 ~  178 (291)
                      +
T Consensus        81 ~   81 (562)
T TIGR01628        81 P   81 (562)
T ss_pred             c
Confidence            4

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

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

Probab=99.55  E-value=1.7e-14  Score=128.71  Aligned_cols=84  Identities=20%  Similarity=0.359  Sum_probs=77.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ..+..++|+|+|||+..-|-||+.+|++||.|.+|+|+.+.-| +|||+||+|++.+||++|-++||+..+.|++|.|..
T Consensus        92 s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERG-SKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~  170 (376)
T KOG0125|consen   92 SKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERG-SKGFGFVTMENPADADRARAELHGTVVEGRKIEVNN  170 (376)
T ss_pred             CCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCC-CCccceEEecChhhHHHHHHHhhcceeeceEEEEec
Confidence            3455689999999999999999999999999999999998643 599999999999999999999999999999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      ++.+.
T Consensus       171 ATarV  175 (376)
T KOG0125|consen  171 ATARV  175 (376)
T ss_pred             cchhh
Confidence            88765

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

Probab=99.54  E-value=2.4e-14  Score=140.36  Aligned_cols=79  Identities=22%  Similarity=0.399  Sum_probs=72.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeC-CeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLD-GKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~-g~~i~V~~a  174 (291)
                      ...++|||+|||++++|++|+++|++||+|.+|+|+.|.++++++||||+|.+.++|++||+.||+.+|. ++.|.|.++
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence            4569999999999999999999999999999999999999999999999999999999999999998885 677666544

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.

>smart00362 RRM_2 RNA recognition motif

Probab=99.54  E-value=5.4e-14  Score=99.10  Aligned_cols=72  Identities=38%  Similarity=0.657  Sum_probs=67.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827          100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus       100 ~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      +|||.|||..+++++|+++|.+||+|..+.+..++ +.++++|||+|.+.++|+.|++.+++..+.++.|+|+
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            58999999999999999999999999999998876 6778999999999999999999999999999998873

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

Probab=99.53  E-value=7.3e-14  Score=136.55  Aligned_cols=82  Identities=23%  Similarity=0.318  Sum_probs=77.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ..++|||+|||+.+|+++|+++|+.||.|..|.|+.+. ++.++|||||+|.+.++|+.||+.||+..|.++.|.|+++.
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~  373 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRAC  373 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECc
Confidence            35799999999999999999999999999999999998 89999999999999999999999999999999999999986


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      ...
T Consensus       374 ~~~  376 (509)
T TIGR01642       374 VGA  376 (509)
T ss_pred             cCC
Confidence            543

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

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

Probab=99.53  E-value=5.9e-14  Score=135.52  Aligned_cols=81  Identities=30%  Similarity=0.518  Sum_probs=76.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ..++|||.|||+.+|+++|+++|+.||.|..|.|+.+. ++.+++||||+|.+.++|++||+.||+..|.+++|+|.++.
T Consensus       185 ~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            36899999999999999999999999999999999998 77999999999999999999999999999999999999987


Q ss_pred             CC
Q 022827          176 TN  177 (291)
Q Consensus       176 ~~  177 (291)
                      ..
T Consensus       265 ~~  266 (457)
T TIGR01622       265 DS  266 (457)
T ss_pred             CC
Confidence            44

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.

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

Probab=99.52  E-value=1e-13  Score=133.87  Aligned_cols=81  Identities=21%  Similarity=0.338  Sum_probs=75.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ....++|||.|||+.+++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|| .|++..|.+++|.|.+
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al-~l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-ALTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHH-HhCCCEECCeeeEEee
Confidence            4467899999999999999999999999999999999998 8999999999999999999999 5899999999999987


Q ss_pred             ecC
Q 022827          174 VGT  176 (291)
Q Consensus       174 a~~  176 (291)
                      +..
T Consensus       165 ~~~  167 (457)
T TIGR01622       165 SQA  167 (457)
T ss_pred             cch
Confidence            653

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.

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

Probab=99.52  E-value=6.4e-14  Score=138.79  Aligned_cols=83  Identities=31%  Similarity=0.547  Sum_probs=79.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ...++|||.||++.+|+++|+++|++||.|.+|.|+.+.++.++|||||+|.+.++|++||+.||+..|.|++|.|.++.
T Consensus       283 ~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~  362 (562)
T TIGR01628       283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQ  362 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEecc
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      .+.
T Consensus       363 ~k~  365 (562)
T TIGR01628       363 RKE  365 (562)
T ss_pred             CcH
Confidence            754

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

>PLN03213 repressor of silencing 3; Provisional

Probab=99.51  E-value=4.7e-14  Score=131.71  Aligned_cols=80  Identities=20%  Similarity=0.330  Sum_probs=73.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCH--HHHHHHHHHhCCceeCCeeeEEEE
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARR--SDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~--~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ....+|||+||++.|+++||..+|..||.|..|.|+.. +|  +|||||+|.+.  +++.+||+.||+..|+|+.|+|..
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE-TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT-KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc-cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            35689999999999999999999999999999999933 66  89999999987  789999999999999999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      |++..
T Consensus        85 AKP~Y   89 (759)
T PLN03213         85 AKEHY   89 (759)
T ss_pred             ccHHH
Confidence            88653

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.51  E-value=1.3e-13  Score=119.98  Aligned_cols=77  Identities=21%  Similarity=0.233  Sum_probs=70.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      .+.+|||+||++.+||++|++||+.||+|.+|.|+.+.  ...+||||+|.++++|+.|| .||+..|.+++|.|.....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~--et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG--EYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC--CcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCcc
Confidence            46899999999999999999999999999999999884  44679999999999999999 8999999999999987653

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

Probab=99.50  E-value=1e-13  Score=128.16  Aligned_cols=84  Identities=26%  Similarity=0.428  Sum_probs=78.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCcee-CCeeeEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLL-DGKPMKIE  172 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l-~g~~i~V~  172 (291)
                      ...+|.|||+.||.++.|++|.-||++.|+|-+++|+.|+ +|.++|||||+|.+.++|++||+.||+++| .|+.|.|+
T Consensus        80 p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc  159 (506)
T KOG0117|consen   80 PPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVC  159 (506)
T ss_pred             CCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEE
Confidence            3678999999999999999999999999999999999998 999999999999999999999999999988 58999998


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++..+.
T Consensus       160 ~Svan~  165 (506)
T KOG0117|consen  160 VSVANC  165 (506)
T ss_pred             Eeeecc
Confidence            877654

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

Probab=99.49  E-value=1.3e-13  Score=120.31  Aligned_cols=79  Identities=25%  Similarity=0.387  Sum_probs=75.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      +..|+|||+||+..+||++|+++|+.||+|.+|+|.++     +|||||.|++.|.|..||..+|+.++.|+.+++.|-+
T Consensus       162 p~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~-----qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGK  236 (321)
T KOG0148|consen  162 PDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD-----QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGK  236 (321)
T ss_pred             CCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc-----cceEEEEecchhhHHHHHHHhcCceeCceEEEEeccc
Confidence            48899999999999999999999999999999999998     8999999999999999999999999999999999987


Q ss_pred             CCCC
Q 022827          176 TNAE  179 (291)
Q Consensus       176 ~~~~  179 (291)
                      ....
T Consensus       237 e~~~  240 (321)
T KOG0148|consen  237 EGDD  240 (321)
T ss_pred             cCCC
Confidence            6654

>smart00360 RRM RNA recognition motif

Probab=99.49  E-value=1.6e-13  Score=96.20  Aligned_cols=70  Identities=40%  Similarity=0.654  Sum_probs=66.0

Q ss_pred             EcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827          103 VSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus       103 V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      |.|||..+++++|+++|++||.|..+.|..++ ++.++++|||+|.+.++|..|++.|++..+.++.|+|+
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            68999999999999999999999999999988 68899999999999999999999999999999998874

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

Probab=99.48  E-value=4.6e-14  Score=116.64  Aligned_cols=80  Identities=28%  Similarity=0.399  Sum_probs=76.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ....||||+||+..++++.|++||-++|+|..+.|..|+ +...+|||||+|.++|+|+-||+.||.+.|.|++|+|..+
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            467899999999999999999999999999999999999 8889999999999999999999999999999999999988


Q ss_pred             c
Q 022827          175 G  175 (291)
Q Consensus       175 ~  175 (291)
                      .
T Consensus        87 s   87 (203)
T KOG0131|consen   87 S   87 (203)
T ss_pred             c
Confidence            7

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

Probab=99.48  E-value=1.4e-13  Score=119.61  Aligned_cols=86  Identities=31%  Similarity=0.456  Sum_probs=81.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      ..+..+.|.|.-||..+|+++|+.||...|+|++|+++.|+ +|++.||+||.|.+++||++||..||+..|..+.|+|+
T Consensus        37 t~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVS  116 (360)
T KOG0145|consen   37 TDESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVS  116 (360)
T ss_pred             cCcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEE
Confidence            34566789999999999999999999999999999999999 99999999999999999999999999999999999999


Q ss_pred             EecCCCC
Q 022827          173 VVGTNAE  179 (291)
Q Consensus       173 ~a~~~~~  179 (291)
                      ++.+..+
T Consensus       117 yARPSs~  123 (360)
T KOG0145|consen  117 YARPSSD  123 (360)
T ss_pred             eccCChh
Confidence            9998764

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

Probab=99.47  E-value=7.3e-14  Score=129.13  Aligned_cols=97  Identities=28%  Similarity=0.402  Sum_probs=82.6

Q ss_pred             CCCCchhhhhhhhhcCC---CCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHH
Q 022827           76 FPWQHDLFEDSLRAAGI---SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDA  152 (291)
Q Consensus        76 ~~~~~d~~~~~~~~~~~---~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A  152 (291)
                      .-|-|....++..+...   ..+..-+.|||.||+.+|||+.|+++|++||.|..|+.+.|       ||||.|.+.++|
T Consensus       234 klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-------YaFVHf~eR~da  306 (506)
T KOG0117|consen  234 KLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-------YAFVHFAEREDA  306 (506)
T ss_pred             eecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc-------eeEEeecchHHH
Confidence            34777766666543322   23455678999999999999999999999999999988866       999999999999


Q ss_pred             HHHHHHhCCceeCCeeeEEEEecCCCC
Q 022827          153 FAALKRYNNVLLDGKPMKIEVVGTNAE  179 (291)
Q Consensus       153 ~~Ai~~lng~~l~g~~i~V~~a~~~~~  179 (291)
                      .+||+.+|+++|+|..|.|.||++...
T Consensus       307 vkAm~~~ngkeldG~~iEvtLAKP~~k  333 (506)
T KOG0117|consen  307 VKAMKETNGKELDGSPIEVTLAKPVDK  333 (506)
T ss_pred             HHHHHHhcCceecCceEEEEecCChhh
Confidence            999999999999999999999998764

>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=99.47  E-value=5.3e-13  Score=94.48  Aligned_cols=74  Identities=39%  Similarity=0.631  Sum_probs=69.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827          100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus       100 ~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      +|+|.|||+.+++++|+++|..||.|..+.+..++...++++|||+|.+.++|..|++.+++..++++.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            58999999999999999999999999999999888657789999999999999999999999999999999864

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).

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

Probab=99.47  E-value=2.4e-13  Score=102.67  Aligned_cols=82  Identities=26%  Similarity=0.347  Sum_probs=73.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      .+....|||.|||+.+|.+++.+||.+||.|..|+|-..+  ..+|.|||.|++..+|.+|++.|++..++++.|.|-+-
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k--~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyy   92 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK--ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYY   92 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc--CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEec
Confidence            3567899999999999999999999999999999887665  33799999999999999999999999999999999887


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      ++..
T Consensus        93 q~~~   96 (124)
T KOG0114|consen   93 QPED   96 (124)
T ss_pred             CHHH
Confidence            6544

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

Probab=99.46  E-value=3.1e-13  Score=119.00  Aligned_cols=79  Identities=32%  Similarity=0.554  Sum_probs=76.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      .++|||+|||+++|+++|.++|.+||.|..|.|..++ ++.+++||||+|.+.++|..||+.+++..|.++.|.|.++..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            5999999999999999999999999999999999997 999999999999999999999999999999999999999653

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

Probab=99.45  E-value=7.6e-13  Score=122.11  Aligned_cols=82  Identities=18%  Similarity=0.397  Sum_probs=75.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHH-hcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFS-EIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~-~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ....+.+||+|||+++.|+||++||. +.|+|.+|.++.|.+++++|+|.|+|+++|.+++|++.||.+++++++|+|+.
T Consensus        41 ~~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKE  120 (608)
T KOG4212|consen   41 AARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKE  120 (608)
T ss_pred             ccccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEec
Confidence            33456799999999999999999995 79999999999999999999999999999999999999999999999999986


Q ss_pred             ecC
Q 022827          174 VGT  176 (291)
Q Consensus       174 a~~  176 (291)
                      ...
T Consensus       121 d~d  123 (608)
T KOG4212|consen  121 DHD  123 (608)
T ss_pred             cCc
Confidence            543

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

Probab=99.44  E-value=5.9e-13  Score=129.59  Aligned_cols=80  Identities=30%  Similarity=0.337  Sum_probs=73.6

Q ss_pred             CCCCcEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHP-GVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~-~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ..++++|||+||++ .+|+++|++||+.||.|.+|.|+.++    ++||||+|.+.++|+.||+.||+..|.|++|+|++
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~  347 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCP  347 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            34678999999998 69999999999999999999999874    68999999999999999999999999999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      ++...
T Consensus       348 s~~~~  352 (481)
T TIGR01649       348 SKQQN  352 (481)
T ss_pred             ccccc
Confidence            86553

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).

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

Probab=99.44  E-value=1.5e-14  Score=119.43  Aligned_cols=81  Identities=23%  Similarity=0.413  Sum_probs=76.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      .+.-|||+|||+++||.||.-+|++||+|+.|.++.|+ ||+++||||+.|++..+..-|+..||+..|.++.|+|..+.
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            56789999999999999999999999999999999999 99999999999999999999999999999999999998765


Q ss_pred             CC
Q 022827          176 TN  177 (291)
Q Consensus       176 ~~  177 (291)
                      ..
T Consensus       114 ~Y  115 (219)
T KOG0126|consen  114 NY  115 (219)
T ss_pred             cc
Confidence            43

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

Probab=99.43  E-value=5e-13  Score=130.14  Aligned_cols=76  Identities=17%  Similarity=0.181  Sum_probs=69.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHh--CCceeCCeeeEEEEe
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY--NNVLLDGKPMKIEVV  174 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~l--ng~~l~g~~i~V~~a  174 (291)
                      ++++|||+|||++++|++|+++|++||.|.+|.|+.+     ++||||+|.+.++|++||+.|  ++..|.|++|.|+++
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~-----k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s   75 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG-----KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYS   75 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC-----CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEec
Confidence            4789999999999999999999999999999999865     689999999999999999875  678999999999998


Q ss_pred             cCC
Q 022827          175 GTN  177 (291)
Q Consensus       175 ~~~  177 (291)
                      ...
T Consensus        76 ~~~   78 (481)
T TIGR01649        76 TSQ   78 (481)
T ss_pred             CCc
Confidence            643

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).

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

Probab=99.42  E-value=3.1e-13  Score=117.97  Aligned_cols=82  Identities=22%  Similarity=0.423  Sum_probs=78.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      -..|||+.|..+++.++|++.|.+||+|.+++|++|. |+++|||+||.|.+.++|+.||..||+..|..+.|+..|++.
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            4579999999999999999999999999999999999 999999999999999999999999999999999999999988


Q ss_pred             CCC
Q 022827          177 NAE  179 (291)
Q Consensus       177 ~~~  179 (291)
                      ++.
T Consensus       142 Kp~  144 (321)
T KOG0148|consen  142 KPS  144 (321)
T ss_pred             Ccc
Confidence            773

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

Probab=99.41  E-value=7.9e-13  Score=124.92  Aligned_cols=84  Identities=32%  Similarity=0.490  Sum_probs=77.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHh-----CC-ceeCCee
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRY-----NN-VLLDGKP  168 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~l-----ng-~~l~g~~  168 (291)
                      ....+|||.|||+++||++|+++|++||+|.++.|+.++ |++++|+|||.|.+..+|++||+..     .+ +.|+|+.
T Consensus       290 ~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~  369 (678)
T KOG0127|consen  290 TEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRL  369 (678)
T ss_pred             cccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccE
Confidence            345899999999999999999999999999999999999 9999999999999999999999876     23 6799999


Q ss_pred             eEEEEecCCCC
Q 022827          169 MKIEVVGTNAE  179 (291)
Q Consensus       169 i~V~~a~~~~~  179 (291)
                      |+|.++.+...
T Consensus       370 Lkv~~Av~Rke  380 (678)
T KOG0127|consen  370 LKVTLAVTRKE  380 (678)
T ss_pred             EeeeeccchHH
Confidence            99999987764

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

Probab=99.39  E-value=8.8e-13  Score=125.05  Aligned_cols=81  Identities=16%  Similarity=0.445  Sum_probs=78.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecCC
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTN  177 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~~  177 (291)
                      +.|||+|||++++|++|.++|+..|.|.++++++|+ +|+++||+|++|.+.++|+.|++.||+.++.+++|+|.|+...
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            899999999999999999999999999999999999 9999999999999999999999999999999999999998766


Q ss_pred             CC
Q 022827          178 AE  179 (291)
Q Consensus       178 ~~  179 (291)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            54

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

Probab=99.38  E-value=2.6e-12  Score=111.68  Aligned_cols=84  Identities=19%  Similarity=0.266  Sum_probs=78.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      .....-.|||-||.++++|.-|++||..||.|..|+|++|. +.+.|||+||++.+.++|..||..||+..|.++.|.|.
T Consensus       274 ~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVs  353 (360)
T KOG0145|consen  274 GPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVS  353 (360)
T ss_pred             CCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEE
Confidence            34456799999999999999999999999999999999999 79999999999999999999999999999999999999


Q ss_pred             EecCC
Q 022827          173 VVGTN  177 (291)
Q Consensus       173 ~a~~~  177 (291)
                      +...+
T Consensus       354 FKtnk  358 (360)
T KOG0145|consen  354 FKTNK  358 (360)
T ss_pred             EecCC
Confidence            87654

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

Probab=99.38  E-value=3.2e-13  Score=114.70  Aligned_cols=82  Identities=24%  Similarity=0.370  Sum_probs=78.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      .-.+|||++|..+|+|.-|...|-.||+|+.|.|..|. +.++++|+||+|...|+|.+||..||..+|.|+.|+|.+++
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            45799999999999999999999999999999999998 99999999999999999999999999999999999999998


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      +..
T Consensus        89 P~k   91 (298)
T KOG0111|consen   89 PEK   91 (298)
T ss_pred             Ccc
Confidence            765

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

Probab=99.37  E-value=6.4e-13  Score=122.45  Aligned_cols=86  Identities=28%  Similarity=0.457  Sum_probs=78.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCc-eeCC--eeeEEEE
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNV-LLDG--KPMKIEV  173 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~-~l~g--~~i~V~~  173 (291)
                      ...+|||+-|+..+||.||+++|++||.|++|.|++|..+.++|||||.|.+.|.|..||+.||+. ++.|  .+|.|.|
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkF  202 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKF  202 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEe
Confidence            467999999999999999999999999999999999999999999999999999999999999994 4555  5999999


Q ss_pred             ecCCCCCcc
Q 022827          174 VGTNAEIPL  182 (291)
Q Consensus       174 a~~~~~~~~  182 (291)
                      +.++.++..
T Consensus       203 ADtqkdk~~  211 (510)
T KOG0144|consen  203 ADTQKDKDG  211 (510)
T ss_pred             cccCCCchH
Confidence            988775543

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

Probab=99.36  E-value=6.9e-13  Score=119.58  Aligned_cols=85  Identities=20%  Similarity=0.360  Sum_probs=80.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      ..++...|||.-|.+-||++||.-+|+.||.|.+|.|+.|+ |+.+..||||+|++.+++++|.-+|+++.|+.+.|+|.
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVD  314 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVD  314 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEee
Confidence            35678899999999999999999999999999999999999 99999999999999999999999999999999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++++-.
T Consensus       315 FSQSVs  320 (479)
T KOG0415|consen  315 FSQSVS  320 (479)
T ss_pred             hhhhhh
Confidence            987654

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

Probab=99.36  E-value=1.4e-12  Score=120.27  Aligned_cols=85  Identities=27%  Similarity=0.452  Sum_probs=76.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCc-eeCC--eeeEE
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNV-LLDG--KPMKI  171 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~-~l~g--~~i~V  171 (291)
                      ....+|||+-||..++|.||++||++||.|.+|.|++|+ ++.++|||||.|.+.++|.+|+.+||+. +|-|  .+|.|
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            456799999999999999999999999999999999999 9999999999999999999999999985 4544  68999


Q ss_pred             EEecCCCCC
Q 022827          172 EVVGTNAEI  180 (291)
Q Consensus       172 ~~a~~~~~~  180 (291)
                      .++..+.+.
T Consensus       112 k~Ad~E~er  120 (510)
T KOG0144|consen  112 KYADGERER  120 (510)
T ss_pred             cccchhhhc
Confidence            988766543

>PF13893 RRM_5: RNA recognition motif

Probab=99.32  E-value=9.3e-12  Score=85.30  Aligned_cols=56  Identities=34%  Similarity=0.535  Sum_probs=51.0

Q ss_pred             HHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827          115 IRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus       115 L~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      |.++|++||+|+.|.+..+.    .++|||+|.+.++|++|++.||+..+.|++|+|+++
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            78999999999999998663    489999999999999999999999999999999986

(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 ....

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

Probab=99.31  E-value=5.7e-12  Score=119.21  Aligned_cols=82  Identities=26%  Similarity=0.405  Sum_probs=77.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      +-.+|.|.||||.+...||+.+|+.||.|..|.|.....++-+|||||.|....+|.+||+.||+..|+|++|.|.||.+
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~  195 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVD  195 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecc
Confidence            46799999999999999999999999999999999877888889999999999999999999999999999999999987


Q ss_pred             CC
Q 022827          177 NA  178 (291)
Q Consensus       177 ~~  178 (291)
                      +.
T Consensus       196 Kd  197 (678)
T KOG0127|consen  196 KD  197 (678)
T ss_pred             cc
Confidence            75

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

Probab=99.31  E-value=1.9e-12  Score=112.87  Aligned_cols=83  Identities=16%  Similarity=0.297  Sum_probs=79.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      +.+|.|||-.||.+..+.||.++|-.||.|++.+|..|+ |..+|+|+||.|+++.+|++||..||+..|.-+.|+|++.
T Consensus       283 PeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLK  362 (371)
T KOG0146|consen  283 PEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLK  362 (371)
T ss_pred             CCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhc
Confidence            578999999999999999999999999999999999999 9999999999999999999999999999999999999998


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      .++.
T Consensus       363 RPkd  366 (371)
T KOG0146|consen  363 RPKD  366 (371)
T ss_pred             Cccc
Confidence            7765

>smart00361 RRM_1 RNA recognition motif

Probab=99.30  E-value=1.3e-11  Score=88.77  Aligned_cols=61  Identities=28%  Similarity=0.486  Sum_probs=54.9

Q ss_pred             HHHHHHHHH----hcCCeeEEE-EeeCC-C--CCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827          112 NDDIRELFS----EIGELKRYA-IHFDK-N--GRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus       112 e~dL~~~F~----~~G~v~~v~-i~~d~-t--g~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      +++|+++|+    .||.|.+|. |+.++ +  +.++||+||+|.+.++|.+|++.||+..+.++.|+++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            578999998    999999995 66665 5  8899999999999999999999999999999999863

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

Probab=99.27  E-value=5.8e-12  Score=111.11  Aligned_cols=73  Identities=22%  Similarity=0.368  Sum_probs=69.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecCCC
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNA  178 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~~~  178 (291)
                      .+|||+|||..+++.+|+.||++||.|.+|.|+++       |+||..++...|+.||..||+.+|+|..|+|+-++.+.
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN-------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN-------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc-------cceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence            58999999999999999999999999999999955       99999999999999999999999999999999988773

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

Probab=99.25  E-value=8.5e-12  Score=118.27  Aligned_cols=82  Identities=30%  Similarity=0.547  Sum_probs=77.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecCCC
Q 022827          100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNA  178 (291)
Q Consensus       100 ~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~~~  178 (291)
                      .|||+||+++++|++|+.+|+.||.|..|.++.|. ||.++||+||+|.+.++|.+|+++||+.+|-|+.|+|.+++...
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~  359 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERV  359 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeec
Confidence            49999999999999999999999999999999998 99999999999999999999999999999999999999988766


Q ss_pred             CCc
Q 022827          179 EIP  181 (291)
Q Consensus       179 ~~~  181 (291)
                      ...
T Consensus       360 ~~~  362 (549)
T KOG0147|consen  360 DTK  362 (549)
T ss_pred             ccc
Confidence            544

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=99.24  E-value=6.4e-11  Score=111.83  Aligned_cols=80  Identities=20%  Similarity=0.383  Sum_probs=67.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ...+|||.|||+++++++|+++|..||+|+...|..-. .++..+|+||+|.+.++++.||++ +-..|+++.|.|+...
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKR  365 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecc
Confidence            34559999999999999999999999999987776644 344449999999999999999976 5788999999999755


Q ss_pred             CC
Q 022827          176 TN  177 (291)
Q Consensus       176 ~~  177 (291)
                      +.
T Consensus       366 ~~  367 (419)
T KOG0116|consen  366 PG  367 (419)
T ss_pred             cc
Confidence            43

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

Probab=99.23  E-value=1.1e-11  Score=109.30  Aligned_cols=77  Identities=29%  Similarity=0.423  Sum_probs=72.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ...+++|+|.||.+.++.++|++.|++||+|++|+|++       .|+||.|+..++|..||+.||+.+|+|++|+|+++
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk-------dy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~s  147 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK-------DYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLS  147 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeeec-------ceeEEEEeeccchHHHHhcccccccccceeeeeee
Confidence            44778999999999999999999999999999999995       49999999999999999999999999999999999


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      ++..
T Consensus       148 tsrl  151 (346)
T KOG0109|consen  148 TSRL  151 (346)
T ss_pred             cccc
Confidence            8775

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

Probab=99.20  E-value=1.6e-10  Score=113.21  Aligned_cols=76  Identities=30%  Similarity=0.431  Sum_probs=71.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      .++||||+.|+..|+|.||..+|++||+|.+|.++..     ++||||++.+..+|++||.+|+++.+..+.|+|.|+..
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~-----R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP-----RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC-----CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            5679999999999999999999999999999999876     89999999999999999999999999999999999875


Q ss_pred             C
Q 022827          177 N  177 (291)
Q Consensus       177 ~  177 (291)
                      .
T Consensus       495 ~  495 (894)
T KOG0132|consen  495 K  495 (894)
T ss_pred             C
Confidence            4

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

Probab=99.20  E-value=1.1e-11  Score=112.28  Aligned_cols=77  Identities=27%  Similarity=0.464  Sum_probs=74.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      --|+|||+.|.+++.|+.|+..|..||+|++|.+.+|+ |+++++||||+|+-+|.|+-|++.||+..|.|+.|+|-.
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr  189 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  189 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC
Confidence            35899999999999999999999999999999999999 999999999999999999999999999999999999974

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

Probab=99.19  E-value=6.1e-11  Score=115.98  Aligned_cols=72  Identities=15%  Similarity=0.300  Sum_probs=60.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhc------------CCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCcee
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEI------------GELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLL  164 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~------------G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l  164 (291)
                      ...+|||+|||+.+|+++|++||.+|            ..|..+.+..     .++||||+|.+.++|..|| .||++.|
T Consensus       174 ~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~-----~kg~afVeF~~~e~A~~Al-~l~g~~~  247 (509)
T TIGR01642       174 QARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINK-----EKNFAFLEFRTVEEATFAM-ALDSIIY  247 (509)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECC-----CCCEEEEEeCCHHHHhhhh-cCCCeEe
Confidence            45789999999999999999999975            2344444443     4899999999999999999 6999999


Q ss_pred             CCeeeEEEEe
Q 022827          165 DGKPMKIEVV  174 (291)
Q Consensus       165 ~g~~i~V~~a  174 (291)
                      .+++|+|...
T Consensus       248 ~g~~l~v~r~  257 (509)
T TIGR01642       248 SNVFLKIRRP  257 (509)
T ss_pred             eCceeEecCc
Confidence            9999999753

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

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

Probab=99.19  E-value=5.9e-11  Score=111.38  Aligned_cols=78  Identities=26%  Similarity=0.488  Sum_probs=73.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecCCCC
Q 022827          100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNAE  179 (291)
Q Consensus       100 ~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~~~~  179 (291)
                      .|||.||++.++..+|.++|+.||+|.+|+|..+.++ ++|| ||+|+++++|++||+.||+..+.+++|.|-+......
T Consensus        78 ~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~e  155 (369)
T KOG0123|consen   78 LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEE  155 (369)
T ss_pred             eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhh
Confidence            3999999999999999999999999999999999988 8999 9999999999999999999999999999988776553

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

Probab=99.15  E-value=1.5e-10  Score=99.22  Aligned_cols=85  Identities=28%  Similarity=0.523  Sum_probs=75.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHH----HHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeee
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRE----LFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPM  169 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~----~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i  169 (291)
                      .+.+..||||.||+..+..++|+.    ||++||.|..|...  ++.+.+|-|||+|.+.+.|-.|+.+|+|..+-|++|
T Consensus         5 ~~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~--kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~m   82 (221)
T KOG4206|consen    5 SVNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF--KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPM   82 (221)
T ss_pred             ccCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec--CCCCccCceEEEecChhHHHHHHHHhcCCcccCchh
Confidence            345566999999999999999887    99999999976655  456789999999999999999999999999999999


Q ss_pred             EEEEecCCCCC
Q 022827          170 KIEVVGTNAEI  180 (291)
Q Consensus       170 ~V~~a~~~~~~  180 (291)
                      +|++|..+...
T Consensus        83 riqyA~s~sdi   93 (221)
T KOG4206|consen   83 RIQYAKSDSDI   93 (221)
T ss_pred             heecccCccch
Confidence            99999987643

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

Probab=99.12  E-value=1.3e-10  Score=96.40  Aligned_cols=85  Identities=28%  Similarity=0.414  Sum_probs=77.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKR-YAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~-v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      ..+.+..|||+||.+.++|..|.++|+.||.|.. -+|+++. |+.+++|+||.|.+.|.+.+||+.+|+..+..++|.|
T Consensus        92 nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv  171 (203)
T KOG0131|consen   92 NLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITV  171 (203)
T ss_pred             cccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEE
Confidence            3456689999999999999999999999998874 4778888 8999999999999999999999999999999999999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      +++..+.
T Consensus       172 ~ya~k~~  178 (203)
T KOG0131|consen  172 SYAFKKD  178 (203)
T ss_pred             EEEEecC
Confidence            9987665

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.10  E-value=3.1e-10  Score=95.94  Aligned_cols=85  Identities=24%  Similarity=0.358  Sum_probs=77.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHHhc-CCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeE
Q 022827           93 SGIEVGTKLYVSNLHPGVTNDDIRELFSEI-GELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMK  170 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~~~te~dL~~~F~~~-G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~  170 (291)
                      +.......+||..||..+.+.+|..+|.+| |.|..+++.+++ ||.+++||||+|++++.|+-|-+.||+..|.++-|.
T Consensus        44 p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~  123 (214)
T KOG4208|consen   44 PEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLE  123 (214)
T ss_pred             CccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheee
Confidence            445566789999999999999999999988 778888887888 999999999999999999999999999999999999


Q ss_pred             EEEecCC
Q 022827          171 IEVVGTN  177 (291)
Q Consensus       171 V~~a~~~  177 (291)
                      |.+..+.
T Consensus       124 c~vmppe  130 (214)
T KOG4208|consen  124 CHVMPPE  130 (214)
T ss_pred             eEEeCch
Confidence            9998776

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

Probab=99.08  E-value=5.9e-11  Score=101.00  Aligned_cols=94  Identities=22%  Similarity=0.279  Sum_probs=84.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           93 SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      +..+...||||.||...|+|+.|.|||-+.|+|.+|.|..++.+..+ ||||+|.++..+.-|++.+|+..|.+.+|+|.
T Consensus         4 aaae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~   82 (267)
T KOG4454|consen    4 AAAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRT   82 (267)
T ss_pred             CCcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhcc
Confidence            44567789999999999999999999999999999999999888888 99999999999999999999999999999999


Q ss_pred             EecCCCCCccccccC
Q 022827          173 VVGTNAEIPLQARVN  187 (291)
Q Consensus       173 ~a~~~~~~~~~~r~~  187 (291)
                      +-......++-.+..
T Consensus        83 ~r~G~shapld~r~~   97 (267)
T KOG4454|consen   83 LRCGNSHAPLDERVT   97 (267)
T ss_pred             cccCCCcchhhhhcc
Confidence            988776666555543

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

Probab=99.07  E-value=4.6e-10  Score=101.32  Aligned_cols=80  Identities=26%  Similarity=0.350  Sum_probs=71.5

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHh-CCceeCCeeeE
Q 022827           92 ISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY-NNVLLDGKPMK  170 (291)
Q Consensus        92 ~~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~l-ng~~l~g~~i~  170 (291)
                      ++.+...++|||.+|...++|.||.++|.+||+|..|.|...     +++|||+|.+.++|+.|.+++ |...|+|+.|+
T Consensus       222 pPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-----~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~  296 (377)
T KOG0153|consen  222 PPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-----KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLK  296 (377)
T ss_pred             CCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-----cccceeeehhhHHHHHHHHhhcceeeecceEEE
Confidence            455667789999999999999999999999999999999877     679999999999999988865 44678999999


Q ss_pred             EEEecC
Q 022827          171 IEVVGT  176 (291)
Q Consensus       171 V~~a~~  176 (291)
                      |.|..+
T Consensus       297 i~Wg~~  302 (377)
T KOG0153|consen  297 IKWGRP  302 (377)
T ss_pred             EEeCCC
Confidence            999887

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

Probab=99.05  E-value=3.6e-10  Score=104.68  Aligned_cols=77  Identities=27%  Similarity=0.333  Sum_probs=69.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      .....|+|||.|||+++||+.|++-|.+||.|.++.|+.  .+++++  .|.|.++++|+.|+..||+..|+|+.|+|.+
T Consensus       532 aarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime--~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y  607 (608)
T KOG4212|consen  532 AARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME--NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTY  607 (608)
T ss_pred             ccccccEEEEecCCccccHHHHHHHHHhccceehhhhhc--cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeee
Confidence            456789999999999999999999999999999999843  466675  8999999999999999999999999999987


Q ss_pred             e
Q 022827          174 V  174 (291)
Q Consensus       174 a  174 (291)
                      .
T Consensus       608 ~  608 (608)
T KOG4212|consen  608 F  608 (608)
T ss_pred             C
Confidence            3

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

Probab=99.05  E-value=5e-10  Score=109.12  Aligned_cols=78  Identities=32%  Similarity=0.459  Sum_probs=71.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCC----CceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGR----PSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~----~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      .++|||.||++++|.++|..+|...|.|.+|.|...+...    +.||+||+|.++++|++|++.|+++.|+|+.|.|++
T Consensus       515 ~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~  594 (725)
T KOG0110|consen  515 ETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKI  594 (725)
T ss_pred             chhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEe
Confidence            3459999999999999999999999999999888776443    459999999999999999999999999999999999


Q ss_pred             ec
Q 022827          174 VG  175 (291)
Q Consensus       174 a~  175 (291)
                      +.
T Consensus       595 S~  596 (725)
T KOG0110|consen  595 SE  596 (725)
T ss_pred             cc
Confidence            88

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

Probab=99.04  E-value=5.6e-10  Score=104.85  Aligned_cols=77  Identities=30%  Similarity=0.394  Sum_probs=72.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecCCC
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNA  178 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~~~  178 (291)
                      ..|||+   ++|||.+|.++|+.+|+|.+|+|+.|. . +.|||||.|.++++|++||++||-..|.|++|+|.|+..++
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t-slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~   76 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T-SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP   76 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C-ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC
Confidence            468998   999999999999999999999999999 5 99999999999999999999999999999999999998776


Q ss_pred             CC
Q 022827          179 EI  180 (291)
Q Consensus       179 ~~  180 (291)
                      ..
T Consensus        77 ~~   78 (369)
T KOG0123|consen   77 SL   78 (369)
T ss_pred             ce
Confidence            43

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

Probab=99.02  E-value=6.8e-10  Score=100.79  Aligned_cols=84  Identities=19%  Similarity=0.339  Sum_probs=77.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      .-.+|||..++++++|+||+.+|+.||+|++|.+..+. .+.++||+||+|.+..+...||..||-..|.|+.|+|-.+.
T Consensus       209 ~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  209 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             hhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccccc
Confidence            45799999999999999999999999999999999999 56789999999999999999999999999999999998777


Q ss_pred             CCCCC
Q 022827          176 TNAEI  180 (291)
Q Consensus       176 ~~~~~  180 (291)
                      +.+..
T Consensus       289 TPP~a  293 (544)
T KOG0124|consen  289 TPPDA  293 (544)
T ss_pred             CCCch
Confidence            66543

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=99.00  E-value=8.5e-10  Score=105.05  Aligned_cols=83  Identities=18%  Similarity=0.310  Sum_probs=76.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      .+..|||++|...|...||+.||++||.|+-.+|+.+. +--.++|+||++.+.++|.+||+.||.++|.|+.|.|+.++
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            45689999999999999999999999999999999987 66668999999999999999999999999999999999988


Q ss_pred             CCCC
Q 022827          176 TNAE  179 (291)
Q Consensus       176 ~~~~  179 (291)
                      ..+.
T Consensus       484 NEp~  487 (940)
T KOG4661|consen  484 NEPG  487 (940)
T ss_pred             cCcc
Confidence            7663

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

Probab=98.99  E-value=4.1e-10  Score=102.74  Aligned_cols=84  Identities=25%  Similarity=0.375  Sum_probs=76.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ..++|||++|+|+++++.|+++|.+||+|.+|.|+.|+ ++++++|+||+|++.+...++|.. ..+.|+++.|.++.+.
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            67999999999999999999999999999999999999 999999999999999998888843 5688999999999888


Q ss_pred             CCCCCc
Q 022827          176 TNAEIP  181 (291)
Q Consensus       176 ~~~~~~  181 (291)
                      +.....
T Consensus        84 ~r~~~~   89 (311)
T KOG4205|consen   84 SREDQT   89 (311)
T ss_pred             Cccccc
Confidence            776443

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

Probab=98.93  E-value=1.2e-09  Score=95.59  Aligned_cols=83  Identities=24%  Similarity=0.446  Sum_probs=75.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCc-eeCC--eeeEEEE
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNV-LLDG--KPMKIEV  173 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~-~l~g--~~i~V~~  173 (291)
                      ..++|||+-|...-+|+|++.||..||+|.+|.|....++.+||+|||.|.+..+|+.||..||+. ++-|  ..|.|++
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~   97 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKF   97 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEe
Confidence            568999999999999999999999999999999999999999999999999999999999999994 4444  5899999


Q ss_pred             ecCCCC
Q 022827          174 VGTNAE  179 (291)
Q Consensus       174 a~~~~~  179 (291)
                      +.++.+
T Consensus        98 ADTdkE  103 (371)
T KOG0146|consen   98 ADTDKE  103 (371)
T ss_pred             ccchHH
Confidence            887763

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

Probab=98.93  E-value=8e-10  Score=107.69  Aligned_cols=84  Identities=24%  Similarity=0.352  Sum_probs=77.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ...++|+|.|||+..+-.+|++||..||.|+.|+|..-. .+.++|||||+|-++.+|.+|+++|..+.|.|+.|.++|+
T Consensus       611 k~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA  690 (725)
T KOG0110|consen  611 KKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWA  690 (725)
T ss_pred             cccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehh
Confidence            346799999999999999999999999999999998874 5667999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 022827          175 GTNAE  179 (291)
Q Consensus       175 ~~~~~  179 (291)
                      .....
T Consensus       691 ~~d~~  695 (725)
T KOG0110|consen  691 KSDNT  695 (725)
T ss_pred             ccchH
Confidence            87764

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

Probab=98.93  E-value=3.4e-09  Score=95.73  Aligned_cols=82  Identities=28%  Similarity=0.404  Sum_probs=75.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCee--------EEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCC
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELK--------RYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDG  166 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~--------~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g  166 (291)
                      ....+.|||+|||.++|.+++.++|++||.|.        .|.|..+..|+.+|-|.+.|...++++-||+.|+...|.|
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            34667899999999999999999999999885        3788888899999999999999999999999999999999


Q ss_pred             eeeEEEEecC
Q 022827          167 KPMKIEVVGT  176 (291)
Q Consensus       167 ~~i~V~~a~~  176 (291)
                      +.|+|+.|+=
T Consensus       211 ~~~rVerAkf  220 (382)
T KOG1548|consen  211 KKLRVERAKF  220 (382)
T ss_pred             cEEEEehhhh
Confidence            9999998763

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

Probab=98.92  E-value=8e-09  Score=88.39  Aligned_cols=83  Identities=23%  Similarity=0.329  Sum_probs=70.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC--CCCCceEEEEEEcCHHHHHHHHHHhCCceeC---CeeeEE
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK--NGRPSGSAEVVYARRSDAFAALKRYNNVLLD---GKPMKI  171 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~--tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~---g~~i~V  171 (291)
                      .-+||||++||.+|...+|..||..|--.+.+.|.+..  ....+-+|||+|.+..+|++|+++||++.|+   ++.|+|
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhi  112 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHI  112 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEe
Confidence            46899999999999999999999998777766665543  2234579999999999999999999999986   679999


Q ss_pred             EEecCCCC
Q 022827          172 EVVGTNAE  179 (291)
Q Consensus       172 ~~a~~~~~  179 (291)
                      ++++.+..
T Consensus       113 ElAKSNtK  120 (284)
T KOG1457|consen  113 ELAKSNTK  120 (284)
T ss_pred             eehhcCcc
Confidence            99998764

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.87  E-value=4.3e-09  Score=92.61  Aligned_cols=82  Identities=24%  Similarity=0.294  Sum_probs=76.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ....+.|||+||.+.+|.++|+..|+.||.|..|.|..|+ .+++++|+||+|.+.+.++.|+. ||+..|.++.|+|.+
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTL  176 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeee
Confidence            3466899999999999999999999999999999999999 77899999999999999999996 999999999999998


Q ss_pred             ecCC
Q 022827          174 VGTN  177 (291)
Q Consensus       174 a~~~  177 (291)
                      ...+
T Consensus       177 ~r~~  180 (231)
T KOG4209|consen  177 KRTN  180 (231)
T ss_pred             eeee
Confidence            7655

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.85  E-value=1.3e-08  Score=92.54  Aligned_cols=85  Identities=24%  Similarity=0.366  Sum_probs=76.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCee--------EEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeC
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELK--------RYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLD  165 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~--------~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~  165 (291)
                      .....+|||.+||..+++++|.++|.+|+.|+        .|.|.+|+ |+.+|+-|.|+|++...|++||+.+++..+.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            44667999999999999999999999999885        36777787 9999999999999999999999999999999


Q ss_pred             CeeeEEEEecCCCC
Q 022827          166 GKPMKIEVVGTNAE  179 (291)
Q Consensus       166 g~~i~V~~a~~~~~  179 (291)
                      +.+|+|.++.....
T Consensus       143 gn~ikvs~a~~r~~  156 (351)
T KOG1995|consen  143 GNTIKVSLAERRTG  156 (351)
T ss_pred             CCCchhhhhhhccC
Confidence            99999998876653

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

Probab=98.84  E-value=4.3e-09  Score=96.13  Aligned_cols=86  Identities=20%  Similarity=0.356  Sum_probs=78.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ...+|||+.||+++++++|+++|++||.|..+.|++|. +.++++|+||+|.+++++.+++ ...-+.|+++.+.|..|.
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~-~~~f~~~~gk~vevkrA~  174 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVT-LQKFHDFNGKKVEVKRAI  174 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceec-ccceeeecCceeeEeecc
Confidence            46799999999999999999999999999999999999 8899999999999999999988 457789999999999999


Q ss_pred             CCCCCccc
Q 022827          176 TNAEIPLQ  183 (291)
Q Consensus       176 ~~~~~~~~  183 (291)
                      ++......
T Consensus       175 pk~~~~~~  182 (311)
T KOG4205|consen  175 PKEVMQST  182 (311)
T ss_pred             chhhcccc
Confidence            88765544

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

Probab=98.74  E-value=8.1e-09  Score=89.18  Aligned_cols=71  Identities=18%  Similarity=0.306  Sum_probs=65.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      ..|||++||+.+.+.||++||..||.|..|.+.       .+|+||+|.+..+|..||..||+.+|.+..+.|+++..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk-------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK-------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee-------cccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            479999999999999999999999999999887       67999999999999999999999999998888887653

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.65  E-value=2.5e-07  Score=70.43  Aligned_cols=78  Identities=19%  Similarity=0.212  Sum_probs=65.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHh--cCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeC----CeeeEE
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSE--IGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLD----GKPMKI  171 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~--~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~----g~~i~V  171 (291)
                      +||.|.|||...|.++|.+++.+  .|...-+.+..|. +..+.|||||.|.+++.|.+-.+.+++..+.    .+.+.|
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            79999999999999999999864  3555567777777 8889999999999999999999999998875    456777


Q ss_pred             EEecC
Q 022827          172 EVVGT  176 (291)
Q Consensus       172 ~~a~~  176 (291)
                      .+|.-
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).

