Citrus Sinensis ID: 024424

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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-------27
Protein Sequence
MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGSGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKLRPRSYSRSPSPRRGRSRSRSYSRGRSDSRSRSPVKRDRSVERFERRTRSPRDSRSPKRRRNSPPSSKGRKRSPTPDERSPQDQRSPSPRDRRQANGSEYSGSPRGKSRSPVDDADGPEDRNYRSPPEENGRSRSRSLSPVPRDDRSPIDDDDNHGDPRGSESN
Secondary Structure (PSIPRED)
ccccEEEEEEcccccHHHHHHHHccccccccEEEEEEccccccccccccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccEEEEEEcccccHHHHHHHccccEccccEEEEEEcccccccccccccccccccccccccEEcccccccccccccccccccccEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHcccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mkrdfafvefsdprdaddaryslngrdvdgsRIIVEFarggprgpggsreylgrgpppgsgrcfncgidghwardckagdwknkcyrcgerghierncqnspkklrprsysrspsprrgrsrsrsysrgrsdsrsrspvkrdrsverferrtrsprdsrspkrrrnsppsskgrkrsptpderspqdqrspsprdrrqangseysgsprgksrspvddadgpedrnyrsppeengrsrsrslspvprddrspiddddnhgdprgsesn
Flexible Loop (DISEMBL)
MKRDFAFVefsdprdaddaryslngrdvdgsriivefarggprgpggsrEYLGRGPPPGSGRCFNCGIDGHwardckagdwKNKCYrcgerghierncqnspkklrprsysrspsprrgrsrsrsysrgrsdsrsrspvkrdrsverferrtrsprdsrspkrrrnsppsskgrkrsptpderspqdqrspsprdrrqangseysgsprgksrspvddadgpedrnyrsppeengrsrsrslspvprddrspiddddnhgdprgsesn
Low Complexity Region (SEG)
MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFArggprgpggSREYLGRGPPPGSGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKLrprsysrspsprrgrsrsrsysrgrsdsrsrspVKRDRSVERFErrtrsprdsrspkrrrnsppsskgrkrsptpDERSPQDQRSPSPRDRRQANGSEYSGSPRGKSRSPVDDADGPEDRNYRSPPEENGrsrsrslspvprddrspiddddNHGDPRGSESN
Disordered region (IsUnstruct)
*************************************************************RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHI******************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
*KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIV*****************************************************************************************************************************************************************************************************************************************
Disordered Region (DISEMBL)
MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGSGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC******************************************************************************************************************************************************DRSPIDDD************
Disordered Region (DISPRO)
*KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG*************RGP**GSGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIE**C**************************************************************************************************************************************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGSGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKLRPRSYSRSPSPRRGRSRSRSYSRGRSDSRSRSPVKRDRSVERFERRTRSPRDSRSPKRRRNSPPSSKGRKRSPTPDERSPQDQRSPSPRDRRQANGSEYSGSPRGKSRSPVDDADGPEDRNYRSPPEENGRSRSRSLSPVPRDDRSPIDDDDNHGDPRGSESN
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	268	2.2.26 [Sep-21-2011]
Q8VYA5	290	Serine/arginine-rich spli	yes	no	0.384	0.355	0.811	7e-47
Q9FYB7	284	Serine/arginine-rich spli	no	no	0.873	0.823	0.527	2e-46
Q02836	1472	Gag-Pol polyprotein OS=Si	N/A	no	0.597	0.108	0.252	4e-08
Q8VE97	489	Serine/arginine-rich spli	yes	no	0.149	0.081	0.625	4e-08
Q08170	494	Serine/arginine-rich spli	yes	no	0.149	0.080	0.625	4e-08
P26686	376	Serine-arginine protein 5	no	no	0.164	0.117	0.568	3e-07
Q13247	344	Serine/arginine-rich spli	no	no	0.149	0.116	0.6	6e-07
Q1A267	1438	Gag-Pol polyprotein OS=Si	no	no	0.444	0.082	0.261	7e-07
Q3B7L6	345	Serine/arginine-rich spli	no	no	0.149	0.115	0.6	7e-07
Q10021	208	Probable splicing factor,	yes	no	0.164	0.211	0.565	8e-07

>sp|Q8VYA5|RSZ33_ARATH Serine/arginine-rich splicing factor RS2Z33 OS=Arabidopsis thaliana GN=RS2Z33 PE=1 SV=1

 Score =  187 bits (475), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 86/106 (81%), Positives = 95/106 (89%), Gaps = 3/106 (2%)

Query: 1   MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGS 60
           MKRD+AFVEF DPRDADDAR+ L+GRD DGSRI VEF+RG PRG   SR++  RGPPPG+
Sbjct: 42  MKRDYAFVEFGDPRDADDARHYLDGRDFDGSRITVEFSRGAPRG---SRDFDSRGPPPGA 98

Query: 61  GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKLR 106
           GRCFNCG+DGHWARDC AGDWKNKCYRCGERGHIERNC+NSPKKLR
Sbjct: 99  GRCFNCGVDGHWARDCTAGDWKNKCYRCGERGHIERNCKNSPKKLR 144

Involved in pre-mRNA splicing.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9FYB7|RSZ32_ARATH Serine/arginine-rich splicing factor RS2Z32 OS=Arabidopsis thaliana GN=RS2Z32 PE=1 SV=1

 Score =  186 bits (472), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 145/275 (52%), Positives = 166/275 (60%), Gaps = 41/275 (14%)

Query: 1   MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGS 60
           MKRD+AFVEFSDPRDADDARY L+GRD DGSRI VE +RG PRG   SR+   RGPPPGS
Sbjct: 42  MKRDYAFVEFSDPRDADDARYYLDGRDFDGSRITVEASRGAPRG---SRDNGSRGPPPGS 98

Query: 61  GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKLRPR---SYSRSPSPR 117
           GRCFNCG+DGHWARDC AGDWKNKCYRCGERGHIERNC+NSP   + R   SYSRSP   
Sbjct: 99  GRCFNCGVDGHWARDCTAGDWKNKCYRCGERGHIERNCKNSPSPKKARQGGSYSRSPV-- 156

Query: 118 RGRSRSRSYSRGRSDSRSRSPVKRDRSVERFERRTRSPRD-SRSPKRRRNSPPSSKGRKR 176
             +SRS    R  S SRS S  +         RR +S  D SRSPK    S  S KGR +
Sbjct: 157 --KSRSPRRRRSPSRSRSYSRGRSYSRSRSPVRREKSVEDRSRSPKAMERS-VSPKGRDQ 213

Query: 177 SPTPDERSPQDQRSPSPRDRRQANGSEYSGSPRGKSRSPVDDADGPEDRNYRSPPEENGR 236
           S +PD +           D     GS+Y GSP+       ++ +G   RN  SP    G 
Sbjct: 214 SLSPDRKVI---------DASPKRGSDYDGSPK-------ENGNG---RNSASPIVGGGE 254

Query: 237 SRSRSLSPVPRD--DRSPIDDDDNHG--DPRGSES 267
                 SPV  +  DRSPIDD+       P+GSES
Sbjct: 255 ------SPVGLNGQDRSPIDDEAELSRPSPKGSES 283

Involved in pre-mRNA splicing.

Arabidopsis thaliana (taxid: 3702)

>sp|Q02836|POL_SIVG1 Gag-Pol polyprotein OS=Simian immunodeficiency virus agm.grivet (isolate AGM gr-1) GN=gag-pol PE=3 SV=2

 Score = 58.9 bits (141), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 48/190 (25%), Positives = 81/190 (42%), Gaps = 30/190 (15%)

Query: 57  PPGSGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKLRPRSYSRSPSP 116
           P G  +CFNCG  GH  R+CKA   + KC++CG+ GH+ ++C+N                
Sbjct: 386 PRGPLKCFNCGKFGHMQRECKAPR-QIKCFKCGKIGHMAKDCKNGQANF----------- 433

Query: 117 RRGRSRSRSYSRGRSDSRSRSPVKRDRSVERFERRTRSPRDSRSPKRRRNSPPSSKGRKR 176
                  R +  GRS+++    ++R  S       T SP +  S +  + +PP+      
Sbjct: 434 ------FRVWPLGRSETKKFCAIQRRHSWS----GTNSPPNGNSLRSSKEAPPAVCREGT 483

Query: 177 SPTPDERSPQD---QRSPS-----PRDRRQANGSEYSGSPRGKSRSPVDDADGPEDRNYR 228
           +P   ER+ ++   +RS       P  RR        G+P         D    ++++  
Sbjct: 484 APERGERTDKETEGERSGGCFLELPLWRRPMKRVIIEGTPVQALLDTGADDTIIQEKDLH 543

Query: 229 SPPEENGRSR 238
            PP +  RS+
Sbjct: 544 FPPHKPWRSK 553

Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein, Vpr and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step, the PIC enters cell nucleus. This process is mediated through integrase and Vpr proteins, and allows the virus to infect a non dividing cell. This ability to enter the nucleus is specific of lentiviruses, other retroviruses cannot and rely on cell division to access cell chromosomes. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The 5'-ends are produced by integrase-catalyzed staggered cuts, 5 bp apart. A Y-shaped, gapped, recombination intermediate results, with the 5'-ends of the viral DNA strands and the 3' ends of target DNA strands remaining unjoined, flanking a gap of 5 bp. The last step is viral DNA integration into host chromosome. This involves host DNA repair synthesis in which the 5 bp gaps between the unjoined strands are filled in and then ligated. Since this process occurs at both cuts flanking the SIV genome, a 5 bp duplication of host DNA is produced at the ends of SIV integration. Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration.

Cercopithecidae (taxid: 9527)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: 2

>sp|Q8VE97|SRSF4_MOUSE Serine/arginine-rich splicing factor 4 OS=Mus musculus GN=Srsf4 PE=2 SV=1

 Score = 58.9 bits (141), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 30/40 (75%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40
          +K  + FVEF D RDADDA Y LNG+D+ G R+IVE ARG
Sbjct: 33 LKNGYGFVEFDDLRDADDAVYELNGKDLCGERVIVEHARG 72

Plays a role in alternative splice site selection during pre-mRNA splicing. Represses the splicing of MAPT/Tau exon 10.

Mus musculus (taxid: 10090)

>sp|Q08170|SRSF4_HUMAN Serine/arginine-rich splicing factor 4 OS=Homo sapiens GN=SRSF4 PE=1 SV=2

 Score = 58.5 bits (140), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 30/40 (75%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40
          +K  + FVEF D RDADDA Y LNG+D+ G R+IVE ARG
Sbjct: 33 LKNGYGFVEFDDLRDADDAVYELNGKDLCGERVIVEHARG 72

Plays a role in alternative splice site selection during pre-mRNA splicing. Represses the splicing of MAPT/Tau exon 10.

Homo sapiens (taxid: 9606)

>sp|P26686|SRR55_DROME Serine-arginine protein 55 OS=Drosophila melanogaster GN=B52 PE=1 SV=4

 Score = 55.8 bits (133), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 25/44 (56%), Positives = 32/44 (72%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRG 44
          +K  + FVEF D RDADDA Y LNG+++ G R++VE ARG  RG
Sbjct: 35 IKNGYGFVEFEDYRDADDAVYELNGKELLGERVVVEPARGTARG 78

Essential for development. May have a critical role in splicing or in controlling alternative splice site use of at least some pre-mRNA in vivo. Not required for all splicing. May play a general role in the condensation or decondensation of chromatin.

Drosophila melanogaster (taxid: 7227)

>sp|Q13247|SRSF6_HUMAN Serine/arginine-rich splicing factor 6 OS=Homo sapiens GN=SRSF6 PE=1 SV=2

 Score = 55.1 bits (131), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 24/40 (60%), Positives = 30/40 (75%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40
          +K  + FVEF D RDADDA Y LNG+++ G R+IVE ARG
Sbjct: 33 LKNGYGFVEFEDSRDADDAVYELNGKELCGERVIVEHARG 72

Plays a role in constitutive splicing and can modulate the selection of alternative splice sites. Represses the splicing of MAPT/Tau exon 10.

Homo sapiens (taxid: 9606)

>sp|Q1A267|POL_SIVMB Gag-Pol polyprotein OS=Simian immunodeficiency virus (isolate MB66) GN=gag-pol PE=3 SV=4

 Score = 54.7 bits (130), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 33/126 (26%), Positives = 61/126 (48%), Gaps = 7/126 (5%)

Query: 15  DADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGSGRCFNCGIDGHWAR 74
           + D+  +   G     +R++ E            R++ G   P    +CFNCG +GH AR
Sbjct: 342 EGDEPAFQGVGGPSHKARVLAEAMSQAQHSNDAKRQFKG---PKRIVKCFNCGKEGHIAR 398

Query: 75  DCKAGDWKNKCYRCGERGHIERNCQNSPKKLRPRSYSRSPSPRRGRSRSRSYSRGRSDSR 134
           +CKA   K  C++CG+ GH  RNC N   + +   +  + + ++G++R       R++S 
Sbjct: 399 NCKAPRRKG-CWKCGQEGHQMRNCTN---ERQANFFRETLAFQQGKAREFPSEETRTNSS 454

Query: 135 SRSPVK 140
           +   ++
Sbjct: 455 TNRELR 460

Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein, Vpr and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step, the PIC enters cell nucleus. This process is mediated through integrase and Vpr proteins, and allows the virus to infect a non dividing cell. This ability to enter the nucleus is specific of lentiviruses, other retroviruses cannot and rely on cell division to access cell chromosomes. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The 5'-ends are produced by integrase-catalyzed staggered cuts, 5 bp apart. A Y-shaped, gapped, recombination intermediate results, with the 5'-ends of the viral DNA strands and the 3' ends of target DNA strands remaining unjoined, flanking a gap of 5 bp. The last step is viral DNA integration into host chromosome. This involves host DNA repair synthesis in which the 5 bp gaps between the unjoined strands are filled in and then ligated. Since this process occurs at both cuts flanking the SIV genome, a 5 bp duplication of host DNA is produced at the ends of SIV integration. Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration.

Pan troglodytes (taxid: 9598)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: 2

>sp|Q3B7L6|SRSF6_BOVIN Serine/arginine-rich splicing factor 6 OS=Bos taurus GN=SRSF6 PE=2 SV=1

 Score = 54.7 bits (130), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 24/40 (60%), Positives = 30/40 (75%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40
          +K  + FVEF D RDADDA Y LNG+++ G R+IVE ARG
Sbjct: 33 LKNGYGFVEFEDSRDADDAVYELNGKELCGERVIVEHARG 72

Plays a role in constitutive splicing and can modulate the selection of alternative splice sites. Represses the splicing of MAPT/Tau exon 10.

Bos taurus (taxid: 9913)

>sp|Q10021|RSP5_CAEEL Probable splicing factor, arginine/serine-rich 5 OS=Caenorhabditis elegans GN=rsp-5 PE=3 SV=3

 Score = 54.3 bits (129), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 26/46 (56%), Positives = 35/46 (76%), Gaps = 2/46 (4%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGS--RIIVEFARGGPRG 44
          MK  FAFV+F D RDA+DA + L+G+ ++GS  R++VE ARG PRG
Sbjct: 33 MKYGFAFVDFEDSRDAEDACHDLDGKTMEGSSMRLVVEMARGKPRG 78

Plays a functionally redundant role in shifting germ cell sexual differentiation in hermaphrodites.

Caenorhabditis elegans (taxid: 6239)

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	268
359486310	304	PREDICTED: uncharacterized protein LOC10	0.947	0.835	0.819	1e-84
356572371	297	PREDICTED: uncharacterized protein LOC10	0.895	0.808	0.641	2e-71
225439817	307	PREDICTED: uncharacterized protein LOC10	0.962	0.840	0.708	2e-70
147774947	306	hypothetical protein VITISV_036556 [Viti	0.958	0.839	0.631	2e-70
449451689	309	PREDICTED: serine/arginine-rich splicing	0.962	0.834	0.743	2e-69
297736448	278	unnamed protein product [Vitis vinifera]	0.735	0.708	0.866	4e-68
255568494	305	arginine/serine-rich splicing factor, pu	0.876	0.770	0.678	6e-68
363807264	299	uncharacterized protein LOC100813237 [Gl	0.899	0.806	0.629	1e-67
118487500	252	unknown [Populus trichocarpa]	0.891	0.948	0.626	3e-67
356572373	287	PREDICTED: uncharacterized protein LOC10	0.888	0.829	0.645	2e-61

>gi|359486310|ref|XP_002281756.2| PREDICTED: uncharacterized protein LOC100251921 [Vitis vinifera]

 Score =  318 bits (816), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 218/266 (81%), Positives = 229/266 (86%), Gaps = 12/266 (4%)

Query: 1   MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGS 60
           MK DFAFVEFSDPRDADDARYSLNGRD DGSRIIVEFA+GGPRGPGGSREYLGRGPPPGS
Sbjct: 42  MKHDFAFVEFSDPRDADDARYSLNGRDFDGSRIIVEFAKGGPRGPGGSREYLGRGPPPGS 101

Query: 61  GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKL-RPRSYSRSPSPRRG 119
           GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKL R RSYSRSPSPRRG
Sbjct: 102 GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKLKRGRSYSRSPSPRRG 161

Query: 120 RSRSRSYSRGRSDSRS----RSPVKRDRSVERFERRTRSPRDSRSPKRRRNSPPSSKGRK 175
           RSRSRS SR  S SRS    RS  KR+RS ER ERR+RSP DSRSPKRR+ SPP SKGRK
Sbjct: 162 RSRSRSRSRSYSRSRSYSQPRSSPKRERSAERLERRSRSPHDSRSPKRRKASPPPSKGRK 221

Query: 176 RSPTPDERSPQDQRSPSPRDRRQ-ANGSEYSGSPRGKSRSPVDDA--DGPEDRNY-RSPP 231
           RSPTPDERSP+ +RSPSPRDR+Q  NGS+YS SPR KSRSP  DA  D P DRNY RSP 
Sbjct: 222 RSPTPDERSPK-ERSPSPRDRKQTTNGSDYSDSPRVKSRSPALDAERDSPRDRNYRRSPD 280

Query: 232 EENGRSRSRSLSPVPRDDRSPIDDDD 257
           EENG   SRS SP+PRDD SP+DDD+
Sbjct: 281 EENG--HSRSPSPIPRDDASPVDDDE 304

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356572371|ref|XP_003554342.1| PREDICTED: uncharacterized protein LOC100789337 [Glycine max]

 Score =  274 bits (701), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 172/268 (64%), Positives = 196/268 (73%), Gaps = 28/268 (10%)

Query: 1   MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGS 60
           MK DFAFVEFSDPRDADDARYSL+GRDV+GSRIIVEFA+GGPRG   SRE LGRG PPGS
Sbjct: 42  MKNDFAFVEFSDPRDADDARYSLDGRDVEGSRIIVEFAKGGPRG---SRENLGRGLPPGS 98

Query: 61  GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKL--RPRSYSRSP---- 114
           GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIE+NC+NSPKK     RS SRSP    
Sbjct: 99  GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIEKNCKNSPKKSSRHGRSLSRSPVRSH 158

Query: 115 SPRRGRSRSRSYSRGRSDSRSRSPVKRDRSVERFERRTRSPRDSRSPKRRRNSPPSSKGR 174
           SPRRGRSR RSYSR R+ SRSRSPV+R+RS                 + R  SP  SK R
Sbjct: 159 SPRRGRSRDRSYSRDRNYSRSRSPVRRERSP--------------VSEDRSQSPEPSKIR 204

Query: 175 KRSPTPDERSPQDQRSPSPRDRRQA---NGSEYSGSPRGKSRSPVDDADGPEDRNYRSPP 231
           K S +PD+ SP+ +  P+P + R A   +GS+YS  PRGKSRSP   A   ++ NY S P
Sbjct: 205 KHSTSPDQSSPRKRGDPAPGNDRLATLQDGSDYSDGPRGKSRSPASPARDHDEGNYDS-P 263

Query: 232 EENGRSRSRSLSPVPRDDRSPIDDDDNH 259
           + +GRS S S SP   DDRSPID+DD++
Sbjct: 264 KASGRSHSPSRSPR-EDDRSPIDEDDDN 290

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225439817|ref|XP_002277105.1| PREDICTED: uncharacterized protein LOC100258584 [Vitis vinifera]

 Score =  271 bits (694), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 194/274 (70%), Positives = 216/274 (78%), Gaps = 16/274 (5%)

Query: 1   MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSR-EYLGRGPPPG 59
           MK DFAFVEFSDPRDADDARY+LNGRD DGSRIIVEFA+GGPRG  G   EYLGRGPPPG
Sbjct: 42  MKHDFAFVEFSDPRDADDARYNLNGRDFDGSRIIVEFAKGGPRGGSGGSREYLGRGPPPG 101

Query: 60  SGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKL--RPRSYSRSP-SP 116
           SGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSP+KL    RSYSRSP   
Sbjct: 102 SGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPRKLSRHGRSYSRSPVRS 161

Query: 117 RRGRSRSRSYSRGRSDSRSRSPVKRDRSVERFERRTRSPRDSRSPKRRRNSPPSSKGRKR 176
           R GRSRSRSYS  RS SRSRSP KRDRS+ER ++R+ SPR  RSP+ +R S P+SK RKR
Sbjct: 162 RHGRSRSRSYSPSRSYSRSRSPPKRDRSIER-DKRSGSPR-YRSPEPKRRSTPTSKPRKR 219

Query: 177 SPTPDERSPQDQRSPSPRDRRQANGSEYSGSPRGKSRSPV-DDADGPEDRNYRSPPEENG 235
           SPTP++  PQ++ SP+   R Q    EYS SPR KSRSPV  + D P  R YRSP + NG
Sbjct: 220 SPTPEDSRPQERISPNVYKREQP---EYSQSPREKSRSPVSSERDSPVARRYRSPSDANG 276

Query: 236 RSRSRSLSPVPRDDRSPIDDDD--NHGDPRGSES 267
           RSRS+S    PRD+RSP+D+D+  N   PRGSES
Sbjct: 277 RSRSQS----PRDERSPLDEDEDNNSRSPRGSES 306

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147774947|emb|CAN60012.1| hypothetical protein VITISV_036556 [Vitis vinifera]

 Score =  271 bits (693), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 173/274 (63%), Positives = 203/274 (74%), Gaps = 17/274 (6%)

Query: 1   MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSR-EYLGRGPPPG 59
           MK DFAFVEFSDPRDADDARY+LNGRD DGSRIIVEFA+GGPRG  G   EYLGRGPPPG
Sbjct: 42  MKHDFAFVEFSDPRDADDARYNLNGRDFDGSRIIVEFAKGGPRGGSGGSREYLGRGPPPG 101

Query: 60  SGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKLRPR---SYSRSPSP 116
           SGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSP+KL      ++      
Sbjct: 102 SGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPRKLSDMDGVTHDLQLDL 161

Query: 117 RRGRSRSRSYSRGRSDSRSRSPVKRDRSVERFERRTRSPRDSRSPKRRRNSPPSSKGRKR 176
               + +   ++  + + SRSP KRDRS+ER ++R+ SPR  RSP+ +R S P+SK RKR
Sbjct: 162 AMAGAGAEVIAQV-AVTGSRSPPKRDRSIER-DKRSGSPR-YRSPEPKRRSTPTSKPRKR 218

Query: 177 SPTPDERSPQDQRSPSPRDRRQANGSEYSGSPRGKSRSPV-DDADGPEDRNYRSPPEENG 235
           SPTP++  PQ++ SP+   R Q    EYS SPR KSRSPV  + D P  R YRSP + NG
Sbjct: 219 SPTPEDSRPQERISPNVYKREQP---EYSQSPREKSRSPVSSERDSPVARRYRSPSDANG 275

Query: 236 RSRSRSLSPVPRDDRSPI--DDDDNHGDPRGSES 267
           RSRS+S    PRD+RSP+  D+DBN   PRGSES
Sbjct: 276 RSRSQS----PRDERSPLDEDEDBNSRSPRGSES 305

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449451689|ref|XP_004143594.1| PREDICTED: serine/arginine-rich splicing factor RS2Z32-like isoform 1 [Cucumis sativus] gi|449451691|ref|XP_004143595.1| PREDICTED: serine/arginine-rich splicing factor RS2Z32-like isoform 2 [Cucumis sativus] gi|449507559|ref|XP_004163066.1| PREDICTED: serine/arginine-rich splicing factor RS2Z32-like isoform 1 [Cucumis sativus] gi|449507562|ref|XP_004163067.1| PREDICTED: serine/arginine-rich splicing factor RS2Z32-like isoform 2 [Cucumis sativus]

 Score =  268 bits (685), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 200/269 (74%), Positives = 224/269 (83%), Gaps = 11/269 (4%)

Query: 1   MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGS 60
           MKRD+AFVEFSDPRDADDARYSLNGRDV GSRIIVE A+G PRGPGGSREYLGRGPP G+
Sbjct: 42  MKRDYAFVEFSDPRDADDARYSLNGRDVHGSRIIVEIAKGVPRGPGGSREYLGRGPP-GT 100

Query: 61  GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKLRPRSYSRSPSPRRGR 120
           GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIE+NCQNSPKKL+  SYSRSPSPRRGR
Sbjct: 101 GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIEKNCQNSPKKLKRGSYSRSPSPRRGR 160

Query: 121 SRSRSYSRGRSDSRSRSPVKRDRSVERFERRTRSPRDSRSPKRRRNSPPSSKGRKRSPTP 180
           SRSRSYSRGRS SRSRSPVKRDRS+ER ++R+RSPR   SPKR   SPP  K  KRSPTP
Sbjct: 161 SRSRSYSRGRSYSRSRSPVKRDRSLERSDKRSRSPRGRSSPKRHSLSPP-PKAMKRSPTP 219

Query: 181 DERSPQD--QRSPSPRDRRQANGSEYSGSPRGKSRSPVD---DADGPEDRNYRSPPEENG 235
           DERSP++  +RS SP +R   +    S SPRG+SRSP+D   D +G   RNYR   EENG
Sbjct: 220 DERSPEEDARRSLSPGNRDSRSPRGRSRSPRGRSRSPMDEGEDFNGGGSRNYRR--EENG 277

Query: 236 RSRSRSLSPVPRDDRSPIDDDDNHGDPRG 264
              SRS SP+PR++RSP++D+DN+G PRG
Sbjct: 278 --YSRSPSPLPREERSPVNDEDNNGSPRG 304

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297736448|emb|CBI25319.3| unnamed protein product [Vitis vinifera]

 Score =  264 bits (674), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 176/203 (86%), Positives = 183/203 (90%), Gaps = 6/203 (2%)

Query: 1   MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGS 60
           MK DFAFVEFSDPRDADDARYSLNGRD DGSRIIVEFA+GGPRGPGGSREYLGRGPPPGS
Sbjct: 74  MKHDFAFVEFSDPRDADDARYSLNGRDFDGSRIIVEFAKGGPRGPGGSREYLGRGPPPGS 133

Query: 61  GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKL-RPRSYSRSPSPRRG 119
           GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKL R RSYSRSPSPRRG
Sbjct: 134 GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKLKRGRSYSRSPSPRRG 193

Query: 120 RSRSRSYSRGRSDSRS----RSPVKRDRSVERFERRTRSPRDSRSPKRRRNSPPSSKGRK 175
           RSRSRS SR  S SRS    RS  KR+RS ER ERR+RSP DSRSPKRR+ SPP SKGRK
Sbjct: 194 RSRSRSRSRSYSRSRSYSQPRSSPKRERSAERLERRSRSPHDSRSPKRRKASPPPSKGRK 253

Query: 176 RSPTPDERSPQDQRSPSPRDRRQ 198
           RSPTPDERSP+ +RSPSPRD+RQ
Sbjct: 254 RSPTPDERSPK-ERSPSPRDQRQ 275

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255568494|ref|XP_002525221.1| arginine/serine-rich splicing factor, putative [Ricinus communis] gi|223535518|gb|EEF37187.1| arginine/serine-rich splicing factor, putative [Ricinus communis]

 Score =  263 bits (672), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 177/261 (67%), Positives = 193/261 (73%), Gaps = 26/261 (9%)

Query: 1   MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGS 60
           MKRD+AFVEFSDPRDADDARY L+G+D+DGSRIIVEFA+G PRG   SREYLGRGPPPGS
Sbjct: 42  MKRDYAFVEFSDPRDADDARYHLDGKDLDGSRIIVEFAKGVPRG---SREYLGRGPPPGS 98

Query: 61  GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKL-RPRSYSRSPSPRRG 119
           GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC+NSPKKL R RSYSRSPSPRRG
Sbjct: 99  GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCKNSPKKLKRGRSYSRSPSPRRG 158

Query: 120 RSRS-RSYSRGRSDSRSRSPVKRDRSVERFERRTRSPRDSRSPKRRRNSPPSSKGRKRSP 178
           RSRS               P KR+RS E  +R       SR PK   N  P SKGRKRSP
Sbjct: 159 RSRSPSYSRGRSYSRSRSPPPKRERSFENEDRSL-----SREPK---NGVP-SKGRKRSP 209

Query: 179 TPDERSPQDQRSPSPRDRR---QANGSEYSGSPRGKSRSPVDDADGPEDRNYRSPPEENG 235
           TPDE SP+    PSP+ R+   Q + S+YSGSPR +SRSP  D   P D  Y SP + NG
Sbjct: 210 TPDEGSPR----PSPKSRKLDDQQDRSDYSGSPR-RSRSP--DRKSPGDGRYGSPAQTNG 262

Query: 236 RSRSRSLSPVPRDDRSPIDDD 256
           RSRS S S  PRD RSP+DDD
Sbjct: 263 RSRSPSPS--PRDGRSPVDDD 281

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363807264|ref|NP_001242616.1| uncharacterized protein LOC100813237 [Glycine max] gi|255647309|gb|ACU24121.1| unknown [Glycine max]

 Score =  262 bits (669), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 170/270 (62%), Positives = 191/270 (70%), Gaps = 29/270 (10%)

Query: 1   MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGS 60
           MK DFAFVEFSDPRDADDARY+L+GRDV+GSRIIVEFA+GGPRG    REY+GRGPPPGS
Sbjct: 42  MKNDFAFVEFSDPRDADDARYNLDGRDVEGSRIIVEFAKGGPRG-SRDREYMGRGPPPGS 100

Query: 61  GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKL--RPRSYSRSPSPRR 118
           GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIE+NC+NSPKKL  R RS SRSP   R
Sbjct: 101 GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIEKNCKNSPKKLSQRGRSLSRSPVRSR 160

Query: 119 GRSRS----RSYSRGRSDSRSRSPVKRDRS-VERFERRTRSPRDSRSPKRRRNSPPSSKG 173
              R     RSYSR  S SRSRSPV+R+RS V     ++R P               SK 
Sbjct: 161 SPRRGRSTDRSYSRDHSYSRSRSPVRRERSPVSEDRSQSREP---------------SKI 205

Query: 174 RKRSPTPDERSPQDQRSPSPRDRRQA---NGSEYSGSPRGKSRSPVDDADGPEDRNYRSP 230
           RK S +PD+ SP+ +   SP + R A   +GS+YS  PRGKSRSP   A   ++  Y S 
Sbjct: 206 RKHSASPDQSSPRKRGDTSPGNDRLATHQDGSDYSDGPRGKSRSPASPARDRDEGGYDS- 264

Query: 231 PEENGRSRSRSLSPVPRDDRSPID-DDDNH 259
           P+ NG SRS S SP   DDRSPID DDDNH
Sbjct: 265 PKVNGHSRSPSRSPRD-DDRSPIDEDDDNH 293

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118487500|gb|ABK95577.1| unknown [Populus trichocarpa]

 Score =  261 bits (666), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 173/276 (62%), Positives = 194/276 (70%), Gaps = 37/276 (13%)

Query: 1   MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGS 60
           MKRD+AFVEFSDPRDADDAR+ L+G++ DGSRIIVEFA+G PRG   SREYLGRGPPPGS
Sbjct: 1   MKRDYAFVEFSDPRDADDARHYLDGKEFDGSRIIVEFAKGVPRG---SREYLGRGPPPGS 57

Query: 61  GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKL-RPRSYSRSP----S 115
           GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC+NSPKKL R +SYSRSP    S
Sbjct: 58  GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCKNSPKKLTRGKSYSRSPGRSRS 117

Query: 116 PRRGRSRS-RSYSRGRSDSRSRSPVKRDRSVERFERRTRSPRDSRSPKRRRNSPPSSKGR 174
           P RGRSRS               P KR+RSVE  E R+ SP            P S+K R
Sbjct: 118 PHRGRSRSPSYSRGRSYSRSRSPPPKRERSVEN-ENRSLSP-----------EPKSTKAR 165

Query: 175 KRSPTPDERSPQDQRSPSPRDRRQANGS--EYSGSPRGKSRSPVDDADGPEDRNYRSPPE 232
           KRSPTPDE SP+    PSP+ R+  +    EYSGSP G+SRS    +  P D  YRS P+
Sbjct: 166 KRSPTPDEGSPR----PSPKSRKLDDEQDREYSGSPTGRSRS---RSRSPRDERYRS-PQ 217

Query: 233 ENGRSRSRSLSPVPRDDRSPIDDD--DNHGDPRGSE 266
            NGRSR     P PRDDRSP+DDD  DN+  PR S+
Sbjct: 218 TNGRSR----IPSPRDDRSPVDDDYEDNNRSPRDSD 249

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356572373|ref|XP_003554343.1| PREDICTED: uncharacterized protein LOC100789862 [Glycine max]

 Score =  241 bits (615), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 177/274 (64%), Positives = 195/274 (71%), Gaps = 36/274 (13%)

Query: 1   MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGS 60
           MK DFAFV+FSDPRDADDARY+L+GRDVDGSRIIVEFA+G PRG   SREYLGRGPPPGS
Sbjct: 42  MKNDFAFVDFSDPRDADDARYNLDGRDVDGSRIIVEFAKGAPRG---SREYLGRGPPPGS 98

Query: 61  GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKL---RPRSYSRSP--- 114
           GRCFNCG+DGHWARDCKAGDWKNKCYRCGERGHIERNC+NSPKKL   R RSYSRSP   
Sbjct: 99  GRCFNCGLDGHWARDCKAGDWKNKCYRCGERGHIERNCKNSPKKLSTRRGRSYSRSPVRS 158

Query: 115 -SPRRGRSRSRSYSRGRSDSRSRSPVKRDRSVERFERRTRSPRDSRSPKRRRNSPPSSKG 173
            SP RGRSR RSYSR RS SRSRSPV+R+ S  R E R++SP         +NSP  SK 
Sbjct: 159 RSPHRGRSRDRSYSRDRSYSRSRSPVRREESPVR-EDRSQSP-------DHKNSPQPSKT 210

Query: 174 RKRSPTPDERSPQDQRSPSPRDRRQANGSEYSGSPRGKSRSPVDDADGPEDRNYRSPPEE 233
           RK SP+PD RSPQ +   SP + R              SRSP  D   PEDR Y S P+ 
Sbjct: 211 RKHSPSPD-RSPQKRGDTSPDNDRL-------------SRSPARD---PEDRGYDS-PKV 252

Query: 234 NGRSRSRSLSPVPRDDRSPIDDDDNHGDPRGSES 267
           NGRS S S SP   D     DD+++   PRGSES
Sbjct: 253 NGRSGSPSCSPRDDDRSPIDDDNNHRHSPRGSES 286

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	268
TAIR|locus:2049766	290	RS2Z33 "arginine/serine-rich z	0.380	0.351	0.761	1.4e-48
TAIR|locus:2083936	284	RS2Z32 "arginine/serine-rich z	0.369	0.348	0.774	3.7e-48
UNIPROTKB|E1BVX5	235	LOC100859609 "Uncharacterized	0.264	0.302	0.416	3.5e-15
UNIPROTKB|Q16629	238	SRSF7 "Serine/arginine-rich sp	0.324	0.365	0.393	2.5e-14
UNIPROTKB|Q5ZMI0	223	SRSF7 "Uncharacterized protein	0.264	0.318	0.444	3.9e-14
UNIPROTKB|Q3T106	235	SRSF7 "Serine/arginine-rich sp	0.324	0.370	0.393	6.2e-14
ZFIN|ZDB-GENE-040426-1798	258	zgc:77155 "zgc:77155" [Danio r	0.317	0.329	0.340	6.7e-14
UNIPROTKB|F1S4R5	268	SRSF7 "Uncharacterized protein	0.264	0.264	0.444	1.2e-13
UNIPROTKB|D4A720	238	Sfrs7 "Protein Sfrs7" [Rattus	0.324	0.365	0.393	1.7e-13
MGI|MGI:1926232	267	Srsf7 "serine/arginine-rich sp	0.324	0.325	0.393	5.6e-13

TAIR|locus:2049766 RS2Z33 "arginine/serine-rich zinc knuckle-containing protein 33" [Arabidopsis thaliana (taxid:3702)]

 Score = 457 (165.9 bits), Expect = 1.4e-48, Sum P(2) = 1.4e-48
 Identities = 80/105 (76%), Positives = 89/105 (84%)

Query:     1 MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAXXXXXXXXXSREYLGRGPPPGS 60
             MKRD+AFVEF DPRDADDAR+ L+GRD DGSRI VEF+         SR++  RGPPPG+
Sbjct:    42 MKRDYAFVEFGDPRDADDARHYLDGRDFDGSRITVEFSRGAPRG---SRDFDSRGPPPGA 98

Query:    61 GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKL 105
             GRCFNCG+DGHWARDC AGDWKNKCYRCGERGHIERNC+NSPKKL
Sbjct:    99 GRCFNCGVDGHWARDCTAGDWKNKCYRCGERGHIERNCKNSPKKL 143

GO:0005634 "nucleus" evidence=ISM

GO:0000245 "spliceosomal complex assembly" evidence=TAS

GO:0000398 "mRNA splicing, via spliceosome" evidence=RCA;TAS

GO:0005515 "protein binding" evidence=IPI

GO:0016607 "nuclear speck" evidence=IDA

GO:0008380 "RNA splicing" evidence=NAS

GO:0005829 "cytosol" evidence=RCA

GO:0048573 "photoperiodism, flowering" evidence=RCA

TAIR|locus:2083936 RS2Z32 "arginine/serine-rich zinc knuckle-containing protein 32" [Arabidopsis thaliana (taxid:3702)]

 Score = 443 (161.0 bits), Expect = 3.7e-48, Sum P(2) = 3.7e-48
 Identities = 79/102 (77%), Positives = 84/102 (82%)

Query:     1 MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAXXXXXXXXXSREYLGRGPPPGS 60
             MKRD+AFVEFSDPRDADDARY L+GRD DGSRI VE           SR+   RGPPPGS
Sbjct:    42 MKRDYAFVEFSDPRDADDARYYLDGRDFDGSRITVE---ASRGAPRGSRDNGSRGPPPGS 98

Query:    61 GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSP 102
             GRCFNCG+DGHWARDC AGDWKNKCYRCGERGHIERNC+NSP
Sbjct:    99 GRCFNCGVDGHWARDCTAGDWKNKCYRCGERGHIERNCKNSP 140

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000398 "mRNA splicing, via spliceosome" evidence=RCA;TAS

GO:0008380 "RNA splicing" evidence=NAS

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

GO:0030422 "production of siRNA involved in RNA interference" evidence=RCA

GO:0035196 "production of miRNAs involved in gene silencing by miRNA" evidence=RCA

GO:0043687 "post-translational protein modification" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

UNIPROTKB|E1BVX5 LOC100859609 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 128 (50.1 bits), Expect = 3.5e-15, Sum P(2) = 3.5e-15
 Identities = 30/72 (41%), Positives = 36/72 (50%)

Query:     5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAXXXXXXXXXSREYLGRGPPPGSGRCF 64
             FAFVEF DPRDA     S   R + GSR+ VE +          R    R P   + RC+
Sbjct:    49 FAFVEFEDPRDAKPLLKSSKSRVICGSRVRVEVSTGMPRRSRYDRPP-ARRPFDPNDRCY 107

Query:    65 NCGIDGHWARDC 76
              CG  GH+A DC
Sbjct:   108 ECGEKGHYAYDC 119

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|Q16629 SRSF7 "Serine/arginine-rich splicing factor 7" [Homo sapiens (taxid:9606)]

 Score = 150 (57.9 bits), Expect = 2.5e-14, Sum P(2) = 2.5e-14
 Identities = 35/89 (39%), Positives = 46/89 (51%)