>PF13865 FoP_duplication: C-terminal duplication domain of Friend of PRMT1

Probab=98.62  E-value=1.3e-07  Score=68.52  Aligned_cols=20  Identities=40%  Similarity=0.652  Sum_probs=17.5

Q ss_pred             CCCCChhHHHHHHHHHHHhh
Q 022827          269 PVDKSADDLDKELDNYHAEA  288 (291)
Q Consensus       269 ~~~~s~~~~d~el~~y~~~~  288 (291)
                      ++++|+||||+|||+||+.+
T Consensus        37 ~~~kT~EeLDaELD~Ym~~~   56 (74)
T PF13865_consen   37 KPPKTAEELDAELDAYMSKT   56 (74)
T ss_pred             CCCCCHHHHHHHHHHHHHHH
Confidence            56899999999999999654

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.62  E-value=3.2e-08  Score=94.49  Aligned_cols=71  Identities=31%  Similarity=0.337  Sum_probs=64.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeE
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMK  170 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~  170 (291)
                      .+..+|+|-|||..|++++|.++|+.||+|+.|+....+    .+.+||+|.+..+|+.|+++|+..++.++.|+
T Consensus        73 ~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~----~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   73 MNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNK----RGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             CccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccccc----CceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            456799999999999999999999999999987665543    78999999999999999999999999999888

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

Probab=98.57  E-value=2.6e-07  Score=87.19  Aligned_cols=81  Identities=23%  Similarity=0.324  Sum_probs=66.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      .+....|.+.+|||.+|++||.+||+.| .|..+.+.. .++++.|-|||+|.++|++++||+ .+...+..+.|.|-.+
T Consensus         7 ~~~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r-~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen    7 GSTAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPR-RNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTA   83 (510)
T ss_pred             CCcceEEEecCCCccccHHHHHHHHhcC-ceeEEEEec-cCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEcc
Confidence            3466788999999999999999999999 577643332 279999999999999999999995 4778888899999877


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      ....
T Consensus        84 ~~~e   87 (510)
T KOG4211|consen   84 GGAE   87 (510)
T ss_pred             CCcc
Confidence            5444

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.56  E-value=9e-08  Score=83.43  Aligned_cols=81  Identities=19%  Similarity=0.348  Sum_probs=75.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      .+...+||++.|..+++++.|...|.+|-.....+++.|+ |++++||.||.|.+.+++..|+++||+..+..++|++..
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRk  266 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRK  266 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhh
Confidence            3456899999999999999999999999988889999999 999999999999999999999999999999999998865


Q ss_pred             ec
Q 022827          174 VG  175 (291)
Q Consensus       174 a~  175 (291)
                      +.
T Consensus       267 S~  268 (290)
T KOG0226|consen  267 SE  268 (290)
T ss_pred             hh
Confidence            44

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.54  E-value=1.5e-07  Score=92.04  Aligned_cols=83  Identities=27%  Similarity=0.348  Sum_probs=74.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCC----CCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN----GRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMK  170 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~t----g~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~  170 (291)
                      ++..+.|||.||++.++|+.|-..|..||+|..|+|++.++    .+..-++||.|.+..+|++|++.|++..+....|+
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            45668999999999999999999999999999999999873    34567899999999999999999999999999999


Q ss_pred             EEEecCC
Q 022827          171 IEVVGTN  177 (291)
Q Consensus       171 V~~a~~~  177 (291)
                      +-|.+.-
T Consensus       251 ~gWgk~V  257 (877)
T KOG0151|consen  251 LGWGKAV  257 (877)
T ss_pred             ecccccc
Confidence            9998543

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

Probab=98.43  E-value=1e-06  Score=81.51  Aligned_cols=78  Identities=26%  Similarity=0.351  Sum_probs=71.1

Q ss_pred             CcEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           98 GTKLYVSNLHPG-VTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        98 ~~~l~V~nL~~~-~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      .+.|.|+||.++ ||.+-|..||..||+|.+|+|.+++    +-.|.|.|.+...|+-|++.|+++.|.|++|+|.+++-
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH  372 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKH  372 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC----CcceeeeecchhHHHHHHHHhhcceecCceEEEeeccC
Confidence            688999999665 9999999999999999999999986    45799999999999999999999999999999999886


Q ss_pred             CCC
Q 022827          177 NAE  179 (291)
Q Consensus       177 ~~~  179 (291)
                      ...
T Consensus       373 ~~v  375 (492)
T KOG1190|consen  373 TNV  375 (492)
T ss_pred             ccc
Confidence            653

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

Probab=98.43  E-value=3.1e-06  Score=70.74  Aligned_cols=64  Identities=22%  Similarity=0.348  Sum_probs=58.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCC
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDG  166 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g  166 (291)
                      ....|.|++||+..+++||+++..+.|+|....|..|      +++.|+|...|+.+-||.+|+...+..
T Consensus       114 Se~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD------g~GvV~~~r~eDMkYAvr~ld~~~~~s  177 (241)
T KOG0105|consen  114 SEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD------GVGVVEYLRKEDMKYAVRKLDDQKFRS  177 (241)
T ss_pred             cceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc------cceeeeeeehhhHHHHHHhhccccccC
Confidence            4578999999999999999999999999999999877      589999999999999999998876643

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

Probab=98.39  E-value=7.6e-07  Score=84.10  Aligned_cols=79  Identities=20%  Similarity=0.273  Sum_probs=67.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKR-YAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~-v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      .....|.+.+||+.||++||.+||+-.-.|.. |.++.+..+++.|-|||.|++.+.|++||. .|...|..+-|.|..+
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEVFRS  179 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHH-HHHHhhccceEEeehh
Confidence            46679999999999999999999997754544 556777788899999999999999999995 4778888899988765


Q ss_pred             c
Q 022827          175 G  175 (291)
Q Consensus       175 ~  175 (291)
                      .
T Consensus       180 s  180 (510)
T KOG4211|consen  180 S  180 (510)
T ss_pred             H
Confidence            4

>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=98.39  E-value=5.6e-07  Score=69.76  Aligned_cols=75  Identities=25%  Similarity=0.373  Sum_probs=47.4

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCC-----ceeCCeeeEEE
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNN-----VLLDGKPMKIE  172 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng-----~~l~g~~i~V~  172 (291)
                      ++.|+|.+++..++.++|+++|+.|++|..|.+...     .-.|||-|.++++|++|++++.-     ..|.+..++++
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G-----~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG-----DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC-----CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            367999999999999999999999999999988765     34799999999999999987754     36677777777


Q ss_pred             EecCC
Q 022827          173 VVGTN  177 (291)
Q Consensus       173 ~a~~~  177 (291)
                      +....
T Consensus        76 vLeGe   80 (105)
T PF08777_consen   76 VLEGE   80 (105)
T ss_dssp             ---HH
T ss_pred             ECCCH
Confidence            65433

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>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=98.36  E-value=2.1e-06  Score=62.88  Aligned_cols=70  Identities=24%  Similarity=0.302  Sum_probs=48.6

Q ss_pred             cEEEEcCCCCCCCHHH----HHHHHHhcC-CeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           99 TKLYVSNLHPGVTNDD----IRELFSEIG-ELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        99 ~~l~V~nL~~~~te~d----L~~~F~~~G-~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      +.|||.|||.+.+...    |++|+..|| .|..|  .       .+.|+|.|.+.+.|..|.+.|++..+-|..|.|.+
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--~-------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~   73 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--S-------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSF   73 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-----------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEES
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--e-------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEE
Confidence            5799999999888765    567777886 45443  2       46899999999999999999999999999999998


Q ss_pred             ecCC
Q 022827          174 VGTN  177 (291)
Q Consensus       174 a~~~  177 (291)
                      ....
T Consensus        74 ~~~~   77 (90)
T PF11608_consen   74 SPKN   77 (90)
T ss_dssp             S--S
T ss_pred             cCCc
Confidence            7433

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

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

Probab=98.27  E-value=8.4e-07  Score=85.34  Aligned_cols=84  Identities=25%  Similarity=0.350  Sum_probs=77.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ....+|||++||..+++.+++|++..||+++...++.|. ++.+++|||.+|.+......|+..||+..+.++.|.|+.+
T Consensus       287 ~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A  366 (500)
T KOG0120|consen  287 DSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRA  366 (500)
T ss_pred             cccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehh
Confidence            445689999999999999999999999999999999998 8999999999999999999999999999999999999988


Q ss_pred             cCCCC
Q 022827          175 GTNAE  179 (291)
Q Consensus       175 ~~~~~  179 (291)
                      .....
T Consensus       367 ~~g~~  371 (500)
T KOG0120|consen  367 IVGAS  371 (500)
T ss_pred             hccch
Confidence            76553

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

Probab=98.22  E-value=1.6e-06  Score=74.44  Aligned_cols=70  Identities=24%  Similarity=0.395  Sum_probs=56.7

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeC
Q 022827           93 SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLD  165 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~  165 (291)
                      +......||||.||..+|||++|+.+|+.|--...++|. .+.|.  ..|||+|++.+.|..||..|++..|.
T Consensus       205 ~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~-~~~g~--~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  205 SGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIR-ARGGM--PVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             ccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEe-cCCCc--ceEeecHHHHHHHHHHHHHhhcceec
Confidence            445566799999999999999999999999776655554 33443  47999999999999999999887653

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

Probab=98.21  E-value=8.9e-07  Score=76.60  Aligned_cols=74  Identities=24%  Similarity=0.327  Sum_probs=65.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      +....+.|+|.||+..+++.+|+++|..+|++..+.+.       ..++||+|.+.++|..||+.|++..|.++.|.+..
T Consensus        95 p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~~-------~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen   95 PSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDAR-------RNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             cccccceeeeccchhhhhHHHHhhhhcccCCCchhhhh-------ccccceeehhhhhhhhcchhccchhhcCceeeecc
Confidence            34567899999999999999999999999999655443       56899999999999999999999999999999954


Q ss_pred             e
Q 022827          174 V  174 (291)
Q Consensus       174 a  174 (291)
                      .
T Consensus       168 ~  168 (216)
T KOG0106|consen  168 N  168 (216)
T ss_pred             c
Confidence            3

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

Probab=98.21  E-value=5.4e-06  Score=71.37  Aligned_cols=78  Identities=18%  Similarity=0.234  Sum_probs=69.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeC-CeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLD-GKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~-g~~i~V~  172 (291)
                      ..++..+||+.|||.+++.+.|..+|.+|.-.+.|.++...    .+.|||+|.+...|..|...+++..+. ...|+|.
T Consensus       142 ~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~  217 (221)
T KOG4206|consen  142 MAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQIT  217 (221)
T ss_pred             CCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC----CceeEEecchhhhhHHHhhhhccceeccCceEEec
Confidence            35678899999999999999999999999999999998765    679999999999999999999998876 7788887


Q ss_pred             Eec
Q 022827          173 VVG  175 (291)
Q Consensus       173 ~a~  175 (291)
                      ++.
T Consensus       218 ~a~  220 (221)
T KOG4206|consen  218 FAK  220 (221)
T ss_pred             ccC
Confidence            654

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

Probab=98.19  E-value=5.7e-07  Score=85.90  Aligned_cols=80  Identities=20%  Similarity=0.280  Sum_probs=74.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      .....+||+.-|...+++-||.+||+.+|.|..|.|+.|+ +..++|.|||+|.+.+.+..|| .|.|..+.|.+|.|+.
T Consensus       176 ERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq~  254 (549)
T KOG0147|consen  176 ERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQL  254 (549)
T ss_pred             HHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEecc
Confidence            3445689999999999999999999999999999999999 8999999999999999999999 8999999999999987


Q ss_pred             ec
Q 022827          174 VG  175 (291)
Q Consensus       174 a~  175 (291)
                      ..
T Consensus       255 sE  256 (549)
T KOG0147|consen  255 SE  256 (549)
T ss_pred             cH
Confidence            54

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.18  E-value=1.9e-05  Score=77.53  Aligned_cols=75  Identities=20%  Similarity=0.306  Sum_probs=68.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCee-EEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELK-RYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~-~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      +.|-|.|+|++|+-+||.+||..|-.+. +|.|.++..|.+.|-|.|.|++.++|.+|...|++..|..+.|+|.+
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            4889999999999999999999996654 67777787999999999999999999999999999999999998875

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.14  E-value=5.1e-06  Score=75.55  Aligned_cols=76  Identities=17%  Similarity=0.219  Sum_probs=66.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcC--CeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIG--ELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G--~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ..+||+||-|++|++||.+.+...|  .+.++++..++ +|.+||||+|...+....++.|+.|...+|.|+.-.|.-.
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~  159 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSY  159 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeecc
Confidence            4799999999999999999887766  55677778888 8999999999999999999999999999999986666443

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=98.01  E-value=4e-05  Score=70.41  Aligned_cols=88  Identities=25%  Similarity=0.291  Sum_probs=76.7

Q ss_pred             CCCCCCCCcEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeee
Q 022827           91 GISGIEVGTKLYVSNLHPG-VTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPM  169 (291)
Q Consensus        91 ~~~~~~~~~~l~V~nL~~~-~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i  169 (291)
                      .+....+++.+.|.+|+.. ++-+.|..||..||.|.+|++++.+    .+.|.|++.+..+.+.||..||+..+-|.+|
T Consensus       280 ~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk----~gtamVemgd~~aver~v~hLnn~~lfG~kl  355 (494)
T KOG1456|consen  280 SPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKL  355 (494)
T ss_pred             CCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc----cceeEEEcCcHHHHHHHHHHhccCccccceE
Confidence            3455678899999999876 5567799999999999999999876    5789999999999999999999999999999


Q ss_pred             EEEEecCCCCCcc
Q 022827          170 KIEVVGTNAEIPL  182 (291)
Q Consensus       170 ~V~~a~~~~~~~~  182 (291)
                      .|.+++.....+.
T Consensus       356 ~v~~SkQ~~v~~~  368 (494)
T KOG1456|consen  356 NVCVSKQNFVSPV  368 (494)
T ss_pred             EEeeccccccccC
Confidence            9999887765444

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

Probab=97.93  E-value=4.5e-05  Score=69.44  Aligned_cols=80  Identities=13%  Similarity=0.296  Sum_probs=64.1

Q ss_pred             CCCCcEEEEcCCC----CCCCH-------HHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCce
Q 022827           95 IEVGTKLYVSNLH----PGVTN-------DDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVL  163 (291)
Q Consensus        95 ~~~~~~l~V~nL~----~~~te-------~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~  163 (291)
                      ....++|.|.||=    +..+.       +||.+-.++||.|.+|.|.-.   ++.|.+.|.|.+.++|..||+.|++..
T Consensus       262 ~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~---hPdGvvtV~f~n~eeA~~ciq~m~GR~  338 (382)
T KOG1548|consen  262 ARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDR---HPDGVVTVSFRNNEEADQCIQTMDGRW  338 (382)
T ss_pred             ccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEecc---CCCceeEEEeCChHHHHHHHHHhcCee
Confidence            4566899999982    23442       455666889999999877633   568999999999999999999999999


Q ss_pred             eCCeeeEEEEecCC
Q 022827          164 LDGKPMKIEVVGTN  177 (291)
Q Consensus       164 l~g~~i~V~~a~~~  177 (291)
                      |+|+.|..++....
T Consensus       339 fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  339 FDGRQLTASIWDGK  352 (382)
T ss_pred             ecceEEEEEEeCCc
Confidence            99999999876533

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.88  E-value=6.6e-06  Score=74.82  Aligned_cols=81  Identities=23%  Similarity=0.405  Sum_probs=71.9

Q ss_pred             CCcEEE-EcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           97 VGTKLY-VSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        97 ~~~~l~-V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ...++| |.||++.+++++|+++|..++.|..+++..+. ++..++|+||.|.+...+..++.. +...+.+.++.|...
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  261 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEED  261 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccC
Confidence            344555 99999999999999999999999999999988 999999999999999999999976 788899999999876


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      .+.+
T Consensus       262 ~~~~  265 (285)
T KOG4210|consen  262 EPRP  265 (285)
T ss_pred             CCCc
Confidence            6553

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.86  E-value=3e-05  Score=70.34  Aligned_cols=81  Identities=21%  Similarity=0.417  Sum_probs=63.8

Q ss_pred             CCcEEEEcCCCCCCCHHH----H--HHHHHhcCCeeEEEEeeCC-CC-CCceE--EEEEEcCHHHHHHHHHHhCCceeCC
Q 022827           97 VGTKLYVSNLHPGVTNDD----I--RELFSEIGELKRYAIHFDK-NG-RPSGS--AEVVYARRSDAFAALKRYNNVLLDG  166 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~d----L--~~~F~~~G~v~~v~i~~d~-tg-~~kG~--afV~F~~~~~A~~Ai~~lng~~l~g  166 (291)
                      .-.-|||-+|++.+..++    |  .++|.+||.|+.|.|.+.. +- ...+.  .||+|.+.|+|..||.+.++..++|
T Consensus       113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DG  192 (480)
T COG5175         113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDG  192 (480)
T ss_pred             ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccC
Confidence            345689999999887776    2  5899999999988776543 11 11222  4999999999999999999999999


Q ss_pred             eeeEEEEecCC
Q 022827          167 KPMKIEVVGTN  177 (291)
Q Consensus       167 ~~i~V~~a~~~  177 (291)
                      +.|+..+-+.+
T Consensus       193 r~lkatYGTTK  203 (480)
T COG5175         193 RVLKATYGTTK  203 (480)
T ss_pred             ceEeeecCchH
Confidence            99999886654

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.85  E-value=1.5e-05  Score=74.36  Aligned_cols=78  Identities=18%  Similarity=0.178  Sum_probs=62.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeC---C-C--CC--------CceEEEEEEcCHHHHHHHHHHhCC
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD---K-N--GR--------PSGSAEVVYARRSDAFAALKRYNN  161 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d---~-t--g~--------~kG~afV~F~~~~~A~~Ai~~lng  161 (291)
                      .++++|.+.|||.+-.-+.|.+||..||.|+.|+|+..   . +  +.        .+-+|+|+|...+.|.+|.+.++.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            47899999999999999999999999999999999887   3 1  21        256899999999999999988866


Q ss_pred             ceeCCeeeEEEE
Q 022827          162 VLLDGKPMKIEV  173 (291)
Q Consensus       162 ~~l~g~~i~V~~  173 (291)
                      ..-.-.-|+|.+
T Consensus       309 e~~wr~glkvkL  320 (484)
T KOG1855|consen  309 EQNWRMGLKVKL  320 (484)
T ss_pred             hhhhhhcchhhh
Confidence            444334444444

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=97.82  E-value=1.1e-05  Score=70.62  Aligned_cols=66  Identities=23%  Similarity=0.356  Sum_probs=55.8

Q ss_pred             HHHHHHHH-hcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecCCC
Q 022827          113 DDIRELFS-EIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNA  178 (291)
Q Consensus       113 ~dL~~~F~-~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~~~  178 (291)
                      +||...|+ +||+|+++.|..+..-+-.|-+||.|...++|++|++.||+..+.|++|..+++....
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT~  149 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVTD  149 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcCc
Confidence            34444445 8999999988777666678899999999999999999999999999999999987655

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

Probab=97.79  E-value=5.5e-05  Score=70.25  Aligned_cols=79  Identities=23%  Similarity=0.318  Sum_probs=66.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCe-eeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGK-PMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~-~i~V~~a  174 (291)
                      +++.+|.++|||..++|++|+++|.+-|-..+......+   .+-+|++.+.+.|+|..|+-.++++.+... -|+|+++
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~k---d~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFS  488 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQK---DRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFS  488 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCceEEeeeecCC---CcceeecccCChhHhhhhccccccccCCCCceEEEEee
Confidence            567899999999999999999999988876655444432   255999999999999999999999998765 8999988


Q ss_pred             cCC
Q 022827          175 GTN  177 (291)
Q Consensus       175 ~~~  177 (291)
                      +..
T Consensus       489 ks~  491 (492)
T KOG1190|consen  489 KST  491 (492)
T ss_pred             ccc
Confidence            753

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

Probab=97.73  E-value=4.5e-05  Score=70.33  Aligned_cols=80  Identities=18%  Similarity=0.270  Sum_probs=69.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCC-eeE--EEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGE-LKR--YAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~-v~~--v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      .+...|.+.+||+..+.+||.+||..|-. |..  |.++.+..|++.|-|||+|.++|+|.+|....+++..+.+.|.|.
T Consensus       278 ~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvf  357 (508)
T KOG1365|consen  278 RSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVF  357 (508)
T ss_pred             CCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEe
Confidence            34568999999999999999999998864 333  889999999999999999999999999999999888888888886


Q ss_pred             Eec
Q 022827          173 VVG  175 (291)
Q Consensus       173 ~a~  175 (291)
                      -+.
T Consensus       358 p~S  360 (508)
T KOG1365|consen  358 PCS  360 (508)
T ss_pred             ecc
Confidence            554

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.73  E-value=0.00019  Score=69.12  Aligned_cols=80  Identities=21%  Similarity=0.240  Sum_probs=64.9

Q ss_pred             CCCcEEEEcCCCCCCCH------HHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeC-Cee
Q 022827           96 EVGTKLYVSNLHPGVTN------DDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLD-GKP  168 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te------~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~-g~~  168 (291)
                      --.+.|+|.|+|---..      .-|..+|+++|+|..+.+..+..+..+||.|++|.+..+|+.|++.||++.|+ .+.
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            45578999999853222      23678899999999999998887779999999999999999999999998886 557


Q ss_pred             eEEEEec
Q 022827          169 MKIEVVG  175 (291)
Q Consensus       169 i~V~~a~  175 (291)
                      +.|.+.+
T Consensus       136 f~v~~f~  142 (698)
T KOG2314|consen  136 FFVRLFK  142 (698)
T ss_pred             EEeehhh
Confidence            7776543

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.72  E-value=8e-05  Score=50.33  Aligned_cols=52  Identities=27%  Similarity=0.358  Sum_probs=42.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHH
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL  156 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai  156 (291)
                      +.|-|.+.+++..+. |..+|.+||+|.++.+...     .-+.||.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~~-----~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPES-----TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCCC-----CcEEEEEECCHHHHHhhC
Confidence            578899999877654 4458999999999877632     458999999999999985

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.59  E-value=0.00023  Score=57.91  Aligned_cols=86  Identities=21%  Similarity=0.327  Sum_probs=52.5

Q ss_pred             hhhhhhhhcCCCCCCCCcEEEEcCCC----C--CCCH---HHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHH
Q 022827           82 LFEDSLRAAGISGIEVGTKLYVSNLH----P--GVTN---DDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDA  152 (291)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~l~V~nL~----~--~~te---~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A  152 (291)
                      .|.+.....+|    +..||.|+=+.    .  ...+   .+|.+.|.+||+|.-|+++-+       .-+|+|.+-+.|
T Consensus        15 Vf~eVi~~~GP----pDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~-------~mwVTF~dg~sA   83 (146)
T PF08952_consen   15 VFEEVISSQGP----PDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD-------TMWVTFRDGQSA   83 (146)
T ss_dssp             -----S---------TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT-------CEEEEESSCHHH
T ss_pred             HHHHHHHhcCC----CCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC-------eEEEEECccHHH
Confidence            34444433443    55566665443    1  2222   256778899999998888754       589999999999


Q ss_pred             HHHHHHhCCceeCCeeeEEEEecCCCC
Q 022827          153 FAALKRYNNVLLDGKPMKIEVVGTNAE  179 (291)
Q Consensus       153 ~~Ai~~lng~~l~g~~i~V~~a~~~~~  179 (291)
                      .+|+ .+++.++.|+.|+|.+..++-.
T Consensus        84 Laal-s~dg~~v~g~~l~i~LKtpdW~  109 (146)
T PF08952_consen   84 LAAL-SLDGIQVNGRTLKIRLKTPDWL  109 (146)
T ss_dssp             HHHH-HGCCSEETTEEEEEEE------
T ss_pred             HHHH-ccCCcEECCEEEEEEeCCccHH
Confidence            9999 7899999999999999887754

; PDB: 1UFW_A 2DNR_A.

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=97.54  E-value=0.00051  Score=63.35  Aligned_cols=81  Identities=21%  Similarity=0.142  Sum_probs=64.9

Q ss_pred             CCCCCcEEEEc--CCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeC--Ceee
Q 022827           94 GIEVGTKLYVS--NLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLD--GKPM  169 (291)
Q Consensus        94 ~~~~~~~l~V~--nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~--g~~i  169 (291)
                      +..+.+.|.+.  |--+.+|.+-|..+...+|+|..|.|... ++   -.|.|||++.+.|++|.+.||+..|.  -+.|
T Consensus       116 s~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk-ng---VQAmVEFdsv~~AqrAk~alNGADIYsGCCTL  191 (494)
T KOG1456|consen  116 SATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK-NG---VQAMVEFDSVEVAQRAKAALNGADIYSGCCTL  191 (494)
T ss_pred             CCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec-cc---eeeEEeechhHHHHHHHhhcccccccccceeE
Confidence            34455555544  55667999999999999999999887754 33   36999999999999999999998763  3699


Q ss_pred             EEEEecCCC
Q 022827          170 KIEVVGTNA  178 (291)
Q Consensus       170 ~V~~a~~~~  178 (291)
                      +|++|++..
T Consensus       192 KIeyAkP~r  200 (494)
T KOG1456|consen  192 KIEYAKPTR  200 (494)
T ss_pred             EEEecCcce
Confidence            999998764

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=97.51  E-value=8.7e-05  Score=71.84  Aligned_cols=83  Identities=22%  Similarity=0.267  Sum_probs=67.2

Q ss_pred             CCCCCCCCcEEEEcCCCCCCCHHHHHHHHH-hcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCcee---CC
Q 022827           91 GISGIEVGTKLYVSNLHPGVTNDDIRELFS-EIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLL---DG  166 (291)
Q Consensus        91 ~~~~~~~~~~l~V~nL~~~~te~dL~~~F~-~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l---~g  166 (291)
                      .++....+..|||.||-.-+|.-.|++|+. .+|.|....|  |   +-+-.|||.|.+.++|.+.+.+||++.+   +.
T Consensus       437 SPsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--D---kIKShCyV~yss~eEA~atr~AlhnV~WP~sNP  511 (718)
T KOG2416|consen  437 SPSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--D---KIKSHCYVSYSSVEEAAATREALHNVQWPPSNP  511 (718)
T ss_pred             CCCCCCccceEeeecccccchHHHHHHHHhhccCchHHHHH--H---HhhcceeEecccHHHHHHHHHHHhccccCCCCC
Confidence            345567788999999999999999999998 6777776633  3   2366799999999999999999999876   56


Q ss_pred             eeeEEEEecCCC
Q 022827          167 KPMKIEVVGTNA  178 (291)
Q Consensus       167 ~~i~V~~a~~~~  178 (291)
                      +.|.|.|+....
T Consensus       512 K~L~adf~~~de  523 (718)
T KOG2416|consen  512 KHLIADFVRADE  523 (718)
T ss_pred             ceeEeeecchhH
Confidence            788888876443

>PF07078 FYTT: Forty-two-three protein; InterPro: IPR009782 This family consists of several hypothetical mammalian proteins of around 320 residues in length

Probab=97.48  E-value=3.8e-05  Score=68.55  Aligned_cols=19  Identities=58%  Similarity=0.786  Sum_probs=16.5

Q ss_pred             CCcCCCChHHHHHhcccCc
Q 022827            2 ATHVDMSLDDIIKSRKKSE   20 (291)
Q Consensus         2 ~~~ld~sLddii~~~~~~~   20 (291)
                      .|||||||||||+-+||-.
T Consensus        26 ~DKIDMSLDDIIKLNKKE~   44 (316)
T PF07078_consen   26 LDKIDMSLDDIIKLNKKEQ   44 (316)
T ss_pred             cccccccHHHHHHhhhhhh
Confidence            4899999999999987753

The function of this family is unknown although several of the family members are annotated as putative 40-2-3 proteins.

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.48  E-value=0.00012  Score=64.28  Aligned_cols=72  Identities=24%  Similarity=0.309  Sum_probs=60.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-C--------CCCce----EEEEEEcCHHHHHHHHHHhCCce
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-N--------GRPSG----SAEVVYARRSDAFAALKRYNNVL  163 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-t--------g~~kG----~afV~F~~~~~A~~Ai~~lng~~  163 (291)
                      ..-.||+++||+.+...-|+++|+.||+|-.|.|.... +        +.+..    -++|+|.+...|..+.+.||+..
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            44589999999999999999999999999999887765 3        22222    35799999999999999999999


Q ss_pred             eCCee
Q 022827          164 LDGKP  168 (291)
Q Consensus       164 l~g~~  168 (291)
                      |.|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            98864

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

Probab=97.47  E-value=0.00033  Score=67.02  Aligned_cols=68  Identities=16%  Similarity=0.278  Sum_probs=62.4

Q ss_pred             CCCCCCCCcEEEEcCCCCCCCHHHHHHHHH-hcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHH
Q 022827           91 GISGIEVGTKLYVSNLHPGVTNDDIRELFS-EIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKR  158 (291)
Q Consensus        91 ~~~~~~~~~~l~V~nL~~~~te~dL~~~F~-~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~  158 (291)
                      ...++++.+||||+.||--++.++|..+|+ .||.|..+-|-.|+ -+.++|-+-|+|.+..+-.+||++
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            345678999999999999999999999998 89999999999995 788999999999999999999974

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

Probab=97.29  E-value=0.0001  Score=74.11  Aligned_cols=81  Identities=17%  Similarity=0.229  Sum_probs=74.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecCC
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTN  177 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~~  177 (291)
                      ..+|+|.|+|+..|.++|+.+|..+|.++++.++..+.++++|.|||.|.++.++..++...+...+.-..+.|.++.+.
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~  815 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNPE  815 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCCc
Confidence            35899999999999999999999999999999999999999999999999999999999888888888888888887664


Q ss_pred             C
Q 022827          178 A  178 (291)
Q Consensus       178 ~  178 (291)
                      .
T Consensus       816 ~  816 (881)
T KOG0128|consen  816 R  816 (881)
T ss_pred             c
Confidence            4

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

Probab=97.24  E-value=0.00099  Score=63.79  Aligned_cols=64  Identities=19%  Similarity=0.283  Sum_probs=49.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC--C--CCCce---EEEEEEcCHHHHHHHHHHhC
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK--N--GRPSG---SAEVVYARRSDAFAALKRYN  160 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~--t--g~~kG---~afV~F~~~~~A~~Ai~~ln  160 (291)
                      .-+++|||+.||++++|+.|...|..||.|. |......  .  -.++|   |+|+.|+++..+.+.|.++.
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~  327 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACS  327 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHh
Confidence            4567999999999999999999999999876 3333211  1  13466   99999999998888776653

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

Probab=97.23  E-value=0.00086  Score=64.91  Aligned_cols=63  Identities=13%  Similarity=0.203  Sum_probs=51.8

Q ss_pred             HHHHHHhcCCeeEEEEeeC-CCC---CCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecCC
Q 022827          115 IRELFSEIGELKRYAIHFD-KNG---RPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTN  177 (291)
Q Consensus       115 L~~~F~~~G~v~~v~i~~d-~tg---~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~~  177 (291)
                      |+.-+++||.|..|.|..+ .+.   -..|..||+|.+.++++.|+++|+|.+|.++.+...|....
T Consensus       426 vr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeD  492 (500)
T KOG0120|consen  426 VRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDED  492 (500)
T ss_pred             HHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHH
Confidence            3444678999999999887 322   34677999999999999999999999999999998886543

>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=97.13  E-value=0.0025  Score=48.86  Aligned_cols=76  Identities=17%  Similarity=0.205  Sum_probs=50.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEE-EeeC-------CCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCee
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYA-IHFD-------KNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKP  168 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~-i~~d-------~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~  168 (291)
                      ..+-|.|-+.|+. ....|.++|++||+|.+.. +..+       +.-....+..|+|+++.+|++|| ..|+..|.+..
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL-~~NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRAL-QKNGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHH-TTTTEEETTCE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHH-HhCCeEEcCcE
Confidence            3466888899987 4467778999999998664 1110       10112458999999999999999 56999999865


Q ss_pred             e-EEEEe
Q 022827          169 M-KIEVV  174 (291)
Q Consensus       169 i-~V~~a  174 (291)
                      | -|.+.
T Consensus        83 mvGV~~~   89 (100)
T PF05172_consen   83 MVGVKPC   89 (100)
T ss_dssp             EEEEEE-
T ss_pred             EEEEEEc
Confidence            4 45555

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.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=97.02  E-value=0.0042  Score=43.20  Aligned_cols=55  Identities=25%  Similarity=0.282  Sum_probs=45.3

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhc---CCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHh
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEI---GELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY  159 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~---G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~l  159 (291)
                      ..+|+|.+|+ +++.+||+.+|..|   .....|.++-|.      .|-|.|.+.+.|.+||.+|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC------cEEEEECCHHHHHHHHHcC
Confidence            4689999996 47889999999988   234578888773      5899999999999999764

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.95  E-value=0.0006  Score=67.32  Aligned_cols=81  Identities=11%  Similarity=0.047  Sum_probs=67.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKR-YAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~-v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      +......|||..||..+++.++.++|...-.|++ |.|.+-.+++-.+.|||+|..++++.+|+..-+.+.+..+.|+|.
T Consensus       430 P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~  509 (944)
T KOG4307|consen  430 PGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVD  509 (944)
T ss_pred             CCCccceEEeccCCccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccccccchhhhcccccccCceEEEee
Confidence            4456789999999999999999999987767776 777777788889999999999888888887666667777788875


Q ss_pred             Ee
Q 022827          173 VV  174 (291)
Q Consensus       173 ~a  174 (291)
                      -.
T Consensus       510 si  511 (944)
T KOG4307|consen  510 SI  511 (944)
T ss_pred             ch
Confidence            43

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=96.90  E-value=0.00088  Score=62.71  Aligned_cols=74  Identities=28%  Similarity=0.309  Sum_probs=59.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcC-CeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCC-ceeCCeeeEEEEecC
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIG-ELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNN-VLLDGKPMKIEVVGT  176 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G-~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng-~~l~g~~i~V~~a~~  176 (291)
                      .+|||.||.+.++..||..+|...- ....-.++.      .+|+||.+.+...|.+|++.+++ .++.|+.+.|+...+
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 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            4799999999999999999997541 111112221      58999999999999999999998 579999999988766


Q ss_pred             CC
Q 022827          177 NA  178 (291)
Q Consensus       177 ~~  178 (291)
                      +.
T Consensus        76 kk   77 (584)
T KOG2193|consen   76 KK   77 (584)
T ss_pred             HH
Confidence            54

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=96.86  E-value=0.0017  Score=60.29  Aligned_cols=75  Identities=16%  Similarity=0.262  Sum_probs=60.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC----CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK----NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~----tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ..|.|.||.+.+|.++++.||.-.|.|..+.|+.+.    -....-+|||.|.+...+..|. .|-+++|-++.|.|-.+
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeeeeEEEEec
Confidence            489999999999999999999999999999887644    1234568999999999888887 67777776766655543

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.84  E-value=0.0037  Score=56.09  Aligned_cols=63  Identities=16%  Similarity=0.155  Sum_probs=52.2

Q ss_pred             HHHHHHHHhcCCeeEEEEeeCCCC--CCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827          113 DDIRELFSEIGELKRYAIHFDKNG--RPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus       113 ~dL~~~F~~~G~v~~v~i~~d~tg--~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      +++++.+++||.|..|.|+..++-  .-.--.||+|+..++|.+|+-.||+..|.|+.+...+..
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            467888999999999988887621  112347999999999999999999999999999887754

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

Probab=96.84  E-value=0.0045  Score=57.45  Aligned_cols=76  Identities=22%  Similarity=0.278  Sum_probs=58.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHh-c---CCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSE-I---GELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~-~---G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      .-.|.+.+||+++++.|+.+||.. |   +.++.|.++...+++..|-|||.|..+++|+.||.+ |...|.-+.|.|..
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElFR  239 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELFR  239 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHHH
Confidence            346778899999999999999962 1   244556666666899999999999999999999965 55556666665543


Q ss_pred             e
Q 022827          174 V  174 (291)
Q Consensus       174 a  174 (291)
                      +
T Consensus       240 S  240 (508)
T KOG1365|consen  240 S  240 (508)
T ss_pred             H
Confidence            3

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.78  E-value=0.0014  Score=57.70  Aligned_cols=63  Identities=30%  Similarity=0.559  Sum_probs=58.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCC
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNN  161 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng  161 (291)
                      ..|||.||...++.+.|.+.|+.||+|....++.|..+++.+-.+|+|...-.|.+|+..++-
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~   94 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCRE   94 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhcc
Confidence            789999999999999999999999999988888888888888999999999999999988754

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

Probab=96.77  E-value=7.5e-05  Score=74.95  Aligned_cols=70  Identities=29%  Similarity=0.381  Sum_probs=59.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeC
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLD  165 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~  165 (291)
                      ...+++||+||++.+.+.||...|..++.|..+.|.... +++.+|+|||+|..++++.+||.....+.+.
T Consensus       665 R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  665 RDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            345789999999999999999999999988887777445 7889999999999999999999655555444

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.51  E-value=0.0079  Score=44.21  Aligned_cols=56  Identities=21%  Similarity=0.246  Sum_probs=42.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCC
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNN  161 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng  161 (291)
                      ....+|. .|......||.+||+.||.|. |..+.|      -.|||.+.+.+.|..|+..+.-
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d------TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND------TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT------TEEEEEECCCHHHHHHHHHHTT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC------CcEEEEeecHHHHHHHHHHhcc
Confidence            3456666 999999999999999999986 555554      2699999999999999988763

; 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.

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

Probab=96.41  E-value=0.0044  Score=62.98  Aligned_cols=81  Identities=16%  Similarity=0.230  Sum_probs=69.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCC--eeeEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDG--KPMKIE  172 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g--~~i~V~  172 (291)
                      ....+.++|..|..++....|...|..||.|..|.+-..     .-||||.|++...|++|+..|-+..|.+  +.|.|.
T Consensus       452 st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg-----q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvd  526 (975)
T KOG0112|consen  452 STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG-----QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVD  526 (975)
T ss_pred             cccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC-----CcceeeecccCccchhhHHHHhcCcCCCCCcccccc
Confidence            446688999999999999999999999999998766543     5699999999999999999999999875  679999


Q ss_pred             EecCCCCC
Q 022827          173 VVGTNAEI  180 (291)
Q Consensus       173 ~a~~~~~~  180 (291)
                      |+.+.-..
T Consensus       527 la~~~~~~  534 (975)
T KOG0112|consen  527 LASPPGAT  534 (975)
T ss_pred             cccCCCCC
Confidence            98765543

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=96.17  E-value=0.0016  Score=59.41  Aligned_cols=80  Identities=19%  Similarity=0.336  Sum_probs=63.1

Q ss_pred             cEEEEcCCCCCCCHHHH---HHHHHhcCCeeEEEEeeCCC----CCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827           99 TKLYVSNLHPGVTNDDI---RELFSEIGELKRYAIHFDKN----GRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL---~~~F~~~G~v~~v~i~~d~t----g~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      .-+||-.|+..+..+++   .+.|.+||.|.+|.+..+.+    -.....++|+|...++|..||...++..++++.|++
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            46788888887666554   35799999999988877652    112234899999999999999999999999999888


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      .+...+.
T Consensus       158 ~~gttky  164 (327)
T KOG2068|consen  158 SLGTTKY  164 (327)
T ss_pred             hhCCCcc
Confidence            8776654

>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=96.06  E-value=0.0088  Score=50.65  Aligned_cols=80  Identities=18%  Similarity=0.278  Sum_probs=50.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHh-cCCe---eEEEEeeCC--CC-CCceEEEEEEcCHHHHHHHHHHhCCceeCCe--
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSE-IGEL---KRYAIHFDK--NG-RPSGSAEVVYARRSDAFAALKRYNNVLLDGK--  167 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~-~G~v---~~v~i~~d~--tg-~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~--  167 (291)
                      ..++|.|.+||+.+||+++.+.++. +++.   ..+.-....  .. ....-|||.|.+.+++...+..++++.|.+.  
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            4579999999999999999987765 5554   333322332  11 2235699999999999999999999776432  


Q ss_pred             ---eeEEEEecC
Q 022827          168 ---PMKIEVVGT  176 (291)
Q Consensus       168 ---~i~V~~a~~  176 (291)
                         ...|++|.-
T Consensus        86 ~~~~~~VE~Apy   97 (176)
T PF03467_consen   86 NEYPAVVEFAPY   97 (176)
T ss_dssp             -EEEEEEEE-SS
T ss_pred             CCcceeEEEcch
Confidence               445666543

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.

>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=96.00  E-value=0.03  Score=40.35  Aligned_cols=67  Identities=21%  Similarity=0.260  Sum_probs=40.1

Q ss_pred             EEEEc-CCCCCCCHHHHHHHHHhcCC-----eeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827          100 KLYVS-NLHPGVTNDDIRELFSEIGE-----LKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus       100 ~l~V~-nL~~~~te~dL~~~F~~~G~-----v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      +|||. +--..++..+|..++.....     |-.|.|..+       |+||+-.. +.|+.+++.|++..+.|++|+|+.
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~-------~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~   73 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN-------FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVER   73 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS--------EEEEE-T-T-HHHHHHHHTT--SSS----EEE
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEeee-------EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEE
Confidence            44553 22446788999999976644     446777744       89999875 588999999999999999999987


Q ss_pred             e
Q 022827          174 V  174 (291)
Q Consensus       174 a  174 (291)
                      |
T Consensus        74 A   74 (74)
T PF03880_consen   74 A   74 (74)
T ss_dssp             -
T ss_pred             C
Confidence            5

; PDB: 2G0C_A 3MOJ_B.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=95.97  E-value=0.01  Score=57.53  Aligned_cols=73  Identities=12%  Similarity=0.209  Sum_probs=59.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHH--hcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCC--ceeCCeeeE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFS--EIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNN--VLLDGKPMK  170 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~--~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng--~~l~g~~i~  170 (291)
                      ...-|.|.|.-||..+-+|+++.||.  .|-.+++|.+-.+.      -=||+|++..||+.|.+.|..  ++|.|++|.
T Consensus       172 ~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~------nWyITfesd~DAQqAykylreevk~fqgKpIm  245 (684)
T KOG2591|consen  172 NHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND------NWYITFESDTDAQQAYKYLREEVKTFQGKPIM  245 (684)
T ss_pred             CcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC------ceEEEeecchhHHHHHHHHHHHHHhhcCcchh
Confidence            34557888999999999999999996  58888888887662      259999999999999988765  567888776


Q ss_pred             EEE
Q 022827          171 IEV  173 (291)
Q Consensus       171 V~~  173 (291)
                      ..+
T Consensus       246 ARI  248 (684)
T KOG2591|consen  246 ARI  248 (684)
T ss_pred             hhh
Confidence            554

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=95.94  E-value=0.0053  Score=58.36  Aligned_cols=74  Identities=20%  Similarity=0.306  Sum_probs=59.5

Q ss_pred             cEEEEcCCCCCC-CHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecCC
Q 022827           99 TKLYVSNLHPGV-TNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTN  177 (291)
Q Consensus        99 ~~l~V~nL~~~~-te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~~  177 (291)
                      +.|-+.-+++.+ +.++|...|.+||+|..|.|-+.     .-.|.|+|.+..+|-.|. +.+...|+++.|+|.|-.+.
T Consensus       373 s~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~-----~~~a~vTF~t~aeag~a~-~s~~avlnnr~iKl~whnps  446 (526)
T KOG2135|consen  373 SPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS-----SLHAVVTFKTRAEAGEAY-ASHGAVLNNRFIKLFWHNPS  446 (526)
T ss_pred             chhhhhccCCCCchHhhhhhhhhhcCccccccccCc-----hhhheeeeeccccccchh-ccccceecCceeEEEEecCC
Confidence            344444455554 44889999999999999988776     346999999999997776 67899999999999998874


Q ss_pred             C
Q 022827          178 A  178 (291)
Q Consensus       178 ~  178 (291)
                      +
T Consensus       447 ~  447 (526)
T KOG2135|consen  447 P  447 (526)
T ss_pred             c
Confidence            4

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

Probab=95.48  E-value=0.0032  Score=63.97  Aligned_cols=79  Identities=20%  Similarity=0.212  Sum_probs=66.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ..+.+||++||+..+++.+|+..|..+|.|.+|.|...+-+.-.-|+||.|.+...+..|+..+.+..|..-.+++-+-
T Consensus       370 ~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  370 RATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            4567999999999999999999999999999999988764444568999999999999999998887775545555544

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.39  E-value=0.084  Score=42.80  Aligned_cols=71  Identities=17%  Similarity=0.225  Sum_probs=51.1

Q ss_pred             CCCcEEEEcCCCCCCCH-HHHH---HHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827           96 EVGTKLYVSNLHPGVTN-DDIR---ELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te-~dL~---~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      ++-.+|.|.=|..++.. +||+   ..++.||+|.+|.++-      +-.|.|+|.+..+|=+|+.+++. ..-|.-+..
T Consensus        84 pPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG------rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qC  156 (166)
T PF15023_consen   84 PPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG------RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQC  156 (166)
T ss_pred             CCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC------CceEEEEehhhHHHHHHHHhhcC-CCCCceEEe
Confidence            45578888755554332 4454   4568999999998763      44799999999999999999876 444555665


Q ss_pred             EE
Q 022827          172 EV  173 (291)
Q Consensus       172 ~~  173 (291)
                      .|
T Consensus       157 sW  158 (166)
T PF15023_consen  157 SW  158 (166)
T ss_pred             ec
Confidence            55

>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=95.33  E-value=0.052  Score=46.29  Aligned_cols=63  Identities=16%  Similarity=0.193  Sum_probs=46.6

Q ss_pred             CHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhC--CceeCCeeeEEEEecCCC
Q 022827          111 TNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN--NVLLDGKPMKIEVVGTNA  178 (291)
Q Consensus       111 te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~ln--g~~l~g~~i~V~~a~~~~  178 (291)
                      ..+.|+++|..|..+..+.++..     -.-..|.|.+.++|.+|...|+  +..+.+..|+|.++....
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s-----FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS-----FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT-----TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC-----CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            34789999999999988777644     4468999999999999999999  899999999999985443

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.