Query:     5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAXXXXXXXXXSREYLGRGPPPGSGRCF 64
             FAFVEF DPRDA+DA   L+G+ + GSR+ VE +          R    R P   + RC+
Sbjct:    49 FAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPP-ARRPFDPNDRCY 107

Query:    65 NCGIDGHWARDCKAGDWKNKCYRCGERGH 93
              CG  GH+A DC     + +  R   R H
Sbjct:   108 ECGEKGHYAYDCHRYSRRRRS-RSRSRSH 135

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=IDA

GO:0006397 "mRNA processing" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0006369 "termination of RNA polymerase II transcription" evidence=TAS

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

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0031124 "mRNA 3'-end processing" evidence=TAS

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

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|Q5ZMI0 SRSF7 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 149 (57.5 bits), Expect = 3.9e-14, Sum P(2) = 3.9e-14
 Identities = 32/72 (44%), Positives = 41/72 (56%)

Query:     5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAXXXXXXXXXSREYLGRGPPPGSGRCF 64
             FAFVEF DPRDA+DA   L+G+ + GSR+ VE +          R    R P   + RC+
Sbjct:    47 FAFVEFEDPRDAEDAVLGLDGKIICGSRVRVEVSTGMPRRSRYDRPP-ARRPFDPNDRCY 105

Query:    65 NCGIDGHWARDC 76
              CG  GH+A DC
Sbjct:   106 ECGEKGHYAYDC 117

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|Q3T106 SRSF7 "Serine/arginine-rich splicing factor 7" [Bos taurus (taxid:9913)]

 Score = 150 (57.9 bits), Expect = 6.2e-14, Sum P(2) = 6.2e-14
 Identities = 35/89 (39%), Positives = 46/89 (51%)

Query:     5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAXXXXXXXXXSREYLGRGPPPGSGRCF 64
             FAFVEF DPRDA+DA   L+G+ + GSR+ VE +          R    R P   + RC+
Sbjct:    49 FAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPP-ARRPFDPNDRCY 107

Query:    65 NCGIDGHWARDCKAGDWKNKCYRCGERGH 93
              CG  GH+A DC     + +  R   R H
Sbjct:   108 ECGEKGHYAYDCHRYSRRRRS-RSRSRSH 135

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

ZFIN|ZDB-GENE-040426-1798 zgc:77155 "zgc:77155" [Danio rerio (taxid:7955)]

 Score = 130 (50.8 bits), Expect = 6.7e-14, Sum P(2) = 6.7e-14
 Identities = 30/88 (34%), Positives = 47/88 (53%)

Query:     5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAXXXXXXXXXSREYLGRGPPPGSGRCF 64
             FAFVE+ D RDA+DA   ++G+ + G+R+ VE +          R    +  P  + RC+
Sbjct:    52 FAFVEYEDARDAEDAVKGMDGKVLCGARVRVELSNGMSRKSRYGRPSRRQFDP--NDRCY 109

Query:    65 NCGIDGHWARDC-KAGDWKNKCYRCGER 91
              CG  GH+A DC +    +++  R G R
Sbjct:   110 QCGETGHYAYDCYRFSKRRSRRSRSGSR 137

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|F1S4R5 SRSF7 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 149 (57.5 bits), Expect = 1.2e-13, Sum P(2) = 1.2e-13
 Identities = 32/72 (44%), Positives = 41/72 (56%)

Query:     5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAXXXXXXXXXSREYLGRGPPPGSGRCF 64
             FAFVEF DPRDA+DA   L+G+ + GSR+ VE +          R    R P   + RC+
Sbjct:    76 FAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPP-ARRPFDPNDRCY 134

Query:    65 NCGIDGHWARDC 76
              CG  GH+A DC
Sbjct:   135 ECGEKGHYAYDC 146

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|D4A720 Sfrs7 "Protein Sfrs7" [Rattus norvegicus (taxid:10116)]

 Score = 150 (57.9 bits), Expect = 1.7e-13, Sum P(2) = 1.7e-13
 Identities = 35/89 (39%), Positives = 46/89 (51%)

Query:     5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAXXXXXXXXXSREYLGRGPPPGSGRCF 64
             FAFVEF DPRDA+DA   L+G+ + GSR+ VE +          R    R P   + RC+
Sbjct:    49 FAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPP-ARRPFDPNDRCY 107

Query:    65 NCGIDGHWARDCKAGDWKNKCYRCGERGH 93
              CG  GH+A DC     + +  R   R H
Sbjct:   108 ECGEKGHYAYDCHRYSRRRRS-RSRSRSH 135

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

MGI|MGI:1926232 Srsf7 "serine/arginine-rich splicing factor 7" [Mus musculus (taxid:10090)]

 Score = 150 (57.9 bits), Expect = 5.6e-13, Sum P(2) = 5.6e-13
 Identities = 35/89 (39%), Positives = 46/89 (51%)

Query:     5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAXXXXXXXXXSREYLGRGPPPGSGRCF 64
             FAFVEF DPRDA+DA   L+G+ + GSR+ VE +          R    R P   + RC+
Sbjct:    78 FAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPP-ARRPFDPNDRCY 136

Query:    65 NCGIDGHWARDCKAGDWKNKCYRCGERGH 93
              CG  GH+A DC     + +  R   R H
Sbjct:   137 ECGEKGHYAYDCHRYSRRRRS-RSRSRSH 164

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=ISO

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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:
	GSVIVG00029498001	SubName- Full=Chromosome chr13 scaffold_48, whole genome shotgun sequence; (288 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00000599001	SubName- Full=Chromosome chr8 scaffold_106, whole genome shotgun sequence; (357 aa)					•	•			0.443

---

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	268
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	2e-11
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	8e-10
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	2e-09
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	7e-09
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	6e-08
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-07
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	1e-07
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-07
smart00360	73	smart00360, RRM, RNA recognition motif	4e-07
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	5e-07
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-06
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	1e-06
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	1e-06
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	3e-06
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	3e-06
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	5e-06
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	6e-06
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	1e-05
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	1e-05
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-05
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-05
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	4e-05
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	4e-05
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	7e-05
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	8e-05
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	1e-04
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	1e-04
PRK12678	672	PRK12678, PRK12678, transcription termination fact	1e-04
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	1e-04
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-04
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	2e-04
PRK12678	672	PRK12678, PRK12678, transcription termination fact	3e-04
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	3e-04
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	3e-04
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	3e-04
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	3e-04
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-04
pfam00098	18	pfam00098, zf-CCHC, Zinc knuckle	5e-04
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	6e-04
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	6e-04
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	7e-04
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	7e-04
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	7e-04
PRK12678	672	PRK12678, PRK12678, transcription termination fact	0.001
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	0.001
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	0.001
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	0.001
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	0.001
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	0.001
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.001
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	0.001
cd12253	79	cd12253, RRM_PIN4_like, RNA recognition motif in y	0.001
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	0.001
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	0.001
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.002
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	0.002
cd12374	85	cd12374, RRM_UHM_SPF45_PUF60, RNA recognition moti	0.002
cd12496	74	cd12496, RRM3_RBM46, RNA recognition motif 3 in ve	0.002
smart00343	17	smart00343, ZnF_C2HC, zinc finger	0.002
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	0.002
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	0.002
smart00343	17	smart00343, ZnF_C2HC, zinc finger	0.003
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	0.003
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	0.003
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	0.003
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	0.004
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	0.004
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	0.004

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

 Score = 57.7 bits (140), Expect = 2e-11
 Identities = 26/40 (65%), Positives = 31/40 (77%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40
          +K  F FVEF DPRDADDA Y LNG+++ G R+IVE ARG
Sbjct: 31 LKNGFGFVEFEDPRDADDAVYELNGKELCGERVIVEHARG 70

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

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

 Score = 53.8 bits (129), Expect = 8e-10
 Identities = 25/40 (62%), Positives = 30/40 (75%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40
          +K  + FVEF D RDADDA Y LNG+D+ G R+IVE ARG
Sbjct: 31 LKNGYGFVEFEDSRDADDAVYELNGKDLCGERVIVEHARG 70

This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 52.4 bits (126), Expect = 2e-09
 Identities = 18/39 (46%), Positives = 26/39 (66%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
          +++ FAFVEF D  DA  A  +L+G  +DGS + VEF +
Sbjct: 32 IRKTFAFVEFEDSEDATKALEALHGSRIDGSVLTVEFVK 70

This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus. Length = 70

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

 Score = 51.1 bits (123), Expect = 7e-09
 Identities = 22/36 (61%), Positives = 29/36 (80%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40
          FAFVEF DPRDA+DA  +L+GR + G+R+ VE +RG
Sbjct: 38 FAFVEFEDPRDAEDAVRALDGRRICGNRVRVELSRG 73

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

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

 Score = 47.9 bits (115), Expect = 6e-08
 Identities = 15/37 (40%), Positives = 20/37 (54%)

Query: 2  KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
          K  FAFVEFS    A+ A   LNG    G  + V+++
Sbjct: 20 KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

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

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

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 17/37 (45%), Positives = 22/37 (59%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
          R F FV F    DAD A   LNG++++G  I VE A+
Sbjct: 43 RGFGFVTFESVEDADAAIRDLNGKELEGRVIKVEKAK 79

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|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 47.7 bits (113), Expect = 1e-07
 Identities = 26/43 (60%), Positives = 31/43 (72%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR 43
          +K  + FVEF D RDADDA Y LNG+D+ G R+IVE ARG  R
Sbjct: 31 LKNGYGFVEFDDLRDADDAVYELNGKDLCGERVIVEHARGPRR 73

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

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

 Score = 46.9 bits (112), Expect = 2e-07
 Identities = 16/34 (47%), Positives = 24/34 (70%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVE 36
          + FAFVEF  P DA+ A  +LNG+++DG ++ V 
Sbjct: 39 KGFAFVEFESPEDAEKALEALNGKELDGRKLKVS 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 = 46.0 bits (110), Expect = 4e-07
 Identities = 15/33 (45%), Positives = 22/33 (66%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIV 35
          + FAFVEF    DA+ A  +LNG+++DG  + V
Sbjct: 41 KGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

Length = 73

>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional

 Score = 47.9 bits (114), Expect = 5e-07
 Identities = 26/63 (41%), Positives = 33/63 (52%), Gaps = 4/63 (6%)

Query: 48  SREYLGRGPPPGSGRCFNCGIDGHWARDC----KAGDWKNKCYRCGERGHIERNCQNSPK 103
           SRE     P  G   C+NCG  GH +R+C    K G  +  CY CG  GHI R+C N+ K
Sbjct: 65  SRECPEAPPGSGPRSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNAGK 124

Query: 104 KLR 106
           +  
Sbjct: 125 RPG 127

Length = 148

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

 Score = 44.9 bits (107), Expect = 1e-06
 Identities = 14/31 (45%), Positives = 21/31 (67%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRI 33
          + FAFVEF D  DA+ A  +LNG+++ G  +
Sbjct: 39 KGFAFVEFEDEEDAEKALEALNGKELGGREL 69

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

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

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 19/44 (43%), Positives = 26/44 (59%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPG 46
          R FAFVE++   DA++A+ +LNG  + GS I V F   G  G  
Sbjct: 44 RGFAFVEYATAEDAEEAQQALNGHSLQGSPIRVSFGNPGRPGAS 87

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

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

 Score = 44.6 bits (105), Expect = 1e-06
 Identities = 22/39 (56%), Positives = 29/39 (74%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
          +KR F FVEF DPRDADDA Y L+G+++   R+ +E AR
Sbjct: 31 LKRGFGFVEFDDPRDADDAVYELDGKELCNERVTIEHAR 69

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 44.2 bits (104), Expect = 3e-06
 Identities = 23/39 (58%), Positives = 29/39 (74%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR 43
          FAFVEF DPRDA+DA   L+G+ + GSR+ VE + G PR
Sbjct: 38 FAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPR 76

This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 77

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

 Score = 43.9 bits (104), Expect = 3e-06
 Identities = 21/33 (63%), Positives = 24/33 (72%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEF 37
          FAFVEF DPRDA+DA    +G D DG R+ VEF
Sbjct: 40 FAFVEFEDPRDAEDAVRGRDGYDFDGYRLRVEF 72

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

>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional

 Score = 44.8 bits (106), Expect = 5e-06
 Identities = 24/64 (37%), Positives = 29/64 (45%), Gaps = 3/64 (4%)

Query: 48  SREYLGRGPPPGSGRCFNCGIDGHWARDCKAGDWKN---KCYRCGERGHIERNCQNSPKK 104
           SRE        G   C+NCG  GH +R+C      +    CY CG+ GHI R C N  K 
Sbjct: 40  SRECPSAPGGRGERSCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRAKG 99

Query: 105 LRPR 108
              R
Sbjct: 100 GAAR 103

Length = 148

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

 Score = 46.8 bits (111), Expect = 6e-06
 Identities = 33/111 (29%), Positives = 43/111 (38%), Gaps = 2/111 (1%)

Query: 95  ERNCQNSPKKLRPRSYSRSPSPRRGRSRSRSYSRGRSDSRSRSPVKRDRSVERFERRTRS 154
           E + +    + R R  S     RR R RSR   R R  SR RS  +  R  +R    +RS
Sbjct: 4   EPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHR-RSRERSYREDSRPRDRRRYDSRS 62

Query: 155 PRDSRSPKRRRN-SPPSSKGRKRSPTPDERSPQDQRSPSPRDRRQANGSEY 204
           PR  R    RR+   P  + R        R     RSPS + R+       
Sbjct: 63  PRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSL 113

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

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

 Score = 42.1 bits (99), Expect = 1e-05
 Identities = 23/35 (65%), Positives = 26/35 (74%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
          FAFVEF DPRDA+DA Y  +G D DG R+ VEF R
Sbjct: 39 FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR 73

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

>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

 Score = 44.1 bits (104), Expect = 1e-05
 Identities = 29/104 (27%), Positives = 38/104 (36%), Gaps = 10/104 (9%)

Query: 63  CFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKLRPRSYSRSPSPRRGRSR 122
           C+NC  DGH +  C       KCY CGE GH+ R+C  +P K + +S     S R     
Sbjct: 81  CYNCSWDGHRSNHCP---KPKKCYNCGETGHLSRDC--NPSKDQQKSCFDCNSTRHSSED 135

Query: 123 -----SRSYSRGRSDSRSRSPVKRDRSVERFERRTRSPRDSRSP 161
                             +       S   F    + PR SR P
Sbjct: 136 CPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKEPRSSRVP 179

Length = 190

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

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 15/37 (40%), Positives = 18/37 (48%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
          R F FVE     +A+ A   LNG D  G  + V  AR
Sbjct: 41 RGFGFVEMETAEEANAAIEKLNGTDFGGRTLTVNEAR 77

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

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

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 19/43 (44%), Positives = 27/43 (62%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGP 45
          R FA+V+F D RDA+DA Y L+     G  I ++FA+G  + P
Sbjct: 42 RGFAYVQFEDVRDAEDALYYLDRTRFLGREIEIQFAQGDRKTP 84

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|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 44.8 bits (106), Expect = 4e-05
 Identities = 32/145 (22%), Positives = 43/145 (29%), Gaps = 1/145 (0%)

Query: 108 RSYSRSPSPRRGRSRSRSYSRGRSDSRSRSPVKRDRSVERFERRTRSPRDSRSPKRRRNS 167
            + + SP+P  GRS +       SDS S S           E     P     P R   +
Sbjct: 214 SASASSPAPAPGRSAADDAGASSSDS-SSSESSGCGWGPENECPLPRPAPITLPTRIWEA 272

Query: 168 PPSSKGRKRSPTPDERSPQDQRSPSPRDRRQANGSEYSGSPRGKSRSPVDDADGPEDRNY 227
              +    R       S   +RSPSP      +G   S      S S   ++      + 
Sbjct: 273 SGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSS 332

Query: 228 RSPPEENGRSRSRSLSPVPRDDRSP 252
                    S   S S  P   R P
Sbjct: 333 SESSRGAAVSPGPSPSRSPSPSRPP 357

Length = 1352

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

 Score = 40.6 bits (96), Expect = 4e-05
 Identities = 14/36 (38%), Positives = 22/36 (61%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVE 36
          + R +A+VEF  P DA+ A   ++G  +DG  + VE
Sbjct: 38 LPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVTVE 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|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional

 Score = 41.7 bits (98), Expect = 7e-05
 Identities = 24/67 (35%), Positives = 32/67 (47%), Gaps = 5/67 (7%)

Query: 48  SREYLGRGPPPGSGR--CFNCGIDGHWARDC---KAGDWKNKCYRCGERGHIERNCQNSP 102
           SRE     P   +    C+ CG  GH +R+C     G  +  CY CG+ GH+ R C  +P
Sbjct: 13  SRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPEAP 72

Query: 103 KKLRPRS 109
               PRS
Sbjct: 73  PGSGPRS 79

Length = 148

>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 40.0 bits (93), Expect = 8e-05
 Identities = 20/37 (54%), Positives = 26/37 (70%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
          RD+AFV FS+  DA DA  +LNG+ +DGS I V  A+
Sbjct: 44 RDYAFVHFSNREDAVDAMNALNGKVIDGSPIEVTLAK 80

This subgroup corresponds to the RRM3 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. ACF contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 83

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 42.9 bits (101), Expect = 1e-04
 Identities = 33/131 (25%), Positives = 39/131 (29%), Gaps = 6/131 (4%)

Query: 106 RPRSYSRSPSPRRGRSRSRSYSRGRSDSRSRSPVKRDRSVERFERRTRSPRDSRSPKRRR 165
            P S     SPR   S S S     S + S S   R  +V      +RSP  SR P    
Sbjct: 302 SPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPSPSRPPPPAD 361

Query: 166 NSPPSSKGRKRSPTPDERSPQDQRSPSPRDRRQANGSEY-----SGSPRGKSRSPVDDAD 220
            S P  + R         +    R    R R    G           P G+ R    DA 
Sbjct: 362 PSSPRKRPRPSRAPS-SPAASAGRPTRRRARAAVAGRARRRDATGRFPAGRPRPSPLDAG 420

Query: 221 GPEDRNYRSPP 231
                 Y   P
Sbjct: 421 AASGAFYARYP 431

Length = 1352

>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 = 39.1 bits (92), Expect = 1e-04
 Identities = 14/34 (41%), Positives = 21/34 (61%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVE 36
          +++ FV   +  DA+DA  +LNG +  G RI VE
Sbjct: 33 KNYGFVHMEEEEDAEDAIKALNGYEFMGKRINVE 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|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 43.0 bits (102), Expect = 1e-04
 Identities = 27/155 (17%), Positives = 51/155 (32%), Gaps = 9/155 (5%)

Query: 108 RSYSRSPSPRRGRSRSRSYSRGRSDSRSRSPVKRDRSVERFERRTRSPRDSRSPKRRRNS 167
           R  +R       +  + + +     +      +R R  +R +R+  + R  R  +  R  
Sbjct: 139 RGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGR 198

Query: 168 PPSSKGRKRSPTPDERSPQDQRSPSPRDRRQANGSEYSGSPRGKSRSPVDDADGPEDRNY 227
               + R+          + ++     +R + +G +  G  R + R      D  EDR  
Sbjct: 199 DGDDRDRRD---------RREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGD 249

Query: 228 RSPPEENGRSRSRSLSPVPRDDRSPIDDDDNHGDP 262
           R   +  GR   R      RD R     D  +   
Sbjct: 250 RDGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNERE 284

Length = 672

>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal EAR1-like proteins

 Score = 39.0 bits (91), Expect = 1e-04
 Identities = 15/35 (42%), Positives = 24/35 (68%)

Query: 2  KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVE 36
          KR+  FVEF D RDA  A  ++NG+++ G  +++E
Sbjct: 37 KREQRFVEFFDVRDAAKALRAMNGKEISGKPVVIE 71

This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 71

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

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 15/37 (40%), Positives = 24/37 (64%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
          +D+AFV F +  DA  A   +NG++++GS I V  A+
Sbjct: 35 KDYAFVHFEERDDAVKAMEEMNGKELEGSPIEVSLAK 71

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

 Score = 38.3 bits (89), Expect = 2e-04
 Identities = 15/34 (44%), Positives = 20/34 (58%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVE 36
          R FAFV       AD A   LNGR++ G +++VE
Sbjct: 34 RQFAFVHLRGEAAADRAIEELNGRELHGRKLVVE 67

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

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 41.8 bits (99), Expect = 3e-04
 Identities = 19/163 (11%), Positives = 44/163 (26%)

Query: 101 SPKKLRPRSYSRSPSPRRGRSRSRSYSRGRSDSRSRSPVKRDRSVERFERRTRSPRDSRS 160
           + K     +   + +     + +   ++ R         +R  + +  E   +   ++R+
Sbjct: 99  AAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEARA 158

Query: 161 PKRRRNSPPSSKGRKRSPTPDERSPQDQRSPSPRDRRQANGSEYSGSPRGKSRSPVDDAD 220
               R        R+R    ++R  + +R    R   +    +       + +    +  
Sbjct: 159 DAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREER 218

Query: 221 GPEDRNYRSPPEENGRSRSRSLSPVPRDDRSPIDDDDNHGDPR 263
           G  D   R         R         D      DD      R
Sbjct: 219 GRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGR 261

Length = 672

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

 Score = 38.3 bits (89), Expect = 3e-04
 Identities = 18/36 (50%), Positives = 24/36 (66%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
          R F FV F +P DA DA  ++NG+ VDG +I V+ A
Sbjct: 42 RGFGFVTFENPDDAKDAMMAMNGKSVDGRQIRVDQA 77

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

>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 38.5 bits (89), Expect = 3e-04
 Identities = 20/43 (46%), Positives = 31/43 (72%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGP 45
          R FA+++F D RDA+DA Y+LN + V G +I ++FA+G  + P
Sbjct: 42 RGFAYIQFEDVRDAEDALYNLNRKWVCGRQIEIQFAQGDRKTP 84

This subgroup corresponds to the RRM of 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). SRSF12 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. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate RNA-binding protein 47 (RBM47)

 Score = 38.1 bits (88), Expect = 3e-04
 Identities = 17/37 (45%), Positives = 24/37 (64%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
          RD+AFV F+   DA  A  +LNG +++GS I V  A+
Sbjct: 37 RDYAFVHFTSREDAVHAMNNLNGTELEGSCIEVTLAK 73

This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 37.9 bits (88), Expect = 3e-04
 Identities = 19/33 (57%), Positives = 22/33 (66%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEF 37
          FAFV F DPRDA+DA +  NG D    R+ VEF
Sbjct: 40 FAFVRFEDPRDAEDAVFGRNGYDFGQCRLRVEF 72

This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

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

 Score = 37.5 bits (88), Expect = 4e-04
 Identities = 16/33 (48%), Positives = 20/33 (60%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRI 33
            R FAFVEF+ P DA+ A   LNG  +DG  +
Sbjct: 36 RPRGFAFVEFASPEDAEAALKKLNGLVLDGRTL 68

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

>gnl|CDD|189387 pfam00098, zf-CCHC, Zinc knuckle

 Score = 36.3 bits (85), Expect = 5e-04
 Identities = 10/18 (55%), Positives = 13/18 (72%)

Query: 61 GRCFNCGIDGHWARDCKA 78
           +C+NCG +GH ARDC  
Sbjct: 1  RKCYNCGKEGHLARDCPE 18

The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger. Length = 18

>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 = 13/35 (37%), Positives = 22/35 (62%)

Query: 4  DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
          ++ FVE+    DA+ A  +LNGR ++ + I V +A
Sbjct: 40 NYGFVEYHQSHDAEIALQTLNGRQIENNEIRVNWA 74

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

 Score = 37.3 bits (87), Expect = 6e-04
 Identities = 13/38 (34%), Positives = 21/38 (55%)

Query: 2  KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
           R + FV F    +A+ A  SLNG+   G +++V +A 
Sbjct: 43 PRGYCFVTFETKEEAEKALKSLNGKTALGKKLVVRWAH 80

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

 Score = 37.2 bits (87), Expect = 7e-04
 Identities = 11/21 (52%), Positives = 16/21 (76%)

Query: 5  FAFVEFSDPRDADDARYSLNG 25
          +AFVEF+ P +A +A  +LNG
Sbjct: 52 YAFVEFATPEEAKEAVKALNG 72

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

>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 37.5 bits (88), Expect = 7e-04
 Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 3/41 (7%)

Query: 1  MKRDFAFVEFSDPRDAD---DARYSLNGRDVDGSRIIVEFA 38
            R FAFVEF    DA    DA  +L+   +DG  + V +A
Sbjct: 44 TSRGFAFVEFPSLEDATQWMDALNNLDPFVIDGRVVRVSYA 84

This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 84

>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 37.5 bits (88), Expect = 7e-04
 Identities = 13/36 (36%), Positives = 24/36 (66%), Gaps = 2/36 (5%)

Query: 6  AFVEFSDPRDADDARYSLNGRDV-DGS-RIIVEFAR 39
          A V+F     A++A+ +LNGR++ DG   + ++F+R
Sbjct: 42 ALVQFDSVESAENAKKALNGRNIYDGCCTLDIQFSR 77

This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. . Length = 85

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 39.9 bits (94), Expect = 0.001
 Identities = 24/165 (14%), Positives = 48/165 (29%), Gaps = 3/165 (1%)

Query: 102 PKKLRPRSYSRSPSPRRGRSRSRSYSRGRSDSRSRSPVKRDRSVERFERRTRSPRDSRSP 161
            ++    +   + +       +R+ +   +++ S     + R         R     ++ 
Sbjct: 87  ARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAG 146

Query: 162 KRRRNSPPSSKGRKRSPTPDERSPQDQRSPSPRDRRQANGSEYSGSPRGKSRSPVDDADG 221
           +        ++      T +E   + +R     DR+           R +     DD D 
Sbjct: 147 EGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERG-ERGRREERGRDGDDRDR 205

Query: 222 PEDRNYRSPPEENGRS--RSRSLSPVPRDDRSPIDDDDNHGDPRG 264
            + R      EE GR     R      RD R    DD+       
Sbjct: 206 RDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDR 250

Length = 672

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

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 15/37 (40%), Positives = 17/37 (45%)

Query: 2  KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
           R F FV F    DA  A    N   +D S+I VE A
Sbjct: 40 SRRFGFVGFKSEEDAQQAVKYFNKTFIDTSKISVELA 76

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|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 22/39 (56%), Positives = 26/39 (66%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR 43
          FAFVEF DPRDA DA   L+GR + G R+ VE + G  R
Sbjct: 43 FAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEKR 81

This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation and tumor induction and maintenance. SRSF3 can shuttle between the nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 81

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

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 12/34 (35%), Positives = 20/34 (58%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
          + FV++ D  DA  A  +LNG ++   R+ V +A
Sbjct: 44 YGFVDYVDENDAQKAINTLNGFEIRNKRLKVSYA 77

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

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

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 14/37 (37%), Positives = 24/37 (64%)

Query: 2  KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
          K+ FAFV+F+   DA+ A   +NG+ + G  + V++A
Sbjct: 39 KKGFAFVQFTSKADAEKAIKGVNGKKIKGRPVAVDWA 75

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

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

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 15/34 (44%), Positives = 21/34 (61%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
          +AFVE+ D R A  A  ++NGR + G  I V +A
Sbjct: 39 YAFVEYYDHRSAAAALQTMNGRLILGQEIKVNWA 72

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

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

 Score = 39.5 bits (92), Expect = 0.001
 Identities = 29/93 (31%), Positives = 37/93 (39%), Gaps = 6/93 (6%)

Query: 108 RSYSRSPSPRRGRSRSRSYSRGRSDSRSRSPVKRDRSVERFERRTRSPRDSRSPKRRRNS 167
           R   R     R  +R     R RS  RSRS   RDRS  R +R     R  RS  R  N 
Sbjct: 1   RYRDRERGRLRNDTRRSDKGRERSRRRSRS---RDRSRRRRDRDYYRGRRGRSRSRSPNR 57

Query: 168 PPSSKGRKRSPTPDERS---PQDQRSPSPRDRR 197
               +G +     D RS    ++  + + RD R
Sbjct: 58  YYRPRGDRSYRRDDRRSGRNTKEPLTEAERDDR 90

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

 Score = 36.7 bits (85), Expect = 0.001
 Identities = 14/36 (38%), Positives = 24/36 (66%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
          R FAFVEFS  ++A +A  +L    + G R+++++A
Sbjct: 41 RGFAFVEFSTAKEALNAMNALKDTHLLGRRLVLQYA 76

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|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast RNA-binding protein PIN4, fission yeast RNA-binding post-transcriptional regulators cip1, cip2 and similar proteins

 Score = 36.7 bits (85), Expect = 0.001
 Identities = 14/37 (37%), Positives = 20/37 (54%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
          R  AF  F  P +A     +LNG ++ G R+ VE+ R
Sbjct: 43 RGLAFANFRSPEEAQTVVEALNGYEISGRRLRVEYKR 79

This subfamily corresponds to the RRM in PIN4, also termed psi inducibility protein 4 or modifier of damage tolerance Mdt1, a novel phosphothreonine (pThr)-containing protein that specifically interacts with the pThr-binding site of the Rad53 FHA1 domain. It is encoded by gene MDT1 (YBL051C) from yeast Saccharomyces cerevisiae. PIN4 is involved in normal G2/M cell cycle progression in the absence of DNA damage and functions as a novel target of checkpoint-dependent cell cycle arrest pathways. It contains an N-terminal RRM, a nuclear localization signal, a coiled coil, and a total of 15 SQ/TQ motifs. cip1 (Csx1-interacting protein 1) and cip2 (Csx1-interacting protein 2) are novel cytoplasmic RRM-containing proteins that counteract Csx1 function during oxidative stress. They are not essential for viability in fission yeast Schizosaccharomyces pombe. Both cip1 and cip2 contain one RRM. Like PIN4, Cip2 also possesses an R3H motif that may function in sequence-specific binding to single-stranded nucleic acids. . Length = 79

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

 Score = 36.3 bits (84), Expect = 0.001
 Identities = 13/35 (37%), Positives = 19/35 (54%)

Query: 2  KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVE 36
           +  AF+ F +   A  A  +LNG  VDG+ I V+
Sbjct: 36 VQPHAFITFENLEAAQLAIETLNGASVDGNCIKVQ 70

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

>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 36.3 bits (84), Expect = 0.001
 Identities = 17/32 (53%), Positives = 22/32 (68%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVE 36
          +AF+EF D RDA+DA    +G D DG R+ VE
Sbjct: 40 YAFIEFEDARDAEDAIRGRDGYDFDGQRLRVE 71

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

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

 Score = 39.1 bits (91), Expect = 0.002
 Identities = 34/120 (28%), Positives = 38/120 (31%), Gaps = 19/120 (15%)

Query: 122 RSRSYSRGRSDSRSRSPVKRDRSVERFERRTRSPRDSRSPKRRRNSPPSSKGRKRSPTPD 181
           R     R R  SR R    RDRS ER  RR+R     R   RR         R+RS   D
Sbjct: 1   RDEEPDREREKSRGRD---RDRSSERPRRRSRDRSRFRDRHRR--------SRERSYRED 49

Query: 182 ERSPQDQRSPSPRDRRQANGSEYSGSPRGKSRSPVDDADGPEDRNYRSPPEENGRSRSRS 241
            R     R     D R      YS     +SR              +       R RS S
Sbjct: 50  SRP----RDRRRYDSRSPRSLRYS--SVRRSRDRPRRRSRSVRSIEQH--RRRLRDRSPS 101

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

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 39.4 bits (92), Expect = 0.002
 Identities = 28/156 (17%), Positives = 39/156 (25%), Gaps = 3/156 (1%)

Query: 113 SPSPRRGRSRSRSYSRGRSDSRSRSPVKRDRSVERFERRTRSPRDSRSPKRRRNSPPSSK 172
             SP      S   +        RS      +        RS  D        +S   S 
Sbjct: 186 PSSPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPGRSAADDAGASSSDSSSSESS 245

Query: 173 GRKRSPTPDERSPQDQRSPSPRDRRQANGSEYSGS---PRGKSRSPVDDADGPEDRNYRS 229
           G    P  +   P+      P    +A+G     S   P   S SP + +  P   +  S
Sbjct: 246 GCGWGPENECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGS 305

Query: 230 PPEENGRSRSRSLSPVPRDDRSPIDDDDNHGDPRGS 265
            P  +    S S S       S              
Sbjct: 306 GPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAV 341

Length = 1352

>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 14/31 (45%), Positives = 18/31 (58%)

Query: 7  FVEFSDPRDADDARYSLNGRDVDGSRIIVEF 37
          FVEFSD  +A  A  +LNGR   G ++   F
Sbjct: 53 FVEFSDADEAIKAVRALNGRFFGGRKVTARF 83

This subfamily corresponds to the RRM found in UHM domain of 45 kDa-splicing factor (SPF45 or RBM17), poly(U)-binding-splicing factor PUF60 (FIR or Hfp or RoBP1 or Siah-BP1), and similar proteins. SPF45 is an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. 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 RRMs and a C-terminal UHM domain. . Length = 85

>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate RNA-binding protein 46 (RBM46)

 Score = 36.2 bits (83), Expect = 0.002
 Identities = 16/37 (43%), Positives = 23/37 (62%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
          RD+AFV F +  DA  A   +NG+ +DG+ I V  A+
Sbjct: 37 RDYAFVHFFNREDAVAAMSVMNGKCIDGASIEVTLAK 73

This subgroup corresponds to the RRM3 of RBM46, also termed cancer/testis antigen 68 (CT68), is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|197667 smart00343, ZnF_C2HC, zinc finger

 Score = 34.7 bits (81), Expect = 0.002
 Identities = 10/16 (62%), Positives = 13/16 (81%)

Query: 62 RCFNCGIDGHWARDCK 77
          +C+NCG +GH ARDC 
Sbjct: 1  KCYNCGKEGHIARDCP 16

Length = 17

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 16/38 (42%), Positives = 23/38 (60%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
            R F FV F    DA +A+  LNG ++DG RI V+++
Sbjct: 39 RSRGFGFVYFESVEDAKEAKERLNGMEIDGRRIRVDYS 76

This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 78

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 16/33 (48%), Positives = 24/33 (72%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIV 35
          R FAFV F D RDA+DA  +++G+++DG  + V
Sbjct: 40 RGFAFVRFYDKRDAEDAMDAMDGKELDGRELRV 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|197667 smart00343, ZnF_C2HC, zinc finger

 Score = 34.0 bits (79), Expect = 0.003
 Identities = 10/17 (58%), Positives = 13/17 (76%)

Query: 84  KCYRCGERGHIERNCQN 100
           KCY CG+ GHI R+C +
Sbjct: 1   KCYNCGKEGHIARDCPS 17

Length = 17

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 35.4 bits (81), Expect = 0.003
 Identities = 12/37 (32%), Positives = 23/37 (62%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
          +D+AF+ F +   A  A   +NG++++G  I + FA+
Sbjct: 35 KDYAFIHFDERDGAVKAMEEMNGKELEGENIEIVFAK 71

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

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

 Score = 35.5 bits (82), Expect = 0.003
 Identities = 16/34 (47%), Positives = 21/34 (61%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
          F FV F++  DAD AR  L+G  V+G +I V  A
Sbjct: 42 FGFVTFANSADADRAREKLHGTVVEGRKIEVNNA 75

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

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

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 15/33 (45%), Positives = 20/33 (60%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIV 35
          R FAFVEF +P DA  A  ++N  ++ G  I V
Sbjct: 40 RGFAFVEFEEPEDAAAAIDNMNESELFGRTIRV 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|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional

 Score = 36.3 bits (84), Expect = 0.004
 Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 5/45 (11%)

Query: 63  CFNCGIDGHWARDCKAGDWKN-----KCYRCGERGHIERNCQNSP 102
           C+ CG  GH +R+C             CY+CGE GH+ R C ++P
Sbjct: 3   CYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAP 47

Length = 148

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

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 12/34 (35%), Positives = 19/34 (55%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVE 36
          + F FV + +P  A  A  ++NG  V G R+ V+
Sbjct: 40 KCFGFVSYDNPESAQAAIKAMNGFQVGGKRLKVQ 73

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

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

 Score = 34.5 bits (80), Expect = 0.004
 Identities = 10/33 (30%), Positives = 19/33 (57%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRI 33
          + + + FV+F +  DA  A    NGR++ G ++
Sbjct: 33 LHKGYGFVQFDNEEDARAAVAGENGREIAGQKL 65

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	268
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.79
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.3
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.08
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.85
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	98.48
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.34
smart00361	70	RRM_1 RNA recognition motif.	98.33
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.3
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.13
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.08
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	97.93
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.92
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	97.87
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	97.8
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	97.76
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	97.73
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	97.71
smart00360	71	RRM RNA recognition motif.	97.71
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	97.7
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	97.61
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	97.59
smart00362	72	RRM_2 RNA recognition motif.	97.57
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	97.55
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	97.54
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	97.51
PTZ00368	148	universal minicircle sequence binding protein (UMS	97.48
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	97.47
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	97.47
PTZ00368	148	universal minicircle sequence binding protein (UMS	97.46
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	97.45
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	97.44
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	97.42
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	97.39
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	97.35
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	97.33
PLN03213	759	repressor of silencing 3; Provisional	97.32
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	97.3
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	97.26
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	97.26
PLN03120	260	nucleic acid binding protein; Provisional	97.22
COG0724	306	RNA-binding proteins (RRM domain) [General functio	97.22
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	97.2
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	97.19
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	97.17
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	97.08
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	97.05
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	96.99
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	96.94
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	96.93
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	96.92
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	96.9
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	96.89
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	96.85
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	96.84
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	96.83
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	96.82
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	96.76
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	96.58
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	96.55
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	96.54
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	96.53
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	96.47
KOG0119	554	consensus Splicing factor 1/branch point binding p	96.44
PLN03121	243	nucleic acid binding protein; Provisional	96.23
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	96.2
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	96.04
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	95.97
PF13696	32	zf-CCHC_2: Zinc knuckle	95.9
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	95.67
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	95.27
KOG1457	284	consensus RNA binding protein (contains RRM repeat	95.23
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	95.1
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	95.09
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	94.81
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	94.68
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	94.66
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	94.59
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	94.56
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	94.4
KOG4207	256	consensus Predicted splicing factor, SR protein su	94.39
KOG0226	290	consensus RNA-binding proteins [General function p	94.29
KOG1548	382	consensus Transcription elongation factor TAT-SF1	94.07
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	93.94
PF13917	42	zf-CCHC_3: Zinc knuckle	93.94
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	93.92
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	93.48
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	93.4
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	93.04
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	92.79
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	92.51
smart00343	26	ZnF_C2HC zinc finger.	92.21
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	91.67
COG5222	427	Uncharacterized conserved protein, contains RING Z	90.63
KOG4660	549	consensus Protein Mei2, essential for commitment t	89.97
KOG2314	698	consensus Translation initiation factor 3, subunit	89.6
KOG1995	351	consensus Conserved Zn-finger protein [General fun	89.59
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	89.52
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	88.62
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	88.02
PF13696	32	zf-CCHC_2: Zinc knuckle	87.87
PF13917	42	zf-CCHC_3: Zinc knuckle	86.8
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	86.35
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	85.98
KOG0533	243	consensus RRM motif-containing protein [RNA proces	85.69
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	84.81
COG5175	480	MOT2 Transcriptional repressor [Transcription]	84.12
PF14392	49	zf-CCHC_4: Zinc knuckle	83.71
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	83.53
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	83.05
PF15288	40	zf-CCHC_6: Zinc knuckle	80.91
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	80.08

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

Probab=99.79  E-value=1.2e-18  Score=146.17  Aligned_cols=73  Identities=53%  Similarity=0.996  Sum_probs=53.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCCcccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGSGRCFNCGIDGHWARDCKA   78 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r~~g~~r~~~~r~~~~~~~rC~~CG~~GH~ardC~~   78 (268)
                      +.|||||||+++.||++||..|||.+|+|.+|+||+..+.+++...+..   . ++.+...||+||..|||++.|..
T Consensus        46 PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~r~~r~gg~---~-~~~g~~~~~r~G~rg~~~r~~~~  118 (195)
T KOG0107|consen   46 PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRPRGSRRGGS---R-PPRGRGFCYRCGERGHIGRNCKD  118 (195)
T ss_pred             CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCccccccCCC---C-CcccccccccCCCcccccccccc
Confidence            5699999999999999999999999999999999999987763322111   1 22222336666666666655544