>PF13865 FoP_duplication: C-terminal duplication domain of Friend of PRMT1

Probab=95.32  E-value=0.035  Score=40.14  Aligned_cols=17  Identities=41%  Similarity=0.690  Sum_probs=14.6

Q ss_pred             CChhHHHHHHHHHHHhh
Q 022827          272 KSADDLDKELDNYHAEA  288 (291)
Q Consensus       272 ~s~~~~d~el~~y~~~~  288 (291)
                      .+...||+|||.||+++
T Consensus        55 ~~~~~LD~~Ld~Y~~~~   71 (74)
T PF13865_consen   55 KTKSKLDAELDSYMSKK   71 (74)
T ss_pred             HHHHHHHHHHHHHHHcc
Confidence            35789999999999976

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=95.04  E-value=0.034  Score=54.00  Aligned_cols=84  Identities=15%  Similarity=0.062  Sum_probs=58.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHH-hcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeC----Cee
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFS-EIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLD----GKP  168 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~-~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~----g~~  168 (291)
                      ..+-+++.|.|+|...|...|...-+ ..+.-.-+.+..|- +....|||||.|.+++++..+.+++|++.+.    .+.
T Consensus       385 e~~rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Ki  464 (549)
T KOG4660|consen  385 ECPRTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKI  464 (549)
T ss_pred             cCchhhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceee
Confidence            34556777777776666555444432 34555556666665 6678999999999999999999999997653    345


Q ss_pred             eEEEEecCCC
Q 022827          169 MKIEVVGTNA  178 (291)
Q Consensus       169 i~V~~a~~~~  178 (291)
                      +.|.||.-+-
T Consensus       465 a~itYArIQG  474 (549)
T KOG4660|consen  465 ASITYARIQG  474 (549)
T ss_pred             eeeehhhhhc
Confidence            6666665443

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=94.81  E-value=0.02  Score=56.65  Aligned_cols=73  Identities=10%  Similarity=0.141  Sum_probs=64.0

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           93 SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      .+.++..+|||+||.+.+.++-++.++..||.|..+....        |+|.+|..+..+..|+..++-..++++.+.+.
T Consensus        35 ~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~--------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~  106 (668)
T KOG2253|consen   35 QPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK--------FGFCEFLKHIGDLRASRLLTELNIDDQKLIEN  106 (668)
T ss_pred             cCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh--------hcccchhhHHHHHHHHHHhcccCCCcchhhcc
Confidence            4556788999999999999999999999999998776652        89999999999999999999889988877765


Q ss_pred             E
Q 022827          173 V  173 (291)
Q Consensus       173 ~  173 (291)
                      .
T Consensus       107 ~  107 (668)
T KOG2253|consen  107 V  107 (668)
T ss_pred             c
Confidence            5

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=94.71  E-value=0.85  Score=46.29  Aligned_cols=68  Identities=13%  Similarity=0.269  Sum_probs=50.9

Q ss_pred             EEEEc-CCCCCCCHHHHHHHHHhcCCee-----EEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827          100 KLYVS-NLHPGVTNDDIRELFSEIGELK-----RYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus       100 ~l~V~-nL~~~~te~dL~~~F~~~G~v~-----~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ++||. +-...++..+|..++..-+.|.     .|.|..       .|.||+.. .+.|...++.|++..+.+++|.|+.
T Consensus       488 ~~~~~~g~~~~~~~~~~~~~i~~~~~~~~~~ig~i~i~~-------~~s~v~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  559 (629)
T PRK11634        488 LYRIEVGRDDGVEVRHIVGAIANEGDISSRYIGNIKLFA-------SHSTIELP-KGMPGEVLQHFTRTRILNKPMNMQL  559 (629)
T ss_pred             EEEEecccccCCCHHHHHHHHHhhcCCChhhCCcEEEeC-------CceEEEcC-hhhHHHHHHHhccccccCCceEEEE
Confidence            45553 2345688889988887655443     566663       38899976 4578899999999999999999998


Q ss_pred             ec
Q 022827          174 VG  175 (291)
Q Consensus       174 a~  175 (291)
                      +.
T Consensus       560 ~~  561 (629)
T PRK11634        560 LG  561 (629)
T ss_pred             CC
Confidence            74

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.32  E-value=0.19  Score=49.26  Aligned_cols=79  Identities=20%  Similarity=0.196  Sum_probs=61.4

Q ss_pred             CCCCcEEEEcCCCCC-CCHHHHHHHHHhc----CCeeEEEEeeCCCCC--------------------------------
Q 022827           95 IEVGTKLYVSNLHPG-VTNDDIRELFSEI----GELKRYAIHFDKNGR--------------------------------  137 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~-~te~dL~~~F~~~----G~v~~v~i~~d~tg~--------------------------------  137 (291)
                      ...+..|-|.||.|+ |...||.-+|+.|    |.|.+|.|....-|+                                
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            456789999999997 7789999999877    578888775432111                                


Q ss_pred             ----------------CceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827          138 ----------------PSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus       138 ----------------~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                                      -.=||.|+|.+.+.|.+..+.++|+.|....+.+.|
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DL  302 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDL  302 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeee
Confidence                            124899999999999999999999999765444443

>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=94.08  E-value=0.53  Score=36.68  Aligned_cols=69  Identities=9%  Similarity=-0.008  Sum_probs=49.0

Q ss_pred             CCcEEEEcC-CCCCCCHHHHHHHHHhcC-CeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCC
Q 022827           97 VGTKLYVSN-LHPGVTNDDIRELFSEIG-ELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDG  166 (291)
Q Consensus        97 ~~~~l~V~n-L~~~~te~dL~~~F~~~G-~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g  166 (291)
                      ..+.|.|-- +|+.++.++|..+.+.+- .|..++|+.|.+. ++-.+.+.|.+.++|..-.+.|||+.++.
T Consensus        11 ~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~p-nrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   11 RRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTP-NRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             CCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCC-ceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            334444444 455555566765556554 5668888887642 46689999999999999999999988764

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>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=93.86  E-value=0.3  Score=34.46  Aligned_cols=55  Identities=20%  Similarity=0.296  Sum_probs=43.3

Q ss_pred             CCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827          109 GVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus       109 ~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      .++-+||+..+..|.- .  .|..|++|     -||.|.+.++|++|....++..+-...|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~--~I~~d~tG-----fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-D--RIRDDRTG-----FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-c--eEEecCCE-----EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            3677999999999953 3  34555433     589999999999999999998887777654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=93.70  E-value=0.054  Score=55.05  Aligned_cols=74  Identities=20%  Similarity=0.205  Sum_probs=61.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCcee--CCeeeEEEEecCC
Q 022827          100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLL--DGKPMKIEVVGTN  177 (291)
Q Consensus       100 ~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l--~g~~i~V~~a~~~  177 (291)
                      +.++.|.+-.++...|..||++||.|.++..+.+     .-.|.|+|.+.+.|..|+++++++++  .|-+.+|.+++.-
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~-----~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~  374 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRD-----LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTL  374 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheeccc-----ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccc
Confidence            4445555667778889999999999999988776     56899999999999999999999775  5778999998865


Q ss_pred             C
Q 022827          178 A  178 (291)
Q Consensus       178 ~  178 (291)
                      +
T Consensus       375 ~  375 (1007)
T KOG4574|consen  375 P  375 (1007)
T ss_pred             c
Confidence            5

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=93.34  E-value=0.051  Score=49.56  Aligned_cols=83  Identities=19%  Similarity=0.231  Sum_probs=66.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ...+++||+++.+.+.+.++..+|.++|.+..+.+.... ...++++++|.|...+.+..|+.......+....+...+.
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            357899999999999999999999999988877776655 7788999999999999999999765555666666655554


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      ....
T Consensus       166 ~~~~  169 (285)
T KOG4210|consen  166 TRRG  169 (285)
T ss_pred             cccc
Confidence            4433

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=93.03  E-value=0.28  Score=44.45  Aligned_cols=74  Identities=24%  Similarity=0.359  Sum_probs=52.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCee-eEEEEecC
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKP-MKIEVVGT  176 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~-i~V~~a~~  176 (291)
                      .+=|-|-+.|+.-. ..|..+|++||+|.+....  .+   --+-+|.|.+..+|++|| ..|+..|++.. |-|.-+..
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~--~n---gNwMhirYssr~~A~KAL-skng~ii~g~vmiGVkpCtD  269 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP--SN---GNWMHIRYSSRTHAQKAL-SKNGTIIDGDVMIGVKPCTD  269 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecC--CC---CceEEEEecchhHHHHhh-hhcCeeeccceEEeeeecCC
Confidence            34566667776544 4567799999999865433  22   348899999999999999 56999998864 44554444


Q ss_pred             CC
Q 022827          177 NA  178 (291)
Q Consensus       177 ~~  178 (291)
                      +.
T Consensus       270 ks  271 (350)
T KOG4285|consen  270 KS  271 (350)
T ss_pred             HH
Confidence            43

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=92.59  E-value=0.32  Score=50.39  Aligned_cols=9  Identities=44%  Similarity=0.933  Sum_probs=3.7

Q ss_pred             CCCccCCCC
Q 022827          224 RGGLRRSSQ  232 (291)
Q Consensus       224 rgG~~~~~g  232 (291)
                      +|||+..++
T Consensus      1232 rgGfrnngg 1240 (1282)
T KOG0921|consen 1232 RGGFRNNGG 1240 (1282)
T ss_pred             CCccccCCC
Confidence            344443333

>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]

Probab=91.91  E-value=0.55  Score=43.41  Aligned_cols=8  Identities=50%  Similarity=0.945  Sum_probs=2.9

Q ss_pred             CCCCCCCC
Q 022827          244 RGRGGGGG  251 (291)
Q Consensus       244 ~grgg~Gg  251 (291)
                      +++|+++|
T Consensus       439 r~gggr~g  446 (465)
T KOG3973|consen  439 RDGGGRDG  446 (465)
T ss_pred             CCCCCCCC
Confidence            33333333

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=91.37  E-value=0.88  Score=43.48  Aligned_cols=69  Identities=13%  Similarity=0.147  Sum_probs=58.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhc-CCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCC
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEI-GELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDG  166 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~-G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g  166 (291)
                      +++.|.|--+|..+|..||-.|...| -.|.+++|++|.... +=.+.|.|.+.++|....+.|||..|+.
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pn-rymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPN-RYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCc-eEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            38899999999999999999998754 467799999876332 4578999999999999999999988764

>KOG4019 consensus Calcineurin-mediated signaling pathway inhibitor DSCR1 [Signal transduction mechanisms; General function prediction only]

Probab=87.84  E-value=0.46  Score=40.05  Aligned_cols=77  Identities=16%  Similarity=0.238  Sum_probs=55.8

Q ss_pred             CCcEEEEcCCCCCCCHH-----HHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCe-eeE
Q 022827           97 VGTKLYVSNLHPGVTND-----DIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGK-PMK  170 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~-----dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~-~i~  170 (291)
                      -.++|++.+|+..|-.+     ..+.+|.+|-+.....++.     +..+.-|.|.+++.|..|..+++...|.++ .++
T Consensus         9 lp~~~~~c~i~~~VF~~~~~k~~~~~lFrq~n~~~~fq~lr-----sfrrvRi~f~~p~~a~~a~i~~~~~~f~~~~~~k   83 (193)
T KOG4019|consen    9 LPTAIIACDIHEEVFVNREDKALFENLFRQINEDATFQLLR-----SFRRVRINFSNPEAAADARIKLHSTSFNGKNELK   83 (193)
T ss_pred             ccceeeeecccHHhhccHHHHHHHHhHHhhhCcchHHHHHH-----hhceeEEeccChhHHHHHHHHhhhcccCCCceEE
Confidence            34678888888765432     3455666666555444443     356788999999999999999999999998 787


Q ss_pred             EEEecCCC
Q 022827          171 IEVVGTNA  178 (291)
Q Consensus       171 V~~a~~~~  178 (291)
                      .-++++.-
T Consensus        84 ~yfaQ~~~   91 (193)
T KOG4019|consen   84 LYFAQPGH   91 (193)
T ss_pred             EEEccCCC
Confidence            77776543

>PF03468 XS: XS domain; InterPro: IPR005380 The XS (rice gene X and SGS3) domain is found in a family of plant proteins including gene X Q9SBW2 from SWISSPROT and SGS3 Q9LDX1 from SWISSPROT

Probab=84.39  E-value=1.9  Score=33.89  Aligned_cols=55  Identities=22%  Similarity=0.312  Sum_probs=30.2

Q ss_pred             EEEEcCCCCC---------CCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcC-HHHHHHHH
Q 022827          100 KLYVSNLHPG---------VTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYAR-RSDAFAAL  156 (291)
Q Consensus       100 ~l~V~nL~~~---------~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~-~~~A~~Ai  156 (291)
                      ++.|-|++..         ++.++|.+.|+.|.+++ |..++++.+ +.+++.|+|.+ -.-...|+
T Consensus        10 mgIi~N~~~~~~~~g~~~g~~~~~l~~~l~~f~p~k-v~~l~~~~g-h~g~aiv~F~~~w~Gf~~A~   74 (116)
T PF03468_consen   10 MGIIVNIPTEKDDDGRWVGMSNEELLDKLAEFNPLK-VKPLYGKQG-HTGFAIVEFNKDWSGFKNAM   74 (116)
T ss_dssp             EEEEE----EE-TTS-EE---SHHHHHHHHH---SE-EEEEEETTE-EEEEEEEE--SSHHHHHHHH
T ss_pred             EEEEEcCccccCCCCceeccCHHHHHHHHHhcCCce-eEECcCCCC-CcEEEEEEECCChHHHHHHH
Confidence            4566677443         45688999999998875 666676654 47899999985 33344444

SGS3 is thought to be involved in post-transcriptional gene silencing (PTGS). This domain contains a conserved aspartate residue that may be functionally important. The XS domain containing proteins contain coiled-coils, which suggests that they will oligomerise. Most coiled-coil proteins form either a dimeric or a trimeric structure. It is possible that different members of the XS domain family could oligomerise via their coiled-coils forming a variety of complexes [].; PDB: 4E8U_C.

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.16  E-value=2.5  Score=39.93  Aligned_cols=55  Identities=16%  Similarity=0.112  Sum_probs=45.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCee-EEEEeeCCCCCCceEEEEEEcCHHHHHHHHHH
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELK-RYAIHFDKNGRPSGSAEVVYARRSDAFAALKR  158 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~-~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~  158 (291)
                      ...|-|.++|.....+||..+|+.|+.-- +|.++-|      -+||..|.+...|..||-.
T Consensus       391 pHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDd------thalaVFss~~~AaeaLt~  446 (528)
T KOG4483|consen  391 PHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDD------THALAVFSSVNRAAEALTL  446 (528)
T ss_pred             cceeEeccCchhhccHHHHHHHHHhhcCCceeEEeec------ceeEEeecchHHHHHHhhc
Confidence            46899999999999999999999997543 4555555      2799999999999999943

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=83.62  E-value=0.058  Score=50.87  Aligned_cols=80  Identities=14%  Similarity=0.283  Sum_probs=66.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      .+.+|-|.|||+...++.|..|+..||.|..|.++...+-  .-..-|+|.+.+.+..||..||+..|....++|.|...
T Consensus        79 rsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~e--tavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiPd  156 (584)
T KOG2193|consen   79 RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSE--TAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIPD  156 (584)
T ss_pred             HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchH--HHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCch
Confidence            4567999999999999999999999999998876443211  22345789999999999999999999999999988654


Q ss_pred             CC
Q 022827          177 NA  178 (291)
Q Consensus       177 ~~  178 (291)
                      ..
T Consensus       157 eq  158 (584)
T KOG2193|consen  157 EQ  158 (584)
T ss_pred             hh
Confidence            43

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=82.99  E-value=0.18  Score=47.23  Aligned_cols=73  Identities=15%  Similarity=0.110  Sum_probs=54.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      .+|+|.+|+..+...++-++|..+|+|.+..+..   +...-+|.|+|........|+ .+++.++.-+...+.+..
T Consensus       152 Rt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~as---k~~s~~c~~sf~~qts~~hal-r~~gre~k~qhsr~ai~k  224 (479)
T KOG4676|consen  152 RTREVQSLISAAILPESGESFERKGEVSYAHTAS---KSRSSSCSHSFRKQTSSKHAL-RSHGRERKRQHSRRAIIK  224 (479)
T ss_pred             hhhhhhcchhhhcchhhhhhhhhcchhhhhhhhc---cCCCcchhhhHhhhhhHHHHH-HhcchhhhhhhhhhhhcC
Confidence            6899999999999999999999999988665543   233457889999888888888 456666654433333333

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	291
2f3j_A	177	The Solution Structure Of The Ref2-I Mrna Export Fa		4e-25
2kt5_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		5e-24
2yka_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		6e-24
1no8_A	106	Solution Structure Of The Nuclear Factor Aly Rbd Do		4e-21
3ulh_A	107	Crystal Structure Of A Rna Binding Domain Of Tho Co		8e-20
1sxl_A	97	Resonance Assignments And Solution Structure Of The		1e-05
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		1e-05
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		1e-05
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		3e-05
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		9e-05
2do0_A	114	Solution Structure Of The Rna Binding Domain Of Het		2e-04
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		3e-04
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		3e-04
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		4e-04
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		4e-04
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		4e-04
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		4e-04
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		5e-04
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		5e-04
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		5e-04
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		7e-04
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		8e-04

>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor (Residues 1-155) Length = 177

Iteration: 1
 Score =  112 bits (279), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 68/182 (37%), Positives = 96/182 (52%), Gaps = 28/182 (15%)
Query: 1   MATHVDMSLDDIIKSRKKSEXXXXXXXXXXXXXXXXXXXXXXXXXXMTGAARRGPLSNAR 60
           MA  +DMSLDDIIK  +                               G  RR   + AR
Sbjct: 15  MADKMDMSLDDIIKLNRNQRRVNR-----------------------GGGPRRNRPAIAR 51
Query: 61  PSSYTIAKSFRRTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIREL 118
                 A  + R +  P  WQHDLF+      G  G+E G KL VSNL  GV++ DI+EL
Sbjct: 52  GGRNRPA-PYSRPKPLPDKWQHDLFDSG--CGGGEGVETGAKLLVSNLDFGVSDADIQEL 108
Query: 119 FSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNA 178
           F+E G LK+ A+ +D++GR  G+A+V + RR+DA  A+K+Y  V LDG+PM I++V +  
Sbjct: 109 FAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI 168
Query: 179 EI 180
           ++
Sbjct: 169 DL 170

>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1 Icp27 Peptide Length = 124

Iteration: 1
 Score =  107 bits (268), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 49/103 (47%), Positives = 72/103 (69%), Gaps = 2/103 (1%)
Query: 78  WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGR 137
           WQHDLF+      G  G+E G KL VSNL  GV++ DI+ELF+E G LK+ A+ +D++GR
Sbjct: 17  WQHDLFDSG--CGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR 74
Query: 138 PSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNAEI 180
             G+A+V + RR+DA  A+K+Y  V LDG+PM I++V +  ++
Sbjct: 75  SLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDL 117

>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs Orf57 Peptide Length = 124

Iteration: 1
 Score =  107 bits (268), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 49/103 (47%), Positives = 72/103 (69%), Gaps = 2/103 (1%)
Query: 78  WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGR 137
           WQHDLF+      G  G+E G KL VSNL  GV++ DI+ELF+E G LK+ A+ +D++GR
Sbjct: 17  WQHDLFDSG--CGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR 74
Query: 138 PSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNAEI 180
             G+A+V + RR+DA  A+K+Y  V LDG+PM I++V +  ++
Sbjct: 75  SLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDL 117

>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain Length = 106

Iteration: 1
 Score = 98.6 bits (244), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 50/105 (47%), Positives = 71/105 (67%), Gaps = 4/105 (3%)
Query: 72  RTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYA 129
           R +  P  WQHDLF+           E G KL VSNL  GV++ DI+ELF+E G LK+ A
Sbjct: 2   RPKQLPDKWQHDLFDSGFGGGAGV--ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAA 59
Query: 130 IHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV 174
           +H+D++GR  G+A+V + R++DA  A+K+YN V LDG+PM I++V
Sbjct: 60  VHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV 104

>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A Resolution Length = 107

Iteration: 1
 Score = 94.0 bits (232), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 49/105 (46%), Positives = 69/105 (65%), Gaps = 4/105 (3%)
Query: 72  RTRNFP--WQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYA 129
           R +  P  WQHDLF+           E G KL VSNL  GV++ DI+ELF+E G LK+ A
Sbjct: 3   RPKQLPDKWQHDLFDSGFGGGAGV--ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAA 60
Query: 130 IHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV 174
           +H+D++GR  G+A+V + R++DA  A K+YN V LDG+P  I++V
Sbjct: 61  VHYDRSGRSLGTADVHFERKADALKAXKQYNGVPLDGRPXNIQLV 105

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 45/78 (57%), Gaps = 3/78 (3%)
Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALK 157
           T LYV+NL   +T+D +  +F + G + +  I  DK  GRP G A V Y +R +A  A+ 
Sbjct: 14  TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 158 RYNNVLLDG--KPMKIEV 173
             NNV+ +G  +P+ + +
Sbjct: 74  ALNNVIPEGGSQPLSVRL 91

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 45/78 (57%), Gaps = 3/78 (3%)
Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALK 157
           T LYV+NL   +T+D +  +F + G + +  I  DK  GRP G A V Y +R +A  A+ 
Sbjct: 90  TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Query: 158 RYNNVLLDG--KPMKIEV 173
             NNV+ +G  +P+ + +
Sbjct: 150 ALNNVIPEGGSQPLSVRL 167

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 45/78 (57%), Gaps = 3/78 (3%)
Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALK 157
           T LYV+NL   +T+D +  +F + G + +  I  DK  GRP G A V Y +R +A  A+ 
Sbjct: 101 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 160
Query: 158 RYNNVLLDG--KPMKIEV 173
             NNV+ +G  +P+ + +
Sbjct: 161 ALNNVIPEGGSQPLSVRL 178

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALKR 158
           +LYV +LH  +T D +R +F   G ++   +  D + GR  G   + ++    A  AL++
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 159 YNNVLLDGKPMKI 171
            N   L G+PMK+
Sbjct: 88  LNGFELAGRPMKV 100

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 43.9 bits (102), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 38/72 (52%)
Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           LYV NL    T + I ELFS+ G++K+  +  DK     G   V Y  R+DA  A++  N
Sbjct: 21  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYIN 80
Query: 161 NVLLDGKPMKIE 172
              LD + ++ +
Sbjct: 81  GTRLDDRIIRTD 92

>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein M Length = 114

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 43/77 (55%)
Query: 97  VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
           +G+ ++V+NL   V    ++E+FS  G + R  I  DK+G+  G   V + +  +A  A+
Sbjct: 14  LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAI 73
Query: 157 KRYNNVLLDGKPMKIEV 173
             +N  LL  +PM +++
Sbjct: 74  SMFNGQLLFDRPMHVKM 90

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 98  GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAAL 156
           G  L+V+ +H   T +DI + F+E GE+K   ++ D + G   G   V Y    +A AA+
Sbjct: 7   GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 157 KRYNNVLLDGKPMKIE 172
           +  N   L G+P+ ++
Sbjct: 67  EGLNGQDLMGQPISVD 82

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 98  GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAAL 156
           G  L+V+ +H   T +DI + F+E GE+K   ++ D + G   G   V Y    +A AA+
Sbjct: 22  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81
Query: 157 KRYNNVLLDGKPMKIE 172
           +  N   L G+P+ ++
Sbjct: 82  EGLNGQDLMGQPISVD 97

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 98  GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAAL 156
           G  L+V+ +H   T +DI + F+E GE+K   ++ D + G   G   V Y    +A AA+
Sbjct: 23  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 82
Query: 157 KRYNNVLLDGKPMKIE 172
           +  N   L G+P+ ++
Sbjct: 83  EGLNGQDLMGQPISVD 98

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 98  GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAAL 156
           G  L+V+ +H   T +DI + F+E GE+K   ++ D + G   G   V Y    +A AA+
Sbjct: 7   GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 157 KRYNNVLLDGKPMKIE 172
           +  N   L G+P+ ++
Sbjct: 67  EGLNGQDLMGQPISVD 82

>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 = 42.0 bits (97), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 98  GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAAL 156
           G  L+V+ +H   T +DI + F+E GE+K   ++ D + G   G   V Y    +A AA+
Sbjct: 9   GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 68
Query: 157 KRYNNVLLDGKPMKIE 172
           +  N   L G+P+ ++
Sbjct: 69  EGLNGQDLMGQPISVD 84

>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 = 42.0 bits (97), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 98  GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAAL 156
           G  L+V+ +H   T +DI + F+E GE+K   ++ D + G   G   V Y    +A AA+
Sbjct: 7   GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 157 KRYNNVLLDGKPMKIE 172
           +  N   L G+P+ ++
Sbjct: 67  EGLNGQDLMGQPISVD 82

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 33/120 (27%), Positives = 56/120 (46%), Gaps = 12/120 (10%)
Query: 54  GPLSNARPSSYTIAKSFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTND 113
           G  SN R + +    S+ R RN        +D L       +E G  L+V+++H     D
Sbjct: 39  GSDSNTREAIH----SYERVRNED------DDELEPGPQRSVE-GWILFVTSIHEEAQED 87
Query: 114 DIRELFSEIGELKRYAIHFD-KNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE 172
           +I+E F + GE+K   ++ D + G   G A V Y     A AA +  N   + G+ ++++
Sbjct: 88  EIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD 147

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/94 (30%), Positives = 47/94 (50%), Gaps = 1/94 (1%)
Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALK 157
           T L V+ L   +T D++R LFS IGE++   +  DK  G   G   V Y    DA  A+ 
Sbjct: 3   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 158 RYNNVLLDGKPMKIEVVGTNAEIPLQARVNVTGV 191
             N + L  K +K+     ++E+   A + ++G+
Sbjct: 63  TLNGLRLQSKTIKVSYARPSSEVIKDANLYISGL 96

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/94 (30%), Positives = 47/94 (50%), Gaps = 1/94 (1%)
Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALK 157
           T L V+ L   +T D++R LFS IGE++   +  DK  G   G   V Y    DA  A+ 
Sbjct: 3   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 158 RYNNVLLDGKPMKIEVVGTNAEIPLQARVNVTGV 191
             N + L  K +K+     ++E+   A + ++G+
Sbjct: 63  TLNGLRLQSKTIKVSYARPSSEVIKDANLYISGL 96

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 98  GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALK 157
           G  L V NL P V+N+ + + FS+ G +++  +  D  GR +G   V +A +  A  AL+
Sbjct: 96  GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALE 155
Query: 158 RYNN--VLLDGKPMKIEV 173
           R  +   LL   P  + V
Sbjct: 156 RCGDGAFLLTTTPRPVIV 173

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 29/105 (27%), Positives = 50/105 (47%), Gaps = 8/105 (7%)
Query: 69  SFRRTRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRY 128
           S+ R RN        +D L       +E G  L+V+++H     D+I+E F + GE+K  
Sbjct: 4   SYERVRNED------DDELEPGPQRSVE-GWILFVTSIHEEAQEDEIQEKFCDYGEIKNI 56
Query: 129 AIHFD-KNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE 172
            ++ D + G   G A V Y     A AA +  N   + G+ ++++
Sbjct: 57  HLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD 101

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	291
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	100.0
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.88
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.88
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.87
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.86
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.85
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.85
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.84
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.84
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.84
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.83
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.83
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.83
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.83
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.83
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.83
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.83
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.83
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.83
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.83
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.83
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.83
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.83
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.83
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.83
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.83
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.83
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.83
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.82
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.82
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.82
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.82
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.82
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.82
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.82
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.82
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.82
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.82
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.82
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.82
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.82
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.82
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.82
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.82
2div_A	99	TRNA selenocysteine associated protein; structural	99.81
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.81
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.81
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.81
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.81
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.81
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.81
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.81
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.81
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.81
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.81
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.81
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.8
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.8
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.8
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.8
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.8
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.8
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.8
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.8
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.8
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.8
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.8
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.8
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.8
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.79
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.79
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.79
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.79
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.79
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.79
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.79
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.79
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.79
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.78
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.78
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.78
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.78
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.78
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.78
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.78
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.78
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.78
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.78
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.78
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.78
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.78
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.78
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.78
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.78
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.77
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.77
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.77
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.77
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.77
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.77
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.77
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.77
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.77
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.77
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.77
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.77
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.77
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.77
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.77
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.77
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.77
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.77
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.77
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.77
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.76
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.76
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.76
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.76
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.76
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.76
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.75
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.75
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.75
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.75
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.75
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.75
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.75
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.75
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.75
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.74
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.74
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.74
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.74
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.74
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.74
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.74
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.74
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.74
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.74
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.74
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.73
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.73
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.73
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.73
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.57
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.72
1x5p_A	97	Negative elongation factor E; structure genomics,	99.72
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.72
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.72
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.71
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.71
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.71
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.71
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.71
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.7
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.7
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.7
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.69
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.69
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.69
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.69
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.68
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.68
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.68
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.67
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.67
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.67
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.67
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.67
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.66
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.66
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.66
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.66
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.65
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.65
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.64
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.64
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.63
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.63
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.62
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.62
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.61
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.61
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.6
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.59
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.59
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.58
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.58
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.57
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.56
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.56
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.55
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.55
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.54
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.54
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.54
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.53
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.52
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.52
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.51
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.49
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.48
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.45
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.38
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.35
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.26
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.09
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.99
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.61
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.09
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.07
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.79
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.68
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.47
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.21
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.02
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.65
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.22
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.94
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	94.84
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	90.88
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	88.69
4eyt_A	129	Telomerase associated protein P65; RNA, LA protein	87.45

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=100.00  E-value=3.2e-34  Score=242.24  Aligned_cols=154  Identities=45%  Similarity=0.755  Sum_probs=121.4

Q ss_pred             CCCcCCCChHHHHHhcccCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccccCCCCCCCc
Q 022827            1 MATHVDMSLDDIIKSRKKSERERGQGRARRGRGRGRGPSGSVSGGRMTGAARRGPLSNARPSSYTIAKSFRRTRNFPWQH   80 (291)
Q Consensus         1 m~~~ld~sLddii~~~~~~~~~~~~~~~~rg~gr~rg~~~~~~~~~g~g~~r~~~~~~~R~~~~~~~~~~~~~~~~~~~~   80 (291)
                      |+++|||||||||+++++..+++      |++++++            ++.++...+..|++||..++    ..+..|+|
T Consensus        15 m~~~ld~sLDdii~~~r~~~r~~------r~~~~r~------------~~~~~~~~g~~r~~~y~~~~----~~~~~w~~   72 (177)
T 2f3j_A           15 MADKMDMSLDDIIKLNRNQRRVN------RGGGPRR------------NRPAIARGGRNRPAPYSRPK----PLPDKWQH   72 (177)
T ss_dssp             CCCSSSCCHHHHHHHHHTCCSCS------SSCCSSS------------SSCCCTTTSSTTTCCSSSCC----CCTTCSSC
T ss_pred             hhhhhccCHHHHHhhcccCCCCC------CCCCCCC------------CCCCCCCCCcCCCCCCCCCc----Cccccccc
Confidence            89999999999999886643211      1110000            01111112245666776543    45889999


Q ss_pred             hhhhhhhhhcCCCCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhC
Q 022827           81 DLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN  160 (291)
Q Consensus        81 d~~~~~~~~~~~~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~ln  160 (291)
                      +.|++..  .......+.++|||.|||+++++++|+++|++||+|+.|.|+.++++.+++||||+|.+.++|++||+.||
T Consensus        73 d~~~~~~--~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~ln  150 (177)
T 2f3j_A           73 DLFDSGC--GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK  150 (177)
T ss_dssp             SSSCSSC--CCCSSCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHST
T ss_pred             ccccccc--CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhC
Confidence            9998765  23345677899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CceeCCeeeEEEEecCCC
Q 022827          161 NVLLDGKPMKIEVVGTNA  178 (291)
Q Consensus       161 g~~l~g~~i~V~~a~~~~  178 (291)
                      +..|++++|+|+++....
T Consensus       151 g~~l~Gr~l~V~~a~~~~  168 (177)
T 2f3j_A          151 GVPLDGRPMDIQLVASQI  168 (177)
T ss_dssp             TCBCSSSBCEEEEESSGG
T ss_pred             CCEECCEEEEEEEecCCC
Confidence            999999999999998654

>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=99.88  E-value=1.9e-22  Score=155.44  Aligned_cols=101  Identities=50%  Similarity=0.886  Sum_probs=79.8

Q ss_pred             CCCCCCCchhhhhhhhhcCCCCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHH
Q 022827           73 TRNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDA  152 (291)
Q Consensus        73 ~~~~~~~~d~~~~~~~~~~~~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A  152 (291)
                      ..+..|+|++|....  ..++...+.++|||.|||+.+|+++|+++|++||.|..|.|+.++++.+++||||+|.+.++|
T Consensus         6 ~~~~~~~~~~~~~~~--~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a   83 (107)
T 3ulh_A            6 QLPDKWQHDLFDSGF--GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADA   83 (107)
T ss_dssp             --------------------CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHH
T ss_pred             CCCcccccccccCCC--CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHH
Confidence            457789999987665  234566788999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhCCceeCCeeeEEEEec
Q 022827          153 FAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus       153 ~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ++||+.||+..|.++.|+|+++.
T Consensus        84 ~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           84 LKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             HHHHHHHTTCEETTEECEEEEEC
T ss_pred             HHHHHHhCCCEeCCcEEEEEEeC
Confidence            99999999999999999999986

>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=99.88  E-value=4.2e-22  Score=152.13  Aligned_cols=81  Identities=33%  Similarity=0.452  Sum_probs=77.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ..+++|||+|||+++|+++|+++|++||+|.+|.|+.++ ++.++|||||+|.+.++|++||+.||+..|+|++|+|+++
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            356899999999999999999999999999999999998 8999999999999999999999999999999999999998


Q ss_pred             cC
Q 022827          175 GT  176 (291)
Q Consensus       175 ~~  176 (291)
                      +|
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            65

>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=99.87  E-value=5.6e-23  Score=180.08  Aligned_cols=82  Identities=20%  Similarity=0.253  Sum_probs=76.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcC--CeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIG--ELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G--~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ..++|||+||+++||+++|+++|++||  .|++|.|+.++ +++++|||||+|.+.++|++||+.||++.|+++.|+|++
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            567999999999999999999999999  99999999998 999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +....
T Consensus       147 a~~~~  151 (229)
T 3q2s_C          147 VNKQF  151 (229)
T ss_dssp             CCHHH
T ss_pred             CCCCc
Confidence            87543

>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=99.86  E-value=2.4e-21  Score=159.37  Aligned_cols=85  Identities=29%  Similarity=0.378  Sum_probs=80.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      ...+.++|||.|||+++|+++|+++|++||+|+.|.|+.++ ++.+++||||+|.+.++|++||+.||++.|+++.|+|+
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  114 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD  114 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34578999999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++.+..
T Consensus       115 ~a~~~~  120 (156)
T 1h2v_Z          115 WDAGFK  120 (156)
T ss_dssp             EESCCC
T ss_pred             ECCCCC
Confidence            997643

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.85  E-value=5.1e-21  Score=151.48  Aligned_cols=104  Identities=47%  Similarity=0.854  Sum_probs=93.2

Q ss_pred             CCCCCCchhhhhhhhhcCCCCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHH
Q 022827           74 RNFPWQHDLFEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAF  153 (291)
Q Consensus        74 ~~~~~~~d~~~~~~~~~~~~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~  153 (291)
                      .+..|+++.+....  ...+...+.++|||+|||+.+++++|+++|++||+|..|.|+.++++.+++||||+|.+.++|+
T Consensus        13 ~~~~~~~~~~~~~~--~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~   90 (124)
T 2kt5_A           13 DPDKWQHDLFDSGC--GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADAL   90 (124)
T ss_dssp             CCCCCCCCCCCCCC--CCCCCCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHH
T ss_pred             CCccccccccccCC--CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHH
Confidence            46689998877654  2334567889999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhCCceeCCeeeEEEEecCCCC
Q 022827          154 AALKRYNNVLLDGKPMKIEVVGTNAE  179 (291)
Q Consensus       154 ~Ai~~lng~~l~g~~i~V~~a~~~~~  179 (291)
                      +||+.||+..|+|+.|+|+++.....
T Consensus        91 ~Ai~~l~g~~~~g~~l~V~~a~~~~~  116 (124)
T 2kt5_A           91 KAMKQYKGVPLDGRPMDIQLVASQID  116 (124)
T ss_dssp             HHHHHHTTEESSSCEEEEEEECCTTC
T ss_pred             HHHHHcCCCEECCcEEEEEEeCCCCC
Confidence            99999999999999999999987654

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.85  E-value=5.1e-21  Score=148.93  Aligned_cols=83  Identities=13%  Similarity=0.184  Sum_probs=78.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      .+.++|||+|||+++++++|+++|++||+|.+|.|+.|+ +++++|||||+|.+.++|++||+.||+..|+|+.|+|+++
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            467899999999999999999999999999999999999 8999999999999999999999999999999999999998


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      ....
T Consensus        84 ~~~~   87 (110)
T 3s8s_A           84 IKGQ   87 (110)
T ss_dssp             STTH
T ss_pred             CCCc
Confidence            6543

>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=99.84  E-value=1.2e-20  Score=139.54  Aligned_cols=82  Identities=20%  Similarity=0.345  Sum_probs=76.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      .+.++|||+|||+++++++|+++|++||.|.+|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+|+.|+|+++
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            467899999999999999999999999999999999997 8999999999999999999999999999999999999999


Q ss_pred             cCC
Q 022827          175 GTN  177 (291)
Q Consensus       175 ~~~  177 (291)
                      .++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            865

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=2.3e-20  Score=140.50  Aligned_cols=83  Identities=28%  Similarity=0.474  Sum_probs=79.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      .+.++|||.|||+++++++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|++++|+|+++
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            467999999999999999999999999999999999998 8999999999999999999999999999999999999998


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      .++.
T Consensus        83 ~~~~   86 (95)
T 2dnz_A           83 TERL   86 (95)
T ss_dssp             SCCC
T ss_pred             cccc
Confidence            7665

>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=99.84  E-value=2.7e-20  Score=141.23  Aligned_cols=86  Identities=23%  Similarity=0.368  Sum_probs=81.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      ...+.++|||.|||+++|+++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+++.|+|+
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (99)
T 1whw_A            4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVL   83 (99)
T ss_dssp             CCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34578999999999999999999999999999999999998 99999999999999999999999999999999999999


Q ss_pred             EecCCCC
Q 022827          173 VVGTNAE  179 (291)
Q Consensus       173 ~a~~~~~  179 (291)
                      ++.++..
T Consensus        84 ~a~~~~~   90 (99)
T 1whw_A           84 PSTIKKE   90 (99)
T ss_dssp             ECCCCST
T ss_pred             EcCCCcc
Confidence            9987753

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=3.4e-20  Score=140.83  Aligned_cols=86  Identities=16%  Similarity=0.310  Sum_probs=80.1

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827           93 SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      +...+.++|||.|||+++++++|+++|++||.|..|.|+.++ ++.+++||||+|.+.++|++||+ ||+..|+++.|+|
T Consensus         5 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V   83 (99)
T 2dgs_A            5 SSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEV   83 (99)
T ss_dssp             CCCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEE
Confidence            345678999999999999999999999999999999999998 89999999999999999999998 9999999999999


Q ss_pred             EEecCCCC
Q 022827          172 EVVGTNAE  179 (291)
Q Consensus       172 ~~a~~~~~  179 (291)
                      +++.+...
T Consensus        84 ~~a~~~~~   91 (99)
T 2dgs_A           84 KRAEPRDS   91 (99)
T ss_dssp             EECCCCCC
T ss_pred             EECCCCcc
Confidence            99987653

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.83  E-value=5.1e-21  Score=143.72  Aligned_cols=81  Identities=19%  Similarity=0.272  Sum_probs=75.4

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcC-CeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhC-CceeCCeeeEEEEe
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIG-ELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYN-NVLLDGKPMKIEVV  174 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G-~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~ln-g~~l~g~~i~V~~a  174 (291)
                      +++|||.|||+++||++|+++|++|| +|.+|.|+.++ ++.++|||||+|.+.++|++||+.++ +..|+|++|+|+++
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            47999999999999999999999999 89999999998 89999999999999999999999875 56899999999999


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      .+++
T Consensus        81 ~~~~   84 (91)
T 2lxi_A           81 DPKP   84 (91)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            8765

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=2.9e-20  Score=141.89  Aligned_cols=86  Identities=21%  Similarity=0.372  Sum_probs=80.8

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827           93 SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      ....+.++|||.|||+++++++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+++.|+|
T Consensus         7 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   86 (102)
T 1x5s_A            7 GMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRV   86 (102)
T ss_dssp             CCCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            344578999999999999999999999999999999999998 8899999999999999999999999999999999999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      +++.+..
T Consensus        87 ~~a~~~~   93 (102)
T 1x5s_A           87 DQAGKSS   93 (102)
T ss_dssp             EEEECCC
T ss_pred             EECCCCC
Confidence            9998765

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=1.4e-20  Score=143.91  Aligned_cols=86  Identities=24%  Similarity=0.336  Sum_probs=80.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827           93 SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      +...+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+++.|+|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2dnm_A            8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRV   87 (103)
T ss_dssp             SCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            345678999999999999999999999999999999999998 7999999999999999999999999999999999999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      +++....
T Consensus        88 ~~a~~~~   94 (103)
T 2dnm_A           88 QVARYGR   94 (103)
T ss_dssp             EECSSCC
T ss_pred             EECCcCC
Confidence            9998664

>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=99.83  E-value=2.9e-20  Score=145.09  Aligned_cols=84  Identities=19%  Similarity=0.323  Sum_probs=79.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ++.++|||.|||+++++++|+++|++||.|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+++.|+|+++
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  102 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK  102 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            467899999999999999999999999999999999998 8999999999999999999999999999999999999998


Q ss_pred             cCCCC
Q 022827          175 GTNAE  179 (291)
Q Consensus       175 ~~~~~  179 (291)
                      .++..
T Consensus       103 ~~~~~  107 (115)
T 2cpz_A          103 RSKND  107 (115)
T ss_dssp             CCSCC
T ss_pred             CCCCc
Confidence            87653

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=4e-20  Score=140.65  Aligned_cols=84  Identities=21%  Similarity=0.378  Sum_probs=79.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ..+.++|||.|||+++|+++|+++|++||+|..|.|+.++++.+++||||+|.+.++|++||+.||+..|+++.|+|+++
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   93 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS   93 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      .+..
T Consensus        94 ~~~~   97 (100)
T 2do4_A           94 NSGP   97 (100)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8765

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=3.3e-20  Score=141.87  Aligned_cols=84  Identities=25%  Similarity=0.375  Sum_probs=79.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ..+.++|||.|||+++++++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+++.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            3567999999999999999999999999999999999997 899999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +.+..
T Consensus        92 a~~~~   96 (103)
T 2cq0_A           92 AKPST   96 (103)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            88765

>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=99.83  E-value=1.9e-20  Score=145.05  Aligned_cols=87  Identities=29%  Similarity=0.486  Sum_probs=81.2

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeE
Q 022827           92 ISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMK  170 (291)
Q Consensus        92 ~~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~  170 (291)
                      +....+.++|||+|||+.+++++|+++|++||+|..|.|+.++ ++.++|||||+|.+.++|++||+.||+..|.|+.|+
T Consensus        20 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~   99 (108)
T 2jrs_A           20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMK   99 (108)
T ss_dssp             CCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            4455678999999999999999999999999999999999997 889999999999999999999999999999999999


Q ss_pred             EEEecCCC
Q 022827          171 IEVVGTNA  178 (291)
Q Consensus       171 V~~a~~~~  178 (291)
                      |+++.++.
T Consensus       100 V~~a~~k~  107 (108)
T 2jrs_A          100 VGHVTERT  107 (108)
T ss_dssp             EECSCSSC
T ss_pred             EEEcccCC
Confidence            99987654

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=2.9e-20  Score=141.89  Aligned_cols=85  Identities=22%  Similarity=0.309  Sum_probs=80.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ..+.++|||.|||+++++++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+++.|+|++
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            4577999999999999999999999999999999999997 899999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 022827          174 VGTNAE  179 (291)
Q Consensus       174 a~~~~~  179 (291)
                      +.+...
T Consensus        89 a~~~~~   94 (102)
T 2cqb_A           89 AKPMRI   94 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            987653

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.83  E-value=8e-20  Score=142.51  Aligned_cols=86  Identities=20%  Similarity=0.366  Sum_probs=81.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ..+.++|||.|||+++++++|+++|++||.|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+++.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4567899999999999999999999999999999999997 899999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 022827          174 VGTNAEI  180 (291)
Q Consensus       174 a~~~~~~  180 (291)
                      +.+....
T Consensus        92 a~~~~~~   98 (115)
T 2dgo_A           92 ATRKPPA   98 (115)
T ss_dssp             SSCCCCC
T ss_pred             ccCCCCC
Confidence            9877643

>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=99.83  E-value=3.9e-20  Score=141.90  Aligned_cols=85  Identities=24%  Similarity=0.349  Sum_probs=80.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      ...+.++|||.|||+++++++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+++.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   90 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   90 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            34577999999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++.+..
T Consensus        91 ~a~~~~   96 (105)
T 1x5u_A           91 KASAHN   96 (105)
T ss_dssp             ETTTTS
T ss_pred             ECCCCC
Confidence            988665

>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=99.83  E-value=6.9e-20  Score=140.49  Aligned_cols=84  Identities=20%  Similarity=0.332  Sum_probs=79.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCC---eeeEEE
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDG---KPMKIE  172 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g---~~i~V~  172 (291)
                      .+.++|||.|||+++++++|+++|++||.|..|.|+.++++.+++||||+|.+.++|++||+.||+..|.+   +.|+|+
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~   92 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVK   92 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEE
Confidence            46799999999999999999999999999999999999999999999999999999999999999999998   999999


Q ss_pred             EecCCCC
Q 022827          173 VVGTNAE  179 (291)
Q Consensus       173 ~a~~~~~  179 (291)
                      ++.+...
T Consensus        93 ~a~~~~~   99 (105)
T 2dnh_A           93 FADTDKE   99 (105)
T ss_dssp             ESCSSCC
T ss_pred             ECccCcc
Confidence            9987763

>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=99.83  E-value=6.2e-20  Score=134.55  Aligned_cols=81  Identities=21%  Similarity=0.392  Sum_probs=77.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      +++|||+|||+++++++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+|++|+|+++.+
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            3689999999999999999999999999999999997 899999999999999999999999999999999999999886


Q ss_pred             CC
Q 022827          177 NA  178 (291)
Q Consensus       177 ~~  178 (291)
                      +.
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.83  E-value=8.3e-20  Score=143.21  Aligned_cols=83  Identities=22%  Similarity=0.360  Sum_probs=79.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ...++|||+|||+++|+++|+++|++||.|..|.|+.++++.+++||||+|.+.++|++||+.||+..|+++.|+|+++.
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   84 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAK   84 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      +..
T Consensus        85 ~~~   87 (116)
T 2fy1_A           85 KPS   87 (116)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            665

>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=99.83  E-value=3.5e-20  Score=136.50  Aligned_cols=81  Identities=23%  Similarity=0.346  Sum_probs=76.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ..+.++|||+|||+++++++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+|++|+|++
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            3577999999999999999999999999999999999986 889999999999999999999999999999999999998


Q ss_pred             ec
Q 022827          174 VG  175 (291)
Q Consensus       174 a~  175 (291)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=1.4e-19  Score=140.86  Aligned_cols=84  Identities=27%  Similarity=0.446  Sum_probs=79.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ..+.++|||.|||+++++++|+++|++||.|.+|.|+.++++.+++||||+|.+.++|++||+.||+..|+++.|+|+++
T Consensus        12 ~~~~~~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           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD   91 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEc
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      ....
T Consensus        92 ~~~~   95 (114)
T 2do0_A           92 ERAL   95 (114)
T ss_dssp             SCCC
T ss_pred             ccCC
Confidence            7554

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.83  E-value=1.3e-20  Score=142.82  Aligned_cols=83  Identities=19%  Similarity=0.231  Sum_probs=76.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCC--eeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCc----eeCC
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGE--LKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNV----LLDG  166 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~--v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~----~l~g  166 (291)
                      ....-.||||.|||+++|+++|+++|++||.  |.+|.|+.|+ ++.++|||||+|.+.++|++||+.||+.    .|+|
T Consensus         5 ~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G   84 (95)
T 2lkz_A            5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG   84 (95)
T ss_dssp             SSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT
T ss_pred             cCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC
Confidence            3455689999999999999999999999995  6789999998 8999999999999999999999999986    5999


Q ss_pred             eeeEEEEecC
Q 022827          167 KPMKIEVVGT  176 (291)
Q Consensus       167 ~~i~V~~a~~  176 (291)
                      ++|.|++|+.
T Consensus        85 r~i~V~~Aks   94 (95)
T 2lkz_A           85 KTIGVDFAKS   94 (95)
T ss_dssp             EEEEEEECCC
T ss_pred             EEEEEEEccC
Confidence            9999999874

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=4.6e-20  Score=138.72  Aligned_cols=82  Identities=29%  Similarity=0.376  Sum_probs=77.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      .++.++|||.|||+++++++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|++++|+|++
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            4567899999999999999999999999999999999998 789999999999999999999999999999999999999


Q ss_pred             ecC
Q 022827          174 VGT  176 (291)
Q Consensus       174 a~~  176 (291)
                      +++
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            764

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=4e-20  Score=138.87  Aligned_cols=81  Identities=27%  Similarity=0.401  Sum_probs=77.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      .++.++|||.|||+++++++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|++++|+|++
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            4567899999999999999999999999999999999998 789999999999999999999999999999999999998


Q ss_pred             ec
Q 022827          174 VG  175 (291)
Q Consensus       174 a~  175 (291)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=4.8e-20  Score=141.62  Aligned_cols=86  Identities=28%  Similarity=0.432  Sum_probs=80.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827           93 SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      ....+.++|||+|||+++++++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus        18 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   97 (106)
T 1p27_B           18 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV   97 (106)
T ss_dssp             CCBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEE
Confidence            334567899999999999999999999999999999999998 8999999999999999999999999999999999999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      +++.++.
T Consensus        98 ~~a~~~~  104 (106)
T 1p27_B           98 DWCFVRG  104 (106)
T ss_dssp             EESEESS
T ss_pred             EeecCCC
Confidence            9987664

>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=99.82  E-value=6.5e-20  Score=141.93  Aligned_cols=86  Identities=20%  Similarity=0.382  Sum_probs=80.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhC------CceeCC
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYN------NVLLDG  166 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~ln------g~~l~g  166 (291)
                      ...+.++|||.|||+++|+++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+.||      +..|++
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            44577899999999999999999999999999999999998 89999999999999999999999999      999999


Q ss_pred             eeeEEEEecCCCC
Q 022827          167 KPMKIEVVGTNAE  179 (291)
Q Consensus       167 ~~i~V~~a~~~~~  179 (291)
                      +.|+|+++.++..
T Consensus        91 ~~l~v~~a~~~~~  103 (111)
T 1x4h_A           91 RQLKVDLAVTRDE  103 (111)
T ss_dssp             CEEEEECCCCCCC
T ss_pred             EEEEEEECCCCcc
Confidence            9999999887653

>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=99.82  E-value=4.3e-20  Score=138.97  Aligned_cols=83  Identities=24%  Similarity=0.402  Sum_probs=78.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ...+.++|||.|||+.+++++|+++|++||+|..|.|+.++++.+++||||+|.+.++|++||+.||+..|++++|+|++
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            34567899999999999999999999999999999999999889999999999999999999999999999999999998


Q ss_pred             ecC
Q 022827          174 VGT  176 (291)
Q Consensus       174 a~~  176 (291)
                      ++.
T Consensus        92 a~~   94 (95)
T 2ywk_A           92 PSS   94 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            753

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.82  E-value=6.7e-20  Score=137.11  Aligned_cols=85  Identities=22%  Similarity=0.352  Sum_probs=79.1

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           93 SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      ++..+.++|||.|||+++++++|+++|++||+|..|.|+.+ ++.+++||||+|.+.++|++||+.||+..|+++.|+|+
T Consensus         3 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~-~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   81 (92)
T 2dgv_A            3 SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVR   81 (92)
T ss_dssp             CSSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            44567899999999999999999999999999999999985 78889999999999999999999999999999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++.+..
T Consensus        82 ~a~~~~   87 (92)
T 2dgv_A           82 IDRNAS   87 (92)
T ss_dssp             ECSCCS
T ss_pred             EcCCCC
Confidence            987664

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=4.6e-20  Score=139.07  Aligned_cols=83  Identities=20%  Similarity=0.326  Sum_probs=78.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEE-EEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRY-AIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v-~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      .+.++|||.|||+++++++|+++|++||.|..| .|+.++ ++.+++||||+|.+.++|++||+.||+..|++++|+|++
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 999996 899999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +.+..
T Consensus        83 a~~~~   87 (96)
T 1x5t_A           83 AFKKD   87 (96)
T ss_dssp             SCCCC
T ss_pred             ecccC
Confidence            88665