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

Probab=99.30  E-value=5.8e-11  Score=102.59  Aligned_cols=40  Identities=48%  Similarity=0.766  Sum_probs=37.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||-|.+..||++||+.|||.+|+|+.|+|++|+-.
T Consensus        54 sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~aryg   93 (256)
T KOG4207|consen   54 SRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARYG   93 (256)
T ss_pred             ccceeEEEeeecchHHHHHHhhcceeeccceeeehhhhcC
Confidence            4799999999999999999999999999999999999743

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

Probab=99.08  E-value=8.6e-11  Score=105.97  Aligned_cols=70  Identities=30%  Similarity=0.729  Sum_probs=57.7

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCCcccCC
Q 024424            1 MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGSGRCFNCGIDGHWARDCKAG   79 (268)
Q Consensus         1 lkrGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r~~g~~r~~~~r~~~~~~~rC~~CG~~GH~ardC~~~   79 (268)
                      |-|+|+||.|+..+||..||.+|||++|.|+.|.|++...+-+...++.         ..-.||.||+.|||...|+..
T Consensus       110 ivkdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlrtapgmg---------Dq~~cyrcGkeghwskEcP~~  179 (346)
T KOG0109|consen  110 IVKDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTAPGMG---------DQSGCYRCGKEGHWSKECPVD  179 (346)
T ss_pred             eecceeEEEEeeccchHHHHhcccccccccceeeeeeeccccccCCCCC---------CHHHheeccccccccccCCcc
Confidence            4589999999999999999999999999999999999886544222221         235799999999999999865

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

Probab=98.85  E-value=2.3e-09  Score=96.83  Aligned_cols=41  Identities=29%  Similarity=0.512  Sum_probs=38.3

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            1 MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         1 lkrGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      |-|+||||.+++...|++||.+|+|..|+|..|.||.++.+
T Consensus        34 IvKNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen   34 IVKNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             eecccceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            45789999999999999999999999999999999998865

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

Probab=98.48  E-value=4.3e-07  Score=75.36  Aligned_cols=42  Identities=33%  Similarity=0.589  Sum_probs=38.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      .+|||||+|.+.++|+.||+.|+|.+|+|+.|+|+++...+.
T Consensus        75 ~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~~~~~  116 (144)
T PLN03134         75 SRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPS  116 (144)
T ss_pred             cceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCCcCCC
Confidence            379999999999999999999999999999999999976543

>PF13893 RRM_5: RNA recognition motif

Probab=98.34  E-value=1e-06  Score=60.76  Aligned_cols=35  Identities=46%  Similarity=0.727  Sum_probs=33.9

Q ss_pred             CeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEec
Q 024424            4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA   38 (268)
Q Consensus         4 GfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a   38 (268)
                      ++|||+|.+.++|+.|+..|+|..|.|..|.|+++
T Consensus        22 ~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen   22 GFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             TEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            89999999999999999999999999999999985

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>smart00361 RRM_1 RNA recognition motif

Probab=98.33  E-value=6.9e-07  Score=64.72  Aligned_cols=34  Identities=35%  Similarity=0.541  Sum_probs=32.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEE
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIV   35 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrV   35 (268)
                      .+|||||+|.+.++|.+||..|||..|+|+.|.+
T Consensus        36 ~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361       36 KRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            4799999999999999999999999999999876

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

Probab=98.30  E-value=1.2e-06  Score=75.09  Aligned_cols=38  Identities=66%  Similarity=1.110  Sum_probs=36.5

Q ss_pred             CeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         4 GfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .||||+|+++.||++||..-||..++|-.|+|||+.+.
T Consensus        46 pfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprgg   83 (241)
T KOG0105|consen   46 PFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGG   83 (241)
T ss_pred             CeeEEEecCccchhhhhhcccccccCcceEEEEeccCC
Confidence            59999999999999999999999999999999999875

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

Probab=98.13  E-value=2.9e-05  Score=70.84  Aligned_cols=40  Identities=35%  Similarity=0.709  Sum_probs=37.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|+++.||+.|+++.+|.+|+|+.|.|.+..+.
T Consensus       142 skGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvERgR  181 (335)
T KOG0113|consen  142 SKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVERGR  181 (335)
T ss_pred             ccceEEEEeccHHHHHHHHHhccCceecCcEEEEEecccc
Confidence            4799999999999999999999999999999999998764

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

Probab=98.08  E-value=2e-06  Score=75.44  Aligned_cols=40  Identities=35%  Similarity=0.528  Sum_probs=37.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|+..+||..||++||+.+|.|+.|+|.+|+...
T Consensus        52 RgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP~k   91 (298)
T KOG0111|consen   52 RGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKPEK   91 (298)
T ss_pred             cceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCCcc
Confidence            6999999999999999999999999999999999998543

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

Probab=97.93  E-value=7.3e-06  Score=75.51  Aligned_cols=39  Identities=41%  Similarity=0.662  Sum_probs=36.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      .||||||+|++.+||++|-.+|+|+.|.|++|.|..+..
T Consensus       135 SKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATa  173 (376)
T KOG0125|consen  135 SKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATA  173 (376)
T ss_pred             CCccceEEecChhhHHHHHHHhhcceeeceEEEEeccch
Confidence            489999999999999999999999999999999998874

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

Probab=97.92  E-value=5.4e-06  Score=72.98  Aligned_cols=42  Identities=57%  Similarity=0.964  Sum_probs=39.1

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            1 MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         1 lkrGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      |++|||||+|++..||++||..||+.+|+|.++.|+++.+..
T Consensus        33 mk~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~   74 (216)
T KOG0106|consen   33 MKNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKR   74 (216)
T ss_pred             eecccceeccCchhhhhcccchhcCceecceeeeeecccccc
Confidence            689999999999999999999999999999999999998643

>PF00076 RRM_1: RNA recognition motif

Probab=97.87  E-value=1.4e-05  Score=56.33  Aligned_cols=33  Identities=39%  Similarity=0.743  Sum_probs=30.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceE
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRII   34 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~Ir   34 (268)
                      .++||||+|.+.++|+.||+.|+|..|+|..|+
T Consensus        38 ~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen   38 SKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             ccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            368999999999999999999999999998874

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=97.80  E-value=2.2e-05  Score=74.02  Aligned_cols=39  Identities=36%  Similarity=0.554  Sum_probs=36.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      .+|||||+|.+.++|+.||..|+|.+|.++.|+|.++..
T Consensus       148 srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~p  186 (346)
T TIGR01659       148 SFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARP  186 (346)
T ss_pred             cCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecccc
Confidence            369999999999999999999999999999999999864

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=97.76  E-value=2.5e-05  Score=72.61  Aligned_cols=38  Identities=37%  Similarity=0.607  Sum_probs=36.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      +|||||+|.+.+||+.||+.|+|..|.|+.|.|+++..
T Consensus        45 ~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~   82 (352)
T TIGR01661        45 LGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP   82 (352)
T ss_pred             ceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecc
Confidence            58999999999999999999999999999999999864

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

>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

Probab=97.73  E-value=1.6e-05  Score=68.32  Aligned_cols=40  Identities=53%  Similarity=1.256  Sum_probs=34.2

Q ss_pred             CCccccCCCCCCCCCccc---------CC------CCCCccccCCCCCccccccC
Q 024424           60 SGRCFNCGIDGHWARDCK---------AG------DWKNKCYRCGERGHIERNCQ   99 (268)
Q Consensus        60 ~~rC~~CG~~GH~ardC~---------~~------~~~~~cyrcg~~GH~~r~c~   99 (268)
                      .-.||+||+.||+.+||+         -+      .+...||.||+.||+..+|.
T Consensus        60 ~~~C~nCg~~GH~~~DCP~~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~  114 (190)
T COG5082          60 NPVCFNCGQNGHLRRDCPHSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCN  114 (190)
T ss_pred             ccccchhcccCcccccCChhHhhhcCCCCcccccCCcccccccccccCccccccC
Confidence            458999999999999999         11      25579999999999999995

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

Probab=97.71  E-value=2.5e-05  Score=63.90  Aligned_cols=39  Identities=26%  Similarity=0.460  Sum_probs=36.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      -+|||+|+|++.++|+.||+.|||.+|.|..|.|.|+--
T Consensus       113 ~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv  151 (170)
T KOG0130|consen  113 VKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFV  151 (170)
T ss_pred             ccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEe
Confidence            479999999999999999999999999999999999853

>smart00360 RRM RNA recognition motif

Probab=97.71  E-value=5.5e-05  Score=52.02  Aligned_cols=34  Identities=44%  Similarity=0.782  Sum_probs=31.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEE
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVE   36 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe   36 (268)
                      +|||||+|.+.++|+.|+..|++..|.|..|.|+
T Consensus        38 ~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360       38 KGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            5899999999999999999999999999988773

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

Probab=97.70  E-value=4.4e-05  Score=76.36  Aligned_cols=41  Identities=44%  Similarity=0.646  Sum_probs=38.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .++||||+|++.++|++||+.|||.+|+|+.|.|.|++...
T Consensus       268 ~rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~  308 (578)
T TIGR01648       268 IRDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVD  308 (578)
T ss_pred             ecCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCC
Confidence            46899999999999999999999999999999999997643

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.

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

Probab=97.61  E-value=5.4e-05  Score=68.33  Aligned_cols=41  Identities=27%  Similarity=0.511  Sum_probs=38.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .||||||.|...+||+.||..|+|.+|.++.|+-.|+..++
T Consensus       103 sKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp  143 (321)
T KOG0148|consen  103 SKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKP  143 (321)
T ss_pred             ccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCc
Confidence            47999999999999999999999999999999999998766

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

Probab=97.59  E-value=8.7e-05  Score=74.60  Aligned_cols=41  Identities=22%  Similarity=0.386  Sum_probs=38.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|++.++|..||..|||++|+|+.|+|.++...+
T Consensus       245 sKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP  285 (612)
T TIGR01645       245 HKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPP  285 (612)
T ss_pred             cCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCc
Confidence            47999999999999999999999999999999999998654

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.

>smart00362 RRM_2 RNA recognition motif

Probab=97.57  E-value=0.00011  Score=50.78  Aligned_cols=34  Identities=44%  Similarity=0.706  Sum_probs=31.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEE
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVE   36 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe   36 (268)
                      .|+|||+|.+.++|+.||..|+|..|.|..|.|.
T Consensus        39 ~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362       39 KGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            5899999999999999999999999999888763

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

Probab=97.55  E-value=9.5e-05  Score=60.03  Aligned_cols=38  Identities=32%  Similarity=0.544  Sum_probs=36.0

Q ss_pred             CeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         4 GfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      ||+||+|...+||+.||..++|+.|+.+.|+|.|..+-
T Consensus        79 GFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~GF  116 (153)
T KOG0121|consen   79 GFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDAGF  116 (153)
T ss_pred             ceEEEEEecchhHHHHHHHhccCcccccceeeeccccc
Confidence            89999999999999999999999999999999998653

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

Probab=97.54  E-value=8.7e-05  Score=72.49  Aligned_cols=39  Identities=36%  Similarity=0.647  Sum_probs=37.3

Q ss_pred             CeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         4 GfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      |||||+|.+..+|..||..|+|.+|+|+.|.|.||....
T Consensus       159 GFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd  197 (678)
T KOG0127|consen  159 GFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKD  197 (678)
T ss_pred             ceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccc
Confidence            999999999999999999999999999999999998654

>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=97.51  E-value=6.3e-05  Score=40.61  Aligned_cols=17  Identities=65%  Similarity=1.425  Sum_probs=13.4

Q ss_pred             ccccCCCCCCCCCcccC
Q 024424           62 RCFNCGIDGHWARDCKA   78 (268)
Q Consensus        62 rC~~CG~~GH~ardC~~   78 (268)
                      .||+||+.||++.+|+.
T Consensus         2 ~C~~C~~~GH~~~~Cp~   18 (18)
T PF00098_consen    2 KCFNCGEPGHIARDCPK   18 (18)
T ss_dssp             BCTTTSCSSSCGCTSSS
T ss_pred             cCcCCCCcCcccccCcc
Confidence            58888888888888863

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional

Probab=97.48  E-value=9.8e-05  Score=61.24  Aligned_cols=41  Identities=37%  Similarity=1.082  Sum_probs=30.2

Q ss_pred             CCccccCCCCCCCCCcccCCC---CCCccccCCCCCccccccCC
Q 024424           60 SGRCFNCGIDGHWARDCKAGD---WKNKCYRCGERGHIERNCQN  100 (268)
Q Consensus        60 ~~rC~~CG~~GH~ardC~~~~---~~~~cyrcg~~GH~~r~c~~  100 (268)
                      ...||+|+..||++.+|+...   ....||.|+..||++.+|+.
T Consensus        27 ~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~Cp~   70 (148)
T PTZ00368         27 ARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPE   70 (148)
T ss_pred             CccCccCCCCCcCcccCcCCCCCCCCcccCCCCCcCcCcccCCC
Confidence            457888888888888887643   23568888888888888865

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

Probab=97.47  E-value=0.00014  Score=71.09  Aligned_cols=40  Identities=35%  Similarity=0.570  Sum_probs=37.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||..|+|..|.|..|.|.++...
T Consensus       336 ~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~  375 (509)
T TIGR01642       336 SKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVG  375 (509)
T ss_pred             cCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccC
Confidence            4799999999999999999999999999999999998643

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

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

Probab=97.47  E-value=0.00013  Score=70.42  Aligned_cols=37  Identities=32%  Similarity=0.652  Sum_probs=35.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|+.||..|+|.+|.|+.|.|.++.
T Consensus       228 ~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       228 KGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             ceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            6899999999999999999999999999999999976

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.

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional

Probab=97.46  E-value=8.5e-05  Score=61.59  Aligned_cols=40  Identities=45%  Similarity=1.158  Sum_probs=27.0

Q ss_pred             CccccCCCCCCCCCcccCCC----CCCccccCCCCCccccccCC
Q 024424           61 GRCFNCGIDGHWARDCKAGD----WKNKCYRCGERGHIERNCQN  100 (268)
Q Consensus        61 ~rC~~CG~~GH~ardC~~~~----~~~~cyrcg~~GH~~r~c~~  100 (268)
                      ..||+|+..||++.+|+...    ....||.|+..||++.+|+.
T Consensus        78 ~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~  121 (148)
T PTZ00368         78 RSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPN  121 (148)
T ss_pred             cccCcCCCCCcccccCCCcccccccchhhcccCcCCcchhcCCC
Confidence            46777777777777776532    23467777777777777776

>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=97.45  E-value=0.00025  Score=49.12  Aligned_cols=35  Identities=49%  Similarity=0.843  Sum_probs=32.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEe
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEF   37 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~   37 (268)
                      .|+|||+|.+.++|..|+..|++..|+|..|.|.+
T Consensus        40 ~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590          40 KGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             ceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            68999999999999999999999999999998864

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=97.44  E-value=0.00045  Score=65.26  Aligned_cols=39  Identities=31%  Similarity=0.443  Sum_probs=34.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecC--cceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDG--SRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~G--r~IrVe~a~~~   41 (268)
                      +|||||+|++.++|++||+.|++..|++  ..|.|.++...
T Consensus       235 kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~  275 (346)
T TIGR01659       235 RGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEH  275 (346)
T ss_pred             ceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCcc
Confidence            5899999999999999999999999977  57888887653

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).

>PF14259 RRM_6: RNA recognition motif (a

Probab=97.42  E-value=0.00015  Score=51.55  Aligned_cols=32  Identities=50%  Similarity=0.808  Sum_probs=29.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceE
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRII   34 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~Ir   34 (268)
                      +|+|||+|.+.++|+.||..++|.+|+|+.|.
T Consensus        39 ~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen   39 RGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            58999999999999999999999999998874

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 ....

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

Probab=97.39  E-value=0.00022  Score=69.92  Aligned_cols=39  Identities=31%  Similarity=0.384  Sum_probs=36.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      ++|||||+|.+.++|+.||..|+|..|.|+.|.|.+++.
T Consensus       312 ~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~  350 (481)
T TIGR01649       312 KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQ  350 (481)
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccc
Confidence            469999999999999999999999999999999999864

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).

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

Probab=97.35  E-value=0.00054  Score=58.36  Aligned_cols=18  Identities=72%  Similarity=1.608  Sum_probs=16.2

Q ss_pred             CccccCCCCCccccccCC
Q 024424           83 NKCYRCGERGHIERNCQN  100 (268)
Q Consensus        83 ~~cyrcg~~GH~~r~c~~  100 (268)
                      ..||.||+.||+.+.|.+
T Consensus       101 ~~~~r~G~rg~~~r~~~~  118 (195)
T KOG0107|consen  101 GFCYRCGERGHIGRNCKD  118 (195)
T ss_pred             cccccCCCcccccccccc
Confidence            349999999999999997

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

Probab=97.33  E-value=0.00027  Score=70.33  Aligned_cols=40  Identities=35%  Similarity=0.619  Sum_probs=37.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||..|+|..|.|+.|.|.++...
T Consensus       325 ~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k  364 (562)
T TIGR01628       325 SRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRK  364 (562)
T ss_pred             cCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCc
Confidence            4699999999999999999999999999999999998753

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=97.32  E-value=0.00024  Score=68.82  Aligned_cols=37  Identities=30%  Similarity=0.471  Sum_probs=34.6

Q ss_pred             CCeEEEEeCCH--HHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDP--RDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~--~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|...  .++.+||..|||.+++|+.|+|+.|+
T Consensus        48 RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAK   86 (759)
T PLN03213         48 RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAK   86 (759)
T ss_pred             CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeecc
Confidence            69999999987  67999999999999999999999876

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

Probab=97.30  E-value=0.00016  Score=61.83  Aligned_cols=38  Identities=34%  Similarity=0.373  Sum_probs=35.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      -+|||||||.+.+||+.||.-|++..|.|+.|+|..+.
T Consensus        50 ~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen   50 HQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             ccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            47999999999999999999999999999999998886

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

Probab=97.26  E-value=0.00028  Score=68.41  Aligned_cols=41  Identities=32%  Similarity=0.618  Sum_probs=38.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .+||||++|.+.++|+.||..|+|.+|.|+.|+|.|+....
T Consensus        59 ~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~~   99 (435)
T KOG0108|consen   59 PKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNRK   99 (435)
T ss_pred             cCceeeEecCchhhHHHHHHhcCCcccCCceEEeecccccc
Confidence            47999999999999999999999999999999999987543

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

Probab=97.26  E-value=0.00033  Score=70.22  Aligned_cols=40  Identities=30%  Similarity=0.600  Sum_probs=37.1

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            1 MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         1 lkrGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      |..|||||+|.+.++|..||..|+|+.|+|..|.|.++..
T Consensus       558 lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~  597 (725)
T KOG0110|consen  558 LSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISEN  597 (725)
T ss_pred             cccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccC
Confidence            3469999999999999999999999999999999999873

>PLN03120 nucleic acid binding protein; Provisional

Probab=97.22  E-value=0.00046  Score=62.43  Aligned_cols=38  Identities=26%  Similarity=0.485  Sum_probs=35.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      .+|||||+|.+.++|+.|| .|+|..|.|+.|.|.++..
T Consensus        42 ~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120         42 RSQIAYVTFKDPQGAETAL-LLSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCCEEEEEeCcHHHHHHHH-HhcCCeeCCceEEEEeccC
Confidence            3689999999999999999 5999999999999999864

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

Probab=97.22  E-value=0.00046  Score=59.40  Aligned_cols=38  Identities=39%  Similarity=0.662  Sum_probs=36.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+|||||+|.+.++|..||..|+|..|.|+.|.|.++.
T Consensus       156 ~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         156 SRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             cCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            47999999999999999999999999999999999975

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=97.20  E-value=0.00033  Score=61.00  Aligned_cols=38  Identities=21%  Similarity=0.218  Sum_probs=34.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+|||||||++.+.|+-|.+.||++.|.+..|.|-+-.
T Consensus        91 SKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmp  128 (214)
T KOG4208|consen   91 SKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMP  128 (214)
T ss_pred             cCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeC
Confidence            37999999999999999999999999999988887754

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

Probab=97.19  E-value=0.00035  Score=70.36  Aligned_cols=38  Identities=34%  Similarity=0.489  Sum_probs=35.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+|||||+|.+.++|+.||..|||..|.|+.|.|.+..
T Consensus       148 skGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       148 HKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             cCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            47999999999999999999999999999999998654

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.

>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

Probab=97.17  E-value=0.00024  Score=61.23  Aligned_cols=41  Identities=34%  Similarity=0.972  Sum_probs=37.6

Q ss_pred             CccccCCCCCCCCCcc-cCCCCCCccccCCCCCccccccCCC
Q 024424           61 GRCFNCGIDGHWARDC-KAGDWKNKCYRCGERGHIERNCQNS  101 (268)
Q Consensus        61 ~rC~~CG~~GH~ardC-~~~~~~~~cyrcg~~GH~~r~c~~s  101 (268)
                      .+||+||..||++.|| +....+..|+.|...+|+..+|+.-
T Consensus        98 ~~C~~Cg~~GH~~~dC~P~~~~~~~C~~C~s~~H~s~~Cp~~  139 (190)
T COG5082          98 KKCYNCGETGHLSRDCNPSKDQQKSCFDCNSTRHSSEDCPSI  139 (190)
T ss_pred             cccccccccCccccccCcccccCcceeccCCCccccccCccc
Confidence            6899999999999999 6777778999999999999999973

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

Probab=97.08  E-value=0.00061  Score=65.30  Aligned_cols=39  Identities=44%  Similarity=0.660  Sum_probs=37.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +.||||.|.+.+||.+|++.|+|++|+|..|.|.+|+..
T Consensus       293 rDYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~  331 (506)
T KOG0117|consen  293 RDYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPV  331 (506)
T ss_pred             cceeEEeecchHHHHHHHHHhcCceecCceEEEEecCCh
Confidence            579999999999999999999999999999999999864

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

Probab=97.05  E-value=0.00066  Score=67.57  Aligned_cols=37  Identities=24%  Similarity=0.525  Sum_probs=35.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.+||+.||+.|++..|.|+.|+|.|+.
T Consensus        42 ~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~   78 (562)
T TIGR01628        42 LGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQ   78 (562)
T ss_pred             ceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccc
Confidence            5899999999999999999999999999999999875

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

>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=96.99  E-value=0.00043  Score=62.66  Aligned_cols=41  Identities=37%  Similarity=1.027  Sum_probs=34.8

Q ss_pred             CccccCCCCCCCCCcccCCCCCCccccCCCCCccccccCCCC
Q 024424           61 GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSP  102 (268)
Q Consensus        61 ~rC~~CG~~GH~ardC~~~~~~~~cyrcg~~GH~~r~c~~s~  102 (268)
                      ..||+||..|||..+|+.. ....||.|+..+|+..+|+...
T Consensus       144 ~~Cy~Cg~~GH~s~~C~~~-~~~~c~~c~~~~h~~~~C~~~~  184 (261)
T KOG4400|consen  144 AKCYSCGEQGHISDDCPEN-KGGTCFRCGKVGHGSRDCPSKQ  184 (261)
T ss_pred             CccCCCCcCCcchhhCCCC-CCCccccCCCcceecccCCccc
Confidence            4599999999999999976 5678999999999999998744

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

Probab=96.94  E-value=0.0008  Score=65.83  Aligned_cols=38  Identities=32%  Similarity=0.514  Sum_probs=35.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      -+|||||+|.+.++|.+|+..|||++|.|+.|+|....
T Consensus       319 skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~  356 (549)
T KOG0147|consen  319 SKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVT  356 (549)
T ss_pred             ccCcceEEEecHHHHHHHHHHhccceecCceEEEEEee
Confidence            47999999999999999999999999999999988754

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

Probab=96.93  E-value=0.001  Score=63.82  Aligned_cols=39  Identities=28%  Similarity=0.441  Sum_probs=34.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCee-cCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDV-DGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l-~Gr~IrVe~a~~   40 (268)
                      -+|||||+|.+.++|+.||+.||+.+| .|+.|.|.....
T Consensus       124 nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Sva  163 (506)
T KOG0117|consen  124 NRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSVA  163 (506)
T ss_pred             CcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEeee
Confidence            479999999999999999999999999 588888887553

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

Probab=96.92  E-value=0.00075  Score=66.01  Aligned_cols=36  Identities=22%  Similarity=0.301  Sum_probs=32.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|..|| .|+|..|.|..|.|....
T Consensus       223 kg~afVeF~~~e~A~~Al-~l~g~~~~g~~l~v~r~~  258 (509)
T TIGR01642       223 KNFAFLEFRTVEEATFAM-ALDSIIYSNVFLKIRRPH  258 (509)
T ss_pred             CCEEEEEeCCHHHHhhhh-cCCCeEeeCceeEecCcc
Confidence            689999999999999999 699999999999886543

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

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

Probab=96.90  E-value=0.0012  Score=63.84  Aligned_cols=38  Identities=32%  Similarity=0.418  Sum_probs=34.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      .+|||||+|.+.++|++||. |+|..|.|..|.|.+...
T Consensus       130 skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~~~  167 (457)
T TIGR01622       130 SKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQA  167 (457)
T ss_pred             cceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeecch
Confidence            37999999999999999995 999999999999988653

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.

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

Probab=96.89  E-value=0.0013  Score=51.61  Aligned_cols=37  Identities=35%  Similarity=0.472  Sum_probs=34.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|-|||.|++..||.+|+++|.|..+++..+.|.+..
T Consensus        57 rGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   57 RGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             CceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            5899999999999999999999999999999988765

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

Probab=96.85  E-value=0.0011  Score=59.85  Aligned_cols=39  Identities=33%  Similarity=0.605  Sum_probs=36.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      -|||||.|-+++||++||..|+|..|.-+.|+|.+++..
T Consensus        83 LGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARPS  121 (360)
T KOG0145|consen   83 LGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARPS  121 (360)
T ss_pred             cccceeeecChHHHHHHHhhhcceeeccceEEEEeccCC
Confidence            489999999999999999999999999999999999854

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

Probab=96.84  E-value=0.0015  Score=59.26  Aligned_cols=39  Identities=23%  Similarity=0.505  Sum_probs=36.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +||+||-|++.|.|..||..|||++|.|..|++.|-+..
T Consensus       200 qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~  238 (321)
T KOG0148|consen  200 QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEG  238 (321)
T ss_pred             cceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccC
Confidence            699999999999999999999999999999999998754

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

Probab=96.83  E-value=0.0014  Score=64.27  Aligned_cols=37  Identities=32%  Similarity=0.486  Sum_probs=33.3

Q ss_pred             CeEEEEeCCHHHHHHHHHhhCCCeecC--cceEEEeccC
Q 024424            4 DFAFVEFSDPRDADDARYSLNGRDVDG--SRIIVEFARG   40 (268)
Q Consensus         4 GfgFVeF~~~~dA~~Ai~~ldG~~l~G--r~IrVe~a~~   40 (268)
                      ++|||+|++.++|+.||..|||.+|.+  ..|+|+|++.
T Consensus       135 ~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~  173 (481)
T TIGR01649       135 FQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKP  173 (481)
T ss_pred             eEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecC
Confidence            689999999999999999999999975  4789999874

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).

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=96.82  E-value=0.00085  Score=62.76  Aligned_cols=39  Identities=26%  Similarity=0.586  Sum_probs=36.3

Q ss_pred             CeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         4 GfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .||||||++.+.+++|+.+||+..|+.++|.|.|.+...
T Consensus       282 qyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQSVs  320 (479)
T KOG0415|consen  282 QYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQSVS  320 (479)
T ss_pred             heeeeeecchhhHHHHHhhhcceeeccceEEeehhhhhh
Confidence            489999999999999999999999999999999987653

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=96.76  E-value=0.0019  Score=59.97  Aligned_cols=39  Identities=33%  Similarity=0.570  Sum_probs=33.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecC--cceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDG--SRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~G--r~IrVe~a~~   40 (268)
                      .+|||||+|++.++|+.||..|+|..+.|  ..|.|.++..
T Consensus       130 ~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~  170 (352)
T TIGR01661       130 SKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANN  170 (352)
T ss_pred             cCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCC
Confidence            36899999999999999999999999987  4577777753

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

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

Probab=96.58  E-value=0.0017  Score=61.06  Aligned_cols=37  Identities=35%  Similarity=0.496  Sum_probs=34.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +||+||||+-++.|.-|++.|||..|.|+.|+|..-.
T Consensus       155 KgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  155 KGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             cceEEEEEeCcHHHHHHHHHhccccccCccccccCCC
Confidence            6999999999999999999999999999999997543

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

Probab=96.55  E-value=0.003  Score=55.83  Aligned_cols=34  Identities=50%  Similarity=0.850  Sum_probs=32.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEE
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIV   35 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrV   35 (268)
                      ..+|+||+|.+.+||..||..|+|.+|.+..|.|
T Consensus       132 ~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen  132 RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISV  165 (216)
T ss_pred             hccccceeehhhhhhhhcchhccchhhcCceeee
Confidence            4689999999999999999999999999999998

>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=96.54  E-value=0.0016  Score=35.08  Aligned_cols=17  Identities=59%  Similarity=1.497  Sum_probs=15.7

Q ss_pred             ccccCCCCCccccccCC
Q 024424           84 KCYRCGERGHIERNCQN  100 (268)
Q Consensus        84 ~cyrcg~~GH~~r~c~~  100 (268)
                      .||.|++.||++.+|+.
T Consensus         2 ~C~~C~~~GH~~~~Cp~   18 (18)
T PF00098_consen    2 KCFNCGEPGHIARDCPK   18 (18)
T ss_dssp             BCTTTSCSSSCGCTSSS
T ss_pred             cCcCCCCcCcccccCcc
Confidence            69999999999999974

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....

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

Probab=96.53  E-value=0.0022  Score=64.37  Aligned_cols=37  Identities=30%  Similarity=0.468  Sum_probs=31.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeec-CcceEEEec
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVD-GSRIIVEFA   38 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~-Gr~IrVe~a   38 (268)
                      .+|||||+|.+.++|+.||+.|++.+|. |+.|.|.++
T Consensus        98 sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        98 NRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             ccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence            4799999999999999999999999885 666655543

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.

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

Probab=96.47  E-value=0.00065  Score=58.31  Aligned_cols=39  Identities=31%  Similarity=0.429  Sum_probs=36.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      .+||||+.|++.....-||++|+|+.|.|+.|+|.+...
T Consensus        76 SKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~  114 (219)
T KOG0126|consen   76 SKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSN  114 (219)
T ss_pred             ccceEEEEecCccceEEEEeccCCceecceeEEeeeccc
Confidence            379999999999999999999999999999999998754

>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]

Probab=96.44  E-value=0.0029  Score=61.42  Aligned_cols=96  Identities=21%  Similarity=0.320  Sum_probs=58.3

Q ss_pred             CeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC-CCCC-CCCCCCCCCCCCCCCCccccCCCCCCCCCcccCC--
Q 024424            4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG-PRGP-GGSREYLGRGPPPGSGRCFNCGIDGHWARDCKAG--   79 (268)
Q Consensus         4 GfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~-~r~~-g~~r~~~~r~~~~~~~rC~~CG~~GH~ardC~~~--   79 (268)
                      .+++|+-++.+..++||..+.......  |.|-..... .+.. ..--...+...-.....|-+||..||-+.+|+..  
T Consensus       205 LH~~Isadt~eki~~Ai~vienli~~a--v~~~e~~n~l~~~Qlrela~lNgt~r~~d~~~c~~cg~~~H~q~~cp~r~~  282 (554)
T KOG0119|consen  205 LHCLISADTQEKIKKAIAVIENLIQSA--VSVPEGQNDLKRLQLRELARLNGTLRDDDNRACRNCGSTGHKQYDCPGRIP  282 (554)
T ss_pred             eeEEEecchHHHHHHHHHHHHHHHHhh--ccCccccccccHHHHHHHHHhCCCCCccccccccccCCCccccccCCcccc
Confidence            368899888888888887665443321  111111000 0000 0000000011122235899999999999999965  


Q ss_pred             CCCCccccCCCCCccccccCCC
Q 024424           80 DWKNKCYRCGERGHIERNCQNS  101 (268)
Q Consensus        80 ~~~~~cyrcg~~GH~~r~c~~s  101 (268)
                      .+...|+.|+-.||+..+|...
T Consensus       283 ~~~n~c~~cg~~gH~~~dc~~~  304 (554)
T KOG0119|consen  283 NTTNVCKICGPLGHISIDCKVN  304 (554)
T ss_pred             cccccccccCCcccccccCCCc
Confidence            4566999999999999999875

>PLN03121 nucleic acid binding protein; Provisional

Probab=96.23  E-value=0.0065  Score=54.43  Aligned_cols=36  Identities=22%  Similarity=0.260  Sum_probs=32.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+||||+|.+.++|+.|| .|+|..|.+..|.|..+.
T Consensus        44 ~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~   79 (243)
T PLN03121         44 ACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWG   79 (243)
T ss_pred             ceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCc
Confidence            479999999999999999 799999999999988764

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

Probab=96.20  E-value=0.0053  Score=58.53  Aligned_cols=40  Identities=28%  Similarity=0.503  Sum_probs=36.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      -|||||.|.++.||+.||+.|+...|.|+.|+|-|....+
T Consensus        37 lgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~   76 (369)
T KOG0123|consen   37 LGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP   76 (369)
T ss_pred             cceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC
Confidence            3899999999999999999999999999999999987543

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

Probab=96.04  E-value=0.0058  Score=61.54  Aligned_cols=38  Identities=34%  Similarity=0.556  Sum_probs=36.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      ++||||.|.+.++|++||.++|++-|+-.+|.|+++..
T Consensus         9 R~F~FiGf~~eeeA~~Ai~~fn~s~i~ts~i~Ve~~~~   46 (725)
T KOG0110|consen    9 RRFGFIGFKSEEEAQKAIKYFNKSFINTSRITVEFCKS   46 (725)
T ss_pred             eeeeEeeeccHHHHHHHHHHhhccccccceEEEEehhh
Confidence            57999999999999999999999999999999999874

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

Probab=95.97  E-value=0.008  Score=57.33  Aligned_cols=37  Identities=30%  Similarity=0.505  Sum_probs=34.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      +|| ||+|++++.|..||+.|||..+.+..|.|.....
T Consensus       116 kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~  152 (369)
T KOG0123|consen  116 KGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFER  152 (369)
T ss_pred             eee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccc
Confidence            689 9999999999999999999999999999977653

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=95.90  E-value=0.0045  Score=38.26  Aligned_cols=23  Identities=43%  Similarity=1.165  Sum_probs=18.4

Q ss_pred             CCCCCccccCCCCCCCCCcccCC
Q 024424           57 PPGSGRCFNCGIDGHWARDCKAG   79 (268)
Q Consensus        57 ~~~~~rC~~CG~~GH~ardC~~~   79 (268)
                      ++..-.|+.|++.|||..||+..
T Consensus         5 pP~~Y~C~~C~~~GH~i~dCP~~   27 (32)
T PF13696_consen    5 PPPGYVCHRCGQKGHWIQDCPTN   27 (32)
T ss_pred             CCCCCEeecCCCCCccHhHCCCC
Confidence            34456899999999999999874

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

Probab=95.67  E-value=0.0078  Score=59.24  Aligned_cols=42  Identities=29%  Similarity=0.401  Sum_probs=38.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      .+|||||+|.=.+|++.||..+.+..|.|+.|.|.++..+.+
T Consensus        46 ~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R~r   87 (678)
T KOG0127|consen   46 KRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKRAR   87 (678)
T ss_pred             ccCccceeeehHhHHHHHHHHhhcCcccceeccccccccccc
Confidence            579999999999999999999999999999999999986543

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

Probab=95.27  E-value=0.019  Score=55.23  Aligned_cols=39  Identities=33%  Similarity=0.524  Sum_probs=36.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      .+|-|+|||.+++.+++|+++|+-++++|+.|.|.+...
T Consensus        85 ~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d  123 (608)
T KOG4212|consen   85 ARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHD  123 (608)
T ss_pred             cCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCc
Confidence            368899999999999999999999999999999988764

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

Probab=95.23  E-value=0.026  Score=50.04  Aligned_cols=39  Identities=33%  Similarity=0.454  Sum_probs=35.2

Q ss_pred             CeEEEEeCCHHHHHHHHHhhCCCeec---CcceEEEeccCCC
Q 024424            4 DFAFVEFSDPRDADDARYSLNGRDVD---GSRIIVEFARGGP   42 (268)
Q Consensus         4 GfgFVeF~~~~dA~~Ai~~ldG~~l~---Gr~IrVe~a~~~~   42 (268)
                      -||||+|.+..+|+.|+..|+|..|+   +..|+||+++...
T Consensus        78 pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiElAKSNt  119 (284)
T KOG1457|consen   78 PVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIELAKSNT  119 (284)
T ss_pred             ceEEEEecchHHHHHHHHHhcCeeeccccCceeEeeehhcCc
Confidence            48999999999999999999999995   7789999998654

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=95.10  E-value=0.031  Score=50.04  Aligned_cols=39  Identities=33%  Similarity=0.556  Sum_probs=36.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+||+||+|.+.+.++.||. |||.+|.|..|.|.+.+..
T Consensus       142 ~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~r~~  180 (231)
T KOG4209|consen  142 PKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLKRTN  180 (231)
T ss_pred             cceeEEEecccHhhhHHHhh-cCCcccccccceeeeeeee
Confidence            37899999999999999998 9999999999999988754

>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=95.09  E-value=0.039  Score=41.83  Aligned_cols=37  Identities=30%  Similarity=0.467  Sum_probs=29.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+-|+|-|.+++.|+.|++.|+|..+-|.+|.|.|..
T Consensus        39 ~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~   75 (90)
T PF11608_consen   39 GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSP   75 (90)
T ss_dssp             TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS-
T ss_pred             CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcC
Confidence            4779999999999999999999999999999999985

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=94.81  E-value=0.021  Score=51.71  Aligned_cols=19  Identities=53%  Similarity=1.349  Sum_probs=16.5

Q ss_pred             CccccCCCCCccccccCCC
Q 024424           83 NKCYRCGERGHIERNCQNS  101 (268)
Q Consensus        83 ~~cyrcg~~GH~~r~c~~s  101 (268)
                      ..||.||+.||+..+|++.
T Consensus       144 ~~Cy~Cg~~GH~s~~C~~~  162 (261)
T KOG4400|consen  144 AKCYSCGEQGHISDDCPEN  162 (261)
T ss_pred             CccCCCCcCCcchhhCCCC
Confidence            4699999999999999964

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

Probab=94.68  E-value=0.023  Score=53.57  Aligned_cols=40  Identities=23%  Similarity=0.390  Sum_probs=36.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||||.+......||..||-+.|.|..|+|..+...+
T Consensus       252 kGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vTPP  291 (544)
T KOG0124|consen  252 KGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPP  291 (544)
T ss_pred             cceeeEEeccccchHHHhhhcchhhcccceEecccccCCC
Confidence            7999999999999999999999999999999998876543

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

Probab=94.66  E-value=0.023  Score=50.62  Aligned_cols=37  Identities=27%  Similarity=0.421  Sum_probs=30.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+|||||+|.|.+.|..|+...+ =.|+|++..+.+|.
T Consensus        53 skGyGfVTf~d~~aa~rAc~dp~-piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   53 SKGYGFVTFRDAEAATRACKDPN-PIIDGRKANCNLAS   89 (247)
T ss_pred             ccceeeEEeecHHHHHHHhcCCC-Ccccccccccchhh
Confidence            47999999999999999997654 56888888777765

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

Probab=94.59  E-value=0.051  Score=52.29  Aligned_cols=42  Identities=36%  Similarity=0.528  Sum_probs=35.6

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHhhCCC-eecC--cceEEEeccCCC
Q 024424            1 MKRDFAFVEFSDPRDADDARYSLNGR-DVDG--SRIIVEFARGGP   42 (268)
Q Consensus         1 lkrGfgFVeF~~~~dA~~Ai~~ldG~-~l~G--r~IrVe~a~~~~   42 (268)
                      +-+|+|||.|.+.+-|..||+.|+|+ .|.|  ..|.|.||....
T Consensus       163 ~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqk  207 (510)
T KOG0144|consen  163 LSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQK  207 (510)
T ss_pred             cccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCC
Confidence            45899999999999999999999997 4555  689999997543