>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=99.82  E-value=1.4e-19  Score=138.32  Aligned_cols=85  Identities=20%  Similarity=0.389  Sum_probs=78.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ...+.++|||.|||+++|+++|+++|++||.|..|.|+.++.. +++||||+|.+.++|++||+.||+..|+++.|+|++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   89 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   89 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456799999999999999999999999999999999998754 899999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 022827          174 VGTNAE  179 (291)
Q Consensus       174 a~~~~~  179 (291)
                      +.+...
T Consensus        90 a~~~~~   95 (103)
T 2cq3_A           90 ATARVM   95 (103)
T ss_dssp             CCSSCC
T ss_pred             cccCCC
Confidence            987764

>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=99.82  E-value=3.8e-20  Score=146.64  Aligned_cols=87  Identities=28%  Similarity=0.417  Sum_probs=81.3

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeE
Q 022827           92 ISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMK  170 (291)
Q Consensus        92 ~~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~  170 (291)
                      +....+.++|||.|||+++|+++|+++|++||.|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+++.|+
T Consensus        16 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   95 (126)
T 3ex7_B           16 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPIS   95 (126)
T ss_dssp             BCCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            3455678899999999999999999999999999999999998 899999999999999999999999999999999999


Q ss_pred             EEEecCCC
Q 022827          171 IEVVGTNA  178 (291)
Q Consensus       171 V~~a~~~~  178 (291)
                      |+++.+..
T Consensus        96 v~~a~~~~  103 (126)
T 3ex7_B           96 VDWCFVRG  103 (126)
T ss_dssp             EEESEESS
T ss_pred             EEEecCCC
Confidence            99998665

>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=99.82  E-value=7.8e-20  Score=138.11  Aligned_cols=83  Identities=19%  Similarity=0.313  Sum_probs=79.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ++++|||+|||+++++++|+++|++||.|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+|+.|+|+++.
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            46899999999999999999999999999999999998 89999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 022827          176 TNAE  179 (291)
Q Consensus       176 ~~~~  179 (291)
                      +...
T Consensus        81 ~~~~   84 (96)
T 2x1f_A           81 NSDI   84 (96)
T ss_dssp             CSSG
T ss_pred             CCCC
Confidence            7753

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.82  E-value=7.7e-20  Score=138.93  Aligned_cols=84  Identities=23%  Similarity=0.419  Sum_probs=78.9

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeE--------EEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCc
Q 022827           92 ISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKR--------YAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNV  162 (291)
Q Consensus        92 ~~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~--------v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~  162 (291)
                      +++..+.++|||+|||+++++++|+++|++||.|..        |.|+.++ ++.++|||||+|.+.++|++||+.||+.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~   86 (99)
T 2la6_A            7 HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   86 (99)
T ss_dssp             CCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            345567899999999999999999999999999999        9999997 8999999999999999999999999999


Q ss_pred             eeCCeeeEEEEec
Q 022827          163 LLDGKPMKIEVVG  175 (291)
Q Consensus       163 ~l~g~~i~V~~a~  175 (291)
                      .|.|+.|+|++++
T Consensus        87 ~~~g~~l~V~~A~   99 (99)
T 2la6_A           87 EFSGNPIKVSFAT   99 (99)
T ss_dssp             BSSSSBCEEEECC
T ss_pred             EeCCcEEEEEecC
Confidence            9999999999874

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=1.5e-19  Score=141.32  Aligned_cols=84  Identities=25%  Similarity=0.362  Sum_probs=78.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      ...+.++|||.|||+++|+++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+.||+ .|+++.|+|+
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~   91 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   91 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEE
Confidence            34567999999999999999999999999999999999998 899999999999999999999999998 8999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++....
T Consensus        92 ~a~~~~   97 (116)
T 2cqd_A           92 LAYLGA   97 (116)
T ss_dssp             ESTTTC
T ss_pred             EcccCC
Confidence            987654

>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=99.82  E-value=6.2e-20  Score=143.60  Aligned_cols=81  Identities=19%  Similarity=0.352  Sum_probs=75.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      ..++|||+|||+++|+++|+++|++||.|.+|.|+.++. .++|||||+|.+.++|++||+.||+..|+|+.|+|+++.+
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~-~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT-EEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCC-CCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            457899999999999999999999999999999999863 4799999999999999999999999999999999999876


Q ss_pred             CC
Q 022827          177 NA  178 (291)
Q Consensus       177 ~~  178 (291)
                      +.
T Consensus        83 ~~   84 (115)
T 4f25_A           83 RK   84 (115)
T ss_dssp             CC
T ss_pred             cc
Confidence            54

>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=99.82  E-value=1.1e-20  Score=141.22  Aligned_cols=81  Identities=19%  Similarity=0.245  Sum_probs=71.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcC--CeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIG--ELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G--~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      .+|||+|||+++|+++|+++|++||  .|.+|.|+.++ ++.++|||||+|.+.++|++||+.||+..|+|+.|+|+++.
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  99999999998 99999999999999999999999999999999999999988


Q ss_pred             CCCC
Q 022827          176 TNAE  179 (291)
Q Consensus       176 ~~~~  179 (291)
                      +.+.
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7654

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.82  E-value=9.4e-20  Score=140.09  Aligned_cols=85  Identities=26%  Similarity=0.362  Sum_probs=80.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeC-C-CCCCceEEEEEEcCHHHHHHHHHHh-CCceeCCeeeE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD-K-NGRPSGSAEVVYARRSDAFAALKRY-NNVLLDGKPMK  170 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d-~-tg~~kG~afV~F~~~~~A~~Ai~~l-ng~~l~g~~i~  170 (291)
                      ...+.++|||.|||+.+++++|+++|++||+|..|.|+.+ + ++.+++||||+|.+.++|++||+.| |+..|.++.|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            4457799999999999999999999999999999999999 5 8999999999999999999999999 99999999999


Q ss_pred             EEEecCCC
Q 022827          171 IEVVGTNA  178 (291)
Q Consensus       171 V~~a~~~~  178 (291)
                      |+++.++.
T Consensus        91 v~~a~~~~   98 (107)
T 2cph_A           91 LEWADSEV   98 (107)
T ss_dssp             EEECCCCC
T ss_pred             EEeCCCCC
Confidence            99998765

>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=99.82  E-value=7.7e-20  Score=140.44  Aligned_cols=85  Identities=19%  Similarity=0.388  Sum_probs=79.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCcee---CCeee
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLL---DGKPM  169 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l---~g~~i  169 (291)
                      ...+.++|||.|||+++++++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..+   .+++|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            34577899999999999999999999999999999999998 799999999999999999999999999987   89999


Q ss_pred             EEEEecCCC
Q 022827          170 KIEVVGTNA  178 (291)
Q Consensus       170 ~V~~a~~~~  178 (291)
                      +|+++.+..
T Consensus        89 ~v~~a~~~~   97 (106)
T 2dgp_A           89 QVKPADSES   97 (106)
T ss_dssp             EEEECCCCS
T ss_pred             EEEECCccc
Confidence            999988665

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=9e-20  Score=139.45  Aligned_cols=84  Identities=24%  Similarity=0.443  Sum_probs=79.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ..+.++|||.|||+++|+++|+++|++||.|..|.|+.+ ++.+++||||+|.+.++|++||+.||+..|.++.|+|+++
T Consensus        12 ~~~~~~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           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA   90 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            347789999999999999999999999999999999999 8899999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 022827          175 GTNAE  179 (291)
Q Consensus       175 ~~~~~  179 (291)
                      .++..
T Consensus        91 ~~~~~   95 (103)
T 2d9p_A           91 QRKEE   95 (103)
T ss_dssp             SSCCC
T ss_pred             ccccc
Confidence            87653

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=1e-19  Score=138.04  Aligned_cols=85  Identities=22%  Similarity=0.342  Sum_probs=79.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCee-EEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCee---
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELK-RYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKP---  168 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~-~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~---  168 (291)
                      ...+.++|||+|||+++++++|+++|++||+|. .|.|+.++ ++.+++||||+|.+.++|++||+.||+..|.++.   
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~   84 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAK   84 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCE
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcce
Confidence            345789999999999999999999999999999 99999998 8999999999999999999999999999999999   


Q ss_pred             -eEEEEecCCC
Q 022827          169 -MKIEVVGTNA  178 (291)
Q Consensus       169 -i~V~~a~~~~  178 (291)
                       |+|+++.+..
T Consensus        85 ~l~v~~a~~~~   95 (99)
T 2div_A           85 RFKLNYATYSG   95 (99)
T ss_dssp             ECCEEETTCCS
T ss_pred             eEEEeecCCCC
Confidence             9999987553

>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=99.81  E-value=8.8e-20  Score=141.17  Aligned_cols=87  Identities=25%  Similarity=0.412  Sum_probs=80.9

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeE
Q 022827           92 ISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMK  170 (291)
Q Consensus        92 ~~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~  170 (291)
                      +....+.++|||+|||+.+|+++|+++|++||.|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+|+.|+
T Consensus        20 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   99 (110)
T 1oo0_B           20 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ   99 (110)
T ss_dssp             BCCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            3445677899999999999999999999999999999999997 899999999999999999999999999999999999


Q ss_pred             EEEecCCC
Q 022827          171 IEVVGTNA  178 (291)
Q Consensus       171 V~~a~~~~  178 (291)
                      |+++.++.
T Consensus       100 V~~a~~~~  107 (110)
T 1oo0_B          100 VDWCFVKG  107 (110)
T ss_dssp             EEESEESS
T ss_pred             EEEcccCC
Confidence            99987654

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.81  E-value=1.6e-19  Score=138.09  Aligned_cols=83  Identities=20%  Similarity=0.350  Sum_probs=77.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      +..+.++|||.|||+++++++|+++|++|+ |..|.|+.++ ++.++|||||+|.+.++|++|| .||+..|.++.|+|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   88 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD   88 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEE
Confidence            345679999999999999999999999996 9999999998 8999999999999999999999 999999999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++.+..
T Consensus        89 ~a~~~~   94 (103)
T 2dng_A           89 IAEGRK   94 (103)
T ss_dssp             ECCCCC
T ss_pred             EecCCC
Confidence            988665

>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=99.81  E-value=1.2e-19  Score=139.04  Aligned_cols=83  Identities=19%  Similarity=0.310  Sum_probs=77.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-C-CCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-N-GRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-t-g~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      ..+.++|||.|||+++++++|+++|++|| |..|.|+.++ + +.+++||||+|.+.++|++|| .||+..|+++.|+|+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   89 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEE
Confidence            35679999999999999999999999999 9999999998 5 899999999999999999999 999999999999999


Q ss_pred             EecCCCC
Q 022827          173 VVGTNAE  179 (291)
Q Consensus       173 ~a~~~~~  179 (291)
                      ++.+...
T Consensus        90 ~a~~~~~   96 (104)
T 1wi8_A           90 VADQAQD   96 (104)
T ss_dssp             ECCCCCC
T ss_pred             EccCCCC
Confidence            9987653

>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=99.81  E-value=1.9e-19  Score=136.19  Aligned_cols=83  Identities=17%  Similarity=0.238  Sum_probs=76.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeee
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIR----ELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPM  169 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~----~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i  169 (291)
                      +....++|||+|||+++++++|+    ++|++||+|.+|.|+.++..  ++||||+|.+.++|++||+.||+..|+|+.|
T Consensus         5 ~~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l   82 (96)
T 2dgx_A            5 SSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKI   82 (96)
T ss_dssp             CCSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            34567899999999999999999    99999999999999998844  8899999999999999999999999999999


Q ss_pred             EEEEecCCC
Q 022827          170 KIEVVGTNA  178 (291)
Q Consensus       170 ~V~~a~~~~  178 (291)
                      +|+++.+..
T Consensus        83 ~V~~a~~~~   91 (96)
T 2dgx_A           83 LVSLATGAS   91 (96)
T ss_dssp             EEEECCCSS
T ss_pred             EEEEcCCCC
Confidence            999997665

>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=99.81  E-value=3.2e-19  Score=136.36  Aligned_cols=84  Identities=30%  Similarity=0.289  Sum_probs=77.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ...+.++|||.|||+++++++|+++|++||.|..|.|+.++.. +++||||+|.+.++|++||+.||+..|.++.|+|++
T Consensus        11 ~~~~~~~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           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC-CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            3457799999999999999999999999999999999998643 689999999999999999999999999999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +.+..
T Consensus        90 a~~~~   94 (103)
T 2cqi_A           90 ATTPS   94 (103)
T ss_dssp             CCCTT
T ss_pred             CCCCc
Confidence            88754

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.2e-19  Score=140.98  Aligned_cols=84  Identities=29%  Similarity=0.491  Sum_probs=79.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCee--------EEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeC
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELK--------RYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLD  165 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~--------~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~  165 (291)
                      ..+.++|||.|||+++|+++|+++|++||.|.        .|.|+.++ ++.+++||||+|.+.++|++||+.||+..|.
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            45679999999999999999999999999999        69999996 8999999999999999999999999999999


Q ss_pred             CeeeEEEEecCCC
Q 022827          166 GKPMKIEVVGTNA  178 (291)
Q Consensus       166 g~~i~V~~a~~~~  178 (291)
                      ++.|+|+++.+..
T Consensus        92 g~~l~V~~a~~~~  104 (113)
T 2cpe_A           92 GSKLKVSLARKKP  104 (113)
T ss_dssp             TEECEEECSSCCC
T ss_pred             CCEEEEEECCCCC
Confidence            9999999988765

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.81  E-value=1.9e-19  Score=145.06  Aligned_cols=85  Identities=21%  Similarity=0.296  Sum_probs=80.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      .....++|||+|||+++++++|+++|+.||+|++|.|+.++ ++.+++||||+|.+.++|++||+.||+..|.++.|+|+
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            44567899999999999999999999999999999999998 88999999999999999999999999999999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++.+..
T Consensus       118 ~a~~~~  123 (139)
T 1u6f_A          118 LAASGH  123 (139)
T ss_dssp             ESSCCC
T ss_pred             ECCCCC
Confidence            988765

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=2.8e-19  Score=133.60  Aligned_cols=83  Identities=14%  Similarity=0.178  Sum_probs=78.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      .....++|||.|||+++++++|+++|+.| .|..|.|+.+.++.++|||||+|.+.++|++||+ ||+..|.++.|+|.+
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            34567899999999999999999999999 9999999999999999999999999999999999 999999999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +.+.+
T Consensus        84 a~~~~   88 (91)
T 2dgw_A           84 EKSGP   88 (91)
T ss_dssp             ESSCC
T ss_pred             CCcCC
Confidence            98764

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.81  E-value=1.5e-19  Score=136.93  Aligned_cols=83  Identities=25%  Similarity=0.435  Sum_probs=77.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCC--C--CCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN--G--RPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~t--g--~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      .+.++|||.|||+++++++|+++|++||+|..|.|+.++.  +  .+++||||+|.+.++|++||+.||+..|+++.|+|
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            4678999999999999999999999999999999998763  3  78999999999999999999999999999999999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      +++.+..
T Consensus        83 ~~a~~~~   89 (98)
T 2cpf_A           83 RISERAT   89 (98)
T ss_dssp             ECSSCSS
T ss_pred             EEccCCC
Confidence            9987665

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=1.1e-19  Score=139.06  Aligned_cols=85  Identities=21%  Similarity=0.333  Sum_probs=79.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHh-cCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCce-eCCeeeEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSE-IGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVL-LDGKPMKI  171 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~-~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~-l~g~~i~V  171 (291)
                      ...+.++|||+|||+++|+++|+++|++ ||.|..|.|+.++++.+++||||+|.+.++|++||+.||+.. |+++.|+|
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            3457799999999999999999999999 999999999999999999999999999999999999999999 99999999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      +++.+..
T Consensus        85 ~~a~~~~   91 (104)
T 2dhg_A           85 SVAIPKA   91 (104)
T ss_dssp             CBCCCCC
T ss_pred             EEccCCC
Confidence            9987664

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.1e-19  Score=139.90  Aligned_cols=81  Identities=15%  Similarity=0.161  Sum_probs=74.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCC--ceeCCeeeEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNN--VLLDGKPMKIE  172 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng--~~l~g~~i~V~  172 (291)
                      ..+.++|||+|||+++||++|+++|++||.|++|.|+.+     +|||||+|.+.++|++||+.|++  ..|.|++|+|+
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   87 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ   87 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            357899999999999999999999999999999999976     79999999999999999998864  78999999999


Q ss_pred             EecCCCCC
Q 022827          173 VVGTNAEI  180 (291)
Q Consensus       173 ~a~~~~~~  180 (291)
                      +++++...
T Consensus        88 ~A~~~~~~   95 (105)
T 1sjq_A           88 FSNHKELK   95 (105)
T ss_dssp             CCSSSSCC
T ss_pred             EcCCCCCC
Confidence            99876543

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=1.2e-19  Score=139.31  Aligned_cols=85  Identities=24%  Similarity=0.291  Sum_probs=79.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      ...+.++|||.|||+++++++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+. |+..|+++.|+|+
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~   90 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPK   90 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEE
Confidence            34577999999999999999999999999999999999997 899999999999999999999988 9999999999999


Q ss_pred             EecCCCC
Q 022827          173 VVGTNAE  179 (291)
Q Consensus       173 ~a~~~~~  179 (291)
                      ++.++..
T Consensus        91 ~a~~~~~   97 (105)
T 2dh8_A           91 PCTPRGM   97 (105)
T ss_dssp             CSCCSSC
T ss_pred             EccCCCC
Confidence            9886653

>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=99.80  E-value=9.8e-20  Score=137.90  Aligned_cols=83  Identities=22%  Similarity=0.235  Sum_probs=77.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      .+..++|||.|||+++++++|+++|++||.|..+.++.++ ++.+++||||+|.+.++|++||+.||+..|+++.|+|++
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            3466899999999999999999999999999988787776 899999999999999999999999999999999999999


Q ss_pred             ecCC
Q 022827          174 VGTN  177 (291)
Q Consensus       174 a~~~  177 (291)
                      +...
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8754

>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=99.80  E-value=4.3e-19  Score=137.12  Aligned_cols=80  Identities=20%  Similarity=0.358  Sum_probs=74.0

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCC-----e
Q 022827           93 SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDG-----K  167 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g-----~  167 (291)
                      ++....++|||.|||+++|+++|+++|++||+|+.|.|+.+      +||||+|.+.++|++||+.||+..|++     +
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~   83 (108)
T 1x4c_A           10 PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETA   83 (108)
T ss_dssp             CCCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcce
Confidence            34456799999999999999999999999999999999876      799999999999999999999999999     9


Q ss_pred             eeEEEEecCCC
Q 022827          168 PMKIEVVGTNA  178 (291)
Q Consensus       168 ~i~V~~a~~~~  178 (291)
                      .|+|+++.++.
T Consensus        84 ~i~V~~a~~~~   94 (108)
T 1x4c_A           84 YIRVKVDGPRS   94 (108)
T ss_dssp             EEEEEESSCCS
T ss_pred             EEEEEeCCCCC
Confidence            99999988754

>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=99.80  E-value=4e-19  Score=169.38  Aligned_cols=84  Identities=24%  Similarity=0.431  Sum_probs=79.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      .+.++|||+|||+.||+++|+++|++||.|+.|.|+.++ ++.++|||||+|.+.++|++||+.||++.|+++.|+|+++
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            456899999999999999999999999999999999997 8999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 022827          175 GTNAE  179 (291)
Q Consensus       175 ~~~~~  179 (291)
                      .+...
T Consensus       180 ~~~~~  184 (437)
T 3pgw_S          180 RGRTV  184 (437)
T ss_pred             CCCCC
Confidence            86653

>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=99.80  E-value=2e-19  Score=133.20  Aligned_cols=82  Identities=27%  Similarity=0.359  Sum_probs=76.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCC-CceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGR-PSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~-~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ..++|||+|||+++|+++|+++|++||.|..|.|+.++ ++. +++||||+|.+.++|++||+.||+..|+|+.|+|+++
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            56899999999999999999999999999999999887 444 8999999999999999999999999999999999998


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7553

>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=99.80  E-value=1.2e-19  Score=145.15  Aligned_cols=85  Identities=29%  Similarity=0.377  Sum_probs=79.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      ..++.++|||.|||+++++++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|++++|+|+
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~  121 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD  121 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEES
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998 88999999999999999999999999999999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++.++.
T Consensus       122 ~a~~~~  127 (129)
T 2kxn_B          122 FSITKR  127 (129)
T ss_dssp             CCSSSS
T ss_pred             EecCCC
Confidence            987654

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.80  E-value=4.6e-20  Score=140.81  Aligned_cols=81  Identities=19%  Similarity=0.225  Sum_probs=77.1

Q ss_pred             CCcEEEEcCCCC------CCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCC-ee
Q 022827           97 VGTKLYVSNLHP------GVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDG-KP  168 (291)
Q Consensus        97 ~~~~l~V~nL~~------~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g-~~  168 (291)
                      .+++|||.|||+      ++++++|+++|++||.|.+|.|+.++ +++++|||||+|.+.++|++||+.||+..|.+ +.
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      99999999999999999999999999 79999999999999999999999999999999 99


Q ss_pred             eEEEEecCC
Q 022827          169 MKIEVVGTN  177 (291)
Q Consensus       169 i~V~~a~~~  177 (291)
                      |+|.++.+.
T Consensus        85 l~V~~a~~~   93 (100)
T 3ns6_A           85 LFLYTMKDV   93 (100)
T ss_dssp             CEEEESHHH
T ss_pred             EEEEECchh
Confidence            999998653

>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=99.80  E-value=7.5e-20  Score=137.63  Aligned_cols=80  Identities=23%  Similarity=0.256  Sum_probs=74.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ++.++|||.|||+++|+++|+++|++||.|..+.++.++ ++.+++||||+|.+.++|++||+.||+..|++++|+|+++
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            456899999999999999999999999999988888877 8899999999999999999999999999999999999987


Q ss_pred             c
Q 022827          175 G  175 (291)
Q Consensus       175 ~  175 (291)
                      .
T Consensus        93 ~   93 (95)
T 2ek1_A           93 S   93 (95)
T ss_dssp             C
T ss_pred             c
Confidence            5

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.80  E-value=1.5e-19  Score=141.60  Aligned_cols=81  Identities=20%  Similarity=0.279  Sum_probs=76.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ..+.++|||.|||+++++++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+++.|+|++
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            4567899999999999999999999999999999999997 899999999999999999999999999999999999998


Q ss_pred             ec
Q 022827          174 VG  175 (291)
Q Consensus       174 a~  175 (291)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            64

>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=99.80  E-value=3.8e-19  Score=132.03  Aligned_cols=79  Identities=27%  Similarity=0.497  Sum_probs=75.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      .++|||+|||+++++++|+++|++||.|..|.|+.++ ++.+++||||+|.+.++|++|| .||+..|+++.|+|+++.+
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            4799999999999999999999999999999999998 8999999999999999999999 9999999999999999875


Q ss_pred             C
Q 022827          177 N  177 (291)
Q Consensus       177 ~  177 (291)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.80  E-value=4.4e-19  Score=131.34  Aligned_cols=80  Identities=21%  Similarity=0.392  Sum_probs=74.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      ...+.++|||+|||+++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++||+ +++..|+|+.|.|+
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~   85 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPK   85 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEE
Confidence            34577899999999999999999999999999999999998 89999999999999999999995 58889999999998


Q ss_pred             Ee
Q 022827          173 VV  174 (291)
Q Consensus       173 ~a  174 (291)
                      +|
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>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=99.80  E-value=8e-19  Score=134.11  Aligned_cols=84  Identities=19%  Similarity=0.309  Sum_probs=77.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      ...+.++|||.|||+++++++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+  +++.|+|+.|+|+
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~   88 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCK   88 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEE
Confidence            34567899999999999999999999999999999999998 89999999999999999999997  4789999999999


Q ss_pred             EecCCCC
Q 022827          173 VVGTNAE  179 (291)
Q Consensus       173 ~a~~~~~  179 (291)
                      ++.++..
T Consensus        89 ~a~~~~~   95 (103)
T 2cqg_A           89 LPNSKQS   95 (103)
T ss_dssp             CCCTTCC
T ss_pred             ecCCCCc
Confidence            9987754

>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=99.80  E-value=5.4e-19  Score=136.54  Aligned_cols=82  Identities=21%  Similarity=0.303  Sum_probs=75.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ..+.++|||.|||+++|+++|+++|++||.|..|.|+.+  +.+++||||+|.+.++|++||+.||+..|+++.|+|+++
T Consensus        19 ~~~~~~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           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   96 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            346789999999999999999999999999999998654  457899999999999999999999999999999999998


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      .+..
T Consensus        97 ~~~~  100 (109)
T 1x4a_A           97 RSGR  100 (109)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            7654

>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=99.79  E-value=9.3e-20  Score=139.42  Aligned_cols=84  Identities=19%  Similarity=0.512  Sum_probs=79.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      .+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|.|+.|+|+++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            356899999999999999999999999999999999997 8999999999999999999999999999999999999998


Q ss_pred             cCCCC
Q 022827          175 GTNAE  179 (291)
Q Consensus       175 ~~~~~  179 (291)
                      .+...
T Consensus        86 ~~~~~   90 (104)
T 1p1t_A           86 ASEKN   90 (104)
T ss_dssp             TCTTH
T ss_pred             CCccc
Confidence            87653

>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=99.79  E-value=5.7e-19  Score=146.69  Aligned_cols=86  Identities=26%  Similarity=0.427  Sum_probs=80.1

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827           93 SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      ....+.++|||.|||+.+|+++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|.++.|.|
T Consensus        67 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  146 (165)
T 1rk8_A           67 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV  146 (165)
T ss_dssp             CCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            344567899999999999999999999999999999999997 9999999999999999999999999999999999999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      .++.+..
T Consensus       147 ~~a~~~~  153 (165)
T 1rk8_A          147 DWCFVKG  153 (165)
T ss_dssp             EESEECC
T ss_pred             EEecCCC
Confidence            9988765

>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=99.79  E-value=1.3e-18  Score=133.08  Aligned_cols=81  Identities=26%  Similarity=0.363  Sum_probs=74.4

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827           92 ISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus        92 ~~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      +....+.++|||.|||+++|+++|+++|++||.|..|.|+       ++||||+|.+.++|++||+.||+..|+++.|+|
T Consensus         5 ~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   77 (103)
T 2dgu_A            5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEI   77 (103)
T ss_dssp             CCCCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEE
Confidence            3445678999999999999999999999999999999987       559999999999999999999999999999999


Q ss_pred             EEecCCCC
Q 022827          172 EVVGTNAE  179 (291)
Q Consensus       172 ~~a~~~~~  179 (291)
                      +++.+...
T Consensus        78 ~~a~~~~~   85 (103)
T 2dgu_A           78 VFAKPPDQ   85 (103)
T ss_dssp             EECCCCCC
T ss_pred             EEcCCCcc
Confidence            99987664

>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=99.79  E-value=2.4e-19  Score=137.51  Aligned_cols=82  Identities=24%  Similarity=0.360  Sum_probs=75.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ....++|||.|||+++|++||+++|+.||. +.|.|+.+++++++|||||+|.+.++|++|| .+|+..|+++.|+|.++
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECCCCCEeeEEEEEECCHHHHHHHH-HhCCCeECCcEEEEEEC
Confidence            346689999999999999999999999995 4999999999999999999999999999999 57999999999999987


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      .+..
T Consensus        90 ~~~~   93 (102)
T 1wez_A           90 STAG   93 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=2.7e-19  Score=137.47  Aligned_cols=80  Identities=16%  Similarity=0.169  Sum_probs=75.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ...++|||+|||+++|+++|+++|++||+|.+|.|+.++.+.++|||||+|.+.++|++||+ +|+..|+|+.|.|.++.
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   87 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEch
Confidence            35689999999999999999999999999999999999889999999999999999999997 89999999999999876


Q ss_pred             C
Q 022827          176 T  176 (291)
Q Consensus       176 ~  176 (291)
                      .
T Consensus        88 ~   88 (103)
T 1s79_A           88 D   88 (103)
T ss_dssp             H
T ss_pred             H
Confidence            5

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.79  E-value=4.9e-19  Score=135.05  Aligned_cols=79  Identities=16%  Similarity=0.207  Sum_probs=72.3

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCce--eCCeeeEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVL--LDGKPMKI  171 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~--l~g~~i~V  171 (291)
                      ..+++++|||+|||+++|+++|+++|++||.|.+|.|+..     ++||||+|.+.++|++||+.||+..  |.|++|.|
T Consensus        17 ~~~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           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK-----KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEE
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEE
Confidence            3457899999999999999999999999999999999854     7999999999999999999998764  88999999


Q ss_pred             EEecCC
Q 022827          172 EVVGTN  177 (291)
Q Consensus       172 ~~a~~~  177 (291)
                      ++++.+
T Consensus        92 ~~S~~k   97 (100)
T 3r27_A           92 NYSTSQ   97 (100)
T ss_dssp             EECSCS
T ss_pred             Eecccc
Confidence            998765

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.79  E-value=5.7e-19  Score=145.67  Aligned_cols=81  Identities=20%  Similarity=0.334  Sum_probs=76.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcC--CeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIG--ELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G--~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ..++|||+|||+++|+++|+++|+.||  .|..|.|+.|+ ++.++|||||+|.+.++|++||+.||+..|+|+.|+|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            568999999999999999999999999  99999999998 999999999999999999999999999999999999999


Q ss_pred             ecCC
Q 022827          174 VGTN  177 (291)
Q Consensus       174 a~~~  177 (291)
                      +.+.
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            8754

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=9.4e-19  Score=130.55  Aligned_cols=79  Identities=24%  Similarity=0.348  Sum_probs=73.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           93 SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      ++..+.++|||+|||+++|+++|+++|++||+|..|.|+       ++||||+|.+.++|++||+.||+..|+++.|+|+
T Consensus         3 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   75 (90)
T 2dnq_A            3 SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVE   75 (90)
T ss_dssp             SCSSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEE
Confidence            345678999999999999999999999999999999998       6799999999999999999999999999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++.+..
T Consensus        76 ~a~~~~   81 (90)
T 2dnq_A           76 ASKNKS   81 (90)
T ss_dssp             CSSCCC
T ss_pred             ECCCCC
Confidence            988765

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.79  E-value=4.6e-19  Score=131.32  Aligned_cols=74  Identities=23%  Similarity=0.262  Sum_probs=70.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      .+..|||+||++.+||++|+++|.+||+|+++.|..     ++|||||+|.++++|++||+.||+++|.+++|+|+++.
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            568999999999999999999999999999999976     49999999999999999999999999999999999984

>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=99.78  E-value=4.7e-19  Score=136.08  Aligned_cols=83  Identities=20%  Similarity=0.257  Sum_probs=76.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKR-YAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~-v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ....++|||.|||+++|+++|+++|+.||.|.. |.|+.+.+++++|||||+|.++++|++||+. |+..|.++.|+|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEE
Confidence            346789999999999999999999999999997 8888888999999999999999999999987 99999999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +....
T Consensus        91 ~~~~~   95 (104)
T 1wg5_A           91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            87543

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=8.2e-20  Score=134.72  Aligned_cols=79  Identities=22%  Similarity=0.273  Sum_probs=74.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      .+.++|||+|||+++++++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+++.|+|.+.
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            577999999999999999999999999999999999997 8999999999999999999999999999999999887654

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.78  E-value=6.2e-19  Score=136.65  Aligned_cols=84  Identities=23%  Similarity=0.313  Sum_probs=75.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ..+.++|||+|||+++|+++|+++|+.||.|..|.|+.++ ++.++|||||+|.+.++|++||+.++ ..|+|+.|+|++
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~-~~l~g~~l~V~~  100 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKV  100 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSC-EEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCC-CcCCCEEEEEEE
Confidence            3467899999999999999999999999999999999998 89999999999999999999998764 999999999999


Q ss_pred             ecCCCC
Q 022827          174 VGTNAE  179 (291)
Q Consensus       174 a~~~~~  179 (291)
                      +.+...
T Consensus       101 a~~~~~  106 (109)
T 2rs2_A          101 AFPRRA  106 (109)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            987654

>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=99.78  E-value=7.6e-19  Score=135.52  Aligned_cols=84  Identities=14%  Similarity=0.196  Sum_probs=77.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEe-eCC-CCCCceEEEEEEcCHHHHHHHHHHhC--CceeCCeeeE
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGE-LKRYAIH-FDK-NGRPSGSAEVVYARRSDAFAALKRYN--NVLLDGKPMK  170 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~-v~~v~i~-~d~-tg~~kG~afV~F~~~~~A~~Ai~~ln--g~~l~g~~i~  170 (291)
                      .+.++|||+|||+++|+++|+++|++||. |..|.|+ .++ ++.+++||||+|.+.++|++||+.||  +..|+++.|+
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            46789999999999999999999999998 9999998 666 78999999999999999999999996  5899999999


Q ss_pred             EEEecCCCC
Q 022827          171 IEVVGTNAE  179 (291)
Q Consensus       171 V~~a~~~~~  179 (291)
                      |+++.+...
T Consensus        86 V~~a~~~~~   94 (109)
T 2dis_A           86 VDWAEPEID   94 (109)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            999987664

>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=99.78  E-value=9.7e-19  Score=132.29  Aligned_cols=79  Identities=16%  Similarity=0.267  Sum_probs=73.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeC--CeeeEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLD--GKPMKIE  172 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~--g~~i~V~  172 (291)
                      ..+.++|||.|||+++|+++|+++|++||+|..|.|+.+     ++||||+|.+.++|++||+.||+..|+  ++.|+|+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-----CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            346789999999999999999999999999999999865     789999999999999999999999999  9999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++.+++
T Consensus        89 ~a~~~~   94 (97)
T 1why_A           89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             ECCCCC
Confidence            998764

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.78  E-value=4.4e-19  Score=139.47  Aligned_cols=83  Identities=17%  Similarity=0.181  Sum_probs=77.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCC---eeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGE---LKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~---v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      ....++|||+|||+++|+++|+++|+.||.   |..|.|+.+++++++|||||+|.+.++|++||+ +|+..|+++.|+|
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   92 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV   92 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEE
Confidence            346789999999999999999999999999   899999999999999999999999999999998 9999999999999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      .++....
T Consensus        93 ~~a~~~~   99 (118)
T 2db1_A           93 FKSHRTE   99 (118)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9986543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=7.2e-19  Score=136.20  Aligned_cols=84  Identities=19%  Similarity=0.366  Sum_probs=77.5

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           93 SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      ......++|||+|||+++++++|+++|++||.|..|.|+.++. .+++||||+|.+.++|++||+.||+..|+|+.|+|+
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  102 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT-BCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC-CCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3445778999999999999999999999999999999998864 489999999999999999999999999999999999


Q ss_pred             EecCC
Q 022827          173 VVGTN  177 (291)
Q Consensus       173 ~a~~~  177 (291)
                      ++.++
T Consensus       103 ~a~~~  107 (109)
T 2err_A          103 NATAR  107 (109)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            98765

>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=99.78  E-value=1.2e-18  Score=143.20  Aligned_cols=84  Identities=25%  Similarity=0.376  Sum_probs=79.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ....++|||+|||+++|+++|+++|+.||.|..|.|+.++ ++.++|||||+|.+.++|++||+.||+..|.+++|+|++
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  146 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  146 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3567899999999999999999999999999999999998 899999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +.+..
T Consensus       147 a~~~~  151 (158)
T 2kn4_A          147 ARYGR  151 (158)
T ss_dssp             ECCSS
T ss_pred             CCCCC
Confidence            98764

>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=99.78  E-value=1.4e-18  Score=133.07  Aligned_cols=80  Identities=16%  Similarity=0.146  Sum_probs=72.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHh--CCceeCCeeeEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY--NNVLLDGKPMKIE  172 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~l--ng~~l~g~~i~V~  172 (291)
                      .+++++|||+|||+++|+++|+++|++||.|..|.|+.+     ++||||+|.+.++|++||+.|  ++..|.|++|+|+
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   86 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   86 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEE
Confidence            357789999999999999999999999999999998866     899999999999999999987  4678999999999


Q ss_pred             EecCCCC
Q 022827          173 VVGTNAE  179 (291)
Q Consensus       173 ~a~~~~~  179 (291)
                      ++..+..
T Consensus        87 ~a~~~~~   93 (101)
T 2cq1_A           87 YSNHKEL   93 (101)
T ss_dssp             ECSCSSC
T ss_pred             EcCcccC
Confidence            9987653

>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=99.78  E-value=1.1e-18  Score=134.39  Aligned_cols=79  Identities=15%  Similarity=0.154  Sum_probs=72.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCC--ceeCCeeeEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNN--VLLDGKPMKIE  172 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng--~~l~g~~i~V~  172 (291)
                      ..++++|||.|||+++++++|+++|++||.|..|.|+.+     ++||||+|.+.++|++||+.|++  ..|.|++|+|+
T Consensus        12 ~~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           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            457799999999999999999999999999999998865     79999999999999999998865  45999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++..+.
T Consensus        87 ~a~~~~   92 (104)
T 1wex_A           87 YSTSKR   92 (104)
T ss_dssp             ECSSSS
T ss_pred             EccCcc
Confidence            998665

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=2e-18  Score=129.22  Aligned_cols=79  Identities=30%  Similarity=0.415  Sum_probs=73.0

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           93 SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      +...+.++|||+|||+++++++|+++|++||.|..|.|+       ++||||+|.+.++|++||+.||+..|+++.|+|+
T Consensus         5 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   77 (92)
T 2dgt_A            5 SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-------KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQ   77 (92)
T ss_dssp             CCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC-------SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE-------CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            345677999999999999999999999999999999998       4499999999999999999999999999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++.+..
T Consensus        78 ~a~~~~   83 (92)
T 2dgt_A           78 LSTSRL   83 (92)
T ss_dssp             ESSCCC
T ss_pred             EccCCC
Confidence            998664

>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=99.78  E-value=4.1e-19  Score=136.26  Aligned_cols=78  Identities=19%  Similarity=0.238  Sum_probs=71.9

Q ss_pred             CCCcEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCC--ceeCCeeeEEE
Q 022827           96 EVGTKLYVSNLHP-GVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNN--VLLDGKPMKIE  172 (291)
Q Consensus        96 ~~~~~l~V~nL~~-~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng--~~l~g~~i~V~  172 (291)
                      +++++|||+|||+ ++|++||+++|++||.|.+|.|+.+     ++||||+|.+.++|++||+.||+  ..|.|++|.|+
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   87 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVH   87 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEE
Confidence            4789999999999 9999999999999999999999876     68999999999999999999885  46999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++....
T Consensus        88 ~a~~~~   93 (102)
T 1x4d_A           88 LSQKYK   93 (102)
T ss_dssp             EECCCT
T ss_pred             ECCCCC
Confidence            998654

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=1e-18  Score=133.01  Aligned_cols=82  Identities=24%  Similarity=0.387  Sum_probs=74.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ...+.++|||.|||+++|+++|+++|++||.|   .|+.+.++.+++||||+|.+.++|++||+.||+..|+++.|+|++
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            34567999999999999999999999999977   566667889999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +.+..
T Consensus        88 a~~~~   92 (101)
T 2fc9_A           88 QGPRG   92 (101)
T ss_dssp             CSSCC
T ss_pred             cCCCC
Confidence            88664

>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=99.78  E-value=5e-19  Score=138.13  Aligned_cols=82  Identities=20%  Similarity=0.235  Sum_probs=77.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCe-eEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGEL-KRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v-~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      .+.++|||.|||+++|+++|+++|+.||.| ..|.|+.+++++++|||||+|.+.++|++||+. |+..|+++.|.|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a   91 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVV   91 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEEC
Confidence            467899999999999999999999999999 899999999999999999999999999999976 999999999999998


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      .+..
T Consensus        92 ~~~~   95 (114)
T 2cpy_A           92 TLED   95 (114)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            7654

>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=99.78  E-value=1e-18  Score=137.64  Aligned_cols=81  Identities=15%  Similarity=0.172  Sum_probs=74.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCC--ceeCCeeeEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNN--VLLDGKPMKI  171 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng--~~l~g~~i~V  171 (291)
                      ..+++++|||+|||+++||++|+++|++||.|++|.|+.+     ++||||+|.+.++|++||+.|++  ..|.|++|+|
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-----GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            3457899999999999999999999999999999999976     79999999999999999999874  6899999999


Q ss_pred             EEecCCCC
Q 022827          172 EVVGTNAE  179 (291)
Q Consensus       172 ~~a~~~~~  179 (291)
                      ++++.+..
T Consensus       102 ~~a~~k~~  109 (119)
T 2ad9_A          102 QFSNHKEL  109 (119)
T ss_dssp             EECSSSSC
T ss_pred             EEccCCCC
Confidence            99987653

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.78  E-value=2.4e-19  Score=144.35  Aligned_cols=84  Identities=25%  Similarity=0.376  Sum_probs=79.2

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ..+.++|||+|||+++|+++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+++.|+|++
T Consensus        44 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  123 (135)
T 2lea_A           44 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  123 (135)
T ss_dssp             GGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3467899999999999999999999999999999999998 899999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +.+..
T Consensus       124 a~~~~  128 (135)
T 2lea_A          124 ARYGR  128 (135)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98664

>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=99.77  E-value=5.4e-19  Score=137.29  Aligned_cols=84  Identities=27%  Similarity=0.459  Sum_probs=77.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHH---HHHHhcCCeeEEEEeeCC-CC---CCceEEEEEEcCHHHHHHHHHHhCCceeCCe
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIR---ELFSEIGELKRYAIHFDK-NG---RPSGSAEVVYARRSDAFAALKRYNNVLLDGK  167 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~---~~F~~~G~v~~v~i~~d~-tg---~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~  167 (291)
                      ....++|||.|||+++++++|+   ++|++||+|..|.|+.++ ++   .++|||||+|.+.++|++||+.||+..|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3467899999999999999999   999999999999999887 33   5669999999999999999999999999999


Q ss_pred             eeEEEEecCCC
Q 022827          168 PMKIEVVGTNA  178 (291)
Q Consensus       168 ~i~V~~a~~~~  178 (291)
                      +|+|+++.++.
T Consensus        92 ~l~V~~a~~k~  102 (111)
T 2cpi_A           92 TLKASLGTTKY  102 (111)
T ss_dssp             EEEEESCCCCS
T ss_pred             EEEEEeccccc
Confidence            99999998765

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.1e-18  Score=136.39  Aligned_cols=81  Identities=19%  Similarity=0.285  Sum_probs=76.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      +.++|||.|||+++|+++|+++|+.||.|..|.|+.++ ++.++|||||+|.+.++|++||+. |+..|+++.|+|+++.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            45899999999999999999999999999999999997 899999999999999999999987 9999999999999988


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      ++.
T Consensus       105 ~~~  107 (116)
T 1x4b_A          105 ARE  107 (116)
T ss_dssp             SCC
T ss_pred             CCc
Confidence            765

>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=99.77  E-value=1.4e-18  Score=135.13  Aligned_cols=82  Identities=18%  Similarity=0.340  Sum_probs=76.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCcee--------CCe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLL--------DGK  167 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l--------~g~  167 (291)
                      .+.++|||.|||+++|+++|+++|+.||.|..|.|+.++++.+++||||+|.+.++|++||+.||+..|        .++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~  102 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE  102 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCC
Confidence            466899999999999999999999999999999999999999999999999999999999999999999        577


Q ss_pred             eeEEEEecCC
Q 022827          168 PMKIEVVGTN  177 (291)
Q Consensus       168 ~i~V~~a~~~  177 (291)
                      +|.|.++.+.
T Consensus       103 ~l~v~~a~p~  112 (114)
T 1x5o_A          103 PLLCKFSGPS  112 (114)
T ss_dssp             CBEEEECCCS
T ss_pred             ceeEEccCCC
Confidence            8999998743

>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=99.77  E-value=6.3e-19  Score=137.26  Aligned_cols=81  Identities=19%  Similarity=0.324  Sum_probs=76.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ..++|||.|||+++++++|+++|++||.|..|.|+.++ ++.+++||||+|.+.++|++|| .||+..|+++.|+|+++.
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  102 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecC
Confidence            45899999999999999999999999999999999998 7999999999999999999999 999999999999999987


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      +..
T Consensus       103 ~~~  105 (114)
T 2cq4_A          103 AEK  105 (114)
T ss_dssp             HHH
T ss_pred             CCc
Confidence            543

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.77  E-value=4e-19  Score=127.88  Aligned_cols=74  Identities=19%  Similarity=0.319  Sum_probs=70.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827          100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus       100 ~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      +|||+|||+++++++|+++|++||+|..|.|+.++ ++.++|||||+|.+.++|++|++ +|+..|+|+.|.|++|
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            59999999999999999999999999999999998 89999999999999999999996 9999999999999874

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.77  E-value=3.3e-19  Score=142.56  Aligned_cols=83  Identities=20%  Similarity=0.243  Sum_probs=78.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeE--EEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCc----eeCCe
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKR--YAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNV----LLDGK  167 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~--v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~----~l~g~  167 (291)
                      ..+.++|||+|||+++|+++|+++|++||.|..  |.|+.|+ +++++|||||+|.+. +|++||+.||+.    .|+|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            356789999999999999999999999999976  9999999 999999999999999 999999999999    99999


Q ss_pred             eeEEEEecCCC
Q 022827          168 PMKIEVVGTNA  178 (291)
Q Consensus       168 ~i~V~~a~~~~  178 (291)
                      .|+|+++.+..
T Consensus        99 ~l~V~~a~~~~  109 (131)
T 2m2b_A           99 TINVEFAKGSK  109 (131)
T ss_dssp             CCCCEECCCSC
T ss_pred             EEEEEECCCCC
Confidence            99999997654

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.77  E-value=1.6e-18  Score=138.15  Aligned_cols=84  Identities=21%  Similarity=0.384  Sum_probs=75.8

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCee
Q 022827           93 SGIEVGTKLYVSNLHPGVTNDDIR----ELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKP  168 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~~~te~dL~----~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~  168 (291)
                      +..++.++|||+|||+.+++++|+    ++|++||+|.+|.|.  .++.++|||||+|.+.++|++||+.||+..|.|++
T Consensus        24 ~~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~--~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~  101 (127)
T 2a3j_A           24 PHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD--LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNP  101 (127)
T ss_dssp             CCCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC--CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec--cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCE
Confidence            445678999999999999999876    699999999988774  46788999999999999999999999999999999


Q ss_pred             eEEEEecCCC
Q 022827          169 MKIEVVGTNA  178 (291)
Q Consensus       169 i~V~~a~~~~  178 (291)
                      |+|+++..+.
T Consensus       102 l~V~~a~~~~  111 (127)
T 2a3j_A          102 LVITFSETPQ  111 (127)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEEccCcc
Confidence            9999998765

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.77  E-value=1e-18  Score=136.09  Aligned_cols=81  Identities=19%  Similarity=0.259  Sum_probs=72.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcC-CeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIG-ELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G-~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ....++|||+|||+++++++|+++|++|| +|..|.|..+   .++|||||+|.+.++|++||+.||+..|+|+.|+|++
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~---~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~  101 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR---DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVER  101 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC---SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC---CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            44678999999999999999999999999 8999988643   4789999999999999999999999999999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +...+
T Consensus       102 a~~~p  106 (111)
T 2jvr_A          102 DDNPP  106 (111)
T ss_dssp             SCC--
T ss_pred             CCCCC
Confidence            87543

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=7.2e-19  Score=136.53  Aligned_cols=79  Identities=19%  Similarity=0.325  Sum_probs=74.0

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      ..++|||.|||+++|++||+++|+.| .|..|.|+.+++++++|||||+|.+.++|++|| .+|+..|.++.|.|..+..
T Consensus        15 ~~~~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           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            45799999999999999999999999 899999999999999999999999999999999 7999999999999988764


Q ss_pred             C
Q 022827          177 N  177 (291)
Q Consensus       177 ~  177 (291)
                      .
T Consensus        93 ~   93 (109)
T 2dnn_A           93 R   93 (109)
T ss_dssp             H
T ss_pred             c
Confidence            3

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.77  E-value=6.5e-19  Score=142.07  Aligned_cols=82  Identities=17%  Similarity=0.177  Sum_probs=76.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCC---eeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGE---LKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~---v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      ....++|||+|||+++|+++|+++|+.||.   |..|.|+.++.++++|||||+|.+.++|++||+ ||+..|+++.|+|
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V  119 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEV  119 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEE
Confidence            346789999999999999999999999999   889999999999999999999999999999998 9999999999999