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=94.56  E-value=0.034  Score=55.16  Aligned_cols=40  Identities=30%  Similarity=0.448  Sum_probs=36.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +-||||+|.+..+|.+||.+|+-++|.|+.|.|+.++.-+
T Consensus       447 RCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKNEp  486 (940)
T KOG4661|consen  447 RCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKNEP  486 (940)
T ss_pred             ceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecccCc
Confidence            4699999999999999999999999999999999987544

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

Probab=94.40  E-value=0.052  Score=49.21  Aligned_cols=41  Identities=32%  Similarity=0.568  Sum_probs=35.8

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHhhCCCeecC--cceEEEeccCC
Q 024424            1 MKRDFAFVEFSDPRDADDARYSLNGRDVDG--SRIIVEFARGG   41 (268)
Q Consensus         1 lkrGfgFVeF~~~~dA~~Ai~~ldG~~l~G--r~IrVe~a~~~   41 (268)
                      |.+|.|||-|+...+|+.||..|+|..-.|  ..|.|.|+...
T Consensus       167 ~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannP  209 (360)
T KOG0145|consen  167 LSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNP  209 (360)
T ss_pred             eecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCc
Confidence            458999999999999999999999998766  57999998643

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

Probab=94.39  E-value=0.43  Score=42.07  Aligned_cols=26  Identities=35%  Similarity=0.433  Sum_probs=21.9

Q ss_pred             EEEEeCCHHHHHHHHHh--hCCCeecCc
Q 024424            6 AFVEFSDPRDADDARYS--LNGRDVDGS   31 (268)
Q Consensus         6 gFVeF~~~~dA~~Ai~~--ldG~~l~Gr   31 (268)
                      -|-+-.+++||++||++  |||.+|.-+
T Consensus        61 rf~~k~daedA~damDG~~ldgRelrVq   88 (256)
T KOG4207|consen   61 RFHDKRDAEDALDAMDGAVLDGRELRVQ   88 (256)
T ss_pred             EeeecchHHHHHHhhcceeeccceeeeh
Confidence            47778899999999998  999998543

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=94.29  E-value=0.03  Score=50.48  Aligned_cols=36  Identities=31%  Similarity=0.498  Sum_probs=32.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEec
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA   38 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a   38 (268)
                      +|||||.|.+..|+..|+..|||..+.-+.|.+.-.
T Consensus       232 kgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  232 KGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             ccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            799999999999999999999999999888776443

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

Probab=94.07  E-value=0.082  Score=49.54  Aligned_cols=40  Identities=23%  Similarity=0.391  Sum_probs=36.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      ..|.+.|.|.+.++|+.||..|+|..|+|+.|..++..+.
T Consensus       313 PdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  313 PDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             CCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCc
Confidence            3588999999999999999999999999999999887654

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

Probab=93.94  E-value=0.057  Score=47.72  Aligned_cols=40  Identities=28%  Similarity=0.432  Sum_probs=37.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|=|||.|.+.+.|-.|+..|+|+-|.|+.|+|++|+...
T Consensus        52 RGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s~s   91 (221)
T KOG4206|consen   52 RGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKSDS   91 (221)
T ss_pred             cCceEEEecChhHHHHHHHHhcCCcccCchhheecccCcc
Confidence            5789999999999999999999999999999999998643

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=93.94  E-value=0.031  Score=36.77  Aligned_cols=18  Identities=44%  Similarity=1.234  Sum_probs=13.8

Q ss_pred             CccccCCCCCCCCCcccC
Q 024424           61 GRCFNCGIDGHWARDCKA   78 (268)
Q Consensus        61 ~rC~~CG~~GH~ardC~~   78 (268)
                      ..|.+|+..|||..+|+.
T Consensus         5 ~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    5 VRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CcCcccCCCCcchhhCCC
Confidence            568888888888887773

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

Probab=93.92  E-value=0.069  Score=45.99  Aligned_cols=40  Identities=25%  Similarity=0.387  Sum_probs=36.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||.|++-+.+..||..|+|..|+.+.|+|.++...
T Consensus       138 ~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~  177 (203)
T KOG0131|consen  138 PKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKK  177 (203)
T ss_pred             CCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEec
Confidence            4689999999999999999999999999999999998743

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

Probab=93.48  E-value=0.075  Score=52.38  Aligned_cols=36  Identities=22%  Similarity=0.318  Sum_probs=34.3

Q ss_pred             CeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         4 GfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      |+.||-|+++++|..|+..|+|++|.|+.|.+.+..
T Consensus       491 g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~  526 (549)
T KOG0147|consen  491 GCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYLP  526 (549)
T ss_pred             ceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEee
Confidence            899999999999999999999999999999998875

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=93.40  E-value=0.053  Score=48.86  Aligned_cols=37  Identities=30%  Similarity=0.375  Sum_probs=34.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .|-+||.|...++|+.|+..|+|.+|.|+.|..++..
T Consensus       110 ~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen  110 VGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             hhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            3568999999999999999999999999999999874

>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A

Probab=93.04  E-value=0.053  Score=34.29  Aligned_cols=19  Identities=42%  Similarity=1.097  Sum_probs=11.7

Q ss_pred             CccccCCCCCCCCCcccCC
Q 024424           61 GRCFNCGIDGHWARDCKAG   79 (268)
Q Consensus        61 ~rC~~CG~~GH~ardC~~~   79 (268)
                      ..|++|++..||+.+|..-
T Consensus         3 ~~CprC~kg~Hwa~~C~sk   21 (36)
T PF14787_consen    3 GLCPRCGKGFHWASECRSK   21 (36)
T ss_dssp             -C-TTTSSSCS-TTT---T
T ss_pred             ccCcccCCCcchhhhhhhh
Confidence            5799999999999999864

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=92.79  E-value=0.13  Score=37.59  Aligned_cols=36  Identities=33%  Similarity=0.555  Sum_probs=22.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEec
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA   38 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a   38 (268)
                      ...|.||+.... .|+.+|..|++..++|+.|.|+.|
T Consensus        39 ~~~~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   39 FDNFSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             -SS-EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             eeeEEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            457899998665 699999999999999999999875

; PDB: 2G0C_A 3MOJ_B.

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=92.51  E-value=0.28  Score=47.58  Aligned_cols=39  Identities=31%  Similarity=0.438  Sum_probs=33.5

Q ss_pred             CeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         4 GfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      .||||+|++...++.||.+- -..|.+++|.||+.+....
T Consensus       331 ~fgFV~f~~~~~~~~~i~As-p~~ig~~kl~Veek~~~~~  369 (419)
T KOG0116|consen  331 CFGFVEFENAAAVQNAIEAS-PLEIGGRKLNVEEKRPGFR  369 (419)
T ss_pred             ceEEEEEeecchhhhhhhcC-ccccCCeeEEEEecccccc
Confidence            79999999999999999776 6788999999999876433

>smart00343 ZnF_C2HC zinc finger

Probab=92.21  E-value=0.072  Score=30.94  Aligned_cols=16  Identities=63%  Similarity=1.566  Sum_probs=13.3

Q ss_pred             ccccCCCCCCCCCccc
Q 024424           62 RCFNCGIDGHWARDCK   77 (268)
Q Consensus        62 rC~~CG~~GH~ardC~   77 (268)
                      .||+||..||++.+|+
T Consensus         1 ~C~~CG~~GH~~~~C~   16 (26)
T smart00343        1 KCYNCGKEGHIARDCP   16 (26)
T ss_pred             CCccCCCCCcchhhCC
Confidence            4888888888888886

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=91.67  E-value=0.27  Score=38.19  Aligned_cols=37  Identities=27%  Similarity=0.440  Sum_probs=29.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeec----CcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVD----GSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~----Gr~IrVe~a~   39 (268)
                      .|||||.|.++++|..-.+.++|....    .+...|.+|+
T Consensus        45 ~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i~yAr   85 (97)
T PF04059_consen   45 LGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEISYAR   85 (97)
T ss_pred             eEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEEehhH
Confidence            599999999999999999999998764    3344555554

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=90.63  E-value=0.12  Score=47.76  Aligned_cols=25  Identities=40%  Similarity=1.194  Sum_probs=19.8

Q ss_pred             CCCCCCCccccCCCCCCCCCcccCC
Q 024424           55 GPPPGSGRCFNCGIDGHWARDCKAG   79 (268)
Q Consensus        55 ~~~~~~~rC~~CG~~GH~ardC~~~   79 (268)
                      ++++-.-.||+||+.|||..+|+-.
T Consensus       171 kppPpgY~CyRCGqkgHwIqnCpTN  195 (427)
T COG5222         171 KPPPPGYVCYRCGQKGHWIQNCPTN  195 (427)
T ss_pred             CCCCCceeEEecCCCCchhhcCCCC
Confidence            3455556899999999999999854

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=89.97  E-value=0.16  Score=50.20  Aligned_cols=33  Identities=52%  Similarity=0.756  Sum_probs=31.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceE
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRII   34 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~Ir   34 (268)
                      ++|..||+|.|..+|+.||+.|++.+|.|+.|.
T Consensus       111 ~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen  111 KRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            578899999999999999999999999999987

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=89.60  E-value=0.29  Score=48.72  Aligned_cols=35  Identities=37%  Similarity=0.647  Sum_probs=29.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecC-cceEEEe
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDG-SRIIVEF   37 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~G-r~IrVe~   37 (268)
                      +||.|+||++..+|+.||..|||..|+- ..+.|..
T Consensus       105 kG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~v~~  140 (698)
T KOG2314|consen  105 KGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFFVRL  140 (698)
T ss_pred             eeEEEEEecChhhHHHHHHhcccceecccceEEeeh
Confidence            6999999999999999999999998864 3444443

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=89.59  E-value=0.23  Score=46.74  Aligned_cols=41  Identities=29%  Similarity=0.354  Sum_probs=36.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .||.|.|.|++...|+.||..|++..|.+..|+|.+|....
T Consensus       115 ~KGeatvS~~D~~~akaai~~~agkdf~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  115 PKGEATVSYEDPPAAKAAIEWFAGKDFCGNTIKVSLAERRT  155 (351)
T ss_pred             cCCceeeeecChhhhhhhhhhhccccccCCCchhhhhhhcc
Confidence            47899999999999999999999999999999998876443

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=89.52  E-value=0.42  Score=49.18  Aligned_cols=40  Identities=28%  Similarity=0.404  Sum_probs=36.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|-|||.+....||++||.+|....|.++.|+|.|+.+.
T Consensus       456 ~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  456 PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccC
Confidence            3578999999999999999999999999999999998764

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=88.62  E-value=0.48  Score=44.59  Aligned_cols=38  Identities=26%  Similarity=0.464  Sum_probs=33.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHh-hCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYS-LNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~-ldG~~l~Gr~IrVe~a~~   40 (268)
                      ++-|||+|.+.+.|+.|..+ ++-..|+|.+|.|.|..+
T Consensus       264 ~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  264 KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            56799999999999998877 566678999999999876

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

Probab=88.02  E-value=0.63  Score=40.42  Aligned_cols=28  Identities=18%  Similarity=0.254  Sum_probs=25.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeec
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVD   29 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~   29 (268)
                      +-|+|+|+|..++||+.||.+|+.+.|.
T Consensus       149 rDg~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  149 RDGVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             cccceeeeeeehhhHHHHHHhhcccccc
Confidence            4689999999999999999999998774

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=87.87  E-value=0.31  Score=30.12  Aligned_cols=20  Identities=35%  Similarity=0.946  Sum_probs=18.1

Q ss_pred             CCccccCCCCCccccccCCC
Q 024424           82 KNKCYRCGERGHIERNCQNS  101 (268)
Q Consensus        82 ~~~cyrcg~~GH~~r~c~~s  101 (268)
                      ...|+.|+..||+..+|+..
T Consensus         8 ~Y~C~~C~~~GH~i~dCP~~   27 (32)
T PF13696_consen    8 GYVCHRCGQKGHWIQDCPTN   27 (32)
T ss_pred             CCEeecCCCCCccHhHCCCC
Confidence            47899999999999999974

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=86.80  E-value=0.34  Score=31.87  Aligned_cols=19  Identities=37%  Similarity=1.106  Sum_probs=17.3

Q ss_pred             CCccccCCCCCccccccCC
Q 024424           82 KNKCYRCGERGHIERNCQN  100 (268)
Q Consensus        82 ~~~cyrcg~~GH~~r~c~~  100 (268)
                      ...|.+|+..||+.++|+.
T Consensus         4 ~~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    4 RVRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CCcCcccCCCCcchhhCCC
Confidence            4689999999999999995

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=86.35  E-value=0.42  Score=42.48  Aligned_cols=37  Identities=24%  Similarity=0.313  Sum_probs=33.5

Q ss_pred             eEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         5 fgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      ||||+|.++.....|+.-|||..|.+..|.|.+-.+.
T Consensus        51 Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~G~   87 (267)
T KOG4454|consen   51 FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCGN   87 (267)
T ss_pred             eeeeecccccchhhhhhhcccchhccchhhcccccCC
Confidence            9999999999999999999999999999888876543

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

Probab=85.98  E-value=0.41  Score=47.37  Aligned_cols=40  Identities=35%  Similarity=0.594  Sum_probs=37.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      -+||+|.+|-+.-....||.+|||..|.+..|+|..|...
T Consensus       330 skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g  369 (500)
T KOG0120|consen  330 SKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVG  369 (500)
T ss_pred             ccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhcc
Confidence            5799999999999999999999999999999999988643

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

Probab=85.69  E-value=1.1  Score=40.38  Aligned_cols=38  Identities=29%  Similarity=0.344  Sum_probs=34.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      .|-|-|.|...+||+.||..|+|..|+|..|.++....
T Consensus       124 ~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen  124 LGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             CccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            47789999999999999999999999999999887653

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=84.81  E-value=1  Score=42.88  Aligned_cols=35  Identities=34%  Similarity=0.542  Sum_probs=31.0

Q ss_pred             EEEEeCCHHHHHHHHHhhCCCeecC--cceEEEeccC
Q 024424            6 AFVEFSDPRDADDARYSLNGRDVDG--SRIIVEFARG   40 (268)
Q Consensus         6 gFVeF~~~~dA~~Ai~~ldG~~l~G--r~IrVe~a~~   40 (268)
                      |+|||++.+-|+.|...|||..|.-  -.|+||+|+.
T Consensus       162 AmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP  198 (494)
T KOG1456|consen  162 AMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKP  198 (494)
T ss_pred             eEEeechhHHHHHHHhhcccccccccceeEEEEecCc
Confidence            8999999999999999999998853  4789999874

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=84.12  E-value=1.2  Score=42.06  Aligned_cols=34  Identities=18%  Similarity=0.406  Sum_probs=30.9

Q ss_pred             EEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            6 AFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         6 gFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .||+|...+||+.||..+||..++|+.|+..+..
T Consensus       168 vYITy~~kedAarcIa~vDgs~~DGr~lkatYGT  201 (480)
T COG5175         168 VYITYSTKEDAARCIAEVDGSLLDGRVLKATYGT  201 (480)
T ss_pred             EEEEecchHHHHHHHHHhccccccCceEeeecCc
Confidence            3999999999999999999999999999877654

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=83.71  E-value=0.42  Score=32.13  Aligned_cols=17  Identities=41%  Similarity=1.032  Sum_probs=15.4

Q ss_pred             CccccCCCCCCCCCccc
Q 024424           61 GRCFNCGIDGHWARDCK   77 (268)
Q Consensus        61 ~rC~~CG~~GH~ardC~   77 (268)
                      ..||+||..||...+|+
T Consensus        32 ~~C~~C~~~gH~~~~C~   48 (49)
T PF14392_consen   32 RFCFHCGRIGHSDKECP   48 (49)
T ss_pred             hhhcCCCCcCcCHhHcC
Confidence            46999999999999986

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=83.53  E-value=1.7  Score=36.28  Aligned_cols=33  Identities=30%  Similarity=0.479  Sum_probs=28.2

Q ss_pred             EEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            6 AFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         6 gFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      -+|+|.+...|..|+ .|+|.+|+|..|.|....
T Consensus        73 mwVTF~dg~sALaal-s~dg~~v~g~~l~i~LKt  105 (146)
T PF08952_consen   73 MWVTFRDGQSALAAL-SLDGIQVNGRTLKIRLKT  105 (146)
T ss_dssp             EEEEESSCHHHHHHH-HGCCSEETTEEEEEEE--
T ss_pred             EEEEECccHHHHHHH-ccCCcEECCEEEEEEeCC
Confidence            479999999999998 699999999999998754

; PDB: 1UFW_A 2DNR_A.

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

Probab=83.05  E-value=0.65  Score=44.93  Aligned_cols=40  Identities=25%  Similarity=0.533  Sum_probs=32.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCC-eecC--cceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGR-DVDG--SRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~-~l~G--r~IrVe~a~~~   41 (268)
                      .+|++||.|...+||..||..|++. .|-|  ..|.|.++.+.
T Consensus        75 s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E  117 (510)
T KOG0144|consen   75 SKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYADGE  117 (510)
T ss_pred             ccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecccchh
Confidence            4799999999999999999999885 4544  46777777643

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=80.91  E-value=1.2  Score=28.90  Aligned_cols=20  Identities=35%  Similarity=0.629  Sum_probs=15.4

Q ss_pred             CccccCCCCCCCCC--cccCCC
Q 024424           61 GRCFNCGIDGHWAR--DCKAGD   80 (268)
Q Consensus        61 ~rC~~CG~~GH~ar--dC~~~~   80 (268)
                      .+|.+||..||...  .|+...
T Consensus         2 ~kC~~CG~~GH~~t~k~CP~~~   23 (40)
T PF15288_consen    2 VKCKNCGAFGHMRTNKRCPMYC   23 (40)
T ss_pred             ccccccccccccccCccCCCCC
Confidence            57999999999875  476543

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=80.08  E-value=2.2  Score=30.69  Aligned_cols=30  Identities=20%  Similarity=0.346  Sum_probs=26.6

Q ss_pred             EEEeCCHHHHHHHHHhhCCCeecCcceEEE
Q 024424            7 FVEFSDPRDADDARYSLNGRDVDGSRIIVE   36 (268)
Q Consensus         7 FVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe   36 (268)
                      ||.|.+..+|+.+....+|+.|-...|.++
T Consensus        37 YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M~   66 (66)
T PF11767_consen   37 YIVFNDSKEAERCFRAEDGTLFFTYRMQME   66 (66)
T ss_pred             EEEECChHHHHHHHHhcCCCEEEEEEEEeC
Confidence            799999999999999999999887776653

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	268
1x4a_A	109	Solution Structure Of Rrm Domain In Splicing Factor		4e-05
2hvz_A	101	Solution Structure Of The Rrm Domain Of Sr Rich Fac		2e-04
2i2y_A	150	Solution Structure Of The Rrm Of Srp20 Bound To The		5e-04
2i38_A	150	Solution Structure Of The Rrm Of Srp20 Length = 150		7e-04

>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2 Length = 109

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/33 (66%), Positives = 25/33 (75%)
Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEF 37
          FAFVEF DPRDA+DA Y  +G D DG R+ VEF
Sbjct: 63 FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF 95

>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8 Length = 101

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/34 (58%), Positives = 26/34 (76%)
Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
          FAFVEF DPRDA+DA   L+G+ + GSR+ VE +
Sbjct: 39 FAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELS 72

>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc Length = 150

Iteration: 1
 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/34 (58%), Positives = 24/34 (70%)
Query: 5   FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
           FAFVEF DPRDA DA   L+GR + G R+ VE +
Sbjct: 112 FAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS 145

>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20 Length = 150

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/34 (58%), Positives = 24/34 (70%)
Query: 5   FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
           FAFVEF DPRDA DA   L+GR + G R+ VE +
Sbjct: 112 FAFVEFEDPRDAADAVRDLDGRTLCGCRVRVELS 145