Q ss_pred             EEecCC
Q 022827          172 EVVGTN  177 (291)
Q Consensus       172 ~~a~~~  177 (291)
                      .++...
T Consensus       120 ~~a~~~  125 (136)
T 2hgl_A          120 FKSHRT  125 (136)
T ss_dssp             EECCHH
T ss_pred             EECChH
Confidence            987643

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.77  E-value=1.6e-18  Score=139.33  Aligned_cols=80  Identities=24%  Similarity=0.355  Sum_probs=75.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ..+.++|||+|||+.+++++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+|+.|+|++
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  139 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL  139 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            3467899999999999999999999999999999999997 899999999999999999999999999999999999997


Q ss_pred             e
Q 022827          174 V  174 (291)
Q Consensus       174 a  174 (291)
                      |
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            5

>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=99.77  E-value=3.3e-19  Score=135.91  Aligned_cols=84  Identities=17%  Similarity=0.260  Sum_probs=74.6

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC--CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeE
Q 022827           93 SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK--NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMK  170 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~--tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~  170 (291)
                      ......++|||+|||+++++++|+++|++|| |.+|.|+.++  +++++|||||+|.+.++|++|| .||+..|+|+.|+
T Consensus        14 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~   91 (100)
T 2j76_E           14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIR   91 (100)
T ss_dssp             ------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEE
Confidence            3446779999999999999999999999999 9999999987  7999999999999999999999 9999999999999


Q ss_pred             EEEecCCC
Q 022827          171 IEVVGTNA  178 (291)
Q Consensus       171 V~~a~~~~  178 (291)
                      |+++.+..
T Consensus        92 V~~a~~~~   99 (100)
T 2j76_E           92 VDVADQAQ   99 (100)
T ss_dssp             CEECCCSC
T ss_pred             EEeccCCC
Confidence            99987653

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.77  E-value=1.4e-18  Score=137.20  Aligned_cols=81  Identities=31%  Similarity=0.492  Sum_probs=76.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ..++|||+|||+++|+++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++|| .||+..|+|+.|+|+++.
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            35899999999999999999999999999999999997 8999999999999999999999 899999999999999987


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      +..
T Consensus       114 ~~~  116 (124)
T 2jwn_A          114 TNM  116 (124)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.77  E-value=2.2e-19  Score=133.79  Aligned_cols=80  Identities=23%  Similarity=0.441  Sum_probs=73.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecCC
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTN  177 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~~  177 (291)
                      ++|||+|||+++++++|+++|++||+|..|.|+.++ ++.+++||||+|.+.+ |++|++.||+..|+|+.|+|+++.+.
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            589999999999999999999999999999999998 7999999999999999 99999999999999999999999876


Q ss_pred             CC
Q 022827          178 AE  179 (291)
Q Consensus       178 ~~  179 (291)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            53

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.77  E-value=3.2e-19  Score=128.83  Aligned_cols=75  Identities=24%  Similarity=0.368  Sum_probs=72.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ++|||+|||+++++++|+++|++||+|..|.|+.++ ++.++|||||+|.+.++|++|++.++ ..|+|+.|+|+++
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            579999999999999999999999999999999998 89999999999999999999999999 9999999999986

>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=99.77  E-value=1.9e-18  Score=127.27  Aligned_cols=78  Identities=23%  Similarity=0.372  Sum_probs=72.3

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHh-CCceeCCeeeEE
Q 022827           93 SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY-NNVLLDGKPMKI  171 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~l-ng~~l~g~~i~V  171 (291)
                      +...+.++|||+|||+++++++|+++|++||.|..|.|+.+     ++||||+|.+.++|++||+.| |+..|+|++|+|
T Consensus         7 ~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~-----kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v   81 (85)
T 2ytc_A            7 GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV   81 (85)
T ss_dssp             CSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCE
T ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC-----CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEE
Confidence            44567789999999999999999999999999999999975     799999999999999999989 999999999999


Q ss_pred             EEec
Q 022827          172 EVVG  175 (291)
Q Consensus       172 ~~a~  175 (291)
                      ++++
T Consensus        82 ~~ak   85 (85)
T 2ytc_A           82 KWGR   85 (85)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9874

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=2.9e-18  Score=127.86  Aligned_cols=78  Identities=23%  Similarity=0.339  Sum_probs=72.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ...+.++|||+|||+++|+++|+++|++||.|..|.|+       ++||||+|.+.++|++||+.||+..|+++.|+|++
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   77 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34577899999999999999999999999999999998       34999999999999999999999999999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +.+..
T Consensus        78 a~~~~   82 (90)
T 2dnp_A           78 STKGQ   82 (90)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            88664

>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=99.77  E-value=4.4e-19  Score=138.17  Aligned_cols=85  Identities=33%  Similarity=0.426  Sum_probs=74.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ..+.++|||.|||+++|+++|+++|++||.|..|.+..+. ++.+++||||+|.+.++|++||+.||+..|+++.|+|++
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3567999999999999999999999999999533222222 788899999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 022827          174 VGTNAE  179 (291)
Q Consensus       174 a~~~~~  179 (291)
                      +.+...
T Consensus       102 a~~~~~  107 (115)
T 2cpx_A          102 GKNKKQ  107 (115)
T ss_dssp             CCCCSC
T ss_pred             ccCCCC
Confidence            987653

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.77  E-value=7.4e-19  Score=135.19  Aligned_cols=83  Identities=18%  Similarity=0.297  Sum_probs=75.7

Q ss_pred             CCCCCcEEEEcCCCCCC------CHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCe
Q 022827           94 GIEVGTKLYVSNLHPGV------TNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGK  167 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~------te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~  167 (291)
                      .....++|||+|||+.+      |+++|+++|++||.|..|.|+ ..++.++|||||+|.+.++|++||+.||+..|+|+
T Consensus        11 ~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~   89 (105)
T 2nlw_A           11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   89 (105)
T ss_dssp             CCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTT
T ss_pred             CCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            34457899999999999      789999999999999999988 45889999999999999999999999999999998


Q ss_pred             -eeEEEEecCC
Q 022827          168 -PMKIEVVGTN  177 (291)
Q Consensus       168 -~i~V~~a~~~  177 (291)
                       +|+|+++...
T Consensus        90 ~~l~V~~a~~~  100 (105)
T 2nlw_A           90 HTFRVNLFTDF  100 (105)
T ss_dssp             CEEEEECSCCC
T ss_pred             ceEEEEEcchH
Confidence             9999998654

>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=99.77  E-value=6.3e-19  Score=140.26  Aligned_cols=99  Identities=17%  Similarity=0.204  Sum_probs=74.5

Q ss_pred             CCCCchhhhhhhhhc-----CCCCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCee--EEEEeeCCCCCCceEEEEEEcC
Q 022827           76 FPWQHDLFEDSLRAA-----GISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELK--RYAIHFDKNGRPSGSAEVVYAR  148 (291)
Q Consensus        76 ~~~~~d~~~~~~~~~-----~~~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~--~v~i~~d~tg~~kG~afV~F~~  148 (291)
                      ..|+++++.......     ........++|||+|||+++|+++|+++|+.| .|+  .|.|+.+++++++|||||+|.+
T Consensus        15 ~~~~~~~~s~~g~~~~~~g~~~~~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~   93 (126)
T 2hgm_A           15 VPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFAS   93 (126)
T ss_dssp             --------------------CTTCSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESS
T ss_pred             cccccccccccCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECC
Confidence            457777665443211     12334567899999999999999999999999 677  8999999999999999999999


Q ss_pred             HHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827          149 RSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus       149 ~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      .++|++||+. ++..|+++.|.|.++..
T Consensus        94 ~e~A~~Al~~-~~~~l~gR~I~V~~a~~  120 (126)
T 2hgm_A           94 QELAEKALGK-HKERIGHRYIEVFKSSQ  120 (126)
T ss_dssp             TTHHHHHHTT-TTCCBTTBCCCCEEECH
T ss_pred             HHHHHHHHHH-CCCEECCEEEEEEECCH
Confidence            9999999975 77999999999998754

>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=99.76  E-value=1.9e-18  Score=131.13  Aligned_cols=79  Identities=28%  Similarity=0.444  Sum_probs=74.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ..+.++|||.|||+.+|+++|+++|++||+|..|.|+.+     ++||||+|.+.++|++||+.||+..|+++.|+|+++
T Consensus        12 ~~~~~~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           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA   86 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEc
Confidence            356789999999999999999999999999999999865     799999999999999999999999999999999998


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      .+..
T Consensus        87 ~~~~   90 (99)
T 2cpj_A           87 CHSA   90 (99)
T ss_dssp             SCCS
T ss_pred             CCCC
Confidence            8765

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=2.6e-18  Score=130.96  Aligned_cols=82  Identities=22%  Similarity=0.311  Sum_probs=74.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      ...+.++|||.|||+++|+++|+++|+.|   ..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+++.|+|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLD   87 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            34577999999999999999999999977   367788887 89999999999999999999999999999999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++.++.
T Consensus        88 ~a~~~~   93 (102)
T 2fc8_A           88 WAKPKG   93 (102)
T ss_dssp             ECCCCC
T ss_pred             EecCCC
Confidence            998664

>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=99.76  E-value=3.4e-18  Score=132.07  Aligned_cols=79  Identities=18%  Similarity=0.307  Sum_probs=74.5

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ...++|||+|||+.+++++|+++|++||.|..|.|+.+     ++||||+|.+.++|++||+.||+..|+|+.|+|+++.
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   97 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   97 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecC
Confidence            46789999999999999999999999999999999977     7899999999999999999999999999999999998


Q ss_pred             CCCC
Q 022827          176 TNAE  179 (291)
Q Consensus       176 ~~~~  179 (291)
                      +...
T Consensus        98 ~~~~  101 (109)
T 1x4g_A           98 ESPD  101 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            7653

>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=99.76  E-value=4.3e-19  Score=140.51  Aligned_cols=82  Identities=17%  Similarity=0.285  Sum_probs=74.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee-CCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHF-DKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~-d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ...++|||.|||+++|+++|+++|+.||.|..+.++. +.+++++|||||+|.+.++|++||+ ||+..|+++.|.|.++
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            4668999999999999999999999999998844444 4499999999999999999999998 9999999999999998


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      ..+.
T Consensus       102 ~~~~  105 (124)
T 1wel_A          102 TKKG  105 (124)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            7654

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=3.1e-18  Score=129.58  Aligned_cols=80  Identities=16%  Similarity=0.331  Sum_probs=72.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      .+..++|||+|||+++|+++|+++|++||.|. +.|+.+   .+++||||+|.+.++|++||+.||+..|+|+.|+|+++
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~---~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ---GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC---CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            34678999999999999999999999999997 666654   57899999999999999999999999999999999998


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      .++.
T Consensus        92 ~~~~   95 (97)
T 2e5j_A           92 RQQR   95 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8654

>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=99.76  E-value=2.2e-18  Score=129.25  Aligned_cols=79  Identities=34%  Similarity=0.454  Sum_probs=70.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCC-ceeCCeeeEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGE-LKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNN-VLLDGKPMKI  171 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~-v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng-~~l~g~~i~V  171 (291)
                      ...+.++|||+|||+++|+++|+++|++||. |..+.|.      +++||||+|.+.++|++||+.||+ ..|+++.|+|
T Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v   77 (93)
T 2cqh_A            4 GSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEV   77 (93)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEE
Confidence            3457789999999999999999999999999 6655553      378999999999999999999999 9999999999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      +++.++.
T Consensus        78 ~~a~~~~   84 (93)
T 2cqh_A           78 DYSVSKK   84 (93)
T ss_dssp             EECCCCC
T ss_pred             EEccCcc
Confidence            9998765

>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=99.75  E-value=1.3e-18  Score=131.33  Aligned_cols=84  Identities=23%  Similarity=0.426  Sum_probs=75.5

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeee
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIR----ELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPM  169 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~----~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i  169 (291)
                      ..++.++|||+|||+++++++|+    ++|++||.|..|.|+.  ++.+++||||+|.+.++|++|++.||+..|.|+.|
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc--CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            34678999999999999999999    9999999999998873  46678999999999999999999999999999999


Q ss_pred             EEEEecCCCC
Q 022827          170 KIEVVGTNAE  179 (291)
Q Consensus       170 ~V~~a~~~~~  179 (291)
                      +|+++.+...
T Consensus        82 ~v~~a~~~~~   91 (97)
T 1nu4_A           82 RIQYAKTDSD   91 (97)
T ss_dssp             EEEECSSCCT
T ss_pred             EEEEccCCCc
Confidence            9999987653

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=9.5e-18  Score=127.27  Aligned_cols=78  Identities=28%  Similarity=0.419  Sum_probs=71.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhc--CCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEI--GELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~--G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      ...+.++|||.|||+++|+++|+++|++|  |.|..|.+.       ++||||+|.+.++|++||+.||+..|+++.|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            34577999999999999999999999999  999988876       679999999999999999999999999999999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      +++.+..
T Consensus        84 ~~a~~~~   90 (99)
T 2cpd_A           84 TLAKPVD   90 (99)
T ss_dssp             ECCCCCC
T ss_pred             EECCCCC
Confidence            9988664

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.75  E-value=4e-19  Score=135.35  Aligned_cols=81  Identities=19%  Similarity=0.222  Sum_probs=74.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      .+.++|||+|||+++|+++|+++|++||.|.. .++.+. ++.++|||||+|.+.++|++||+ ||+..|.++.|+|+++
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            46789999999999999999999999999987 555565 78999999999999999999998 9999999999999998


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      .+..
T Consensus        93 ~~~~   96 (101)
T 1fj7_A           93 KGRD   96 (101)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8665

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.75  E-value=2.5e-18  Score=130.86  Aligned_cols=76  Identities=26%  Similarity=0.396  Sum_probs=72.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecCCC
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNA  178 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~~~  178 (291)
                      ++|||+|||+++|+++|+++|++||+|..|.|+.+    +++||||+|.+.++|++||+.||+..|+++.|+|+++.+..
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   76 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMP   76 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCC
Confidence            58999999999999999999999999999999877    68999999999999999999999999999999999998765

>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=99.75  E-value=9.5e-18  Score=127.19  Aligned_cols=78  Identities=21%  Similarity=0.367  Sum_probs=71.6

Q ss_pred             CCCCCCcEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827           93 SGIEVGTKLYVSNLHP-GVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~-~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      ...++.++|||+|||+ ++++++|+++|++||.|..|.|.       ++||||+|.+.++|++||+.||+..|+|+.|+|
T Consensus        17 ~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   89 (97)
T 2xnq_A           17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL   89 (97)
T ss_dssp             --CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            3456789999999998 99999999999999999999884       789999999999999999999999999999999


Q ss_pred             EEecCC
Q 022827          172 EVVGTN  177 (291)
Q Consensus       172 ~~a~~~  177 (291)
                      +++...
T Consensus        90 ~~a~~~   95 (97)
T 2xnq_A           90 EVSSSN   95 (97)
T ss_dssp             EECCCC
T ss_pred             EecCCC
Confidence            998765

>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=99.75  E-value=2.7e-18  Score=134.32  Aligned_cols=75  Identities=21%  Similarity=0.388  Sum_probs=65.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCee-----e
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKP-----M  169 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~-----i  169 (291)
                      ....++|||.|||+++|+++|+++|++||+|+.|.|+.+      +||||+|.+.++|++||+.||+.+|+|+.     |
T Consensus        13 ~r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i   86 (115)
T 3beg_B           13 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   86 (115)
T ss_dssp             ----CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEE
Confidence            356789999999999999999999999999999999865      89999999999999999999999999998     5


Q ss_pred             EEEEec
Q 022827          170 KIEVVG  175 (291)
Q Consensus       170 ~V~~a~  175 (291)
                      +|..+.
T Consensus        87 ~v~~~~   92 (115)
T 3beg_B           87 RVKVDG   92 (115)
T ss_dssp             EEEECC
T ss_pred             EeccCC
Confidence            555444

>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=99.75  E-value=1e-18  Score=134.88  Aligned_cols=83  Identities=13%  Similarity=0.207  Sum_probs=77.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCC---eeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGE---LKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMK  170 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~---v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~  170 (291)
                      .....++|||+|||+++|+++|+++|+.||.   |..|.|+.++.++++|||||+|.+.++|++||+ +|+..|.++.|+
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            3457789999999999999999999999998   899999999899999999999999999999998 999999999999


Q ss_pred             EEEecCC
Q 022827          171 IEVVGTN  177 (291)
Q Consensus       171 V~~a~~~  177 (291)
                      |.++.+.
T Consensus        86 V~~a~~~   92 (107)
T 2lmi_A           86 VYEINNE   92 (107)
T ss_dssp             CEECCHH
T ss_pred             EEECCHH
Confidence            9998754

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.75  E-value=3.5e-18  Score=130.10  Aligned_cols=76  Identities=17%  Similarity=0.224  Sum_probs=71.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ...++|||+|||+++++++|+++|++||.|.+|.|..     +++||||+|.+.++|++||+.||+..|+|+.|+|++++
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP-----EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            4678999999999999999999999999999999983     48999999999999999999999999999999999886


Q ss_pred             C
Q 022827          176 T  176 (291)
Q Consensus       176 ~  176 (291)
                      +
T Consensus       100 ~  100 (101)
T 2la4_A          100 E  100 (101)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.75  E-value=1.6e-18  Score=126.83  Aligned_cols=73  Identities=21%  Similarity=0.348  Sum_probs=68.0

Q ss_pred             CcEEEEcCCCCCC------CHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCe-eeE
Q 022827           98 GTKLYVSNLHPGV------TNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGK-PMK  170 (291)
Q Consensus        98 ~~~l~V~nL~~~~------te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~-~i~  170 (291)
                      +++|||+|||+.+      ++++|+++|++||+|.+|.|+ ..++.++|||||+|.+.++|++||+.||+..|+|+ +|+
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            4799999999999      779999999999999999887 44889999999999999999999999999999999 887


Q ss_pred             E
Q 022827          171 I  171 (291)
Q Consensus       171 V  171 (291)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.74  E-value=4.6e-18  Score=128.46  Aligned_cols=78  Identities=22%  Similarity=0.350  Sum_probs=71.4

Q ss_pred             CCCCCcEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHP-GVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~-~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      ..++.++|||+|||+ .+++++|+++|++||.|..|.|.       ++||||+|.+.++|++||+.||+..|.++.|+|+
T Consensus         6 ~~~~~~~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            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            345789999999999 99999999999999999999985       7899999999999999999999999999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++.+..
T Consensus        79 ~a~~~~   84 (96)
T 2kvi_A           79 VSSSNA   84 (96)
T ss_dssp             EEECCC
T ss_pred             EcCcCC
Confidence            998664

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.74  E-value=6.7e-18  Score=130.64  Aligned_cols=78  Identities=22%  Similarity=0.346  Sum_probs=72.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ...+.++|||+|||+++|+++|+++|++||.|..|.|+       ++||||+|.+.++|++||+.||+..|+|+.|+|++
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   99 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY   99 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEES
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34577999999999999999999999999999999998       78999999999999999999999999999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +.+..
T Consensus       100 a~~~~  104 (108)
T 2jvo_A          100 SKLPA  104 (108)
T ss_dssp             CSCCC
T ss_pred             ecCCC
Confidence            88765

>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=99.74  E-value=3.3e-18  Score=133.26  Aligned_cols=79  Identities=20%  Similarity=0.315  Sum_probs=71.5

Q ss_pred             CCCCcEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhC--CceeCCeeeEE
Q 022827           95 IEVGTKLYVSNLHPG-VTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN--NVLLDGKPMKI  171 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~-~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~ln--g~~l~g~~i~V  171 (291)
                      ..++++|||+|||++ +|+++|+++|++||.|.+|.|+..     ++||||+|.+.++|++||+.||  ...|.|++|+|
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   96 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   96 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            346899999999998 999999999999999999999854     8999999999999999999886  46699999999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      +++....
T Consensus        97 ~~a~~~~  103 (112)
T 1x4f_A           97 DLSEKYK  103 (112)
T ss_dssp             EEECSCS
T ss_pred             EECcccc
Confidence            9997654

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=2.4e-18  Score=136.40  Aligned_cols=81  Identities=20%  Similarity=0.249  Sum_probs=74.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCe----eEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGEL----KRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v----~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      ...++|||.|||+++|++||+++|++||.|    ..|.|+.+++++++|||||+|.+.++|++||+. |+..|.++.|.|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V   99 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIEL   99 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEE
Confidence            357899999999999999999999999986    689999999999999999999999999999976 999999999999


Q ss_pred             EEecCC
Q 022827          172 EVVGTN  177 (291)
Q Consensus       172 ~~a~~~  177 (291)
                      ..+...
T Consensus       100 ~~a~~~  105 (123)
T 2dha_A          100 FRSTAA  105 (123)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            988654

>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=99.74  E-value=5.5e-18  Score=131.73  Aligned_cols=78  Identities=22%  Similarity=0.236  Sum_probs=72.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      ..++|||.|||+++++++|+++|++||.|..|.|+..     ++||||+|.+.++|++||+.||+..|++++|+|+|+..
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   83 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-----GITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSS-----SSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            4689999999999999999999999999999988753     78999999999999999999999999999999999987


Q ss_pred             CCC
Q 022827          177 NAE  179 (291)
Q Consensus       177 ~~~  179 (291)
                      ...
T Consensus        84 ~~~   86 (111)
T 1whx_A           84 GVF   86 (111)
T ss_dssp             TTT
T ss_pred             Ccc
Confidence            653

>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=99.74  E-value=7.3e-19  Score=142.29  Aligned_cols=81  Identities=23%  Similarity=0.361  Sum_probs=74.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ...++|||.|||+++|++||+++|++|| |+.|.|+++++++++|||||+|.+.++|++|| .+|+..|+++.|+|.++.
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~  121 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNS  121 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECC
Confidence            4568999999999999999999999999 77999999999999999999999999999999 889999999999999876


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      ...
T Consensus       122 ~~~  124 (139)
T 2hgn_A          122 TTG  124 (139)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            543

>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=99.74  E-value=5.5e-18  Score=137.21  Aligned_cols=87  Identities=28%  Similarity=0.372  Sum_probs=76.4

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEE------EEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCC
Q 022827           93 SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRY------AIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDG  166 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v------~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g  166 (291)
                      .+..+.++|||+|||+.+|+++|+++|++||.|..|      .|....++.++|||||+|.+.++|++||+.||+..|.|
T Consensus        40 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g  119 (143)
T 3egn_A           40 EPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFG  119 (143)
T ss_dssp             CCCSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCC
Confidence            445678999999999999999999999999999874      23333478899999999999999999999999999999


Q ss_pred             eeeEEEEecCCCC
Q 022827          167 KPMKIEVVGTNAE  179 (291)
Q Consensus       167 ~~i~V~~a~~~~~  179 (291)
                      +.|+|+++.+...
T Consensus       120 ~~l~V~~a~~~~~  132 (143)
T 3egn_A          120 KPMVVQFARSARP  132 (143)
T ss_dssp             EECEEEECCCSCC
T ss_pred             cEEEEEECCCCCC
Confidence            9999999976543

>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=99.74  E-value=1.5e-18  Score=124.78  Aligned_cols=74  Identities=19%  Similarity=0.387  Sum_probs=70.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827          100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus       100 ~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      +|||+|||+++++++|+++|++||+|..|.|+.++ ++.+++||||+|.+.++|++||+. ++..|+|+.|.|+++
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            69999999999999999999999999999999998 899999999999999999999974 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=99.74  E-value=1.1e-17  Score=144.10  Aligned_cols=85  Identities=31%  Similarity=0.370  Sum_probs=77.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      +..+.++|||+|||+++||++|+++|++||+|.+|.|+.|+ +++++|||||+|.+.++|++||+.+|+..+.++.|+|.
T Consensus        11 p~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~   90 (213)
T 4f02_A           11 PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIM   90 (213)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccc
Confidence            34567899999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++....
T Consensus        91 ~~~~~~   96 (213)
T 4f02_A           91 WSQRDP   96 (213)
T ss_dssp             ECCCCT
T ss_pred             cccccc
Confidence            887554

>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=99.74  E-value=1e-17  Score=130.52  Aligned_cols=81  Identities=22%  Similarity=0.347  Sum_probs=74.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      .++.++|||+|||+.+|+++|+++|+.||.|..|.|+.+  +.+++||||+|.+.++|++||+.||+..|+|+.|+|+++
T Consensus         5 ~~~~~~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            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            356789999999999999999999999999999999876  445899999999999999999999999999999999998


Q ss_pred             cCC
Q 022827          175 GTN  177 (291)
Q Consensus       175 ~~~  177 (291)
                      .+.
T Consensus        83 ~~~   85 (115)
T 3lqv_A           83 NAN   85 (115)
T ss_dssp             CHH
T ss_pred             cCC
Confidence            754

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.74  E-value=3.8e-18  Score=128.60  Aligned_cols=81  Identities=21%  Similarity=0.423  Sum_probs=73.1

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ...+.++|||+|||+.+++++|+++|++||.|..+    ..++.++|||||+|.+.++|++||+.||+..|+|+.|+|++
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   87 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34567899999999999999999999999988765    34778899999999999999999999999999999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +.+..
T Consensus        88 a~~~~   92 (96)
T 1fjc_A           88 TGEKG   92 (96)
T ss_dssp             CSSSC
T ss_pred             cCCCC
Confidence            87664

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.73  E-value=3.3e-18  Score=130.41  Aligned_cols=82  Identities=18%  Similarity=0.325  Sum_probs=76.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.++++.++|||||+|.+.++|++||+  ++..|+|+.|.|.++
T Consensus         6 ~~~~~~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            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            345689999999999999999999999999999999999999999999999999999999997  999999999999998


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      ....
T Consensus        84 ~~~~   87 (102)
T 2xs2_A           84 IRKQ   87 (102)
T ss_dssp             EECC
T ss_pred             CcCc
Confidence            7654

>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=99.73  E-value=1.5e-17  Score=128.61  Aligned_cols=76  Identities=25%  Similarity=0.473  Sum_probs=70.7

Q ss_pred             CCCCcEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPG-VTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~-~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ....++|||.|||++ +++++|+++|++||+|..|.|       +++||||+|.+.++|++||+.||+..|+++.|+|++
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   96 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINM   96 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            345689999999999 999999999999999999998       378999999999999999999999999999999999


Q ss_pred             ecCC
Q 022827          174 VGTN  177 (291)
Q Consensus       174 a~~~  177 (291)
                      +...
T Consensus        97 a~~~  100 (110)
T 1wf1_A           97 AGEP  100 (110)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8754

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=1.8e-17  Score=124.58  Aligned_cols=77  Identities=21%  Similarity=0.253  Sum_probs=68.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ...++|||+|||+++|+++|+++|++||.|.+|  +.++ ++.   ||||+|.+.++|++||+ ||+..|+|+.|.|+++
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            456899999999999999999999999999987  4454 554   99999999999999998 9999999999999987


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      ....
T Consensus        80 ~~~~   83 (94)
T 2e5g_A           80 EQKE   83 (94)
T ss_dssp             CCSC
T ss_pred             CcCC
Confidence            6554

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=1.5e-17  Score=125.32  Aligned_cols=82  Identities=18%  Similarity=0.310  Sum_probs=73.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEE-EEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRY-AIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v-~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      .....++|||+|||+++++++|+++|++||.|..| .|+.++.   .+.|||+|.+.++|++||+.||+..|+|+.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~---~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   87 (96)
T 2e44_A           11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNVTYSSKDQARQALDKLNGFQLENFTLKVA   87 (96)
T ss_dssp             CCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSS---SEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCC---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            33467899999999999999999999999999999 5887752   2349999999999999999999999999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++.++.
T Consensus        88 ~a~~~~   93 (96)
T 2e44_A           88 YIPDEM   93 (96)
T ss_dssp             ECCCCC
T ss_pred             EcCccc
Confidence            998763

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.57  E-value=3e-19  Score=139.61  Aligned_cols=83  Identities=24%  Similarity=0.451  Sum_probs=78.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeE--------EEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCC
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKR--------YAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDG  166 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~--------v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g  166 (291)
                      .+.++|||+|||+++++++|+++|++||.|..        |.|+.++ ++.+++||||+|.+.++|++||+.||+..|++
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            46789999999999999999999999999998        8999997 89999999999999999999999999999999


Q ss_pred             eeeEEEEecCCC
Q 022827          167 KPMKIEVVGTNA  178 (291)
Q Consensus       167 ~~i~V~~a~~~~  178 (291)
                      +.|+|+++.++.
T Consensus        85 ~~l~V~~a~~~~   96 (116)
T 2lcw_A           85 NPIKVSFATRRA   96 (116)
Confidence            999999987654

>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=99.72  E-value=1.8e-17  Score=135.23  Aligned_cols=80  Identities=23%  Similarity=0.340  Sum_probs=74.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ...+.++|||+|||+++|+++|+++|++||.|.+|.|+.+    ++|||||+|.+.++|++||+.||+..|.|++|+|++
T Consensus        69 ~~~~~~~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           69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVEL  144 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3456789999999999999999999999999999999877    589999999999999999999999999999999999


Q ss_pred             ecCC
Q 022827          174 VGTN  177 (291)
Q Consensus       174 a~~~  177 (291)
                      +.++
T Consensus       145 a~~~  148 (150)
T 2i2y_A          145 SNGE  148 (150)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8765

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=5.9e-17  Score=122.46  Aligned_cols=76  Identities=22%  Similarity=0.363  Sum_probs=70.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      .+.++|||.||  ++|+++|+++|++||+|..|.|.     .+++||||+|.+.++|++||+.||+..|+++.|+|+++.
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~   85 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD-----PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   85 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE-----TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCS
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec-----CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECC
Confidence            46789999996  89999999999999999999985     458999999999999999999999999999999999988


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      +..
T Consensus        86 ~~~   88 (97)
T 1x5p_A           86 KQP   88 (97)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            765

>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=99.72  E-value=4.6e-17  Score=133.33  Aligned_cols=82  Identities=29%  Similarity=0.427  Sum_probs=78.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      +.++|||+|||+++|+++|+++|+.||+|..|.|+.++ ++.+++||||+|.+.++|++|++.||+..+.+++|+|.++.
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            35899999999999999999999999999999999998 99999999999999999999999999999999999999987


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      +..
T Consensus        81 ~~~   83 (167)
T 1fxl_A           81 PSS   83 (167)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            654

>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=99.72  E-value=1.7e-17  Score=123.34  Aligned_cols=77  Identities=19%  Similarity=0.310  Sum_probs=71.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ...++|||+|||+++++++|+++|++| .|.+|.|.     .++|||||+|.+.++|++||+.||+..|+|++|+|+++.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            356899999999999999999999999 99999885     468999999999999999999999999999999999987


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      ...
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            654

>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=99.71  E-value=2.3e-17  Score=128.68  Aligned_cols=80  Identities=13%  Similarity=0.113  Sum_probs=71.7

Q ss_pred             CCCCCcEEEE--cCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCcee-----CC
Q 022827           94 GIEVGTKLYV--SNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLL-----DG  166 (291)
Q Consensus        94 ~~~~~~~l~V--~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l-----~g  166 (291)
                      ...+.++|||  +||++++|+++|+++|++||+|..|.|+.+     ++||||+|.+.++|++||+.||+.+|     .+
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~-----rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEEccccCCC
Confidence            3456789999  669999999999999999999999888654     78999999999999999999999988     68


Q ss_pred             eeeEEEEecCCC
Q 022827          167 KPMKIEVVGTNA  178 (291)
Q Consensus       167 ~~i~V~~a~~~~  178 (291)
                      ++|.|.++..-+
T Consensus        96 ~~l~v~~a~~~p  107 (114)
T 2cq2_A           96 ITLYLNFVEKVQ  107 (114)
T ss_dssp             EECEEEEESCCC
T ss_pred             cEEEEEecccCc
Confidence            999999987554

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=5e-17  Score=121.58  Aligned_cols=79  Identities=24%  Similarity=0.247  Sum_probs=68.8

Q ss_pred             CCCCcE-EEEcCCCCCCCHHH----HHHHHHhc-CCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCee
Q 022827           95 IEVGTK-LYVSNLHPGVTNDD----IRELFSEI-GELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKP  168 (291)
Q Consensus        95 ~~~~~~-l~V~nL~~~~te~d----L~~~F~~~-G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~  168 (291)
                      .+++.| |||.|||+.+++++    |+++|++| |+|.+|      ++   |+|||+|.+.++|++|++.||+..|.|++
T Consensus         5 ~~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            5 SSGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI------TG---CSAILRFINQDSAERAQKRMENEDVFGNR   75 (96)
T ss_dssp             CCCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSC
T ss_pred             CCCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE------ec---CEEEEEECCHHHHHHHHHHhcCCccCCce
Confidence            345555 99999999999988    55899999 599987      22   99999999999999999999999999999


Q ss_pred             eEEEEecCCCCCcc
Q 022827          169 MKIEVVGTNAEIPL  182 (291)
Q Consensus       169 i~V~~a~~~~~~~~  182 (291)
                      |+|++++.+...-.
T Consensus        76 i~v~~A~~~sd~~~   89 (96)
T 2diu_A           76 IIVSFTPKNRELCE   89 (96)
T ss_dssp             CEEESSCCSCCCCC
T ss_pred             EEEEecCCCcceeE
Confidence            99999998875433

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.71  E-value=5.9e-17  Score=138.65  Aligned_cols=84  Identities=21%  Similarity=0.405  Sum_probs=79.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ...++|||.|||+++|+++|+++|++||.|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+|+.|+|.++
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            356899999999999999999999999999999999997 8999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 022827          175 GTNAE  179 (291)
Q Consensus       175 ~~~~~  179 (291)
                      .+.+.
T Consensus       203 ~~~~~  207 (216)
T 2qfj_A          203 VTPPM  207 (216)
T ss_dssp             SSCSS
T ss_pred             cCCCC
Confidence            87753

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.71  E-value=7.9e-17  Score=131.81  Aligned_cols=82  Identities=21%  Similarity=0.392  Sum_probs=77.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      ...+.++|||.|||+.+|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|++.||+..|+|++|+|+
T Consensus        83 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  162 (166)
T 3md3_A           83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN  162 (166)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Confidence            44567899999999999999999999999999999999997 89999999999999999999999999999999999999


Q ss_pred             Eec
Q 022827          173 VVG  175 (291)
Q Consensus       173 ~a~  175 (291)
                      +++
T Consensus       163 ~a~  165 (166)
T 3md3_A          163 WAA  165 (166)
T ss_dssp             ESC
T ss_pred             ecC
Confidence            985

>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=99.71  E-value=6e-17  Score=133.93  Aligned_cols=80  Identities=19%  Similarity=0.173  Sum_probs=71.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCC--eeeEEEE
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDG--KPMKIEV  173 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g--~~i~V~~  173 (291)
                      ....+|||.||++.+|+++|+++|++||+|++|.|....   +++||||+|.+.++|++|++.||+..|.+  +.|+|++
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~---~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~  120 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  120 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS---SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEE
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC---CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEE
Confidence            445679999999999999999999999999999987542   57899999999999999999999999965  9999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +++..
T Consensus       121 Ak~~~  125 (164)
T 1sjr_A          121 SKLTS  125 (164)
T ss_dssp             CSSSS
T ss_pred             ecCCc
Confidence            98764

>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=99.70  E-value=4.9e-17  Score=133.60  Aligned_cols=82  Identities=26%  Similarity=0.352  Sum_probs=78.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      +.++|||+|||+++++++|+++|++||+|.+|.|+.++ ++.++|||||+|.+.++|++|++.||+..|.++.|+|.++.
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            56899999999999999999999999999999999997 89999999999999999999999999999999999999988


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      +..
T Consensus        82 ~~~   84 (168)
T 1b7f_A           82 PGG   84 (168)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            655

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.70  E-value=3.1e-17  Score=129.51  Aligned_cols=78  Identities=18%  Similarity=0.314  Sum_probs=71.2

Q ss_pred             cEEEEcCC----CCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcC----HHH----HHHHHH--HhCCce
Q 022827           99 TKLYVSNL----HPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYAR----RSD----AFAALK--RYNNVL  163 (291)
Q Consensus        99 ~~l~V~nL----~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~----~~~----A~~Ai~--~lng~~  163 (291)
                      ++|||+||    |+.|++++|+++|++||+|.+|.++.|+ |+.++|||||+|.+    +++    |.+||+  .+|+..
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            78999999    9999999999999999999999999999 99999999999996    333    889988  789999


Q ss_pred             eCCeeeEEEEecC
Q 022827          164 LDGKPMKIEVVGT  176 (291)
Q Consensus       164 l~g~~i~V~~a~~  176 (291)
                      |+|+.|+|.+...
T Consensus        83 I~Gr~irV~ln~~   95 (136)
T 2j8a_A           83 IMGFKFEVILNKH   95 (136)
T ss_dssp             ETTEEEEEEECCT
T ss_pred             ecCcEEEEEECcc
Confidence            9999999998654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.70  E-value=7.8e-17  Score=127.71  Aligned_cols=75  Identities=21%  Similarity=0.165  Sum_probs=67.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceE-EEEEEcCHHHHHHHHHHhCCceeCC--eeeEEEEec
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGS-AEVVYARRSDAFAALKRYNNVLLDG--KPMKIEVVG  175 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~-afV~F~~~~~A~~Ai~~lng~~l~g--~~i~V~~a~  175 (291)
                      ..|||.||++.+|+++|+++|++||+|++|.|+..     .|| |||+|.+.++|++||+.||+..|.+  +.|+|++++
T Consensus        26 l~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           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR  100 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCS
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEec
Confidence            45789999999999999999999999999998653     376 9999999999999999999999987  689999988


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      +..
T Consensus       101 ~~~  103 (124)
T 2e5i_A          101 PTR  103 (124)
T ss_dssp             CSC
T ss_pred             CCc
Confidence            664

>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=99.69  E-value=6.8e-17  Score=119.22  Aligned_cols=71  Identities=21%  Similarity=0.454  Sum_probs=67.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhc----C-------CeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCcee
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEI----G-------ELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLL  164 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~----G-------~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l  164 (291)
                      .+.++|||+|||+++++++|+++|++|    |       +|.+|.+..+     ++||||+|.+.++|++|| .||+..|
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-----kg~afV~f~~~~~a~~A~-~l~g~~~   77 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAM-AFDGIIF   77 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-----SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-----CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            467899999999999999999999999    8       8999999866     899999999999999999 9999999


Q ss_pred             CCeeeEEE
Q 022827          165 DGKPMKIE  172 (291)
Q Consensus       165 ~g~~i~V~  172 (291)
                      +|+.|+|+
T Consensus        78 ~g~~l~V~   85 (87)
T 2hzc_A           78 QGQSLKIR   85 (87)
T ss_dssp             TTEECEEE
T ss_pred             CCeEEEEe
Confidence            99999997

>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=99.69  E-value=9.9e-17  Score=135.21  Aligned_cols=85  Identities=22%  Similarity=0.287  Sum_probs=77.2

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827           93 SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      ......++|||+|||+++|+++|+++|+.||+|.+|.|+.++ ++.++|||||+|.+.++|++||+. ++..|.++.|.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v   86 (196)
T 1l3k_A            8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEP   86 (196)
T ss_dssp             CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeee
Confidence            344577899999999999999999999999999999999998 899999999999999999999965 899999999999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      .++....
T Consensus        87 ~~~~~~~   93 (196)
T 1l3k_A           87 KRAVSRE   93 (196)
T ss_dssp             EECCC--
T ss_pred             ecccCcc
Confidence            9987654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.69  E-value=1.1e-16  Score=127.66  Aligned_cols=79  Identities=19%  Similarity=0.180  Sum_probs=70.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceE-EEEEEcCHHHHHHHHHHhCCceeCC--eeeEEE
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGS-AEVVYARRSDAFAALKRYNNVLLDG--KPMKIE  172 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~-afV~F~~~~~A~~Ai~~lng~~l~g--~~i~V~  172 (291)
                      ..-..|||.||++.+|+++|+++|++||+|.+|.|...    .++| |||+|.+.++|++||+.||+..|.+  +.|+|+
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~  101 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  101 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEE
Confidence            34457889999999999999999999999999988764    2677 9999999999999999999999988  899999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++++..
T Consensus       102 ~ak~~~  107 (130)
T 3zzy_A          102 FSKLTS  107 (130)
T ss_dssp             ECSCSS
T ss_pred             ecCCCc
Confidence            998653

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.69  E-value=1.3e-16  Score=130.41  Aligned_cols=80  Identities=29%  Similarity=0.363  Sum_probs=75.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecCCC
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNA  178 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~~~  178 (291)
                      ++|||+|||+++|+++|+++|++||+|.+|.|+.++++.+++||||+|.+.++|++|++.||+..|.++.|+|.++....
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            58999999999999999999999999999999999988899999999999999999999999999999999999987654

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.68  E-value=2.1e-16  Score=133.40  Aligned_cols=83  Identities=23%  Similarity=0.369  Sum_probs=79.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      .+.++|||.|||+.+++++|+++|++||.|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+|+.|+|+++
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            567899999999999999999999999999999999998 9999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      .+..
T Consensus       192 ~~~~  195 (198)
T 2yh0_A          192 SVGA  195 (198)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8764

>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=99.68  E-value=1.7e-16  Score=131.03  Aligned_cols=80  Identities=23%  Similarity=0.348  Sum_probs=76.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ...++|||.|||+.+|+++|+++|++||+|..|.|+.++ ++.++|||||+|.+.++|++|++.||+..|+|+.|.|++|
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            457899999999999999999999999999999999997 9999999999999999999999999999999999999987


Q ss_pred             c
Q 022827          175 G  175 (291)
Q Consensus       175 ~  175 (291)
                      .
T Consensus       172 s  172 (172)
T 2g4b_A          172 S  172 (172)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=1.4e-16  Score=124.10  Aligned_cols=80  Identities=23%  Similarity=0.246  Sum_probs=69.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-C---CCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-N---GRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMK  170 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-t---g~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~  170 (291)
                      ....++|||+|||+++|+++|+++|++||+|. +.++.+. +   ++++|||||+|.+.++|++||+.|+  .|+|+.|.
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~   81 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYL   81 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEE
Confidence            45679999999999999999999999999999 8888776 5   7999999999999999999999984  47888877


Q ss_pred             EEEecCC
Q 022827          171 IEVVGTN  177 (291)
Q Consensus       171 V~~a~~~  177 (291)
                      +..+...
T Consensus        82 ~~~~~~~   88 (114)
T 2dnl_A           82 CVSSPTI   88 (114)
T ss_dssp             EECCSSS
T ss_pred             eccCCCc
Confidence            7654433

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.67  E-value=1.5e-16  Score=137.01  Aligned_cols=81  Identities=19%  Similarity=0.337  Sum_probs=75.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      ..++|||.|||+.+|+++|+++|++||.|..|.|+.+.. .++|||||+|.+.++|++||+.||+..|+|++|+|.++.+
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~-~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT-EEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCC-CCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            457999999999999999999999999999999998863 3699999999999999999999999999999999999876


Q ss_pred             CC
Q 022827          177 NA  178 (291)
Q Consensus       177 ~~  178 (291)
                      +.
T Consensus       181 ~~  182 (213)
T 4f02_A          181 RK  182 (213)
T ss_dssp             HH
T ss_pred             Cc
Confidence            53

>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=99.67  E-value=1e-16  Score=119.63  Aligned_cols=77  Identities=18%  Similarity=0.251  Sum_probs=62.8

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCc--eeCCeeeEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNV--LLDGKPMKI  171 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~--~l~g~~i~V  171 (291)
                      ...+.++|||+|||+++|+++|+++|++||.|.+|.|+.+    ++|||||+|.+.++|++    +++.  .+.++.|.|
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v   78 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHI   78 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEE
Confidence            3457799999999999999999999999999999999875    68999999999999984    3444  456999999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      .++.++.
T Consensus        79 ~~a~~k~   85 (89)
T 3d2w_A           79 SNAEPKH   85 (89)
T ss_dssp             EECC---
T ss_pred             EEcCCCC
Confidence            9987654

>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=99.67  E-value=2.1e-16  Score=135.85  Aligned_cols=78  Identities=23%  Similarity=0.253  Sum_probs=73.0

Q ss_pred             CCcEEEEcCCC-CCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLH-PGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~-~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ++++|||+||| +.+|+++|+++|++||.|.+|.|+.++    +|||||+|.+.++|++||+.||+..|.|++|+|.+++
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~----~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~   78 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSK   78 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcc
Confidence            67899999999 899999999999999999999998763    7999999999999999999999999999999999987


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      ...
T Consensus        79 ~~~   81 (205)
T 3tyt_A           79 QPA   81 (205)
T ss_dssp             CSC
T ss_pred             CCc
Confidence            554

>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=99.67  E-value=2.4e-16  Score=132.84  Aligned_cols=83  Identities=16%  Similarity=0.307  Sum_probs=74.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ...++|||.|||+++|+++|+++|+.||.|..|.|+.++ ++.++|||||+|.+.++|++||+. ++..|+|+.|.|.++
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a  180 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKA  180 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEEC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEec
Confidence            456899999999999999999999999999999999998 899999999999999999999976 899999999999999


Q ss_pred             cCCCC
Q 022827          175 GTNAE  179 (291)
Q Consensus       175 ~~~~~  179 (291)
                      .++..
T Consensus       181 ~~k~~  185 (196)
T 1l3k_A          181 LSKQE  185 (196)
T ss_dssp             C----
T ss_pred             CChhH
Confidence            87764

>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=99.67  E-value=1.2e-16  Score=131.22  Aligned_cols=80  Identities=19%  Similarity=0.332  Sum_probs=75.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      +.++|||.|||+++|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|++ +|+..|+|++|+|.++.
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecC
Confidence            45799999999999999999999999999999999997 89999999999999999999997 89999999999999987


Q ss_pred             CC
Q 022827          176 TN  177 (291)
Q Consensus       176 ~~  177 (291)
                      ++
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.66  E-value=4.2e-16  Score=128.68  Aligned_cols=80  Identities=25%  Similarity=0.393  Sum_probs=74.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeC---CeeeEEE
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLD---GKPMKIE  172 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~---g~~i~V~  172 (291)
                      ...++|||.|||+.+|+++|+++|++||.|..|.|+.++++.+++||||+|.+.++|++||+.||+..+.   +++|+|.
T Consensus        93 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~  172 (175)
T 3nmr_A           93 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK  172 (175)
T ss_dssp             GGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEE
T ss_pred             CCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEE
Confidence            3668999999999999999999999999999999999999999999999999999999999999998776   4999999


Q ss_pred             Eec
Q 022827          173 VVG  175 (291)
Q Consensus       173 ~a~  175 (291)
                      ++.
T Consensus       173 ~ad  175 (175)
T 3nmr_A          173 FAD  175 (175)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            873

>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=99.66  E-value=9.7e-17  Score=119.01  Aligned_cols=77  Identities=19%  Similarity=0.266  Sum_probs=66.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      .+.++|||+|||+++|+++|+++|++||+|.+|.|+.+    +++||||+|.+.++|++|+..  ...+.++.|+|.++.
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecC
Confidence            46799999999999999999999999999999999865    589999999999999865432  356689999999887


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      ++.
T Consensus        77 ~~~   79 (88)
T 1wf0_A           77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.66  E-value=6.3e-16  Score=126.94  Aligned_cols=80  Identities=35%  Similarity=0.601  Sum_probs=75.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCC--eeeEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDG--KPMKI  171 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g--~~i~V  171 (291)
                      ..+.++|||.|||+.+++++|+++|++||.|..|.|+.++ ++.+++||||+|.+.++|++|++.||+..|.+  ++|+|
T Consensus        86 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V  165 (168)
T 1b7f_A           86 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV  165 (168)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEE
Confidence            3467899999999999999999999999999999999998 89999999999999999999999999999988  99999


Q ss_pred             EEe
Q 022827          172 EVV  174 (291)
Q Consensus       172 ~~a  174 (291)
                      ++|
T Consensus       166 ~~A  168 (168)
T 1b7f_A          166 RLA  168 (168)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            985

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.65  E-value=3.4e-16  Score=133.88  Aligned_cols=82  Identities=26%  Similarity=0.414  Sum_probs=74.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ..++|||.|||+++|+++|+++|++||+|.+|.|+.++ ++.+++||||+|.+.++|++||+.||+..|.++.|+|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            46899999999999999999999999999999999998 89999999999999999999999999999999999998876


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      ...
T Consensus       107 ~~~  109 (216)
T 2qfj_A          107 NIG  109 (216)
T ss_dssp             CCG
T ss_pred             Ccc
Confidence            543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.65  E-value=1.3e-15  Score=117.30  Aligned_cols=81  Identities=12%  Similarity=0.083  Sum_probs=72.7

Q ss_pred             CCCcEEEEcCCCC-----CCCHHHHHHHHHhcCCeeEEEEeeCC--CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCee
Q 022827           96 EVGTKLYVSNLHP-----GVTNDDIRELFSEIGELKRYAIHFDK--NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKP  168 (291)
Q Consensus        96 ~~~~~l~V~nL~~-----~~te~dL~~~F~~~G~v~~v~i~~d~--tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~  168 (291)
                      .++++|+|.||..     +.++++|+++|++||.|.+|.|+.++  +++++|||||+|.+.++|++|++.||+..|+|+.
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            3678999999963     24789999999999999999999986  3688999999999999999999999999999999


Q ss_pred             eEEEEecC
Q 022827          169 MKIEVVGT  176 (291)
Q Consensus       169 i~V~~a~~  176 (291)
                      |.|+++..
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

>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=99.64  E-value=1e-15  Score=126.36  Aligned_cols=83  Identities=19%  Similarity=0.368  Sum_probs=74.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CC--CCceEEEEEEcCHHHHHHHHHHhCCceeC---CeeeE
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NG--RPSGSAEVVYARRSDAFAALKRYNNVLLD---GKPMK  170 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg--~~kG~afV~F~~~~~A~~Ai~~lng~~l~---g~~i~  170 (291)
                      ..++|||+|||+++|+++|+++|++||+|.+|.|+.++ ++  .+++||||+|.+.++|++||+.||+..+.   .+.|.
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            56899999999999999999999999999999999998 44  88999999999999999999999998775   67888


Q ss_pred             EEEecCCCC
Q 022827          171 IEVVGTNAE  179 (291)
Q Consensus       171 V~~a~~~~~  179 (291)
                      |.++.....
T Consensus        82 ~~~~~~~~~   90 (175)
T 3nmr_A           82 MKPADSEKN   90 (175)
T ss_dssp             EEECGGGCC
T ss_pred             Ecccccccc
Confidence            887765543

>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=99.64  E-value=8.8e-16  Score=130.80  Aligned_cols=80  Identities=16%  Similarity=0.169  Sum_probs=73.8

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      ..++|||.|||+++|+++|+++|++||+|..|.|+.+.++.++|||||+|.+.++|++||+.+ +..|+|+.|.|.++..
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            348999999999999999999999999999999999989999999999999999999999765 4699999999998765


Q ss_pred             C
Q 022827          177 N  177 (291)
Q Consensus       177 ~  177 (291)
                      -
T Consensus       187 y  187 (193)
T 2voo_A          187 Y  187 (193)
T ss_dssp             C
T ss_pred             H
Confidence            4

>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=99.63  E-value=1.3e-15  Score=124.56  Aligned_cols=79  Identities=25%  Similarity=0.407  Sum_probs=73.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCee--eEEE
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKP--MKIE  172 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~--i~V~  172 (291)
                      ...++|||.|||+.+++++|+++|++||.|..|.|+.+. ++.+++||||+|.+.++|++|++.||+..|.|+.  |+|.
T Consensus        86 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~  165 (167)
T 1fxl_A           86 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK  165 (167)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEE
Confidence            456899999999999999999999999999999999998 8999999999999999999999999999999965  7777


Q ss_pred             Ee
Q 022827          173 VV  174 (291)
Q Consensus       173 ~a  174 (291)
                      ||
T Consensus       166 ~A  167 (167)
T 1fxl_A          166 FA  167 (167)
T ss_dssp             EC
T ss_pred             eC
Confidence            64

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.63  E-value=1.4e-15  Score=135.91  Aligned_cols=83  Identities=23%  Similarity=0.426  Sum_probs=76.4

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeee
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIR----ELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPM  169 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~----~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i  169 (291)
                      ...+.++|||+|||+++|+++|+    ++|+.||.|.+|.|+.  +++++|||||+|.+.++|++||+.||+..|.++.|
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~--~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   82 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   82 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC--CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            45678999999999999999966    8999999999998875  67889999999999999999999999999999999


Q ss_pred             EEEEecCCC
Q 022827          170 KIEVVGTNA  178 (291)
Q Consensus       170 ~V~~a~~~~  178 (291)
                      +|+++....
T Consensus        83 ~v~~a~~~~   91 (282)
T 3pgw_A           83 RIQYAKTDS   91 (282)
T ss_pred             EEEEeccCc
Confidence            999997655

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.62  E-value=6.1e-16  Score=135.74  Aligned_cols=81  Identities=19%  Similarity=0.277  Sum_probs=72.0

Q ss_pred             CCCCCcEEEEcCCCCCC---------CHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCcee
Q 022827           94 GIEVGTKLYVSNLHPGV---------TNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLL  164 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~---------te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l  164 (291)
                      .....++|||+||++.+         +|++|+++|++||+|.+|.|+.+     ++||||+|.+.++|+.|+++||+..|
T Consensus       130 ~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~-----kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          130 FRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES-----KNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             -CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             cccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC-----CCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            35678899999999998         79999999999999999999965     89999999999999999999999999


Q ss_pred             ------------CCeeeEEEEecCCCC
Q 022827          165 ------------DGKPMKIEVVGTNAE  179 (291)
Q Consensus       165 ------------~g~~i~V~~a~~~~~  179 (291)
                                  .++.|.|.|+...+.
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             eccccccccccCCCCEEEEEEccCCCC
Confidence                        899999999987764

>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=99.62  E-value=9.3e-16  Score=127.15  Aligned_cols=78  Identities=22%  Similarity=0.428  Sum_probs=72.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      .+.++|||.|||+.+|+++|+++|++||.|..+    ..++.+++||||+|.+.++|++||+.||+..|+|+.|+|+++.
T Consensus        97 ~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  172 (175)
T 1fje_B           97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG  172 (175)
T ss_dssp             GGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECS
T ss_pred             ccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecC
Confidence            456899999999999999999999999988755    5588899999999999999999999999999999999999997


Q ss_pred             CC
Q 022827          176 TN  177 (291)
Q Consensus       176 ~~  177 (291)
                      ++
T Consensus       173 ~k  174 (175)
T 1fje_B          173 EK  174 (175)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>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=99.61  E-value=8.2e-16  Score=126.24  Aligned_cols=79  Identities=24%  Similarity=0.385  Sum_probs=73.1

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ++++|||+|||+++|+++|+++|++||+|.+|.|+.++ ++.++|||||+|.+.++|++||+.  ...|+|+.|.|.++.
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            46899999999999999999999999999999999997 899999999999999999999984  578999999999876


Q ss_pred             CC
Q 022827          176 TN  177 (291)
Q Consensus       176 ~~  177 (291)
                      +.
T Consensus        80 ~~   81 (167)
T 2cjk_A           80 PR   81 (167)
T ss_dssp             CH
T ss_pred             ch
Confidence            54

>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=99.61  E-value=1.5e-15  Score=132.18  Aligned_cols=80  Identities=33%  Similarity=0.417  Sum_probs=74.8

Q ss_pred             CCCCcEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHP-GVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~-~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ..++++|||+|||+ ++++++|+++|++||.|.+|.|+.++    ++||||+|.+.++|++||+.||+..|.++.|.|++
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~  106 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL  106 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEEC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            45789999999999 99999999999999999999999885    78999999999999999999999999999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +....
T Consensus       107 a~~~~  111 (229)
T 2adc_A          107 SKHQN  111 (229)
T ss_dssp             CSCCC
T ss_pred             ecCcc
Confidence            87654

>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=99.60  E-value=4e-15  Score=133.02  Aligned_cols=86  Identities=17%  Similarity=0.249  Sum_probs=80.5

Q ss_pred             CCCCCcEEEEcCCCCCC-CHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGV-TNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~-te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      .....++|||.|||+.+ |+++|+++|+.||.|..|.|+.+.++.+++||||+|.+.++|.+||+.||+..|.|++|+|.
T Consensus       180 ~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  259 (284)
T 3smz_A          180 ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVS  259 (284)
T ss_dssp             TTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             ccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEE
Confidence            34567899999999995 99999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCC
Q 022827          173 VVGTNAE  179 (291)
Q Consensus       173 ~a~~~~~  179 (291)
                      ++.+...
T Consensus       260 ~a~~~~~  266 (284)
T 3smz_A          260 FCAPGPP  266 (284)
T ss_dssp             ECCSSSC
T ss_pred             EecCCCc
Confidence            9987764

>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=99.59  E-value=3e-15  Score=134.38  Aligned_cols=83  Identities=19%  Similarity=0.338  Sum_probs=77.2

Q ss_pred             CCCCcEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeeCCC--CCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827           95 IEVGTKLYVSNLHPG-VTNDDIRELFSEIGELKRYAIHFDKN--GRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~-~te~dL~~~F~~~G~v~~v~i~~d~t--g~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      ..+.++|||.|||+. +|+++|+++|+.||.|..|.|+.+.+  +.+++||||+|.+.++|++|| .||+..|.|+.|.|
T Consensus       207 ~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V  285 (292)
T 2ghp_A          207 TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISV  285 (292)
T ss_dssp             CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEE
T ss_pred             CCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEE
Confidence            456789999999999 99999999999999999999999886  999999999999999999999 99999999999999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      .++.+++
T Consensus       286 ~~a~~k~  292 (292)
T 2ghp_A          286 SLADKKP  292 (292)
T ss_dssp             EECCCCC
T ss_pred             EEecCCC
Confidence            9998753

>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=99.59  E-value=9.9e-15  Score=113.28  Aligned_cols=80  Identities=16%  Similarity=0.376  Sum_probs=69.6

Q ss_pred             CCCcEEEEcCCCCCCC-----------HHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCcee
Q 022827           96 EVGTKLYVSNLHPGVT-----------NDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLL  164 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~t-----------e~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l  164 (291)
                      .++++|+|.||.....           +++|+++|++||+|.+|.| .++  .++|||||+|.+.++|++||+.||+..|
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~--~~~G~afV~f~~~~~A~~Ai~~lng~~~   89 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR--HPDGVASVSFRDPEEADYCIQTLDGRWF   89 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT--CTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC--CCCEEEEEEECCHHHHHHHHHHcCCCEE
Confidence            4678999999944332           5899999999999999965 554  3799999999999999999999999999


Q ss_pred             CCeeeEEEEecCCC
Q 022827          165 DGKPMKIEVVGTNA  178 (291)
Q Consensus       165 ~g~~i~V~~a~~~~  178 (291)
                      ++++|+|+++.+..
T Consensus        90 ~gr~l~v~~a~~~~  103 (112)
T 2dit_A           90 GGRQITAQAWDGTT  103 (112)
T ss_dssp             TTEECEEEECCSCC
T ss_pred             CCcEEEEEEeCCCC
Confidence            99999999987654

>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=99.58  E-value=4.5e-15  Score=127.53  Aligned_cols=78  Identities=21%  Similarity=0.261  Sum_probs=70.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCe--eEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCe----ee
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGEL--KRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGK----PM  169 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v--~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~----~i  169 (291)
                      +++++|||.|||+++|+++|+++|++||.|  .+|.|+.++ +..++||||+|.+.++|.+||..||+..|.+.    ++
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~-~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~  199 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK-SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY  199 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC-SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCE
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC-CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcce
Confidence            467899999999999999999999999999  889888776 45569999999999999999999999999887    67


Q ss_pred             EEEEe
Q 022827          170 KIEVV  174 (291)
Q Consensus       170 ~V~~a  174 (291)
                      .|+++
T Consensus       200 ~vk~~  204 (205)
T 3tyt_A          200 TLKLC  204 (205)
T ss_dssp             ECEEE
T ss_pred             EEEec
Confidence            77765

>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=99.58  E-value=7.8e-15  Score=131.01  Aligned_cols=77  Identities=18%  Similarity=0.171  Sum_probs=72.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeC-CeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLD-GKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~-g~~i~V~~  173 (291)
                      ..+.++|||.|||+.+|+++|+++|++||.|.+|.|+.++    ++||||+|.+.++|++||+.||+..|. ++.|+|+|
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~  279 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISF  279 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEE
Confidence            4567899999999999999999999999999999999764    589999999999999999999999999 99999999


Q ss_pred             ec
Q 022827          174 VG  175 (291)
Q Consensus       174 a~  175 (291)
                      ++
T Consensus       280 ak  281 (282)
T 3pgw_A          280 AK  281 (282)
T ss_pred             ec
Confidence            85

>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=99.57  E-value=1.4e-14  Score=129.39  Aligned_cols=83  Identities=20%  Similarity=0.328  Sum_probs=78.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      +..++|||.|||+.+|+++|+++|+.||.|..|.|+.++ ++.++|||||+|.+.++|.+|++.||+..|.++.|.|.++
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a  172 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT  172 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            356899999999999999999999999999999999998 8999999999999999999999999999999999999998


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      .+..
T Consensus       173 ~~~~  176 (284)
T 3smz_A          173 DAGQ  176 (284)
T ss_dssp             CGGG
T ss_pred             CCCC
Confidence            7654

>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=99.56  E-value=1.5e-15  Score=125.80  Aligned_cols=84  Identities=18%  Similarity=0.199  Sum_probs=73.2

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ...+.++|||+|||+++|+++|+++|++||.|..+.|....++.++|||||+|.+.++|++|| +||+..|.++.|+|.+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~   87 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK   87 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEec
Confidence            446789999999999999999999999999877633333347888999999999999999999 5999999999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +....
T Consensus        88 ~~~~~   92 (175)
T 1fje_B           88 PKGRD   92 (175)
T ss_dssp             CCCSS
T ss_pred             CCCcc
Confidence            87654

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.56  E-value=4.8e-15  Score=125.51  Aligned_cols=78  Identities=33%  Similarity=0.446  Sum_probs=73.1

Q ss_pred             CCcEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHP-GVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~-~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      .+++|||+|||+ .+++++|+++|++||.|.+|.|+.++    ++||||+|.+.++|++||+.||+..|.++.|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            468999999999 99999999999999999999999875    7899999999999999999999999999999999987


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      ...
T Consensus        78 ~~~   80 (198)
T 1qm9_A           78 HQN   80 (198)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            654

>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=99.55  E-value=1.3e-14  Score=128.74  Aligned_cols=79  Identities=25%  Similarity=0.392  Sum_probs=73.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ....++|||+|||+++|+++|+++|+.||.|..|.|..+     ++||||+|.+.++|++||+.||+..|.++.|.|.++
T Consensus        19 ~~~~~~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           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA   93 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeec
Confidence            356689999999999999999999999999999999755     799999999999999999999999999999999998


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      .+..
T Consensus        94 ~~~~   97 (261)
T 3sde_A           94 THGA   97 (261)
T ss_dssp             CCSS
T ss_pred             ccCC
Confidence            7643

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.55  E-value=1.3e-14  Score=122.86  Aligned_cols=79  Identities=22%  Similarity=0.326  Sum_probs=72.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcC-CeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeC-CeeeEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIG-ELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLD-GKPMKIE  172 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G-~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~-g~~i~V~  172 (291)
                      .++.++|||.|||+.+++++|+++|++|| .|..|.|+.+.    ++||||+|.+.++|++||+.||+..|. +++|+|.
T Consensus       117 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  192 (198)
T 1qm9_A          117 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  192 (198)
T ss_dssp             CCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEE
Confidence            34689999999999999999999999999 99999997643    789999999999999999999999999 9999999


Q ss_pred             EecCC
Q 022827          173 VVGTN  177 (291)
Q Consensus       173 ~a~~~  177 (291)
                      ++++.
T Consensus       193 ~a~~~  197 (198)
T 1qm9_A          193 FSKST  197 (198)
T ss_dssp             EECCC
T ss_pred             eeccc
Confidence            98764

>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=99.54  E-value=4.2e-15  Score=114.18  Aligned_cols=72  Identities=22%  Similarity=0.398  Sum_probs=64.9

Q ss_pred             EcCCCCCCCHHHHHHHH------------HhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeE
Q 022827          103 VSNLHPGVTNDDIRELF------------SEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMK  170 (291)
Q Consensus       103 V~nL~~~~te~dL~~~F------------~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~  170 (291)
                      +.+|++.+++++|+++|            ++||+|.+|.|+.+.+++++|||||+|.+.++|++|++.||+..|+|++|+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            56677777887777666            999999999999988889999999999999999999999999999999999


Q ss_pred             EEEe
Q 022827          171 IEVV  174 (291)
Q Consensus       171 V~~a  174 (291)
                      |+++
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9986

>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=99.54  E-value=2.2e-14  Score=110.33  Aligned_cols=81  Identities=15%  Similarity=0.135  Sum_probs=70.9

Q ss_pred             CCCcEEEEcCC--CCCCC--------HHHHHHHHHhcCCeeEEEEeeCCC---CCCceEEEEEEcCHHHHHHHHHHhCCc
Q 022827           96 EVGTKLYVSNL--HPGVT--------NDDIRELFSEIGELKRYAIHFDKN---GRPSGSAEVVYARRSDAFAALKRYNNV  162 (291)
Q Consensus        96 ~~~~~l~V~nL--~~~~t--------e~dL~~~F~~~G~v~~v~i~~d~t---g~~kG~afV~F~~~~~A~~Ai~~lng~  162 (291)
                      .+++.|.|.|+  |.++.        ++||+++|++||+|.+|.|+.++.   ..++|||||+|.+.++|++|++.||+.
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            36789999998  43443        368999999999999999998873   367999999999999999999999999


Q ss_pred             eeCCeeeEEEEecC
Q 022827          163 LLDGKPMKIEVVGT  176 (291)
Q Consensus       163 ~l~g~~i~V~~a~~  176 (291)
                      .|+|+.|+|+++..
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            99999999999754

>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=99.54  E-value=2.5e-14  Score=124.46  Aligned_cols=79  Identities=22%  Similarity=0.320  Sum_probs=72.5

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcC-CeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeC-CeeeEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIG-ELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLD-GKPMKIE  172 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G-~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~-g~~i~V~  172 (291)
                      ..+.++|||.|||+.+++++|+++|++|| .|..|.|+.+    .++||||+|.+.++|++||+.||+..|. ++.|+|.
T Consensus       148 ~~~~~~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          148 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  223 (229)
T ss_dssp             CCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEE
Confidence            34679999999999999999999999999 9999999653    2789999999999999999999999999 9999999


Q ss_pred             EecCC
Q 022827          173 VVGTN  177 (291)
Q Consensus       173 ~a~~~  177 (291)
                      |+++.
T Consensus       224 ~a~~~  228 (229)
T 2adc_A          224 FSKST  228 (229)
T ss_dssp             ECSSC
T ss_pred             EecCC
Confidence            98764

>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=99.53  E-value=2.9e-14  Score=117.44  Aligned_cols=76  Identities=20%  Similarity=0.398  Sum_probs=68.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhc----C-------CeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeC
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEI----G-------ELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLD  165 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~----G-------~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~  165 (291)
                      +.++|||+|||+++|+++|+++|++|    |       .|.++.+..+     ++||||+|.+.++|++|| .||+..|.
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~-----~g~afV~f~~~~~A~~A~-~~~~~~~~   76 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETT-----TTEEEEEESSHHHHHHHG-GGTTCEET
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCC-----CCEEEEEeCCHHHHHHHH-HhCCcEec
Confidence            56899999999999999999999999    6       6777777644     899999999999999999 99999999


Q ss_pred             CeeeEEEEecCCC
Q 022827          166 GKPMKIEVVGTNA  178 (291)
Q Consensus       166 g~~i~V~~a~~~~  178 (291)
                      ++.|+|.++....
T Consensus        77 g~~i~v~~~~~~~   89 (172)
T 2g4b_A           77 GQSLKIRRPHDYQ   89 (172)
T ss_dssp             TEECEEECCSSCC
T ss_pred             CceeeecCCcccC
Confidence            9999999876553

>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=99.52  E-value=4e-14  Score=125.58  Aligned_cols=83  Identities=29%  Similarity=0.461  Sum_probs=75.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCC-ceeC---CeeeEE
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNN-VLLD---GKPMKI  171 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng-~~l~---g~~i~V  171 (291)
                      .+.++|||.|||+.+|+++|+++|+.||.|..|.|+.+.++.++|||||+|.+.++|.+||+.||+ ..+.   +++|.|
T Consensus        94 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v  173 (261)
T 3sde_A           94 THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIV  173 (261)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEE
T ss_pred             ccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEE
Confidence            457899999999999999999999999999999999999999999999999999999999999954 4444   899999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      .++....
T Consensus       174 ~~~~~~~  180 (261)
T 3sde_A          174 EPMEQFD  180 (261)
T ss_dssp             EECCCEE
T ss_pred             eeccccC
Confidence            9987653

>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=99.52  E-value=2.8e-14  Score=128.01  Aligned_cols=83  Identities=17%  Similarity=0.237  Sum_probs=71.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcC-CeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIG-ELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G-~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ...++|||.|||+.+++++|+++|+.|| .|..|.|+.++.+.+++||||+|.+.++|++||+.||+..|.++.|.|.++
T Consensus       115 ~~~~~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          115 LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            3578999999999999999999999999 999999999888889999999999999999999999999999999999998


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      .+..
T Consensus       195 ~~~~  198 (292)
T 2ghp_A          195 NPLE  198 (292)
T ss_dssp             CCC-
T ss_pred             CCCc
Confidence            7654

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.51  E-value=4.2e-14  Score=119.15  Aligned_cols=76  Identities=18%  Similarity=0.404  Sum_probs=66.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhc----C-------CeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeC
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEI----G-------ELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLD  165 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~----G-------~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~  165 (291)
                      ..++|||+|||+++|+++|+++|++|    |       .|.++.+.     .+++||||+|.+.++|++|| .||+..|.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~-----~~~g~afV~F~~~~~A~~Al-~l~g~~~~   76 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-----QDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE-----TTTTEEEEEESCSHHHHHHG-GGTTEEET
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec-----CCCCEEEEEeCCHHHHHHHH-HhcCCEEc
Confidence            56899999999999999999999999    5       56666554     44899999999999999999 89999999


Q ss_pred             CeeeEEEEecCCC
Q 022827          166 GKPMKIEVVGTNA  178 (291)
Q Consensus       166 g~~i~V~~a~~~~  178 (291)
                      ++.|+|.++....
T Consensus        77 g~~i~v~~~~~~~   89 (198)
T 2yh0_A           77 GQSLKIRRPHDYQ   89 (198)
T ss_dssp             TEEEEEECCCCCC
T ss_pred             CceEEEeCCCCCC
Confidence            9999999876553

>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=99.49  E-value=1e-13  Score=108.89  Aligned_cols=80  Identities=18%  Similarity=0.214  Sum_probs=70.3

Q ss_pred             CCcEEEEcCCC--CC---CCHHHHHHHHHhcCCeeEEEEeeCCC-----CCCceEEEEEEcCHHHHHHHHHHhCCceeCC
Q 022827           97 VGTKLYVSNLH--PG---VTNDDIRELFSEIGELKRYAIHFDKN-----GRPSGSAEVVYARRSDAFAALKRYNNVLLDG  166 (291)
Q Consensus        97 ~~~~l~V~nL~--~~---~te~dL~~~F~~~G~v~~v~i~~d~t-----g~~kG~afV~F~~~~~A~~Ai~~lng~~l~g  166 (291)
                      ++++|+|.||-  .+   -.++||+++|++||+|.+|.|+.++.     ++++||+||+|.+.++|++|++.||+..|+|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            67999999983  22   23689999999999999999998862     4678999999999999999999999999999


Q ss_pred             eeeEEEEecC
Q 022827          167 KPMKIEVVGT  176 (291)
Q Consensus       167 ~~i~V~~a~~  176 (291)
                      +.|+|+++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999764

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=4.2e-13  Score=102.24  Aligned_cols=76  Identities=22%  Similarity=0.263  Sum_probs=63.8

Q ss_pred             CcEEEEcCCC-------CCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeE
Q 022827           98 GTKLYVSNLH-------PGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMK  170 (291)
Q Consensus        98 ~~~l~V~nL~-------~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~  170 (291)
                      ..+|.|.-..       ..+++++|+++|++||+|..|.|+    +.++|||||+|.+.++|++||+.++  .+.+++|+
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~----~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l~   83 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS----SKKPGTAVVEFATVKAAELAVQNEV--GLVDNPLK   83 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE----SSSSSEEEEEESCHHHHHHHHHTCC--BCSSSBCE
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc----cCCCCEEEEEECCHHHHHHHHHhcC--CCCCCeEE
Confidence            4566665443       568999999999999999999998    3579999999999999999998854  46799999


Q ss_pred             EEEecCCCC
Q 022827          171 IEVVGTNAE  179 (291)
Q Consensus       171 V~~a~~~~~  179 (291)
                      |+++.+.+.
T Consensus        84 V~~a~~~~~   92 (100)
T 2d9o_A           84 ISWLEGQPQ   92 (100)
T ss_dssp             EECSSCCCC
T ss_pred             EEEccCCCC
Confidence            999887754

>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=99.45  E-value=1.5e-13  Score=126.50  Aligned_cols=77  Identities=16%  Similarity=0.164  Sum_probs=66.7

Q ss_pred             CCCCCcEEEEcC--CCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeC---Ce-
Q 022827           94 GIEVGTKLYVSN--LHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLD---GK-  167 (291)
Q Consensus        94 ~~~~~~~l~V~n--L~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~---g~-  167 (291)
                      ...++.+|||+|  |++.+||++|+++|++||+|++|.|..     +++||||+|.+.++|++||+.||+.++.   |+ 
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            356789999999  589999999999999999999887754     3799999999999999999999998873   34 


Q ss_pred             -eeEEEEec
Q 022827          168 -PMKIEVVG  175 (291)
Q Consensus       168 -~i~V~~a~  175 (291)
                       +|.|.++.
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             67777774

>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=99.38  E-value=2.6e-12  Score=100.16  Aligned_cols=79  Identities=18%  Similarity=0.169  Sum_probs=66.6

Q ss_pred             CCCcEEEEcCCCCCC----------CHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeC
Q 022827           96 EVGTKLYVSNLHPGV----------TNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLD  165 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~----------te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~  165 (291)
                      .+++.|.|.|+=...          .++||+++|++||.|.+|.|..+.   ++||+||+|.+.++|++|++.||+..|+
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~---~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS---AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC---TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC---CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            467889999982211          125789999999999999887653   5899999999999999999999999999


Q ss_pred             CeeeEEEEecCC
Q 022827          166 GKPMKIEVVGTN  177 (291)
Q Consensus       166 g~~i~V~~a~~~  177 (291)
                      |+.|+|+++...
T Consensus        82 GR~i~v~~~~~~   93 (114)
T 3s6e_A           82 GKMITAAYVPLP   93 (114)
T ss_dssp             TEECEEEEECHH
T ss_pred             CEEEEEEEEcHH
Confidence            999999998643

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.35  E-value=3.3e-12  Score=100.24  Aligned_cols=84  Identities=24%  Similarity=0.294  Sum_probs=74.2

Q ss_pred             CCCCCCCCcEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcC-HHHHHHHHHHhC--CceeCC
Q 022827           91 GISGIEVGTKLYVSNLHPG-VTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYAR-RSDAFAALKRYN--NVLLDG  166 (291)
Q Consensus        91 ~~~~~~~~~~l~V~nL~~~-~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~-~~~A~~Ai~~ln--g~~l~g  166 (291)
                      +.-..++++.|||.||+++ +++++|+++|++||+|.+|.|..+.     -+|||.|.+ +++|+.|++.||  +..|++
T Consensus        11 ~~~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~-----~tgfVrf~~~~~~A~~av~~ln~~~~~i~g   85 (121)
T 1owx_A           11 GSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA-----KEGIILFKEKAKEALGKAKDANNGNLQLRN   85 (121)
T ss_dssp             CCCSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC-----SEEEEEESSCHHHHHHHHHHTTTSCBCTTS
T ss_pred             CcccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-----CEEEEEECCChHHHHHHHHHhhcCCcEEeC
Confidence            4456679999999999999 9999999999999999999999884     369999999 899999999995  688999


Q ss_pred             eeeEEEEecCCCC
Q 022827          167 KPMKIEVVGTNAE  179 (291)
Q Consensus       167 ~~i~V~~a~~~~~  179 (291)
                      ..+++++.....+
T Consensus        86 ~~~~~evL~GeeE   98 (121)
T 1owx_A           86 KEVTWEVLEGEVE   98 (121)
T ss_dssp             SSEEEEECCHHHH
T ss_pred             cEEEEEECCCHHH
Confidence            9999998775543

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.26  E-value=1.8e-11  Score=90.65  Aligned_cols=75  Identities=21%  Similarity=0.264  Sum_probs=63.5

Q ss_pred             CCCcEEEEcCCCC----CCCH----HHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCe
Q 022827           96 EVGTKLYVSNLHP----GVTN----DDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGK  167 (291)
Q Consensus        96 ~~~~~l~V~nL~~----~~te----~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~  167 (291)
                      ++..||+|.-++.    +.-.    .+|.+.|++||+|..++|+.++       +||+|.+.++|.+||+ ||+..+.|+
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~-------~fVtF~d~~sAlaAi~-mnG~~v~Gr   76 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK-------MWVTFLEGSSALNVLS-LNGKELLNR   76 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS-------EEEEESSHHHHHHGGG-GTTCEETTE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC-------EEEEECChHHHHHHHh-cCCeEeCCe
Confidence            3667888877652    2333    5789999999999999999873       8999999999999997 999999999


Q ss_pred             eeEEEEecCCC
Q 022827          168 PMKIEVVGTNA  178 (291)
Q Consensus       168 ~i~V~~a~~~~  178 (291)
                      .|+|+++++.-
T Consensus        77 ~LkV~lkt~dW   87 (91)
T 2dnr_A           77 TITIALKSPSG   87 (91)
T ss_dssp             EEEEEECCCSS
T ss_pred             EEEEEeCCCCc
Confidence            99999988764

>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=99.09  E-value=1.8e-10  Score=85.75  Aligned_cols=72  Identities=15%  Similarity=0.272  Sum_probs=61.8

Q ss_pred             CCCcEEEEcCCCCC------CCH---HHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCC
Q 022827           96 EVGTKLYVSNLHPG------VTN---DDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDG  166 (291)
Q Consensus        96 ~~~~~l~V~nL~~~------~te---~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g  166 (291)
                      ++..||+|.-++..      ..+   .+|.+.|++||+|..++|+.++       +||+|.+.++|.+||+ ||+..+.|
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~-------~fVtF~d~~sAl~AI~-ldG~~v~G   84 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ-------MLVTFADSHSALSVLD-VDGMKVKG   84 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE-------EEEECSCSHHHHHHHH-GGGSEETT
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc-------EEEEEcChHHHHHHHh-cCCeeeCC
Confidence            47789999988643      221   4689999999999999999883       9999999999999997 99999999


Q ss_pred             eeeEEEEec
Q 022827          167 KPMKIEVVG  175 (291)
Q Consensus       167 ~~i~V~~a~  175 (291)
                      +.|+|.+..
T Consensus        85 r~L~V~~k~   93 (95)
T 1ufw_A           85 RAVKISGPS   93 (95)
T ss_dssp             EEEEEECCC
T ss_pred             eEEEEeccC
Confidence            999999754

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.99  E-value=2.1e-09  Score=92.63  Aligned_cols=84  Identities=17%  Similarity=0.201  Sum_probs=68.6

Q ss_pred             CCCCCCcEEEEcCC-----CCCCCHHHHHHHHHhcCCeeEEEEeeCC-----CCCCceEEEEEEcCHHHHHHHHHHhCCc
Q 022827           93 SGIEVGTKLYVSNL-----HPGVTNDDIRELFSEIGELKRYAIHFDK-----NGRPSGSAEVVYARRSDAFAALKRYNNV  162 (291)
Q Consensus        93 ~~~~~~~~l~V~nL-----~~~~te~dL~~~F~~~G~v~~v~i~~d~-----tg~~kG~afV~F~~~~~A~~Ai~~lng~  162 (291)
                      ........+.+.|+     ..+-.+++|.+.|++||.|.+|.|+.+.     +++++|++||+|.+.++|++||+.||+.
T Consensus       119 ~~~~~s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr  198 (222)
T 3dxb_A          119 GSAMESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGR  198 (222)
T ss_dssp             CSCCBCSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             ccccccccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCc
Confidence            33444556666665     2234567899999999999999998654     4488999999999999999999999999


Q ss_pred             eeCCeeeEEEEecC
Q 022827          163 LLDGKPMKIEVVGT  176 (291)
Q Consensus       163 ~l~g~~i~V~~a~~  176 (291)
                      .|+|+.|.|+++..
T Consensus       199 ~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          199 WFAGRKVVAEVYDQ  212 (222)
T ss_dssp             BSSSSBCEEEECCH
T ss_pred             eECCeEEEEEEcCH
Confidence            99999999999753

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.61  E-value=2.3e-07  Score=70.45  Aligned_cols=74  Identities=18%  Similarity=0.195  Sum_probs=68.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhc-----CCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeee
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEI-----GELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPM  169 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~-----G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i  169 (291)
                      .+..++|-|-|||..|+++.|+.|++++     +.|++|.+..|     .+-|+|+|.+...|-+|.-+|++.+|++++|
T Consensus        18 ~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD-----H~GAivef~d~~~AgKasLaL~G~ef~gr~L   92 (117)
T 2l9w_A           18 KELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD-----FNGAIIIFRDSKFAAKMLMILNGSQFQGKVI   92 (117)
T ss_dssp             TTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT-----TTEEEEECSCHHHHHHHHHHHSSEEETTEEE
T ss_pred             ccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC-----CCceEEEEccchhhHHHHhhcCCeeecCeEE
Confidence            3457899999999999999999999999     99999999988     5569999999999999999999999999999


Q ss_pred             EEEE
Q 022827          170 KIEV  173 (291)
Q Consensus       170 ~V~~  173 (291)
                      ++--
T Consensus        93 r~gT   96 (117)
T 2l9w_A           93 RSGT   96 (117)
T ss_dssp             EEEC
T ss_pred             EecC
Confidence            9863

>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=98.09  E-value=8.6e-06  Score=61.43  Aligned_cols=77  Identities=16%  Similarity=0.133  Sum_probs=64.3

Q ss_pred             CCcEEEEcCCCCCC-CH----HHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827           97 VGTKLYVSNLHPGV-TN----DDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus        97 ~~~~l~V~nL~~~~-te----~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      -.++|+|.||+.+| +.    +.++++|..|.++........     -.=..|.|.++++|.+|-..||+..+.|+.|+|
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS-----FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc-----ceEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            45789999998865 32    467899999999988776644     235789999999999999999999999999999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      -++++..
T Consensus        79 YFgq~~~   85 (104)
T 1wey_A           79 YFAQTLH   85 (104)
T ss_dssp             ECCCCSS
T ss_pred             EecCCCC
Confidence            9988543

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.07  E-value=5.6e-05  Score=56.79  Aligned_cols=76  Identities=17%  Similarity=0.220  Sum_probs=61.8

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhc-----CCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeee
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEI-----GELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPM  169 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~-----G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i  169 (291)
                      ....++|.|.|||+.++++.|+-+|+.-     |+|..|....       ..|+|+|.+.+.|++.|++ ..+.|++.+|
T Consensus         5 ~~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-------~~AvItF~d~~va~rVL~k-~~H~L~~~~L   76 (104)
T 2dhx_A            5 SSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-------CGGVLTFREPADAERVLAQ-ADHELHGAQL   76 (104)
T ss_dssp             CCCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-------TEEEEEESSHHHHHHHHTC-SCCBSSSSBC
T ss_pred             ccCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-------CcEEEEEcChHHHHHHhcC-CcceecCeEE
Confidence            3467899999999999999999999862     5888877753       4799999999999999853 4688999999


Q ss_pred             EEEEecCCC
Q 022827          170 KIEVVGTNA  178 (291)
Q Consensus       170 ~V~~a~~~~  178 (291)
                      .|.-..+..
T Consensus        77 sV~P~~~~~   85 (104)
T 2dhx_A           77 SLRPAPPRA   85 (104)
T ss_dssp             EEEECCCCC
T ss_pred             EEEcCCCCC
Confidence            997644443

>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=97.79  E-value=0.00015  Score=53.49  Aligned_cols=67  Identities=13%  Similarity=0.264  Sum_probs=55.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CC--CCceEEEEEEcCHHHHHHHHHHhCCceeC
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NG--RPSGSAEVVYARRSDAFAALKRYNNVLLD  165 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg--~~kG~afV~F~~~~~A~~Ai~~lng~~l~  165 (291)
                      ++|.|.+||+.+||+++.+.+..+..+.....+..+ +.  ..-.-|||.|.+.+++....+.++++.+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            689999999999999999999988877766665554 22  23467999999999999999999998764

>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=97.68  E-value=0.00015  Score=53.93  Aligned_cols=55  Identities=22%  Similarity=0.233  Sum_probs=45.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhC
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN  160 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~ln  160 (291)
                      ...++| ++|.++...||.++|+.||.|. |..+.|.      .|||.|.+++.|..|+..+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv~-I~WidDT------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSCC-CEEEETT------EEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCEE-EEEEcCC------eEEEEecCHHHHHHHHHhcc
Confidence            345555 9999999999999999999554 6666662      79999999999999998763

>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=97.47  E-value=0.00036  Score=53.91  Aligned_cols=74  Identities=12%  Similarity=0.065  Sum_probs=58.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCC-eeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDG-KPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g-~~i~V~~  173 (291)
                      ....+-|.|-+.|+.. ...|...|++||+|.+.....     ...+..|.|.++.+|++|| ..|+..|.+ .-|-|..
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~-----~~NWihI~Y~s~~~A~rAL-~kNG~ii~g~~mIGV~p   93 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN-----TGNWMHIRYQSKLQARKAL-SKDGRIFGESIMIGVKP   93 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS-----SSSEEEEEESSHHHHHHHH-TTTTCEETTTEECEEEE
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC-----CCCeEEEEeCCHHHHHHHH-HhCCeEecCCEEEEEEE
Confidence            3456889999999885 466778999999999876621     1458999999999999999 569999985 5566665


Q ss_pred             ec
Q 022827          174 VG  175 (291)
Q Consensus       174 a~  175 (291)
                      ..
T Consensus        94 ~~   95 (119)
T 1wwh_A           94 CI   95 (119)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=97.21  E-value=0.00047  Score=51.36  Aligned_cols=54  Identities=22%  Similarity=0.202  Sum_probs=45.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhC
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN  160 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~ln  160 (291)
                      ..++| ++|.++...||.++|+.||. ..|..+.|.      .|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fgg-v~I~WidDT------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEETT------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCC-EEEEEEcCC------eEEEEecCHHHHHHHHHhcc
Confidence            45556 99999999999999999994 446777662      79999999999999998764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.02  E-value=0.00089  Score=49.81  Aligned_cols=78  Identities=13%  Similarity=0.249  Sum_probs=54.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CC--CCceEEEEEEcCHHHHHHHHHHhCCceeCCe-----e
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NG--RPSGSAEVVYARRSDAFAALKRYNNVLLDGK-----P  168 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg--~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~-----~  168 (291)
                      -+-+|.|..||+.+||+++.+.+..+-++.....+..+ +-  ..-.-|||.|.+.+++....+.+++..+-+.     +
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~   87 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYP   87 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEE
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEee
Confidence            45689999999999999988888765444322222222 11  1124589999999999999999999876432     3


Q ss_pred             eEEEEe
Q 022827          169 MKIEVV  174 (291)
Q Consensus       169 i~V~~a  174 (291)
                      ..|++|
T Consensus        88 a~VE~A   93 (97)
T 2l08_A           88 AVVEFA   93 (97)
T ss_dssp             EEEEEC
T ss_pred             eEEEec
Confidence            445554

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.65  E-value=0.001  Score=63.15  Aligned_cols=56  Identities=7%  Similarity=0.067  Sum_probs=42.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHH
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR  158 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~  158 (291)
                      .++|||. +|..+++.+|.++|++||+|.++.+..++    .-||.|+|.+.+++.++++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~----g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF----GLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS----SEEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC----CeEEEEEeCCHHHHHHHHhc
Confidence            4799998 89999999999999999999988776553    46999999999999977643

>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=96.22  E-value=0.0052  Score=49.13  Aligned_cols=35  Identities=17%  Similarity=0.266  Sum_probs=28.6

Q ss_pred             EEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCc
Q 022827          127 RYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNV  162 (291)
Q Consensus       127 ~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~  162 (291)
                      .+.|+.+.. .++||+||+|.+.++|++|++.+++.
T Consensus         2 ~~kl~ln~~-~~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A            2 QYKLILNGK-TLKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             EEEEEEECS-SCEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             cEEEEecCc-cccchhHHHHHHHHhHHHHHHhhccc
Confidence            355666654 57999999999999999999988753

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.94  E-value=0.013  Score=45.93  Aligned_cols=78  Identities=13%  Similarity=0.213  Sum_probs=54.3

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeeC--------C-CC-----CCceEEEEEEcCHHHHHHHHHHhCC
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKR-YAIHFD--------K-NG-----RPSGSAEVVYARRSDAFAALKRYNN  161 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~-v~i~~d--------~-tg-----~~kG~afV~F~~~~~A~~Ai~~lng  161 (291)
                      ..+-|.|-+.|+..+ ..+-+.|++||.|.+ +.+..+        + ..     ....+..|+|+++.+|++|| ..|+
T Consensus         6 ~e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL-~~NG   83 (132)
T 3p3d_A            6 GELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDAL-LENG   83 (132)
T ss_dssp             --CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHH-TTTT
T ss_pred             CceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHH-HhCC
Confidence            346677888877665 456668999999875 221110        0 00     02457899999999999999 6799


Q ss_pred             ceeCCeeeEEEEecC
Q 022827          162 VLLDGKPMKIEVVGT  176 (291)
Q Consensus       162 ~~l~g~~i~V~~a~~  176 (291)
                      ..|.|.-|-|....+
T Consensus        84 ~ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           84 AVFNGVLLGVIPYTK   98 (132)
T ss_dssp             CEETTEECEEEECCH
T ss_pred             eEeCcEEEEEEECCH
Confidence            999999888876643

>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=94.84  E-value=0.008  Score=47.71  Aligned_cols=39  Identities=18%  Similarity=0.199  Sum_probs=35.6

Q ss_pred             CCceEEEEEEcCHHHHHHHHHHh-CCceeCCeeeEEEEecC
Q 022827          137 RPSGSAEVVYARRSDAFAALKRY-NNVLLDGKPMKIEVVGT  176 (291)
Q Consensus       137 ~~kG~afV~F~~~~~A~~Ai~~l-ng~~l~g~~i~V~~a~~  176 (291)
                      ..+|+++|+|.+.++|++|++.| |+..|+| .|.|.++..
T Consensus        11 ~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             SSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             cccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            56899999999999999999999 9999999 999987654

>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=90.88  E-value=0.52  Score=45.14  Aligned_cols=55  Identities=22%  Similarity=0.232  Sum_probs=44.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhC
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN  160 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~ln  160 (291)
                      ...++|+ +|..+...+|.++|+.||.| +|.++.+      -.|||.|.+.+.|..+++.++
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS------SEEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC------CeEEEEECCHHHHHHHHHHHH
Confidence            3466665 88899999999999999954 4555544      369999999999999999885

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=88.69  E-value=0.81  Score=31.65  Aligned_cols=68  Identities=19%  Similarity=0.227  Sum_probs=43.2

Q ss_pred             EEEEcC-CCCCCCHHHHHHHHHhcCC-----eeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827          100 KLYVSN-LHPGVTNDDIRELFSEIGE-----LKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus       100 ~l~V~n-L~~~~te~dL~~~F~~~G~-----v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      +|||.- -...++..+|..++..-+.     |-.|.|..+       |.||+-.. +.|..+++.|+...+.++.+.|+.
T Consensus         2 ~~~i~~Grk~~~~p~~ivg~i~~~~gi~~~~IG~I~i~d~-------~s~v~v~~-~~~~~~~~~l~~~~i~g~~~~v~~   73 (76)
T 2g0c_A            2 KLYFNGGKKKKIRAVDFVGTIAKIDGVSADDIGIITIMDN-------ASYVEILN-GKGPHVLKVMKNTTVKGKQLKVNK   73 (76)
T ss_dssp             EEEESCCCC----CHHHHHHHHTSTTCCGGGEEEEEECSS-------CEEEEECT-TCHHHHHHHHTTCCC---CCCEEE
T ss_pred             EEEEeCCCccCCCHHHHHHHHHHccCCChhhccEEEEeCC-------cEEEEECH-HHHHHHHHHhccccCcCceEEEEE
Confidence            456642 2344677788888865443     446677533       78888775 468889999999999999999987


Q ss_pred             ec
Q 022827          174 VG  175 (291)
Q Consensus       174 a~  175 (291)
                      +.
T Consensus        74 ~~   75 (76)
T 2g0c_A           74 AN   75 (76)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>4eyt_A Telomerase associated protein P65; RNA, LA protein, LARP7, RRM, XRRM, RNA binding protein; 2.50A {Tetrahymena thermophila} PDB: 4erd_A

Probab=87.45  E-value=3.4  Score=29.87  Aligned_cols=58  Identities=12%  Similarity=0.184  Sum_probs=47.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHh
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY  159 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~l  159 (291)
                      ....|-|.|-|||..+-..++.-.....|---.|..+       .|.|.|.|.+.++..-||..|
T Consensus         9 ikqnclikiinipqgtlkaevvlavrhlgyefycdyi-------dgqamirfqnsdeqrlaiqkl   66 (129)
T 4eyt_A            9 IKQNCLIKIINIPQGTLKAEVVLAVRHLGYEFYCDYI-------DGQAMIRFQNSDEQRLAIQKL   66 (129)
T ss_dssp             -CCSCEEEEECCCTTCCHHHHHHHHHTTCCCEEEEEC-------SSCEEEEESSHHHHHHHHHHH
T ss_pred             hhhCcEEEEEecCCCceeeeeEEeehhcCeeEeeeee-------cCeeEEEecCChHHHHHHHHH
Confidence            4567899999999999999887777777766666665       467999999999999999877

---

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	291
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-17
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-15
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-15
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-15
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	5e-15
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-14
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-14
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-14
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	5e-14
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-13
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-13
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	6e-13
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-12
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-12
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-12
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-12
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-12
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	5e-12
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	5e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	6e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-11
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-11
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-11
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-11
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-11
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-11
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-11
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:) 3e-11
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	9e-11
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-10
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-10
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-10
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	1e-10
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	4e-10
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	4e-10
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	5e-10
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	6e-10
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-09
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-09
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-09
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-09
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-09
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-09
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-09
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	3e-09
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-09
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-08
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-08
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-08
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-08
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	3e-08
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-08
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	8e-08
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-07
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-07
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-07
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-07
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	3e-07
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	4e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	5e-07
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	9e-07
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	1e-06
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-06
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	4e-06
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	4e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	5e-06
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	6e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-05
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	5e-05
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	6e-05
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	8e-05
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	1e-04
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	4e-04
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-04
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	5e-04
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	0.001
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	0.001

>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 = 73.8 bits (181), Expect = 1e-17
 Identities = 40/75 (53%), Positives = 59/75 (78%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY 159
           KL VSNL  GV++ DI+ELF+E G LK+ A+H+D++GR  G+A+V + R++DA  A+K+Y
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 160 NNVLLDGKPMKIEVV 174
           N V LDG+PM I++V
Sbjct: 62  NGVPLDGRPMNIQLV 76

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.0 bits (166), Expect = 2e-15
 Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 3/80 (3%)

Query: 96  EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN--GRPSGSAEVVYARRSDAF 153
           +  +K+ V N+       +IRELFS  GELK   +       G   G   V +  + DA 
Sbjct: 6   QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 65

Query: 154 AALKR-YNNVLLDGKPMKIE 172
            A     ++  L G+ + +E
Sbjct: 66  KAFNALCHSTHLYGRRLVLE 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 67.7 bits (165), Expect = 2e-15
 Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 98  GTKLYVSNLHPGVTNDDIRELFSEIGELK-RYAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
            T LYV+NL   +T+D +  +F + G +  +  +     GRP G A V Y +R +A  A+
Sbjct: 6   DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 65

Query: 157 KRYNNVLLDGKPMKIEV 173
              NNV+ +G    + V
Sbjct: 66  SALNNVIPEGGSQPLSV 82

>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 = 67.3 bits (164), Expect = 3e-15
 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAI-HFDKNGRPSGSAEVVYARRSDAFAALKR 158
            LYV +LHP VT   + E FS  G +    +       R  G A V + + +DA  AL  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 159 YNNVLLDGKPMKIE 172
            N  ++ GKP++I 
Sbjct: 62  MNFDVIKGKPVRIM 75

>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 = 66.9 bits (163), Expect = 5e-15
 Identities = 25/79 (31%), Positives = 40/79 (50%), Gaps = 1/79 (1%)

Query: 95  IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAF 153
           ++    LYV NL    T + I ELFS+ G++K+  +  DK      G   V Y  R+DA 
Sbjct: 4   LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 63

Query: 154 AALKRYNNVLLDGKPMKIE 172
            A++  N   LD + ++ +
Sbjct: 64  NAMRYINGTRLDDRIIRTD 82

>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 = 65.8 bits (160), Expect = 1e-14
 Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKR-YAIHFDKNGRPSGSAEVVYARRSDAFAALK 157
           T L V+ L   +T+ ++  LF  IG +     +   K G   G A V +    D+  A+K
Sbjct: 3   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 62

Query: 158 RYNNVLLDGKPMKIE 172
             N + +  K +K+ 
Sbjct: 63  VLNGITVRNKRLKVS 77

>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 = 65.8 bits (160), Expect = 1e-14
 Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 1/77 (1%)

Query: 98  GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPS-GSAEVVYARRSDAFAAL 156
              LYVS L   +T  ++ +LFS+ G +    I  D+    S G   + + +R +A  A+
Sbjct: 6   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 65

Query: 157 KRYNNVLLDGKPMKIEV 173
           K  N     G    I V
Sbjct: 66  KGLNGQKPSGATEPITV 82

>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 = 65.1 bits (158), Expect = 2e-14
 Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 4/77 (5%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN----GRPSGSAEVVYARRSDAFAAL 156
           L++ NL+   T + ++ +FS++G +K   I   KN        G   V Y +   A  AL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 157 KRYNNVLLDGKPMKIEV 173
           K+     +DG  +++ +
Sbjct: 61  KQLQGHTVDGHKLEVRI 77

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 63.8 bits (155), Expect = 5e-14
 Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 2/75 (2%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKR 158
           K+++  L    T + +RE F + GE+K   +  D    R  G   V +  ++     L +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 159 YNNVLLDGKPMKIEV 173
            +   LD K +  +V
Sbjct: 62  -SRHELDSKTIDPKV 75

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.2 bits (153), Expect = 1e-13
 Identities = 22/75 (29%), Positives = 33/75 (44%), Gaps = 1/75 (1%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGEL-KRYAIHFDKNGRPSGSAEVVYARRSDAFAALK 157
           T L V+ L   +T ++ R LF  IGE+     +     G+  G   V Y    DA  A+ 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 158 RYNNVLLDGKPMKIE 172
             N + L  K +K+ 
Sbjct: 63  TLNGLRLQTKTIKVS 77

>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 = 62.4 bits (151), Expect = 2e-13
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 96  EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSG-SAEVVYARRSDAFA 154
           +    L V  L    T  D+RE+FS+ G +   +I +D+  R S   A V +    DA  
Sbjct: 7   DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 66

Query: 155 ALKRYNNVLLDGKPMKI 171
           A +R N + LDG+ +++
Sbjct: 67  AKERANGMELDGRRIRV 83

>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 = 62.0 bits (150), Expect = 6e-13
 Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 96  EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAA 155
           EV   LY+ NL   +T +++ ++F + G +++  +      R  G+A VVY    DA  A
Sbjct: 5   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR--GTAYVVYEDIFDAKNA 62

Query: 156 LKRYNNVLLDGKPMKIE 172
               +   +  + + + 
Sbjct: 63  CDHLSGFNVCNRYLVVL 79

>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 = 60.8 bits (147), Expect = 1e-12
 Identities = 17/90 (18%), Positives = 35/90 (38%), Gaps = 9/90 (10%)

Query: 83  FEDSLRAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSA 142
           FED +  +          +Y   +  G+T+  +R+ FS  G++    +         G +
Sbjct: 7   FEDVVNQSSPKN----CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF-----PEKGYS 57

Query: 143 EVVYARRSDAFAALKRYNNVLLDGKPMKIE 172
            V ++    A  A+   N   ++G  +K  
Sbjct: 58  FVRFSTHESAAHAIVSVNGTTIEGHVVKCY 87

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 3e-12
 Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALK 157
             + V+NL       D++ELF   G + R  +  DK  G+  G A + + RR DA  A+ 
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 158 RYNNVLLDGKPMKIE 172
             +    D   + +E
Sbjct: 69  GVSGFGYDHLILNVE 83

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 3e-12
 Identities = 18/74 (24%), Positives = 28/74 (37%), Gaps = 1/74 (1%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSG-SAEVVYARRSDAFAALKR 158
            LYV  L   V +  +   F   G++    I  D         A V +    DA AA+  
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 159 YNNVLLDGKPMKIE 172
            N   L G+ +++ 
Sbjct: 67  MNESELFGRTIRVN 80

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 3e-12
 Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 1/75 (1%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAE-VVYARRSDAFAALK 157
             +YV  L   V+   + ELF + G +    +  D+          V +    DA  A+K
Sbjct: 10  ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 69

Query: 158 RYNNVLLDGKPMKIE 172
             + + L GKP+++ 
Sbjct: 70  IMDMIKLYGKPIRVN 84

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 59.0 bits (142), Expect = 4e-12
 Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 98  GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSG-SAEVVYARRSDAFAAL 156
           G  L+V+++H     D+I+E F + GE+K   ++ D+    S   A V Y     A AA 
Sbjct: 7   GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 66

Query: 157 KRYNNVLLDGKPMKIE 172
           +  N   + G+ ++++
Sbjct: 67  EALNGAEIMGQTIQVD 82

>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 = 58.9 bits (142), Expect = 5e-12
 Identities = 13/79 (16%), Positives = 29/79 (36%), Gaps = 5/79 (6%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAI---HFDKNGRPSGSAEVVYARRSDAFAA 155
            +L++  +      ++I E  +++ E     I         +  G A V Y     A  A
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 156 LKRYNN--VLLDGKPMKIE 172
            ++     + L G  + ++
Sbjct: 62  RRKLMPGRIQLWGHQIAVD 80

>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 = 58.8 bits (142), Expect = 5e-12
 Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 3/81 (3%)

Query: 94  GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPS-GSAEVVYARRSDA 152
            ++  + L V  L    T  D++E FS  GE+    +  D     S G   V +      
Sbjct: 4   AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 63

Query: 153 FAALKRYNNVLLDGKPMKIEV 173
              + + +  ++DG+    ++
Sbjct: 64  VKVMSQRH--MIDGRWCDCKL 82

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.4 bits (141), Expect = 6e-12
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 5/74 (6%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           ++L+V NL P +T +++R+LF + G+     IH DK         +    R+ A  A   
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG-----FGFIRLETRTLAEIAKVE 63

Query: 159 YNNVLLDGKPMKIE 172
            +N+ L GK +++ 
Sbjct: 64  LDNMPLRGKQLRVR 77

>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 = 58.2 bits (140), Expect = 1e-11
 Identities = 16/74 (21%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
            +L+VSN+     + D+R++F + G++    I F++     G   V +   +DA  A ++
Sbjct: 12  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREK 70

Query: 159 YNNVLLDGKPMKIE 172
            +  +++G+ +++ 
Sbjct: 71  LHGTVVEGRKIEVN 84

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 57.5 bits (138), Expect = 1e-11
 Identities = 14/76 (18%), Positives = 33/76 (43%), Gaps = 1/76 (1%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELK-RYAIHFDKNGRPSGSAEVVYARRSDAFAALK 157
             L+++N  P  T  +IR+L  +I  +     +   +       A +    + DA   ++
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 158 RYNNVLLDGKPMKIEV 173
           + N + ++G  +  +V
Sbjct: 62  KLNGLKIEGYTLVTKV 77

>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 = 57.3 bits (138), Expect = 2e-11
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKR 158
           KL++  L   + +D ++EL +  G LK + +  D   G   G A   Y   +    A+  
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 159 YNNVLLDGKPMKIE 172
            N + L  K + ++
Sbjct: 63  LNGMQLGDKKLLVQ 76

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.9 bits (137), Expect = 2e-11
 Identities = 13/75 (17%), Positives = 27/75 (36%), Gaps = 2/75 (2%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGS-AEVVYARRSDAFAALKR 158
           K++V  L P    + IRE F   GE++   +  D           + +         +++
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 159 YNNVLLDGKPMKIEV 173
                +     +I+V
Sbjct: 61  -KYHNVGLSKCEIKV 74

>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 = 56.9 bits (137), Expect = 2e-11
 Identities = 14/74 (18%), Positives = 30/74 (40%), Gaps = 2/74 (2%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGS-AEVVYARRSDAFAALKR 158
           K+++  L    T  D+++ FS+ GE+    +  D     S     V++         + +
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 159 YNNVLLDGKPMKIE 172
                L+GK +  +
Sbjct: 61  -KEHKLNGKVIDPK 73

>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 = 57.1 bits (137), Expect = 2e-11
 Identities = 15/74 (20%), Positives = 31/74 (41%), Gaps = 2/74 (2%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAI--HFDKNGRPSGSAEVVYARRSDAFAALKR 158
           +++ NL P +    + + FS  G + +          G   G A + +A    + AA++ 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 159 YNNVLLDGKPMKIE 172
            N   L  +P+ + 
Sbjct: 61  MNGQYLCNRPITVS 74

>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 = 57.0 bits (137), Expect = 2e-11
 Identities = 24/74 (32%), Positives = 32/74 (43%), Gaps = 1/74 (1%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
             LYV NL   VT   I +LFS+IG  K   +  +          V +    DA AAL  
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYC-FVEFYEHRDAAAALAA 67

Query: 159 YNNVLLDGKPMKIE 172
            N   + GK +K+ 
Sbjct: 68  MNGRKILGKEVKVN 81

>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 = 57.4 bits (138), Expect = 3e-11
 Identities = 14/74 (18%), Positives = 31/74 (41%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           + + +   +     +   E+  + GE++   +  +      G+  V + R  DA  A+  
Sbjct: 28  SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVID 87

Query: 159 YNNVLLDGKPMKIE 172
            NN   +G+P+  E
Sbjct: 88  LNNRWFNGQPIHAE 101

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 55.4 bits (133), Expect = 9e-11
 Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 4/75 (5%)

Query: 98  GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALK 157
              L   NL   +T D+++E+F +            ++G+  G A + +   +DA   L+
Sbjct: 16  ARTLLAKNLSFNITEDELKEVFEDA----LEIRLVSQDGKSKGIAYIEFKSEADAEKNLE 71

Query: 158 RYNNVLLDGKPMKIE 172
                 +DG+ + + 
Sbjct: 72  EKQGAEIDGRSVSLY 86

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.5 bits (133), Expect = 1e-10
 Identities = 14/76 (18%), Positives = 29/76 (38%), Gaps = 1/76 (1%)

Query: 98  GTKLYVSNLHPGVTNDDIRELFSEIGELKR-YAIHFDKNGRPSGSAEVVYARRSDAFAAL 156
           G  L++ +L     + D+ ++F   G +         +         V Y     A AA+
Sbjct: 18  GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 77

Query: 157 KRYNNVLLDGKPMKIE 172
           +  N   +  K +K++
Sbjct: 78  QSMNGFQIGMKRLKVQ 93

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.3 bits (130), Expect = 1e-10
 Identities = 12/74 (16%), Positives = 29/74 (39%), Gaps = 2/74 (2%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAE-VVYARRSDAFAALKR 158
           K++V  L    T +D++  F + G++    + FDK          V +          + 
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE- 59

Query: 159 YNNVLLDGKPMKIE 172
            +   ++ K ++ +
Sbjct: 60  IHFHEINNKMVECK 73

>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 = 54.7 bits (131), Expect = 1e-10
 Identities = 16/74 (21%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
             +++ NL   + N  + + FS  G +    +  D+NG   G   V +  +  A  A+++
Sbjct: 9   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEK 67

Query: 159 YNNVLLDGKPMKIE 172
            N +LL+ + + + 
Sbjct: 68  MNGMLLNDRKVFVG 81

>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 = 55.2 bits (132), Expect = 1e-10
 Identities = 14/74 (18%), Positives = 25/74 (33%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           T LY+SNL   +   ++  +    G++    I  D +G   G             A +  
Sbjct: 19  TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 78

Query: 159 YNNVLLDGKPMKIE 172
           +N   +   P    
Sbjct: 79  FNGKFIKTPPGVSA 92

>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 = 54.0 bits (129), Expect = 4e-10
 Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 9/84 (10%)

Query: 98  GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFD---------KNGRPSGSAEVVYAR 148
            + +YV  L+  VT DD+ + F + G +K                + G+P G A V Y  
Sbjct: 8   NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 67

Query: 149 RSDAFAALKRYNNVLLDGKPMKIE 172
              A AA++ ++     G  +K+ 
Sbjct: 68  PPTAKAAVEWFDGKDFQGSKLKVS 91

>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 = 53.2 bits (127), Expect = 4e-10
 Identities = 10/74 (13%), Positives = 26/74 (35%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY 159
           K++V  +        +R+ F + G+++   I  D+          V     D+   +   
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 63

Query: 160 NNVLLDGKPMKIEV 173
               ++G   ++  
Sbjct: 64  KYHTVNGHNCEVRK 77

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.2 bits (127), Expect = 5e-10
 Identities = 13/74 (17%), Positives = 25/74 (33%), Gaps = 1/74 (1%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
             +Y+       T DDI+E   + G++    +    +    GS  VV+     A   ++ 
Sbjct: 7   RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET 66

Query: 159 YNNVLLDGKPMKIE 172
                     + I 
Sbjct: 67  -PGQKYKETDLLIL 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 = 52.7 bits (126), Expect = 6e-10
 Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 2/74 (2%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN-GRPSGSAEVVYARRSDAFAALKR 158
           KL++  L    T++ +R  F + G L    +  D N  R  G   V YA   +  AA+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 159 YNNVLLDGKPMKIE 172
                +DG+ ++ +
Sbjct: 68  -RPHKVDGRVVEPK 80

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.4 bits (125), Expect = 1e-09
 Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 1/83 (1%)

Query: 91  GISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPS-GSAEVVYARR 149
           G SG     +L+V NL    + +D+ +LFS  G L       D   +   G A V +   
Sbjct: 1   GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60

Query: 150 SDAFAALKRYNNVLLDGKPMKIE 172
             A  A    +  +  G+ + + 
Sbjct: 61  EHAVKAYAEVDGQVFQGRMLHVL 83

>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 = 52.1 bits (124), Expect = 2e-09
 Identities = 17/87 (19%), Positives = 36/87 (41%), Gaps = 7/87 (8%)

Query: 93  SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPS-GSAEVVYARRSD 151
           S +  G  +++ NL      + + E+  + G+LK   +    +   S G A   +  +  
Sbjct: 3   SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 62

Query: 152 AFAALKRYN------NVLLDGKPMKIE 172
           A   L   +       + LDG+ +K++
Sbjct: 63  AQKCLAAASLEAEGGGLKLDGRQLKVD 89

>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 = 52.3 bits (125), Expect = 2e-09
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 2/75 (2%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNG-RPSGSAEVVYARRSDAFAALK 157
             ++   L   +   D+ + FS +G+++   I  D+N  R  G A V +        A+ 
Sbjct: 19  RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG 78

Query: 158 RYNNVLLDGKPMKIE 172
                 L G P+ ++
Sbjct: 79  -LTGQRLLGVPIIVQ 92

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.0 bits (124), Expect = 2e-09
 Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 2/78 (2%)

Query: 96  EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN-GRPSGSAEVVYARRSDAFA 154
           E   KL++  L    T + +R  + + G+L    +  D    R  G   V ++  ++  A
Sbjct: 18  EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDA 77

Query: 155 ALKRYNNVLLDGKPMKIE 172
           A+       +DG+ ++ +
Sbjct: 78  AMA-ARPHSIDGRVVEPK 94

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.4 bits (123), Expect = 2e-09
 Identities = 17/78 (21%), Positives = 38/78 (48%), Gaps = 8/78 (10%)

Query: 96  EVGTKLYVSNLHPGVTND-DIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFA 154
            + +++++ NL+  V    D+  +FS+ G++   ++H        G A V Y    +A A
Sbjct: 13  SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK-------GFAFVQYVNERNARA 65

Query: 155 ALKRYNNVLLDGKPMKIE 172
           A+   +  ++ G+ + I 
Sbjct: 66  AVAGEDGRMIAGQVLDIN 83

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.9 bits (124), Expect = 2e-09
 Identities = 16/82 (19%), Positives = 31/82 (37%), Gaps = 3/82 (3%)

Query: 92  ISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSD 151
           ++G     ++ V NL   VT D + ++FS+ G + +       N      A + YA    
Sbjct: 1   MAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ---FQALLQYADPVS 57

Query: 152 AFAALKRYNNVLLDGKPMKIEV 173
           A  A    +   +      + +
Sbjct: 58  AQHAKLSLDGQNIYNACCTLRI 79

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.2 bits (122), Expect = 2e-09
 Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY 159
            LYV NL    + + I + F+            ++  +    A V ++ R DA  A+K  
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFN-----NIKPGAVERVKKIRDYAFVHFSNREDAVEAMKAL 64

Query: 160 NNVLLDGKPMKIE 172
           N  +LDG P+++ 
Sbjct: 65  NGKVLDGSPIEVT 77

>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 = 51.2 bits (122), Expect = 3e-09
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 6/78 (7%)

Query: 99  TKLYVSNLHPGVTNDDIR----ELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFA 154
             +Y++NL+  +  D+++     +FS  G++    +      R  G A V++   S A  
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR--GQAFVIFKEVSSATN 61

Query: 155 ALKRYNNVLLDGKPMKIE 172
           AL+         KPM+I+
Sbjct: 62  ALRSMQGFPFYDKPMRIQ 79

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.8 bits (121), Expect = 3e-09
 Identities = 20/82 (24%), Positives = 40/82 (48%), Gaps = 1/82 (1%)

Query: 93  SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELK-RYAIHFDKNGRPSGSAEVVYARRSD 151
           SG    T + V N+   V+ D+I + F     +     + +++ G P+G A V +  R +
Sbjct: 4   SGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDE 63

Query: 152 AFAALKRYNNVLLDGKPMKIEV 173
           A AA+   N+  +  + +K+ +
Sbjct: 64  ATAAVIDLNDRPIGSRKVKLVL 85

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.0 bits (116), Expect = 1e-08
 Identities = 15/71 (21%), Positives = 26/71 (36%), Gaps = 1/71 (1%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIH-FDKNGRPSGSAEVVYARRSDAFAALKRY 159
           LY+  L PG T+ D+ +L    G++            +  G   V +   S A  A+   
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 160 NNVLLDGKPMK 170
               +  +  K
Sbjct: 61  KASGVQAQMAK 71

>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 = 49.4 bits (117), Expect = 1e-08
 Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRY-AIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           KL+V  L        + ++FS+ G++     +   +  R  G   V +    DA  A+  
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 159 YNNVLLDGKPMKIE 172
            N   +DG+ ++++
Sbjct: 67  MNGKSVDGRQIRVD 80

>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 = 49.3 bits (117), Expect = 2e-08
 Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 2/74 (2%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
            ++YV NL P +   DI ++F + G ++   +   + G     A V +    DA  A+  
Sbjct: 15  CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGP--PFAFVEFEDPRDAEDAVYG 72

Query: 159 YNNVLLDGKPMKIE 172
            +    DG  +++E
Sbjct: 73  RDGYDYDGYRLRVE 86

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.0 bits (116), Expect = 2e-08
 Identities = 25/75 (33%), Positives = 33/75 (44%), Gaps = 1/75 (1%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPS-GSAEVVYARRSDAFAALK 157
             LY+ NL P VT  D+  LF+   E K   I F        G A + +  +  A+ AL 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 158 RYNNVLLDGKPMKIE 172
             N   L GK + IE
Sbjct: 79  LVNGYKLYGKILVIE 93

>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 = 48.6 bits (115), Expect = 3e-08
 Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNG-RPSGSAEVVYARRSDAFAALK 157
           TK++V  L    T+  +R+ F   G+++   +  D+   +  G   V  A R+ A  A K
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 70

Query: 158 RYNNVLLDGKPMKIEV 173
             N + +DG+   + +
Sbjct: 71  DPNPI-IDGRKANVNL 85

>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 = 47.8 bits (113), Expect = 3e-08
 Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 6/74 (8%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY 159
           KLY+ NL P VT DD+R+LF +        +         G A V Y  ++ A  A++  
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS-----GYAFVDYPDQNWAIRAIETL 57

Query: 160 N-NVLLDGKPMKIE 172
           +  V L GK M+++
Sbjct: 58  SGKVELHGKIMEVD 71

>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 = 47.0 bits (111), Expect = 8e-08
 Identities = 15/79 (18%), Positives = 34/79 (43%), Gaps = 4/79 (5%)

Query: 98  GTKLYVSNLHPGVTN-DDIRELFSEIGEL--KRYAIHFDKNGRPSGSAEVVYARRSDAFA 154
           G ++ + NL   + + + +RE F   G +          ++   +  A +V+  +  A  
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 155 ALKRYNNVLLDGKPMKIEV 173
           AL+  N  LL  + + + +
Sbjct: 64  ALQ-MNRSLLGNREISVSL 81

>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 = 47.6 bits (112), Expect = 1e-07
 Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 1/87 (1%)

Query: 96  EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNG-RPSGSAEVVYARRSDAFA 154
           +V   L V+ +   V    +R+LF   G ++   I  D+   +  G   V +   S A  
Sbjct: 40  DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99

Query: 155 ALKRYNNVLLDGKPMKIEVVGTNAEIP 181
           A+   N   +  K +K+ +  +  + P
Sbjct: 100 AIAGLNGFNILNKRLKVALAASGHQRP 126

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (109), Expect = 2e-07
 Identities = 17/75 (22%), Positives = 36/75 (48%), Gaps = 4/75 (5%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
             L++SN+ P V+ +D++ LFS  G + +    F K+ + +    +      +A  AL  
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMA---LIQMGSVEEAVQALID 67

Query: 159 YNN-VLLDGKPMKIE 172
            +N  L +   +++ 
Sbjct: 68  LHNHDLGENHHLRVS 82

>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 = 48.1 bits (113), Expect = 2e-07
 Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 1/63 (1%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKR-YAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           KL++  L    T++ +R  F + G L     +      R  G   V YA   +  AA+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 159 YNN 161
             +
Sbjct: 68  RPH 70

>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 = 46.0 bits (108), Expect = 2e-07
 Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 7/79 (8%)

Query: 100 KLYVSNLHPGVTNDDIRELF---SEIGELKRYAIHFDKNGR----PSGSAEVVYARRSDA 152
            ++V  L   + + ++ +      + G++ +  I+   +      PS SA V Y R  DA
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 153 FAALKRYNNVLLDGKPMKI 171
             A++  NNV++DG+ +K 
Sbjct: 70  LRAIQCVNNVVVDGRTLKA 88

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (109), Expect = 2e-07
 Identities = 15/74 (20%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRY-AIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
            ++V N+    T + ++++FSE+G +  +  ++  + G+P G     Y  +  A +A++ 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 159 YNNVLLDGKPMKIE 172
            N     G+ ++++
Sbjct: 70  LNGREFSGRALRVD 83

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.5 bits (107), Expect = 3e-07
 Identities = 13/78 (16%), Positives = 33/78 (42%), Gaps = 7/78 (8%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKR------YAIHFDKNGRPSGSAEVVYARRSDAF 153
           +LYV N+  G+T + + + F+    L          +   +  +    A + +    +  
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 154 AALKRYNNVLLDGKPMKI 171
            A+  ++ ++  G+ +KI
Sbjct: 63  QAM-AFDGIIFQGQSLKI 79

>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 = 45.3 bits (106), Expect = 3e-07
 Identities = 15/75 (20%), Positives = 30/75 (40%), Gaps = 1/75 (1%)

Query: 98  GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALK 157
              L++ NL+P  +  +++   SE+      A+   + G       V +    D   AL 
Sbjct: 13  PFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL- 71

Query: 158 RYNNVLLDGKPMKIE 172
               + + G  +K+E
Sbjct: 72  ELTGLKVFGNEIKLE 86

>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 = 45.1 bits (106), Expect = 4e-07
 Identities = 13/80 (16%), Positives = 29/80 (36%), Gaps = 6/80 (7%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           + + V NL       ++ +L  +      Y            +A V       A  A++ 
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDR------NKRTAFVTLLNGEQAQNAIQM 59

Query: 159 YNNVLLDGKPMKIEVVGTNA 178
           ++     GK + +++  T+A
Sbjct: 60  FHQYSFRGKDLIVQLQPTDA 79

>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 = 45.1 bits (106), Expect = 5e-07
 Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 5/75 (6%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           T+L+V  L P  +   +   F      +  +I    + +    A + Y     A AA  +
Sbjct: 18  TRLWVGGLGPNTSLAALAREFD-----RFGSIRTIDHVKGDSFAYIQYESLDAAQAACAK 72

Query: 159 YNNVLLDGKPMKIEV 173
                L G   ++ V
Sbjct: 73  MRGFPLGGPDRRLRV 87

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.4 bits (104), Expect = 9e-07
 Identities = 11/79 (13%), Positives = 22/79 (27%), Gaps = 10/79 (12%)

Query: 99  TKLYVSNLHPGVTND-----DIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAF 153
           + L     +  V ++         LF    +   +               + ++    A 
Sbjct: 6   SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF-----KRVRINFSNPLSAA 60

Query: 154 AALKRYNNVLLDGKPMKIE 172
            A  R +     GK MK+ 
Sbjct: 61  DARLRLHKTEFLGKEMKLY 79

>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 = 43.0 bits (100), Expect = 1e-06
 Identities = 16/78 (20%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN 160
           + +  L   VTN ++ +L S+      Y + +    +  G+A V       A AA+  ++
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSD------YELKYCFVDKYKGTAFVTLLNGEQAEAAINTFH 54

Query: 161 NVLLDGKPMKIEVVGTNA 178
              L  + + +++  T+A
Sbjct: 55  QSRLRERELSVQLQPTDA 72

>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 = 43.6 bits (102), Expect = 2e-06
 Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 5/76 (6%)

Query: 99  TKLYVSNLHP-GVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALK 157
           + L VSNL+P  VT   +  LF   G+++R  I F+K       A V  A  + A  A+ 
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN----ALVQMADGNQAQLAMS 58

Query: 158 RYNNVLLDGKPMKIEV 173
             N   L GKP++I +
Sbjct: 59  HLNGHKLHGKPIRITL 74

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 41.8 bits (97), Expect = 4e-06
 Identities = 13/74 (17%), Positives = 28/74 (37%), Gaps = 2/74 (2%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           T + V NL      + + + F   G +    +      +    A + +AR   A AA+ +
Sbjct: 1   TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK-KNFRFARIEFARYDGALAAITK 59

Query: 159 YNNVLLDGKPMKIE 172
            + V +    + + 
Sbjct: 60  THKV-VGQNEIIVS 72

>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 = 4e-06
 Identities = 18/99 (18%), Positives = 36/99 (36%), Gaps = 13/99 (13%)

Query: 79  QHDLFEDSLRAAGISGIEVGTK---LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKN 135
           +H L    LR  GI  +   T+   +    L  GV+ + +  +  + G +    +  +K 
Sbjct: 2   KHTL----LRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP 57

Query: 136 GRPSGSAEVVYARRSDAFAALKRYNN-VLLDGKPMKIEV 173
                 +   Y    ++  A    N   ++D    KI +
Sbjct: 58  -----YSFARYRTTEESKRAYVTLNGKEVVDDLGQKITL 91

>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 = 41.9 bits (98), Expect = 5e-06
 Identities = 14/74 (18%), Positives = 30/74 (40%), Gaps = 6/74 (8%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           + ++V      +T D++RE FS+ G++    I             V +A    A +    
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAF----VTFADDQIAQSLCG- 60

Query: 159 YNNVLLDGKPMKIE 172
             ++++ G  + I 
Sbjct: 61  -EDLIIKGISVHIS 73

>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 = 42.0 bits (98), Expect = 6e-06
 Identities = 13/74 (17%), Positives = 24/74 (32%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY 159
             ++ NL   VT + I+E F  +            N               D+  +    
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 76

Query: 160 NNVLLDGKPMKIEV 173
           N   L  K ++++V
Sbjct: 77  NEESLGNKRIRVDV 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 = 39.8 bits (92), Expect = 4e-05
 Identities = 13/80 (16%), Positives = 25/80 (31%), Gaps = 7/80 (8%)

Query: 95  IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFA 154
           + V   ++V  L   V   D+ E   + G +    +   K       A V +     A  
Sbjct: 12  VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR-----QALVEFENIDSAKE 66

Query: 155 ALKRYNN--VLLDGKPMKIE 172
            +    +  V + G+     
Sbjct: 67  CVTFAADVPVYIAGQQAFFN 86

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 39.1 bits (90), Expect = 5e-05
 Identities = 13/75 (17%), Positives = 27/75 (36%), Gaps = 5/75 (6%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
             L+++NL        +  LF++    K   +  +++      A V +     + AA + 
Sbjct: 9   QILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDI----AFVEFTTELQSNAAKEA 64

Query: 159 YNNV-LLDGKPMKIE 172
                +     MKI 
Sbjct: 65  LQGFKITPTHAMKIT 79

>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 = 39.0 bits (90), Expect = 6e-05
 Identities = 15/87 (17%), Positives = 32/87 (36%), Gaps = 6/87 (6%)

Query: 88  RAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYA 147
            + G        ++ VS L P  +  D+++   E G++    +  D          V Y 
Sbjct: 5   SSGGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGM------GMVEYL 58

Query: 148 RRSDAFAALKRYNNVLLDGKPMKIEVV 174
           R+ D   AL++ ++        +   +
Sbjct: 59  RKEDMEYALRKLDDTKFRSHEGETSYI 85

>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 = 38.5 bits (89), Expect = 8e-05
 Identities = 18/89 (20%), Positives = 34/89 (38%), Gaps = 8/89 (8%)

Query: 95  IEVGTKLYVSNLHPG-VTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAF 153
           +E    +++ +   G      + +L    G +  + I    N      A +  A   DA 
Sbjct: 5   VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN-----EAFIEMATTEDAQ 59

Query: 154 AALKRY--NNVLLDGKPMKIEVVGTNAEI 180
           AA+  Y     L+ GKP+++ +      I
Sbjct: 60  AAVDYYTTTPALVFGKPVRVHLSQKYKRI 88

>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 = 38.3 bits (88), Expect = 1e-04
 Identities = 12/75 (16%), Positives = 23/75 (30%), Gaps = 7/75 (9%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY 159
            L++  L   VT  ++  L           +      +    A +  A    A   +  Y
Sbjct: 10  VLHIRKLPGEVTETEVIALGL-----PFGKVTNILMLKGKNQAFLELATEEAAITMVNYY 64

Query: 160 --NNVLLDGKPMKIE 172
                 L  +P+ I+
Sbjct: 65  SAVTPHLRNQPIYIQ 79

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.2 bits (85), Expect = 4e-04
 Identities = 17/88 (19%), Positives = 37/88 (42%), Gaps = 2/88 (2%)

Query: 88  RAAGISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVY 146
           R+   S  E G  +Y+  L     N  + + F ++  ++         NG+ +G   V +
Sbjct: 8   RSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEF 67

Query: 147 ARRSDAFAALKRYNNVLLDGKPMKIEVV 174
              +D  AAL R+   +   + +++  +
Sbjct: 68  RNEADYKAALCRHKQYM-GNRFIQVHPI 94

>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 = 36.8 bits (84), Expect = 5e-04
 Identities = 20/106 (18%), Positives = 32/106 (30%), Gaps = 5/106 (4%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           T +   NL  G    +I+E FS  G L R             +A V +    +A  A + 
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRV-----LLPEGGITAIVEFLEPLEARKAFRH 65

Query: 159 YNNVLLDGKPMKIEVVGTNAEIPLQARVNVTGVNGRRKRTVVMTSG 204
                    P+ +E            + +        K     +SG
Sbjct: 66  LAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESGPSSG 111

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.7 bits (84), Expect = 5e-04
 Identities = 15/77 (19%), Positives = 31/77 (40%), Gaps = 2/77 (2%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALK 157
              +++N+   +T  D+ +    I   +         NG+  G A V +    DA  + +
Sbjct: 9   VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER 68

Query: 158 RYNNVLLDGKPMKIEVV 174
             +   L+G+   + VV
Sbjct: 69  L-HRKKLNGREAFVHVV 84

>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 = 35.6 bits (81), Expect = 0.001
 Identities = 12/82 (14%), Positives = 30/82 (36%), Gaps = 6/82 (7%)

Query: 100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY 159
           ++ VS L P  +  D+++        +        +    G+  V + R+ D   A+++ 
Sbjct: 2   RVVVSGLPPSGSWQDLKDHM------REAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKL 55

Query: 160 NNVLLDGKPMKIEVVGTNAEIP 181
           +N        +   +    + P
Sbjct: 56  DNTKFRSHEGETAYIRVKVDGP 77

>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 = 35.3 bits (81), Expect = 0.001
 Identities = 10/75 (13%), Positives = 19/75 (25%), Gaps = 8/75 (10%)

Query: 99  TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKR 158
           T + V        +  + +        +   I             + Y  +  A  AL  
Sbjct: 5   TWVTVFGFPQASASYILLQFA------QYGNILKHVMSNTGNWMHIRYQSKLQARKALS- 57

Query: 159 YNNVLLDGKPMKIEV 173
            +  +     M I V
Sbjct: 58  KDGRIFGESIM-IGV 71

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	291
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.87
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.87
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.86
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.86
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.86
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.86
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.86
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.86
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.86
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.85
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.85
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.85
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.84
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.84
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.84
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.84
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.84
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.84
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.84
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.83
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.83
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.83
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.83
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.83
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.83
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.83
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.82
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.82
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.82
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.81
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.81
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.81
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.81
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.81
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.81
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.81
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.8
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.8
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.8
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.8
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.8
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.79
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.79
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.79
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.79
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.78
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.78
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.78
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.78
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.78
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.78
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.77
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.77
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.77
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.77
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.77
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.77
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.77
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.77
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.76
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.76
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.76
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.76
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.75
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.75
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.75
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.74
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.74
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.74
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.73
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.7
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.7
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.69
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.66
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.64
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.63
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	99.62
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.58
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.55
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.52
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.49
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.41
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.4
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.95
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.91
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.72
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.52

>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=99.87  E-value=2.4e-22  Score=146.25  Aligned_cols=79  Identities=27%  Similarity=0.365  Sum_probs=76.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      +++|||+|||+++|+++|+++|++||+|++|.|+.++ ++.+++||||+|.+.++|++||+.||+..|.+++|+|+++++
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            5789999999999999999999999999999999987 899999999999999999999999999999999999999864

>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=99.87  E-value=6.3e-22  Score=149.30  Aligned_cols=85  Identities=22%  Similarity=0.358  Sum_probs=80.0

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      .....++|||+|||+++|+++|+++|++||+|.+|.|+.++ ++.++|||||+|.+.++|++||+.||+..|++++|+|+
T Consensus         4 ~~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~   83 (99)
T d1whwa_           4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVL   83 (99)
T ss_dssp             CCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++..+.
T Consensus        84 ~a~~~~   89 (99)
T d1whwa_          84 PSTIKK   89 (99)
T ss_dssp             ECCCCS
T ss_pred             ECCCCC
Confidence            988764

>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=99.87  E-value=6.4e-22  Score=146.14  Aligned_cols=82  Identities=27%  Similarity=0.456  Sum_probs=77.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ..+++|||+|||+++|+++|+++|++||+|.+|.|+.++ ++.++|||||+|.+.++|++||+.||+..|+|+.|+|+|+
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a   84 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC   84 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            467899999999999999999999999999999999998 8999999999999999999999999999999999999998


Q ss_pred             cCC
Q 022827          175 GTN  177 (291)
Q Consensus       175 ~~~  177 (291)
                      .++
T Consensus        85 ~~k   87 (88)
T d1rk8a_          85 FVK   87 (88)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            754

>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=99.86  E-value=7.1e-22  Score=142.58  Aligned_cols=77  Identities=52%  Similarity=0.916  Sum_probs=74.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827          100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus       100 ~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      +|||+|||+++++++|+++|++||+|.+|.|+.+++++++|||||+|.+.++|++||+.||+..|.|++|+|+++.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999863

>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=99.86  E-value=1.2e-21  Score=146.21  Aligned_cols=82  Identities=30%  Similarity=0.400  Sum_probs=78.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ..+++|||+|||+++|+++|+++|++||+|.+|.|+.++ ++.++|||||+|.+.++|+.||+.||+..|++++|+|+|+
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            467899999999999999999999999999999999998 8999999999999999999999999999999999999998


Q ss_pred             cCC
Q 022827          175 GTN  177 (291)
Q Consensus       175 ~~~  177 (291)
                      ...
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            644

>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=99.86  E-value=1.2e-21  Score=142.41  Aligned_cols=79  Identities=30%  Similarity=0.439  Sum_probs=75.6

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      .++|||+|||+++++++|+++|++||+|.+|.|+.+. ++.++|||||+|.++++|++|++.||+..|.+++|+|++++|
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            3689999999999999999999999999999999987 889999999999999999999999999999999999999875

>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=99.86  E-value=7.5e-22  Score=147.27  Aligned_cols=83  Identities=24%  Similarity=0.370  Sum_probs=78.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ...++|||+|||+.+|+++|+++|++||+|.+|.|+.++ ++.++|||||+|.+.++|++||+.||+..|.|++|+|++|
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            456899999999999999999999999999999999998 8999999999999999999999999999999999999998


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      .++.
T Consensus        87 ~~~~   90 (93)
T d1x5ua1          87 SAHN   90 (93)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            8764

>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=99.86  E-value=9.5e-22  Score=145.76  Aligned_cols=83  Identities=25%  Similarity=0.382  Sum_probs=78.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ++.++|||+|||+.+++++|+++|++||+|.+|.|+.++ ++.++|||||+|.+.++|++||+.||+..|+++.|+|+++
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            466899999999999999999999999999999999998 8999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      ++..
T Consensus        86 kp~~   89 (90)
T d2cq0a1          86 KPST   89 (90)
T ss_dssp             SCCC
T ss_pred             eCCC
Confidence            8653

>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=99.86  E-value=1.3e-21  Score=148.36  Aligned_cols=83  Identities=19%  Similarity=0.316  Sum_probs=79.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      +++++|||+|||+++++++|+++|++||.|.+|.++.++ ++.++|||||+|.+.++|+.||+.||+..|.+++|+|+++
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            456889999999999999999999999999999999998 8999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      .++.
T Consensus        96 ~~k~   99 (102)
T d2cpza1          96 RSKN   99 (102)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            8765

>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=99.86  E-value=1.2e-21  Score=142.02  Aligned_cols=77  Identities=34%  Similarity=0.444  Sum_probs=74.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827          100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus       100 ~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      +|||+|||+++|+++|+++|++||+|.+|.|+.|+ ++.+++||||+|.++++|+.||+.||+..|.|++|+|++++.
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~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            69999999999999999999999999999999998 899999999999999999999999999999999999999853

>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=99.85  E-value=9.5e-22  Score=145.46  Aligned_cols=81  Identities=23%  Similarity=0.341  Sum_probs=77.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ..++|||+|||+++|+++|+++|++||+|.+|.|+.|+ ++.++|||||+|.+.++|++||+.||+..|+|++|+|+++.
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            46799999999999999999999999999999999998 89999999999999999999999999999999999999987


Q ss_pred             CC
Q 022827          176 TN  177 (291)
Q Consensus       176 ~~  177 (291)
                      +.
T Consensus        84 p~   85 (89)
T d2cqba1          84 PM   85 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.85  E-value=3.3e-21  Score=154.03  Aligned_cols=86  Identities=22%  Similarity=0.332  Sum_probs=79.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ...++|||+|||+++|+++|+++|++||+|++|.|+.++ ++.++|||||+|.+.++|++||+.||++.|+|+.|+|+++
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            445789999999999999999999999999999999998 8999999999999999999999999999999999999998


Q ss_pred             cCCCCCc
Q 022827          175 GTNAEIP  181 (291)
Q Consensus       175 ~~~~~~~  181 (291)
                      ......+
T Consensus       120 ~~~~~~p  126 (139)
T d1u6fa1         120 ASGHQRP  126 (139)
T ss_dssp             SCCCCCC
T ss_pred             CCCCCCC
Confidence            8665443

>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=99.85  E-value=2.4e-21  Score=141.33  Aligned_cols=76  Identities=32%  Similarity=0.430  Sum_probs=73.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      ++.++|||+|||+++|+++|+++|++||+|.+|.|+.++ ++.+++||||+|.+.++|++||+.||+..|+|++|+|
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            456899999999999999999999999999999999998 8999999999999999999999999999999999987

>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=99.85  E-value=3.5e-21  Score=143.88  Aligned_cols=84  Identities=26%  Similarity=0.364  Sum_probs=78.3

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC--CCCCceEEEEEEcCHHHHHHHHHHh-CCceeCCeeeEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK--NGRPSGSAEVVYARRSDAFAALKRY-NNVLLDGKPMKI  171 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~--tg~~kG~afV~F~~~~~A~~Ai~~l-ng~~l~g~~i~V  171 (291)
                      ....++|||.|||+++++++|+++|++||.|..|.|+.+.  ++.++|||||+|.+.++|++||+.| |+..|+|++|+|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            3567899999999999999999999999999999998875  7899999999999999999999998 899999999999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      +||..+.
T Consensus        85 ~~A~~~~   91 (94)
T d2cpha1          85 EWADSEV   91 (94)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9998765

>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=99.84  E-value=4.5e-21  Score=140.52  Aligned_cols=79  Identities=35%  Similarity=0.616  Sum_probs=74.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCC--eeeEEE
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDG--KPMKIE  172 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g--~~i~V~  172 (291)
                      ...++|||+|||+++++++|+++|++||+|.+|.|+.++ ++.++|||||+|.+.++|++||+.||+..+.+  ++|+|+
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            356789999999999999999999999999999999998 89999999999999999999999999999977  889999


Q ss_pred             Ee
Q 022827          173 VV  174 (291)
Q Consensus       173 ~a  174 (291)
                      +|
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>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=99.84  E-value=6e-21  Score=139.91  Aligned_cols=78  Identities=27%  Similarity=0.462  Sum_probs=73.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCC--eeeEEEE
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDG--KPMKIEV  173 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g--~~i~V~~  173 (291)
                      ..++|||+|||+++|+++|+++|++||+|.+|.|+.++ ++.+++||||+|.++++|++||+.||+..|.|  ++|+|.|
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            46789999999999999999999999999999999998 89999999999999999999999999999997  5688887


Q ss_pred             e
Q 022827          174 V  174 (291)
Q Consensus       174 a  174 (291)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.84  E-value=2.3e-21  Score=142.14  Aligned_cols=80  Identities=24%  Similarity=0.373  Sum_probs=76.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecCC
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTN  177 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~~  177 (291)
                      .+|||+|||+.+|+++|+++|++||+|.+|.|+.|+ ++.+++||||+|.++++|+.||+.||+..|.+++|+|+++.+.
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            479999999999999999999999999999999998 8999999999999999999999999999999999999999765


Q ss_pred             C
Q 022827          178 A  178 (291)
Q Consensus       178 ~  178 (291)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.84  E-value=3.6e-21  Score=139.68  Aligned_cols=79  Identities=18%  Similarity=0.248  Sum_probs=69.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      .+||||+|||+++|+++|+++|++||+|..+.++.+. ++.+++||||+|.+.++|++||+.||+..|+|++|+|+++.|
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            3799999999999999999999999999988887776 889999999999999999999999999999999999999875

>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=99.84  E-value=6.4e-21  Score=141.11  Aligned_cols=82  Identities=22%  Similarity=0.405  Sum_probs=77.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ...+|||+|||+++|+++|+++|++||.|..|.++.+. ++.++|||||+|.++++|++||+.||+..|.|++|+|+++.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            56789999999999999999999999999999998887 89999999999999999999999999999999999999987


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      ++.
T Consensus        84 ~~~   86 (90)
T d1x5sa1          84 KSS   86 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            664

>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=99.84  E-value=7.1e-21  Score=141.05  Aligned_cols=82  Identities=20%  Similarity=0.317  Sum_probs=75.6

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ....++|||.|||+++|+++|+++|++||+|..|.|+.|+ ++.++|||||+|.+.++|++||+.  ...|+|+.|.|++
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~   82 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKL   82 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEEC
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEe
Confidence            3467899999999999999999999999999999999998 899999999999999999999974  4589999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +.++.
T Consensus        83 a~~k~   87 (90)
T d2cqga1          83 PNSKQ   87 (90)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            87654

>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=99.84  E-value=1.4e-20  Score=142.94  Aligned_cols=82  Identities=26%  Similarity=0.390  Sum_probs=75.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ...++|||+|||+.+|+++|+++|++||+|.+|.|+.++ ++.++|||||+|.+.++|++||+.+|. .|+|++|.|+++
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a   86 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLA   86 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEES
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEc
Confidence            345789999999999999999999999999999999998 899999999999999999999988875 799999999998


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      ....
T Consensus        87 ~~~~   90 (103)
T d2cqda1          87 YLGA   90 (103)
T ss_dssp             TTTC
T ss_pred             CCCC
Confidence            7654

>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=99.83  E-value=2.8e-20  Score=138.58  Aligned_cols=82  Identities=21%  Similarity=0.419  Sum_probs=76.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ...++|||+|||+.+++++|+++|++||+|+.|.|+.++.+ +++||||+|.+.++|++||+.||+..|+|+.|+|++++
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~   87 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   87 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            45678999999999999999999999999999999988744 68999999999999999999999999999999999998


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      ++.
T Consensus        88 ~r~   90 (93)
T d2cq3a1          88 ARV   90 (93)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            765

>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=99.83  E-value=1.8e-20  Score=137.11  Aligned_cols=78  Identities=23%  Similarity=0.296  Sum_probs=73.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ..++|||+|||+++|+++|+++|++||+|..|.|+.|+ ++.++|||||+|.+.++|++||+ ++++.|+|+.|+|..|.
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            44799999999999999999999999999999999998 89999999999999999999996 68999999999999875

>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=99.83  E-value=2e-20  Score=140.28  Aligned_cols=87  Identities=21%  Similarity=0.386  Sum_probs=79.0

Q ss_pred             CCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhC------CceeC
Q 022827           93 SGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYN------NVLLD  165 (291)
Q Consensus        93 ~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~ln------g~~l~  165 (291)
                      ......++|||+|||+++|+++|+++|++||+|..+.++.++ ++.++|||||+|.+.++|++||+.||      +..|+
T Consensus         3 ~~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~   82 (98)
T d1x4ha1           3 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   82 (98)
T ss_dssp             CCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             cCCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEEC
Confidence            345567899999999999999999999999999999999988 88899999999999999999999886      57789


Q ss_pred             CeeeEEEEecCCCC
Q 022827          166 GKPMKIEVVGTNAE  179 (291)
Q Consensus       166 g~~i~V~~a~~~~~  179 (291)
                      |+.|+|+++.++.+
T Consensus        83 gr~l~v~~a~~k~~   96 (98)
T d1x4ha1          83 GRQLKVDLAVTRDE   96 (98)
T ss_dssp             SCEEEEECCCCCCC
T ss_pred             CEEEEEEECCCCCc
Confidence            99999999887653

>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=99.83  E-value=3.1e-21  Score=146.72  Aligned_cols=81  Identities=20%  Similarity=0.529  Sum_probs=76.9

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      .++|||+|||+++|+++|+++|++||+|.+|.|+.++ ++.++|||||+|.+.++|++||+.||+..|.++.|+|+++.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999999999999988 899999999999999999999999999999999999999876


Q ss_pred             CC
Q 022827          177 NA  178 (291)
Q Consensus       177 ~~  178 (291)
                      ..
T Consensus        88 ~~   89 (104)
T d1p1ta_          88 EK   89 (104)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.83  E-value=2.8e-21  Score=139.10  Aligned_cols=75  Identities=24%  Similarity=0.366  Sum_probs=71.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      |+|||+|||+++|+++|+++|++||+|.+|.|+.|+ +++++|||||+|.++++|++||+ +|++.|+|+.|+|.+|
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            689999999999999999999999999999999998 89999999999999999999996 6999999999999976

>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=99.83  E-value=1e-20  Score=137.91  Aligned_cols=78  Identities=22%  Similarity=0.356  Sum_probs=72.9

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEE-EEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecCCC
Q 022827          101 LYVSNLHPGVTNDDIRELFSEIGELKRY-AIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNA  178 (291)
Q Consensus       101 l~V~nL~~~~te~dL~~~F~~~G~v~~v-~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~~~  178 (291)
                      |||+|||+++|+++|+++|++||.|.++ .|+.++ +++++|||||+|.+.++|++||+.||+..|+|++|+|+++.++.
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            8999999999999999999999999764 778887 89999999999999999999999999999999999999988654

>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=99.83  E-value=4.1e-20  Score=136.80  Aligned_cols=82  Identities=30%  Similarity=0.311  Sum_probs=75.2

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      .+.++|||+|||+++|+++|+++|++||+|.+|.|+.++.. .++||||+|.+.++|++||+.||+..|.++.|+|.++.
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~-~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc-cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            35679999999999999999999999999999999988733 37899999999999999999999999999999999987


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      +..
T Consensus        85 ~~~   87 (90)
T d2cqia1          85 TPS   87 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            654

>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=99.82  E-value=1.3e-20  Score=139.31  Aligned_cols=80  Identities=19%  Similarity=0.355  Sum_probs=74.4

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecCC
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTN  177 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~~  177 (291)
                      ..+|||+|||+++|+++|+++|++||.|..|.|+.++. .+++||||+|.+.++|++||+.||+..|+|+.|+|++++++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT-BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC-CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            46899999999999999999999999999999998874 36899999999999999999999999999999999999866


Q ss_pred             C
Q 022827          178 A  178 (291)
Q Consensus       178 ~  178 (291)
                      .
T Consensus        87 ~   87 (89)
T d1cvja2          87 K   87 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.82  E-value=2e-20  Score=136.95  Aligned_cols=77  Identities=25%  Similarity=0.437  Sum_probs=71.4

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CC---CCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827          101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NG---RPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus       101 l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg---~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      |||+|||+++|+++|+++|++||+|.+|.|+.++ ++   .++|||||+|.+.++|++||+.||+..|+|++|+|+++..
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            8999999999999999999999999999999887 33   4689999999999999999999999999999999999854


Q ss_pred             C
Q 022827          177 N  177 (291)
Q Consensus       177 ~  177 (291)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.82  E-value=2e-20  Score=137.39  Aligned_cols=81  Identities=20%  Similarity=0.357  Sum_probs=71.6

Q ss_pred             CCcEEEEcCCCCCCC-HHHHHHHHHhcCCeeEEEEeeCC--CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           97 VGTKLYVSNLHPGVT-NDDIRELFSEIGELKRYAIHFDK--NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        97 ~~~~l~V~nL~~~~t-e~dL~~~F~~~G~v~~v~i~~d~--tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ..++|||+|||+++| +++|+++|++||+|.+|.|+.+.  ++.++|||||+|.+.++|++|| +||+..|+|+.|+|++
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 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHH-hcCCCEECCEEEEEEE
Confidence            568999999999976 56699999999999999987653  8899999999999999999999 5999999999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +.++|
T Consensus        82 a~~kP   86 (86)
T d2ghpa3          82 ADKKP   86 (86)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98654

>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=99.82  E-value=1.6e-20  Score=134.37  Aligned_cols=73  Identities=22%  Similarity=0.426  Sum_probs=69.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827          100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus       100 ~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      +|||+|||+++||++|+++|++||+|..|.|+.++ +++++|||||+|.++++|++||+ +++..|+|+.|.|..
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~r   74 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKR   74 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeE
Confidence            59999999999999999999999999999999998 89999999999999999999996 799999999999864

>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=99.81  E-value=3.8e-20  Score=139.61  Aligned_cols=85  Identities=28%  Similarity=0.483  Sum_probs=76.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCee--------EEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCcee
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELK--------RYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLL  164 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~--------~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l  164 (291)
                      .....++|||+|||+.+|+++|+++|++||+|.        .+.+..++ ++++++||||+|.++++|++||+.||+..|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            345678999999999999999999999999884        45667776 789999999999999999999999999999


Q ss_pred             CCeeeEEEEecCCC
Q 022827          165 DGKPMKIEVVGTNA  178 (291)
Q Consensus       165 ~g~~i~V~~a~~~~  178 (291)
                      +|++|+|+++++++
T Consensus        84 ~gr~i~V~~a~~~~   97 (101)
T d2cpea1          84 QGSKLKVSLARKKP   97 (101)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCEEEEEEEcCCCC
Confidence            99999999998764

>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=99.81  E-value=6.7e-20  Score=137.34  Aligned_cols=78  Identities=18%  Similarity=0.313  Sum_probs=73.6

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      ..++|||+|||+++++++|+++|++||+|.+|.|+.+     ++||||+|.+.++|++||+.||+..|.++.|+|+|+++
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~-----kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~   91 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   91 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            5689999999999999999999999999999999977     79999999999999999999999999999999999987


Q ss_pred             CCC
Q 022827          177 NAE  179 (291)
Q Consensus       177 ~~~  179 (291)
                      ++.
T Consensus        92 ~p~   94 (96)
T d1x4ga1          92 SPD   94 (96)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            653

>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=99.81  E-value=3.7e-20  Score=140.52  Aligned_cols=80  Identities=19%  Similarity=0.287  Sum_probs=75.2

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      .++|||+|||+++|+++|+++|++||+|..|.|+.|+ ++.++|||||+|.+.++|++|| .++++.|+|+.|+|.++.+
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 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHH-TSCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHH-HhCCCeECCEEEEEEECcc
Confidence            3789999999999999999999999999999999998 8899999999999999999999 5799999999999999886


Q ss_pred             CC
Q 022827          177 NA  178 (291)
Q Consensus       177 ~~  178 (291)
                      +.
T Consensus        99 ke  100 (103)
T d1x4ba1          99 RE  100 (103)
T ss_dssp             CC
T ss_pred             cC
Confidence            64

>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=99.81  E-value=6.7e-20  Score=137.00  Aligned_cols=82  Identities=21%  Similarity=0.307  Sum_probs=73.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ...+.++|||+|||+++|+++|+++|++||.|..|.+..+  ..+++||||+|.+.++|++||+.||++.|++++|+|++
T Consensus        10 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~--~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~   87 (95)
T d1x4aa1          10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc--ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            3456789999999999999999999999999998887654  45689999999999999999999999999999999999


Q ss_pred             ecCC
Q 022827          174 VGTN  177 (291)
Q Consensus       174 a~~~  177 (291)
                      ++..
T Consensus        88 a~~~   91 (95)
T d1x4aa1          88 PRSG   91 (95)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            8643

>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=99.81  E-value=2.1e-20  Score=141.42  Aligned_cols=78  Identities=19%  Similarity=0.346  Sum_probs=74.0

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      .++|||+|||+++|+++|+++|+.||+|.+|.|+.++ +++++|||||+|.+.++|++|| .||+..|.|+.|.|+++.+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~-~l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHH-HHCCCEECCEEEEEEECCC
Confidence            3689999999999999999999999999999999998 8999999999999999999999 5999999999999998753

>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=99.81  E-value=8.3e-20  Score=131.66  Aligned_cols=76  Identities=16%  Similarity=0.326  Sum_probs=72.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      .++|||+|||+++|+++|+++|++||.|..+.++.++ ++.++|||||+|.++++|++|+ .+|++.|+|+.|+|+.|
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            4799999999999999999999999999999999998 8899999999999999999999 58999999999999876

>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=99.81  E-value=9.6e-20  Score=140.48  Aligned_cols=79  Identities=22%  Similarity=0.321  Sum_probs=73.3

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      +.+++|||+|||+++|+++|+++|++||+|++|.|..+  +.++|||||+|.+.++|..||+.||+..|+|+.|.|.++.
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~--~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc--CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            46789999999999999999999999999999988754  5668999999999999999999999999999999999976


Q ss_pred             C
Q 022827          176 T  176 (291)
Q Consensus       176 ~  176 (291)
                      .
T Consensus        83 ~   83 (114)
T d2f9da1          83 A   83 (114)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=99.80  E-value=4.4e-20  Score=131.71  Aligned_cols=74  Identities=19%  Similarity=0.319  Sum_probs=70.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827          100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus       100 ~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      +|||+|||+++|+++|+++|++||.|..+.++.++ ++.+++||||+|.+.++|++||+ +|++.|+|++|+|++|
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            59999999999999999999999999999999988 88999999999999999999995 9999999999999875

>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=99.80  E-value=1.8e-20  Score=141.74  Aligned_cols=84  Identities=33%  Similarity=0.449  Sum_probs=78.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      +++++|||+|||+++++++|+++|++||.|..+.|+.+. ++.+++||||+|.+.++|+.||+.||+..|.|++|+|+++
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            467899999999999999999999999999999888887 8999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 022827          175 GTNAE  179 (291)
Q Consensus       175 ~~~~~  179 (291)
                      +++.+
T Consensus        96 k~k~~  100 (102)
T d2cpxa1          96 KNKKQ  100 (102)
T ss_dssp             CCCSC
T ss_pred             CCccc
Confidence            87653

>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=99.80  E-value=2.7e-20  Score=133.16  Aligned_cols=74  Identities=19%  Similarity=0.366  Sum_probs=69.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827          100 KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus       100 ~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      +|||+|||+++|+++|+++|++||+|..|.|+.++ ++.++|||||+|.+.++|++||+ .+++.|+|+.|.|.+|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            69999999999999999999999999999999998 89999999999999999999995 4778899999999864

>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=99.80  E-value=9.5e-21  Score=140.64  Aligned_cols=81  Identities=19%  Similarity=0.213  Sum_probs=75.0

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      .....+|||+|||+++|+++|+++|++||.|..|.|+.+.+++++|||||+|.+.++|++||+ ||+..|.|++|+|+++
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            345679999999999999999999999999999988877799999999999999999999995 9999999999999998


Q ss_pred             cC
Q 022827          175 GT  176 (291)
Q Consensus       175 ~~  176 (291)
                      +.
T Consensus        89 k~   90 (91)
T d1fjeb1          89 KG   90 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=99.80  E-value=1.2e-19  Score=132.92  Aligned_cols=79  Identities=23%  Similarity=0.352  Sum_probs=72.8

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKR-YAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~-v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      +..++|||+|||++++++||+++|+.|+.|.. +.+..+.++.++|||||+|.+.++|++||+.||+..|.+++|+|+++
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45678999999999999999999999999975 56777779999999999999999999999999999999999999974

>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=99.79  E-value=1.7e-19  Score=136.86  Aligned_cols=82  Identities=18%  Similarity=0.283  Sum_probs=73.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC--CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK--NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~--tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      ..+.++|||.|||+++|+++|+++|+.|| |+.+.++.+.  ++.++|||||+|.+.++|++|+ .||+..|+++.|+|+
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~   89 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEE
Confidence            34568999999999999999999999998 7777777765  7889999999999999998777 699999999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++.+..
T Consensus        90 ~a~~~~   95 (104)
T d1wi8a_          90 VADQAQ   95 (104)
T ss_dssp             ECCCCC
T ss_pred             ECCCCC
Confidence            987654

>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=99.79  E-value=5.6e-20  Score=139.00  Aligned_cols=79  Identities=18%  Similarity=0.271  Sum_probs=74.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ..++|||+|||+++++++|+++|++||+|..+.+..+.++.+++||||+|.+.++|++||+.||+..|.+++|.|..+.
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~   95 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE   95 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCC
Confidence            4579999999999999999999999999999999998889999999999999999999999999999999999886544

>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=99.79  E-value=1.7e-19  Score=132.31  Aligned_cols=77  Identities=29%  Similarity=0.451  Sum_probs=72.5

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      ..++|||+|||+++++++|+++|++||+|.+|.+..+     ++||||+|.+.++|++||+.||+..|+|+.|+|++|..
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-----k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~   81 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   81 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            4578999999999999999999999999999999876     78999999999999999999999999999999999886


Q ss_pred             CC
Q 022827          177 NA  178 (291)
Q Consensus       177 ~~  178 (291)
                      ..
T Consensus        82 ~~   83 (86)
T d2cpja1          82 SA   83 (86)
T ss_dssp             CS
T ss_pred             cC
Confidence            64

>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=99.79  E-value=2.9e-19  Score=130.83  Aligned_cols=77  Identities=17%  Similarity=0.188  Sum_probs=73.1

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      .++|||+|||+++|+++|+++|+.||+|..|.|..+.++.++|||||+|.++++|++|| ++++..|.|+.|.|++..
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al-~~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV-ETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHH-TCCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHH-HHCCCEECCEEEEEEEcC
Confidence            47999999999999999999999999999999999889999999999999999999999 579999999999999864

>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=99.78  E-value=2.5e-19  Score=129.30  Aligned_cols=76  Identities=21%  Similarity=0.315  Sum_probs=70.6

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ..+++|||+||+  +|+++|+++|++||+|.+|.+..+     ++||||+|.+.++|++||+.||+..|+|+.|+|+|++
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~-----~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   75 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   75 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC-----CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            467899999996  899999999999999999999865     7899999999999999999999999999999999998


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      +++
T Consensus        76 ~~P   78 (79)
T d2bz2a1          76 KQP   78 (79)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            664

>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=99.78  E-value=3.9e-19  Score=129.44  Aligned_cols=76  Identities=17%  Similarity=0.192  Sum_probs=70.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCcee-CCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLL-DGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l-~g~~i~V~~a  174 (291)
                      +++++|||.|||+++|+++|+++|++||+|+.|.|+.++    ++||||+|.+.++|++|++.||+..| ++++|+|+|+
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~a   81 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFA   81 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEe
Confidence            467899999999999999999999999999999998653    68999999999999999999999888 5689999998


Q ss_pred             c
Q 022827          175 G  175 (291)
Q Consensus       175 ~  175 (291)
                      +
T Consensus        82 k   82 (83)
T d2b0ga1          82 K   82 (83)
T ss_dssp             C
T ss_pred             c
Confidence            6

>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=2.7e-19  Score=134.52  Aligned_cols=81  Identities=17%  Similarity=0.249  Sum_probs=73.6

Q ss_pred             CCCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEE
Q 022827           92 ISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKI  171 (291)
Q Consensus        92 ~~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V  171 (291)
                      ++......+|||+|||++++++||+++|++||+|++|.|..      ++||||+|.+.++|++||+.||+..|+++.|+|
T Consensus         9 p~~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v   82 (98)
T d1wg4a_           9 PPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGET   82 (98)
T ss_dssp             CCCCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEE
Confidence            34455678999999999999999999999999999999863      589999999999999999999999999999999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      .++....
T Consensus        83 ~~~~~~~   89 (98)
T d1wg4a_          83 SYIRVYP   89 (98)
T ss_dssp             EEEEEEC
T ss_pred             EEEecCC
Confidence            9987654

>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=99.78  E-value=2.8e-19  Score=137.00  Aligned_cols=77  Identities=22%  Similarity=0.248  Sum_probs=71.4

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      ..++|||+|||+++++++|++||+.||+|..|.|..     +++||||+|.+.++|++||+.||+..|.+++|+|+++..
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~-----~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~   83 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec-----cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCC
Confidence            457999999999999999999999999999998854     378999999999999999999999999999999999876


Q ss_pred             CC
Q 022827          177 NA  178 (291)
Q Consensus       177 ~~  178 (291)
                      ..
T Consensus        84 ~~   85 (111)
T d1whxa_          84 GV   85 (111)
T ss_dssp             TT
T ss_pred             Cc
Confidence            55

>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=99.78  E-value=9.1e-19  Score=128.23  Aligned_cols=79  Identities=25%  Similarity=0.319  Sum_probs=72.1

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      +...++|||+|||+++|+++|+++|++||.|..+.+...     ++||||+|.+.++|++||+.||+..|.|+.|+|+++
T Consensus         5 ~~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~-----rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~a   79 (86)
T d2cpda1           5 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-----RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA   79 (86)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-----SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC
T ss_pred             ccCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccc-----cEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            345689999999999999999999999999998887654     789999999999999999999999999999999998


Q ss_pred             cCCC
Q 022827          175 GTNA  178 (291)
Q Consensus       175 ~~~~  178 (291)
                      ++..
T Consensus        80 kP~~   83 (86)
T d2cpda1          80 KPVD   83 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            7654

>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=99.78  E-value=3.5e-19  Score=133.85  Aligned_cols=76  Identities=22%  Similarity=0.437  Sum_probs=69.2

Q ss_pred             CCCCcEEEEcCCC-CCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLH-PGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~-~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ....++|||.||| +.+++++|+++|++||+|++|.|.       ++||||+|.+.++|++||+.||+..|+|++|+|++
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~-------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE-------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe-------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3456789999997 578899999999999999999984       78999999999999999999999999999999999


Q ss_pred             ecCC
Q 022827          174 VGTN  177 (291)
Q Consensus       174 a~~~  177 (291)
                      +.+.
T Consensus        85 a~~~   88 (98)
T d1wf2a_          85 AAEP   88 (98)
T ss_dssp             TTSC
T ss_pred             CCCC
Confidence            8654

>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=99.78  E-value=6.2e-19  Score=129.71  Aligned_cols=79  Identities=22%  Similarity=0.321  Sum_probs=70.9

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCcee-CCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLL-DGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l-~g~~i~V~~a  174 (291)
                      +++++|||+|||+++|+++|+++|++||.|..+.+...   +.++||||+|.+.++|.+|+..||+..| ++++|+|+++
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~---~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS---SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee---cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            36789999999999999999999999999988877654   3467999999999999999999999988 6899999998


Q ss_pred             cCC
Q 022827          175 GTN  177 (291)
Q Consensus       175 ~~~  177 (291)
                      ++.
T Consensus        85 k~~   87 (88)
T d2adca2          85 KST   87 (88)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            764

>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=99.77  E-value=3.8e-19  Score=131.01  Aligned_cols=76  Identities=18%  Similarity=0.267  Sum_probs=67.2

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      .+++|||+|||++++++||+++|++|| ++.+.+..     +++||||+|.+.++|++||+.||+..|+|+.|+|+++..
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~~-----~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~   77 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDR-----NKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEEG-----GGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeeec-----cCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            467999999999999999999999999 34344443     489999999999999999999999999999999999876


Q ss_pred             CC
Q 022827          177 NA  178 (291)
Q Consensus       177 ~~  178 (291)
                      +.
T Consensus        78 ~~   79 (88)
T d1wg1a_          78 DA   79 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.77  E-value=5e-19  Score=135.18  Aligned_cols=77  Identities=34%  Similarity=0.466  Sum_probs=71.1

Q ss_pred             CcEEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           98 GTKLYVSNLHP-GVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        98 ~~~l~V~nL~~-~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      +++|||+||++ .+|+++|+++|+.||+|++|.|+.++    +|||||+|++.++|++||+.||+..|.|+.|+|++++.
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~~   77 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH   77 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            57999999965 59999999999999999999999875    78999999999999999999999999999999999865


Q ss_pred             CC
Q 022827          177 NA  178 (291)
Q Consensus       177 ~~  178 (291)
                      ..
T Consensus        78 ~~   79 (109)
T d2adca1          78 QN   79 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.77  E-value=2.7e-19  Score=129.46  Aligned_cols=75  Identities=32%  Similarity=0.434  Sum_probs=68.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCc-eeCCeeeEEEEecCC
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNV-LLDGKPMKIEVVGTN  177 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~-~l~g~~i~V~~a~~~  177 (291)
                      .+|||+|||+++|+++|+++|++||.|..+.+...     ++||||+|.+.++|++||+.||+. .|+|++|+|+++.++
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-----rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k   76 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   76 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE-----TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc-----cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCc
Confidence            47999999999999999999999999987777655     789999999999999999999985 799999999999876


Q ss_pred             C
Q 022827          178 A  178 (291)
Q Consensus       178 ~  178 (291)
                      .
T Consensus        77 ~   77 (80)
T d2cqha1          77 K   77 (80)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.77  E-value=4.3e-19  Score=132.77  Aligned_cols=81  Identities=21%  Similarity=0.411  Sum_probs=72.6

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      ...+.++|||+|||+++|+++|+++|++||.|..+..    ++.+++||||+|.+.++|++||+.||+..|+|++|+|++
T Consensus        12 ~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3456789999999999999999999999998875532    567799999999999999999999999999999999999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +.++.
T Consensus        88 a~~k~   92 (96)
T d1fjca_          88 TGEKG   92 (96)
T ss_dssp             CSSSC
T ss_pred             eCCCC
Confidence            98765

>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=99.77  E-value=5.9e-19  Score=131.98  Aligned_cols=82  Identities=15%  Similarity=0.214  Sum_probs=73.7

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEeeCC--CCCCceEEEEEEcCHHHHHHHHHHhCC--ceeCCeeeEEE
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGE-LKRYAIHFDK--NGRPSGSAEVVYARRSDAFAALKRYNN--VLLDGKPMKIE  172 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~-v~~v~i~~d~--tg~~kG~afV~F~~~~~A~~Ai~~lng--~~l~g~~i~V~  172 (291)
                      +|+|||+|||.++|+++|+++|++||+ |..|.|+.+.  +++++|||||+|.+.++|..||+.|++  ..+.+++|+|+
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            478999999999999999999999996 8899998876  688999999999999999999999965  55689999999


Q ss_pred             EecCCCC
Q 022827          173 VVGTNAE  179 (291)
Q Consensus       173 ~a~~~~~  179 (291)
                      ||.+...
T Consensus        81 ~A~p~~~   87 (96)
T d2disa1          81 WAEPEID   87 (96)
T ss_dssp             ESCSSCS
T ss_pred             EcCCCCC
Confidence            9987653

>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=99.77  E-value=1e-18  Score=131.02  Aligned_cols=78  Identities=18%  Similarity=0.302  Sum_probs=71.7

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCC--eeeEEEE
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDG--KPMKIEV  173 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g--~~i~V~~  173 (291)
                      .+.++|||+|||+++++++|+++|++||+|..|.|..+     ++||||+|.+.++|++|++.||+..|.+  ++|+|+|
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~-----~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~   89 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-----ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            46789999999999999999999999999999999866     7899999999999999999999999986  5899999


Q ss_pred             ecCCC
Q 022827          174 VGTNA  178 (291)
Q Consensus       174 a~~~~  178 (291)
                      +++.+
T Consensus        90 ak~~~   94 (97)
T d1whya_          90 AKSGP   94 (97)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            88654

>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=99.77  E-value=4.8e-19  Score=133.98  Aligned_cols=81  Identities=25%  Similarity=0.365  Sum_probs=74.0

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ....+|||.|||+++|++||+++|+.|+ |..|.++++.++.++|||||+|.++++|++||+ +|+..|.++.|+|.++.
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~   90 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcC
Confidence            4567999999999999999999999997 557888888899999999999999999999995 89999999999999988


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      ...
T Consensus        91 ~~~   93 (102)
T d1weza_          91 TAG   93 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            664

>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=99.77  E-value=1.1e-18  Score=124.70  Aligned_cols=74  Identities=16%  Similarity=0.240  Sum_probs=68.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ++|||+|||+++++++|+++|+.||+|+.|.|+.++.+. ++||||+|.++++|++|| .+|+..|+|++|.|+.+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~-~~~afV~F~~~~~a~~Al-~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN-FRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS-SEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc-ceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            589999999999999999999999999999999988554 579999999999999999 68999999999999865

>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=99.76  E-value=1.1e-18  Score=132.41  Aligned_cols=84  Identities=18%  Similarity=0.166  Sum_probs=73.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      ......+|||.|||+++|++||+++|..|+.|..+.++.+. ++.++|||||+|.++++|++|| .+|+..|.++.|.|.
T Consensus        11 ~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~-~~~~~~i~gR~i~V~   89 (104)
T d1wg5a_          11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL-KKHKERIGHRYIEIF   89 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHH-TTTTCCSSSSCCEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHH-hhCCCEEcceEEEEE
Confidence            34456689999999999999999999999998875555544 8999999999999999999999 489999999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      ++.+..
T Consensus        90 ~~~~~~   95 (104)
T d1wg5a_          90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            987654

>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=99.76  E-value=4.8e-19  Score=130.75  Aligned_cols=76  Identities=29%  Similarity=0.514  Sum_probs=69.4

Q ss_pred             CCcEEEEcCCCCCCCHHHH---HHHHHhcCCeeEEEEeeCC-CCC---CceEEEEEEcCHHHHHHHHHHhCCceeCCeee
Q 022827           97 VGTKLYVSNLHPGVTNDDI---RELFSEIGELKRYAIHFDK-NGR---PSGSAEVVYARRSDAFAALKRYNNVLLDGKPM  169 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL---~~~F~~~G~v~~v~i~~d~-tg~---~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i  169 (291)
                      ..++|||.|||++++++||   +++|++||+|.+|.|+.++ ++.   +.+||||+|.+.++|++||+.||+..|+|++|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            4578999999999999999   7789999999999999987 443   45999999999999999999999999999999


Q ss_pred             EEE
Q 022827          170 KIE  172 (291)
Q Consensus       170 ~V~  172 (291)
                      +|+
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            985

>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=99.76  E-value=1.5e-19  Score=132.87  Aligned_cols=74  Identities=19%  Similarity=0.331  Sum_probs=68.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecCCC
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNA  178 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~~~  178 (291)
                      .+|||+|||+++|+++|+++|++||+|.+|.|+.+      |||||+|.+.++|++||+.||+..|.++.|+|.++....
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~   74 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            36999999999999999999999999999998753      799999999999999999999999999999998876544

>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=99.76  E-value=2.3e-19  Score=126.98  Aligned_cols=70  Identities=24%  Similarity=0.350  Sum_probs=67.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeE
Q 022827          101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMK  170 (291)
Q Consensus       101 l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~  170 (291)
                      |||+|||+++|+++|+++|++||.|..+.++.++ ++.+++||||+|.+.++|++||+.||+..|+|+.|+
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            8999999999999999999999999999999988 899999999999999999999999999999998874

>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=99.75  E-value=9.4e-19  Score=129.59  Aligned_cols=80  Identities=24%  Similarity=0.445  Sum_probs=71.7

Q ss_pred             CCcEEEEcCCCCCCCHHHHHH----HHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           97 VGTKLYVSNLHPGVTNDDIRE----LFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~----~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      |+++|||+|||+.++++||++    +|++||+|.+|.+..  ++.+++||||+|.+.++|.+||+.||+..|++++|+|+
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~--~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~   79 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   79 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee--eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            578999999999999999864    589999999887643  45678999999999999999999999999999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      +++++.
T Consensus        80 ~ak~~~   85 (91)
T d1nu4a_          80 YAKTDS   85 (91)
T ss_dssp             ECSSCC
T ss_pred             EeCCCc
Confidence            998764

>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=99.75  E-value=6.6e-19  Score=129.66  Aligned_cols=77  Identities=19%  Similarity=0.268  Sum_probs=69.1

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      ..+++|||+|||+++|+++|+++|++||+|.+|.+..+    +++||||+|.+.++|++||.  +++.|+|++|+|+++.
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~----~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec----cCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCC
Confidence            46789999999999999999999999999999877644    57899999999999999984  7889999999999987


Q ss_pred             CCC
Q 022827          176 TNA  178 (291)
Q Consensus       176 ~~~  178 (291)
                      ++.
T Consensus        77 ~k~   79 (88)
T d1wf0a_          77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.75  E-value=3.3e-18  Score=122.12  Aligned_cols=72  Identities=24%  Similarity=0.375  Sum_probs=65.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecCCC
Q 022827          101 LYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGTNA  178 (291)
Q Consensus       101 l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~~~  178 (291)
                      |||+|||+++++++|+++|++|| +..+.+.     ++++||||+|.+.++|++|++.||+..|.|++|+|++++.+.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~-----~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD-----KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE-----TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec-----ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            79999999999999999999998 5555554     358999999999999999999999999999999999997654

>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=99.74  E-value=5.5e-18  Score=124.55  Aligned_cols=79  Identities=16%  Similarity=0.159  Sum_probs=71.9

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHh--CCceeCCeeeEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY--NNVLLDGKPMKIE  172 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~l--ng~~l~g~~i~V~  172 (291)
                      .+++++|||+|||+++++++|+++|++||.|.+|.+..+     ++||||+|.+.++|++|++.+  ++..+.|++|+|+
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~-----~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~   79 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   79 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc-----ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEE
Confidence            458899999999999999999999999999999999866     689999999999999999865  5789999999999


Q ss_pred             EecCCC
Q 022827          173 VVGTNA  178 (291)
Q Consensus       173 ~a~~~~  178 (291)
                      +++.+.
T Consensus        80 ~sk~~~   85 (88)
T d2cq1a1          80 YSNHKE   85 (88)
T ss_dssp             ECSCSS
T ss_pred             ECCCCC
Confidence            987553

>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=99.74  E-value=2.5e-18  Score=131.34  Aligned_cols=80  Identities=19%  Similarity=0.161  Sum_probs=71.7

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCcee--CCeeeEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLL--DGKPMKIE  172 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l--~g~~i~V~  172 (291)
                      ..+..+|||+|||+.+|+++|+++|++||.|.+|.|+.++   +++||||+|.+.++|++||+.||+..|  .++.|+|.
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~---~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET---TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC---CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            3466799999999999999999999999999999998774   489999999999999999999999988  47788888


Q ss_pred             EecCC
Q 022827          173 VVGTN  177 (291)
Q Consensus       173 ~a~~~  177 (291)
                      +++..
T Consensus        81 ~s~~~   85 (108)
T d2adba1          81 FSKLT   85 (108)
T ss_dssp             ECSSC
T ss_pred             ecCCc
Confidence            87654

>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=99.74  E-value=1.3e-17  Score=126.44  Aligned_cols=80  Identities=15%  Similarity=0.127  Sum_probs=71.9

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHh--CCceeCCeeeEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY--NNVLLDGKPMKI  171 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~l--ng~~l~g~~i~V  171 (291)
                      ...++.+|||.|||+.+||+||.++|+.||.|++|.|..+     +++|||+|.+.++|++||+.|  +...+.+++|+|
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~-----k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v   85 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec-----ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEE
Confidence            3457899999999999999999999999999999999865     789999999999999999988  456789999999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      ++++.+.
T Consensus        86 ~~s~~~~   92 (104)
T d1wexa_          86 NYSTSKR   92 (104)
T ss_dssp             EECSSSS
T ss_pred             EEcCCCc
Confidence            9987653

>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=99.73  E-value=3.3e-18  Score=129.41  Aligned_cols=81  Identities=20%  Similarity=0.253  Sum_probs=72.4

Q ss_pred             CCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           96 EVGTKLYVSNLHPGVTNDDIRELFSEIGELKR-YAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~-v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      ....+|||+|||+++|+++|+++|+.||.|.. +.+..+.++.++|||||+|.+.++|++||+ +|+..|+|+.|.|.++
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            34578999999999999999999999999876 556666699999999999999999999995 8999999999999987


Q ss_pred             cCC
Q 022827          175 GTN  177 (291)
Q Consensus       175 ~~~  177 (291)
                      ...
T Consensus        85 ~~~   87 (103)
T d2cpya1          85 TLE   87 (103)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            543

>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=99.70  E-value=1.6e-17  Score=124.90  Aligned_cols=79  Identities=20%  Similarity=0.312  Sum_probs=71.2

Q ss_pred             CCCCcEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHH--HhCCceeCCeeeEE
Q 022827           95 IEVGTKLYVSNLHPG-VTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALK--RYNNVLLDGKPMKI  171 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~-~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~--~lng~~l~g~~i~V  171 (291)
                      ..++++|||+|||++ +|+++|.++|+.||.|.+|.|+.+     ++||||+|.+.++|.+||+  .+++..|.|+.|+|
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~-----k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V   89 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   89 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec-----CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEE
Confidence            356789999999985 899999999999999999999866     7899999999999999998  57888999999999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      ++++...
T Consensus        90 ~~s~~~~   96 (99)
T d1x4fa1          90 DLSEKYK   96 (99)
T ss_dssp             EEECSCS
T ss_pred             EEcCCcc
Confidence            9997654

>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=99.70  E-value=2.8e-17  Score=121.06  Aligned_cols=79  Identities=20%  Similarity=0.274  Sum_probs=71.2

Q ss_pred             CCCCcEEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHh--CCceeCCeeeEE
Q 022827           95 IEVGTKLYVSNLHPG-VTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRY--NNVLLDGKPMKI  171 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~-~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~l--ng~~l~g~~i~V  171 (291)
                      .+++.+|||+|||.. +|++||.++|+.||.|.+|.|+.+     +++|||+|++.++|++|++.|  ++..+.|++|+|
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~-----k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V   79 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   79 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc-----ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEE
Confidence            457899999999986 889999999999999999999876     578999999999999999966  678899999999


Q ss_pred             EEecCCC
Q 022827          172 EVVGTNA  178 (291)
Q Consensus       172 ~~a~~~~  178 (291)
                      ++++...
T Consensus        80 ~~s~~~~   86 (89)
T d1x4da1          80 HLSQKYK   86 (89)
T ss_dssp             EEECCCT
T ss_pred             EECCCcc
Confidence            9997543

>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=99.69  E-value=7.6e-18  Score=129.43  Aligned_cols=82  Identities=18%  Similarity=0.325  Sum_probs=72.4

Q ss_pred             CCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEE-EEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEE
Q 022827           95 IEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRY-AIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEV  173 (291)
Q Consensus        95 ~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v-~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~  173 (291)
                      .....+|||.|||+++|++||+++|+.||.|..+ .+..+.++.++|||||+|.+.++|++|| .||+..|+++.|.|..
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al-~~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHH-TSCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHH-HcCCCcCCCEEEEEEE
Confidence            4467799999999999999999999999998764 4455559999999999999999999999 5899999999999998


Q ss_pred             ecCC
Q 022827          174 VGTN  177 (291)
Q Consensus       174 a~~~  177 (291)
                      +...
T Consensus        94 ~~~~   97 (112)
T d1wela1          94 ITKK   97 (112)
T ss_dssp             ECHH
T ss_pred             cChH
Confidence            7643

>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=99.66  E-value=3.7e-17  Score=123.89  Aligned_cols=78  Identities=15%  Similarity=0.132  Sum_probs=69.9

Q ss_pred             CCCcEEEEcCCCCCC-CH----HHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeE
Q 022827           96 EVGTKLYVSNLHPGV-TN----DDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMK  170 (291)
Q Consensus        96 ~~~~~l~V~nL~~~~-te----~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~  170 (291)
                      ...++|||.||+.++ ++    ++|+++|+.||+|++|.++..     ++||||+|.+.++|++||+.||+..|+|++|+
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~-----~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC-----CCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            467899999999986 33    569999999999999999854     78999999999999999999999999999999


Q ss_pred             EEEecCCC
Q 022827          171 IEVVGTNA  178 (291)
Q Consensus       171 V~~a~~~~  178 (291)
                      |.|+++..
T Consensus        78 v~~a~~~~   85 (104)
T d1weya_          78 LYFAQTLH   85 (104)
T ss_dssp             EECCCCSS
T ss_pred             EeecccCC
Confidence            99997664

>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=99.64  E-value=6.2e-16  Score=127.69  Aligned_cols=83  Identities=14%  Similarity=0.273  Sum_probs=76.7

Q ss_pred             CCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           94 GIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        94 ~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      .....++|||.|||+.+|+++|+++|+.||.|..|.|+.+. ++.+++||||+|.+.++|++||+ +++..|+|+.|+|.
T Consensus        93 ~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~  171 (183)
T d1u1qa_          93 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVR  171 (183)
T ss_dssp             TTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEE
T ss_pred             cccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEE
Confidence            34567899999999999999999999999999999999988 79999999999999999999995 78899999999999


Q ss_pred             EecCC
Q 022827          173 VVGTN  177 (291)
Q Consensus       173 ~a~~~  177 (291)
                      +|.++
T Consensus       172 ~A~~k  176 (183)
T d1u1qa_         172 KALSK  176 (183)
T ss_dssp             ECCCH
T ss_pred             ecCCc
Confidence            98754

>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=99.63  E-value=3.6e-18  Score=126.07  Aligned_cols=75  Identities=17%  Similarity=0.362  Sum_probs=65.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEe-----eC-CCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEE
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIH-----FD-KNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIE  172 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~-----~d-~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~  172 (291)
                      ++|||+|||+++||++|+++|++||.|..+.+.     .+ .++.+++||||+|.+.++|++|+ +||+..|+|+.|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhCCcEECCEEEEEC
Confidence            689999999999999999999999988765543     22 26778999999999999999999 599999999999997


Q ss_pred             Ee
Q 022827          173 VV  174 (291)
Q Consensus       173 ~a  174 (291)
                      .+
T Consensus        81 r~   82 (90)
T d1u2fa_          81 RP   82 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            43

>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=99.62  E-value=4.2e-17  Score=123.59  Aligned_cols=76  Identities=18%  Similarity=0.272  Sum_probs=72.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      +.++|.+++.+++|++|+++|++||+|++|.|+.+.+++++|||||+|.+.++|.+||+.||+..|+|++|+|+++
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 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            4688889999999999999999999999999998889999999999999999999999999999999999999985

>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=99.58  E-value=2.2e-15  Score=113.32  Aligned_cols=73  Identities=18%  Similarity=0.164  Sum_probs=62.8

Q ss_pred             CCCCCcEEEEcC--CCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCcee-CCeeeE
Q 022827           94 GIEVGTKLYVSN--LHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLL-DGKPMK  170 (291)
Q Consensus        94 ~~~~~~~l~V~n--L~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l-~g~~i~  170 (291)
                      ...+..+|||.|  ||+++|+++|+++|++||.|+.|.+..+     ++||||+|.+.++|++|++.||+..| ++..++
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-----k~~aFV~f~~~e~A~~A~~~lng~~i~~~~~~~   88 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-----ccEEEEEECCHHHHHHHHHHhCCCCCCCCCCcE
Confidence            345678899966  9999999999999999999999988866     67999999999999999999999876 444333


Q ss_pred             E
Q 022827          171 I  171 (291)
Q Consensus       171 V  171 (291)
                      |
T Consensus        89 i   89 (101)
T d2cq2a1          89 I   89 (101)
T ss_dssp             E
T ss_pred             E
Confidence            3

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=4.4e-15  Score=113.93  Aligned_cols=76  Identities=18%  Similarity=0.262  Sum_probs=66.3

Q ss_pred             CCc-EEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCH-HHHHHHHHHhCCceeCCeeeEEEEe
Q 022827           97 VGT-KLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARR-SDAFAALKRYNNVLLDGKPMKIEVV  174 (291)
Q Consensus        97 ~~~-~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~-~~A~~Ai~~lng~~l~g~~i~V~~a  174 (291)
                      .++ .+||+|||+.+|+++|+++|++||+|.+|.|+.+     ++||||.|.+. ++|.+|+..||+..|.++.+.|.+.
T Consensus         9 ~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~-----kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_           9 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-----CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             CCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC-----CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            344 5699999999999999999999999999999866     79999999985 7899999999999888887777776


Q ss_pred             cCC
Q 022827          175 GTN  177 (291)
Q Consensus       175 ~~~  177 (291)
                      ...
T Consensus        84 ~~~   86 (113)
T d1owxa_          84 VLE   86 (113)
T ss_dssp             ECC
T ss_pred             ecc
Confidence            544

>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=99.52  E-value=2.2e-14  Score=107.32  Aligned_cols=84  Identities=14%  Similarity=0.278  Sum_probs=71.3

Q ss_pred             CCCCCCCcEEEEcCC--CCCCC---------HHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhC
Q 022827           92 ISGIEVGTKLYVSNL--HPGVT---------NDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN  160 (291)
Q Consensus        92 ~~~~~~~~~l~V~nL--~~~~t---------e~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~ln  160 (291)
                      |+....+++|+|.||  |.++.         ++||++.|++||.|..|.+..+   .++|||||+|.+.++|.+|++.||
T Consensus         2 p~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~---~~~G~~fV~f~~~e~A~~A~~~ln   78 (99)
T d2dita1           2 PSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLD   78 (99)
T ss_dssp             CCCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT---CTTCEEEEECSCHHHHHHHHHHST
T ss_pred             CCCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC---CCccEEEEEECCHHHHHHHHHHhC
Confidence            445567899999999  54432         2678899999999999988765   457999999999999999999999


Q ss_pred             CceeCCeeeEEEEecCCC
Q 022827          161 NVLLDGKPMKIEVVGTNA  178 (291)
Q Consensus       161 g~~l~g~~i~V~~a~~~~  178 (291)
                      +..|+|++|+|++..+..
T Consensus        79 g~~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          79 GRWFGGRQITAQAWDGTT   96 (99)
T ss_dssp             TCEETTEECEEEECCSCC
T ss_pred             CcEECCEEEEEEEeCCcC
Confidence            999999999999986553

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=8e-14  Score=114.74  Aligned_cols=80  Identities=23%  Similarity=0.309  Sum_probs=71.5

Q ss_pred             CcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEecC
Q 022827           98 GTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVGT  176 (291)
Q Consensus        98 ~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~~  176 (291)
                      .++|||+|||+++|+++|+++|++||+|.++.|+.+. ++.+++||||+|.+.++|++|++. ++..+..+.+.+.....
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            3799999999999999999999999999999999998 899999999999999999999954 66778888888877654


Q ss_pred             CC
Q 022827          177 NA  178 (291)
Q Consensus       177 ~~  178 (291)
                      ..
T Consensus        85 ~~   86 (183)
T d1u1qa_          85 RE   86 (183)
T ss_dssp             TT
T ss_pred             cc
Confidence            43

>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=99.41  E-value=1.7e-13  Score=98.61  Aligned_cols=73  Identities=11%  Similarity=0.091  Sum_probs=61.9

Q ss_pred             CCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCee-eEEEEec
Q 022827           97 VGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKP-MKIEVVG  175 (291)
Q Consensus        97 ~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~-i~V~~a~  175 (291)
                      ..+.|+|.+||++++++.| ++|++||+|.++.+..+     ++||||+|.++++|++|| .+|+..|+|+. |.|..+.
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~-----~~~~fV~f~~~~~A~~Al-~~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT-----GNWMHIRYQSKLQARKAL-SKDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS-----SSEEEEEESSHHHHHHHH-TTTTCEETTTEECEEEECC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC-----CCEEEEEEcccHHHHHHH-hcCCCeECCcEEEEEEeCC
Confidence            3578999999999987666 57999999999987644     789999999999999999 59999999974 5677654


Q ss_pred             C
Q 022827          176 T  176 (291)
Q Consensus       176 ~  176 (291)
                      .
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=99.40  E-value=1.8e-13  Score=103.21  Aligned_cols=81  Identities=15%  Similarity=0.135  Sum_probs=69.0

Q ss_pred             CCCcEEEEcCC--CCCCC--------HHHHHHHHHhcCCeeEEEEeeCCC---CCCceEEEEEEcCHHHHHHHHHHhCCc
Q 022827           96 EVGTKLYVSNL--HPGVT--------NDDIRELFSEIGELKRYAIHFDKN---GRPSGSAEVVYARRSDAFAALKRYNNV  162 (291)
Q Consensus        96 ~~~~~l~V~nL--~~~~t--------e~dL~~~F~~~G~v~~v~i~~d~t---g~~kG~afV~F~~~~~A~~Ai~~lng~  162 (291)
                      +|+++|.|.||  +.++.        .+||++.|++||.|++|.|..+..   ....|++||+|.+.++|.+|++.||+.
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            36789999999  54433        357899999999999999987662   345689999999999999999999999


Q ss_pred             eeCCeeeEEEEecC
Q 022827          163 LLDGKPMKIEVVGT  176 (291)
Q Consensus       163 ~l~g~~i~V~~a~~  176 (291)
                      .++|+.|.|.++..
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999763

>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=97.95  E-value=9.8e-06  Score=57.42  Aligned_cols=70  Identities=16%  Similarity=0.278  Sum_probs=55.7

Q ss_pred             CCcEEEEcCCCCCC------CH---HHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCe
Q 022827           97 VGTKLYVSNLHPGV------TN---DDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGK  167 (291)
Q Consensus        97 ~~~~l~V~nL~~~~------te---~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~  167 (291)
                      +.-||.|.=+.+..      .|   .+|.+.|.+||+|.-|+++.+       ..+|+|.+-+.|.+|+ .+++.++.|+
T Consensus        14 pDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d-------~mwVTF~dG~SAL~al-~l~g~~v~G~   85 (95)
T d1ufwa_          14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG-------QMLVTFADSHSALSVL-DVDGMKVKGR   85 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT-------EEEEECSCSHHHHHHH-HGGGSEETTE
T ss_pred             CCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC-------eEEEEECCcHHHHHHh-ccCCeEEcce
Confidence            55667665333222      22   357788999999999999966       6999999999999999 7899999999


Q ss_pred             eeEEEEe
Q 022827          168 PMKIEVV  174 (291)
Q Consensus       168 ~i~V~~a  174 (291)
                      .|+|...
T Consensus        86 ~l~It~~   92 (95)
T d1ufwa_          86 AVKISGP   92 (95)
T ss_dssp             EEEEECC
T ss_pred             EEEEecC
Confidence            9999853

>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=97.91  E-value=3.8e-05  Score=51.69  Aligned_cols=65  Identities=15%  Similarity=0.257  Sum_probs=55.4

Q ss_pred             CCCHHH----HHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhCCceeCCeeeEEEEec
Q 022827          109 GVTNDD----IRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYNNVLLDGKPMKIEVVG  175 (291)
Q Consensus       109 ~~te~d----L~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~lng~~l~g~~i~V~~a~  175 (291)
                      .+++.+    |.+.|.+++.|.++.|.....+..  .|-|...+.++|..|+..|+-.+|..+.|.|.+++
T Consensus         3 ~L~~kelqq~L~~~f~~h~~V~sv~l~~~~dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1           3 RLSRKELQQLLQEAFARHGKVKSVELSPHTDYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             TSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             cCCHHHHHHHHHHHHHhheeEEEEEEEeccCCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            345555    456789999999999987766655  49999999999999999999999999999999976

>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=97.72  E-value=8.2e-05  Score=53.11  Aligned_cols=67  Identities=13%  Similarity=0.264  Sum_probs=57.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCC-CC--CCceEEEEEEcCHHHHHHHHHHhCCceeC
Q 022827           99 TKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDK-NG--RPSGSAEVVYARRSDAFAALKRYNNVLLD  165 (291)
Q Consensus        99 ~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~-tg--~~kG~afV~F~~~~~A~~Ai~~lng~~l~  165 (291)
                      ++|.|..||+.+||+++.+.+...+++.....+..+ +-  ..-.-|||.|.+.+++....+.++++.+.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            689999999999999999999998888877777665 22  22367999999999999999999998774

>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=96.52  E-value=0.0044  Score=44.11  Aligned_cols=63  Identities=17%  Similarity=0.142  Sum_probs=50.9

Q ss_pred             CCCCCCCCcEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeeCCCCCCceEEEEEEcCHHHHHHHHHHhC
Q 022827           91 GISGIEVGTKLYVSNLHPGVTNDDIRELFSEIGELKRYAIHFDKNGRPSGSAEVVYARRSDAFAALKRYN  160 (291)
Q Consensus        91 ~~~~~~~~~~l~V~nL~~~~te~dL~~~F~~~G~v~~v~i~~d~tg~~kG~afV~F~~~~~A~~Ai~~ln  160 (291)
                      ++.+.+.-..||.-..|......||.+||+.||.|.- ..+.|      -.|||...+.++|+.+++.++
T Consensus         8 G~d~~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~V-swIdd------TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_           8 GPDLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQI-SWIDD------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSCCCCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCC-EEEET------TEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCCCCcceeEEEeCCcccchhHHHHHhcCCCceEE-EEecC------ceEEEEecCHHHHHHHHHHhc
Confidence            4445566678999999999999999999999998873 34433      269999999999999987654