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	268
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	6e-15
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-14
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-14
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-14
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	5e-14
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	1e-12
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-12
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-12
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-12
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-11
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	3e-11
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	5e-11
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-10
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-10
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	9e-10
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	1e-09
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	3e-09
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	7e-09
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	2e-08
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-08
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	4e-08
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	5e-08
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	6e-08
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	7e-08
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	8e-08
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	1e-07
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	9e-05
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	6e-04
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-07
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-07
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-07
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-07
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-07
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	5e-07
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	5e-07
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	6e-07
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	6e-07
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	6e-07
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	7e-07
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	7e-07
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	7e-07
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	8e-07
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	9e-07
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-06
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	1e-06
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-06
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	5e-04
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-06
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-05
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-06
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-06
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-06
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-06
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-06
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-06
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-06
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-06
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-06
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-06
1x5p_A	97	Negative elongation factor E; structure genomics,	2e-06
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-06
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-06
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-06
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-06
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-06
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	4e-06
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-06
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	4e-06
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-06
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-06
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-04
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-06
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-04
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	5e-06
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-06
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	6e-06
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	7e-06
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	8e-06
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	9e-06
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	9e-06
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-05
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-05
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	1e-05
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-05
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-05
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-05
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-05
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-04
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-05
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-05
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-05
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-05
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-05
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	3e-05
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	3e-05
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-05
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-05
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	8e-05
1x4e_A	85	RNA binding motif, single-stranded interacting pro	4e-05
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	5e-05
2dis_A	109	Unnamed protein product; structural genomics, RRM	5e-05
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-05
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-04
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	7e-05
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	7e-05
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	8e-05
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	9e-05
2div_A	99	TRNA selenocysteine associated protein; structural	1e-04
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-04
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-04
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-04
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-04
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-04
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-04
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-04
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	1e-04
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-04
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-04
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-04
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-04
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-04
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	3e-04
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-04
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-04
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	4e-04
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	5e-04
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	5e-04
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-04
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-04
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-04
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	6e-04
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	7e-04
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	7e-04
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	8e-04
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	9e-04
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	9e-04

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 67.6 bits (166), Expect = 6e-15
 Identities = 19/49 (38%), Positives = 26/49 (53%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSR 49
          + +D+AFV      DA  A   LNG++V G RI VE +  G +  G S 
Sbjct: 41 VVKDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQKKSGPSS 89

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 66.9 bits (164), Expect = 1e-14
 Identities = 11/51 (21%), Positives = 23/51 (45%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREY 51
          +K  F F++F +P+   DA    +     G ++I+E +    R      ++
Sbjct: 43 IKNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNARPQFDHGDH 93

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 66.5 bits (163), Expect = 1e-14
 Identities = 12/47 (25%), Positives = 23/47 (48%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGG 47
          + +++ FV   D   A+DA  +L+   + G  I VE ++   +   G
Sbjct: 40 IIKNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKASSG 86

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 65.8 bits (161), Expect = 3e-14
 Identities = 11/43 (25%), Positives = 21/43 (48%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR 43
          +K  F F++F +P+   DA    +     G ++I+E +    R
Sbjct: 55 IKNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNAR 97

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 64.9 bits (159), Expect = 5e-14
 Identities = 13/47 (27%), Positives = 22/47 (46%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGG 47
          + +D+AFV      DA +A   L+  +  G R+ V+ +    R   G
Sbjct: 42 IVKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTASG 88

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 63

 Score = 60.7 bits (147), Expect = 1e-12
 Identities = 17/60 (28%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 57  PPGSGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKLRPRSYSRSPSP 116
                RC+NCG   H A++CK      KC+ C    H+  +C    ++  P +    PS 
Sbjct: 4   GSSGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQQ-GPSAQGSGPSS 62

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 61.5 bits (150), Expect = 1e-12
 Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 2/61 (3%)

Query: 1   MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP--RGPGGSREYLGRGPPP 58
             +D+AF+ F +   A  A   +NG+D++G  I + FA+     R    ++     GP  
Sbjct: 43  KLKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGPSS 102

Query: 59  G 59
           G
Sbjct: 103 G 103

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 61.2 bits (149), Expect = 2e-12
 Identities = 25/52 (48%), Positives = 31/52 (59%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGP 56
          FAFVEF DPRDA+DA   L+G+ + GSR+ VE + G PR     R    R  
Sbjct: 39 FAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPPARRKL 90

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 60.8 bits (148), Expect = 3e-12
 Identities = 22/59 (37%), Positives = 30/59 (50%), Gaps = 8/59 (13%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPG 59
            RD+AFV FS+  DA +A  +LNG+ +DGS I V  A+   +           GP  G
Sbjct: 49 KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDS--------SGPSSG 99

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 59.5 bits (144), Expect = 2e-11
 Identities = 22/41 (53%), Positives = 26/41 (63%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR 43
             FAFVEF DPRDA DA   L+GR + G R+ VE + G  R
Sbjct: 110 PGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEKR 150

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Length = 74

 Score = 57.3 bits (138), Expect = 3e-11
 Identities = 18/63 (28%), Positives = 27/63 (42%), Gaps = 3/63 (4%)

Query: 45  PGGSREYLGRGPPPGSG---RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNS 101
           P GS    G+          RC+NCG   H A++CK      KC+ C    H+  +C   
Sbjct: 6   PRGSHMPKGKSMQKRRSKGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLK 65

Query: 102 PKK 104
            ++
Sbjct: 66  AQQ 68

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 57.4 bits (139), Expect = 5e-11
 Identities = 13/47 (27%), Positives = 22/47 (46%)

Query: 1   MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGG 47
           + + +AFV++S+ R A  A    NGR + G  + +  A        G
Sbjct: 60  VHKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSG 106

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 56.5 bits (137), Expect = 1e-10
 Identities = 10/43 (23%), Positives = 20/43 (46%)

Query: 1   MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR 43
           +   FAFVEF +   A  A   ++G+      + V +++   +
Sbjct: 63  ILNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAK 105

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 55.0 bits (133), Expect = 4e-10
 Identities = 27/48 (56%), Positives = 30/48 (62%), Gaps = 1/48 (2%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG-PRGPGGSR 49
             FAFVEF DPRDA+DA Y  +G D DG R+ VEF R G   G G S 
Sbjct: 61  PPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGSGPSS 108

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61

 Score = 52.6 bits (126), Expect = 9e-10
 Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 4/55 (7%)

Query: 59  GSGRCFNCGIDGHWARDC----KAGDWKNKCYRCGERGHIERNCQNSPKKLRPRS 109
             G C+ CG  GH+   C    K+G+ + +C  C   GH  + C+        R 
Sbjct: 3   ARGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRKRDGNQGQRP 57

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A* Length = 148

 Score = 54.6 bits (131), Expect = 1e-09
 Identities = 20/65 (30%), Positives = 28/65 (43%)

Query: 44  GPGGSREYLGRGPPPGSGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPK 103
           GPGG         P G  RC+NCG   H A++CK      KC+ C    H+  +C    +
Sbjct: 81  GPGGVFCIGSERRPKGGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKAQ 140

Query: 104 KLRPR 108
           +    
Sbjct: 141 QGPSS 145

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 52.3 bits (126), Expect = 3e-09
 Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGR-DVDGSRIIVEFARG-GPRGPGGS 48
          +K  +AFV++ D   A  A  +L+G+ ++ G  + V+++     R  G S
Sbjct: 42 LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLRSSGPS 91

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 51.5 bits (124), Expect = 7e-09
 Identities = 21/47 (44%), Positives = 28/47 (59%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSR 49
           R FAFV F D RDA DA  +++G ++DG  + V+ AR G R   G  
Sbjct: 55  RGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGPS 101

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus} Length = 37

 Score = 48.4 bits (115), Expect = 2e-08
 Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 3/39 (7%)

Query: 62  RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQN 100
            C+NCG  GH +  C+A      C++C + GH  + C++
Sbjct: 2   TCYNCGKPGHLSSQCRAP---KVCFKCKQPGHFSKQCRS 37

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 50.0 bits (120), Expect = 3e-08
 Identities = 22/66 (33%), Positives = 30/66 (45%), Gaps = 3/66 (4%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRG---PPPG 59
           R FAF+ F +P DA +A   +NG+ + G  I VE A+      GG R          P G
Sbjct: 48  RGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSG 107

Query: 60  SGRCFN 65
           S    +
Sbjct: 108 SLEHHH 113

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 49.2 bits (118), Expect = 4e-08
 Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 2/56 (3%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPP 58
           + + F E+ D   A  A  +LNGR+  G  + V+ A           + LG G P 
Sbjct: 50  KGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA--SEKNKEELKSLGTGAPV 103

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 48.7 bits (117), Expect = 5e-08
 Identities = 17/39 (43%), Positives = 22/39 (56%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41
          R FAFV F +  DA +A+   NG ++DG RI V     G
Sbjct: 57 RGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPSSG 95

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A Length = 60

 Score = 47.6 bits (113), Expect = 6e-08
 Identities = 15/48 (31%), Positives = 20/48 (41%), Gaps = 7/48 (14%)

Query: 61  GRCFNCGIDGHWARDCKAGDWKNK-------CYRCGERGHIERNCQNS 101
           G CF CG  GH+A++C      N        C RC    H    C++ 
Sbjct: 2   GSCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKSK 49

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 48.4 bits (116), Expect = 7e-08
 Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 2/43 (4%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGS--RIIVEFARGGPR 43
            FA++++     A  A   + G  + G   R+ V+FA+ GP 
Sbjct: 53 DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPS 95

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 48.4 bits (116), Expect = 8e-08
 Identities = 14/47 (29%), Positives = 23/47 (48%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSR 49
          + +AF+EF+   DA +A  S N R+++G  I +E          G  
Sbjct: 53 KGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNSGPS 99

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124

 Score = 48.6 bits (115), Expect = 1e-07
 Identities = 12/68 (17%), Positives = 23/68 (33%)

Query: 58  PGSGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPKKLRPRSYSRSPSPR 117
           P + +C  C   GH+   C     K +C  C  + H +  C +  +       +    P+
Sbjct: 40  PKAIQCSKCDEVGHYRSQCPHKWKKVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPK 99

Query: 118 RGRSRSRS 125
                +  
Sbjct: 100 VLPFHTIY 107

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124

 Score = 40.1 bits (93), Expect = 9e-05
 Identities = 13/43 (30%), Positives = 18/43 (41%), Gaps = 5/43 (11%)

Query: 62  RCFNCGIDGHWARDCKAGDWKNKCYRCG-ERGHIERNCQNSPK 103
           +C NC   GH  +DC        C  CG    H  R+C  + +
Sbjct: 6   KCNNCSQRGHLKKDCP----HIICSYCGATDDHYSRHCPKAIQ 44

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124

 Score = 37.8 bits (87), Expect = 6e-04
 Identities = 11/41 (26%), Positives = 15/41 (36%)

Query: 58  PGSGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 98
           P   R +    D   A+          CY CG +GH   +C
Sbjct: 81  PSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDC 121

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 47.5 bits (114), Expect = 1e-07
 Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 2/43 (4%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGP 45
          + +A+VEF +P +A+ A   ++G  +DG  I           P
Sbjct: 47 KGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVL--APWP 87

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 47.7 bits (114), Expect = 1e-07
 Identities = 15/43 (34%), Positives = 19/43 (44%), Gaps = 4/43 (9%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRD----VDGSRIIVEFARGG 41
          R FAFV+ S   DA      L        +DG  I V+FA+  
Sbjct: 53 RGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKSA 95

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 10/37 (27%), Positives = 18/37 (48%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
          R  AFV F +   A +A  S+ G       + +++A+
Sbjct: 51 RGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK 87

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 46.9 bits (112), Expect = 2e-07
 Identities = 10/46 (21%), Positives = 18/46 (39%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGS 48
          + F F+       A+ A+  L+   + G ++ V FA        G 
Sbjct: 51 KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSGP 96

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 46.9 bits (112), Expect = 3e-07
 Identities = 12/47 (25%), Positives = 27/47 (57%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSR 49
           + F FV+F+   DA  A+ ++   ++DG+++ +++A+    G  G  
Sbjct: 54  KGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSGPS 100

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 46.1 bits (110), Expect = 5e-07
 Identities = 10/41 (24%), Positives = 19/41 (46%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR 43
          +  A+VE+ +   A  A   ++G  +  + I V  +  GP 
Sbjct: 58 KGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPS 98

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 46.1 bits (110), Expect = 5e-07
 Identities = 9/44 (20%), Positives = 18/44 (40%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPG 46
          +  A++EF    DA+       G ++DG  + + +        G
Sbjct: 53 KGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTRG 96

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 46.0 bits (109), Expect = 6e-07
 Identities = 11/39 (28%), Positives = 15/39 (38%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41
          R  AF+ + D   A  A   L G  +    + V  AR  
Sbjct: 56 RRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ 94

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 47.2 bits (113), Expect = 6e-07
 Identities = 15/49 (30%), Positives = 24/49 (48%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLG 53
          + FV + DP+DA+ A  +LNG  +    I V +AR        +  Y+ 
Sbjct: 46 YGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVS 94

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 45.7 bits (109), Expect = 6e-07
 Identities = 18/47 (38%), Positives = 24/47 (51%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSR 49
           R F FV F +  DA DA  ++NG+ VDG +I V+ A        G  
Sbjct: 54  RGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSGPS 100

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 45.7 bits (109), Expect = 7e-07
 Identities = 17/47 (36%), Positives = 22/47 (46%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSR 49
           + F FV F +  DAD AR  L+G  V+G +I V  A        G  
Sbjct: 55  KGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSGPS 101

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 45.6 bits (109), Expect = 7e-07
 Identities = 16/51 (31%), Positives = 22/51 (43%), Gaps = 2/51 (3%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLG 53
          + + F+ FSD   A  A   LNG ++ G  + V       R  GGS    G
Sbjct: 47 KGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVT--ERLDGGSGPSSG 95

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 46.2 bits (110), Expect = 7e-07
 Identities = 11/40 (27%), Positives = 19/40 (47%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP 42
          R  A+V + D  DA +A   L+G +V    ++V +     
Sbjct: 47 RGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANR 86

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 45.9 bits (109), Expect = 8e-07
 Identities = 10/37 (27%), Positives = 16/37 (43%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41
           A V F+  R A +   +L+   V G+ I  +    G
Sbjct: 50 LARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIKG 86

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 46.3 bits (110), Expect = 9e-07
 Identities = 15/46 (32%), Positives = 22/46 (47%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGS 48
           R + FV+F     A  A   LNG ++   R+ V  A  G + PG +
Sbjct: 84  RGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIA 129

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 14/43 (32%), Positives = 19/43 (44%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGG 47
          F FVE+  P  A  A   L G  VDG ++ V  +    +   G
Sbjct: 52 FGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATKPASG 94

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic} Length = 39

 Score = 43.3 bits (102), Expect = 1e-06
 Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 1/37 (2%)

Query: 62 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 98
           CFNCG  GH AR C+    +  C+ CG + H    C
Sbjct: 2  TCFNCGKPGHTARMCRQPR-QEGCWNCGSKEHRFAQC 37

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 46.4 bits (111), Expect = 1e-06
 Identities = 16/49 (32%), Positives = 24/49 (48%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLG 53
          +AFV+F+   D+  A   LNG  V   R+ V +AR G      +  Y+ 
Sbjct: 47 YAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVT 95

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 38.7 bits (91), Expect = 5e-04
 Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 2/38 (5%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGS--RIIVEFA 38
           R  AFV ++   +A +A  +LN    +G    + V  A
Sbjct: 131 RGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 47.7 bits (114), Expect = 1e-06
 Identities = 9/37 (24%), Positives = 19/37 (51%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
           R FA+++ +   DA      LNG  ++G  ++ + + 
Sbjct: 159 RRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN 195

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 42.3 bits (100), Expect = 7e-05
 Identities = 9/36 (25%), Positives = 14/36 (38%), Gaps = 1/36 (2%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
              AF+ F +   A+ A   +N   +    I V  A
Sbjct: 254 NCCAFMVFENKDSAERA-LQMNRSLLGNREISVSLA 288

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 44.4 bits (106), Expect = 1e-06
 Identities = 15/37 (40%), Positives = 20/37 (54%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
          R FAFVEF    DA  A  ++N  ++ G  I V  A+
Sbjct: 49 RGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK 85

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 44.5 bits (106), Expect = 1e-06
 Identities = 13/39 (33%), Positives = 15/39 (38%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41
          + F FV F  P     A   LNG  + G  I V     G
Sbjct: 57 KSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPSSG 95

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 9/36 (25%), Positives = 16/36 (44%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
          +  AF+ F D   A +   ++N + + G  I    A
Sbjct: 58 KGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 7/47 (14%), Positives = 13/47 (27%), Gaps = 2/47 (4%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSR 49
          + FA V       +      L  R++ G   +V  +           
Sbjct: 45 KGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN--KLEHHHHH 89

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 14/47 (29%), Positives = 21/47 (44%), Gaps = 2/47 (4%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSR 49
           + FAF+ F    DA  A   ++G   D   + VE+A+  P    G  
Sbjct: 57  KGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAK--PSTNSGPS 101

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG-GPRGPGGS 48
           R  AF+ F +   A  A + +NG  + G  +++EF +    R  G S
Sbjct: 67  RGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRSSGPS 113

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 45.1 bits (107), Expect = 2e-06
 Identities = 12/35 (34%), Positives = 18/35 (51%)

Query: 5   FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
           F FV F +P  A  A  ++NG  V   R+ V+  +
Sbjct: 84  FGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 19/44 (43%), Positives = 26/44 (59%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPG 46
           R FAFV F D RDA+DA  +++G  +DG  + V+ AR G     
Sbjct: 112 RGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDS 155

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 44.1 bits (105), Expect = 2e-06
 Identities = 9/49 (18%), Positives = 19/49 (38%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREY 51
          + +AF+EF D   +  A  +LNG  +    +   ++            +
Sbjct: 44 KGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDISGVSLEHH 92

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 16/46 (34%), Positives = 21/46 (45%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGS 48
          R+ AFV +     AD A   LNG  V+  ++ V  AR  P    G 
Sbjct: 49 RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDSGP 94

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 43.7 bits (104), Expect = 3e-06
 Identities = 18/51 (35%), Positives = 23/51 (45%), Gaps = 2/51 (3%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLG 53
           R FAFVEF    DA  A  ++N  ++ G  I V  A+  P     S    G
Sbjct: 54  RGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK--PMRIKESGPSSG 102

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 43.6 bits (103), Expect = 3e-06
 Identities = 8/35 (22%), Positives = 13/35 (37%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
             V +S    A  A   LNG  ++   + V +  
Sbjct: 56 VVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIP 90

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 44.5 bits (105), Expect = 3e-06
 Identities = 6/38 (15%), Positives = 15/38 (39%)

Query: 2   KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
               A++ F+    A     +  G    G+ +++ F+ 
Sbjct: 71  NSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSE 108

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 46.2 bits (110), Expect = 3e-06
 Identities = 10/41 (24%), Positives = 17/41 (41%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR 43
          R F F+       A+ A+  L+G  +    + + FA  G  
Sbjct: 58 RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGAA 98

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 43.8 bits (104), Expect = 3e-06
 Identities = 16/37 (43%), Positives = 21/37 (56%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
           + F FV F +  DAD AR  L+G  V+G +I V  A 
Sbjct: 69  KGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT 105

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 13/36 (36%), Positives = 18/36 (50%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
          +  A V F DP  A  A    +G++  G+ I V FA
Sbjct: 63 KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 43.7 bits (104), Expect = 4e-06
 Identities = 11/43 (25%), Positives = 17/43 (39%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGP 45
          + FAFV F  P  A  A   ++G+   G  + V  +       
Sbjct: 50 KGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEAS 92

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 43.9 bits (104), Expect = 4e-06
 Identities = 17/59 (28%), Positives = 22/59 (37%), Gaps = 2/59 (3%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGSG 61
           +  A V F DP  A  A    +G++  G+ I V FA    R         GRG      
Sbjct: 57  KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT--RRADFNRGGGNGRGGLEHHH 113

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 46.1 bits (110), Expect = 4e-06
 Identities = 13/42 (30%), Positives = 22/42 (52%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRG 44
           + FA +E+     A++A+   +G  + GS + V F   GP G
Sbjct: 226 KGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPG 267

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 46.1 bits (110), Expect = 4e-06
 Identities = 9/46 (19%), Positives = 16/46 (34%)

Query: 5   FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSRE 50
           + F E+     A  A+  L G+ +    + V +   G   P     
Sbjct: 139 YGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHS 184

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 41.9 bits (99), Expect = 1e-04
 Identities = 6/41 (14%), Positives = 14/41 (34%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR 43
          +  AFV   +   A+ A  + +   +    + V+       
Sbjct: 57 KGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDAL 97

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 45.0 bits (107), Expect = 5e-06
 Identities = 12/39 (30%), Positives = 20/39 (51%)

Query: 5   FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR 43
           +AF E+ D    D A   LNG  +   +++V+ A  G +
Sbjct: 158 YAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK 196

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 13/59 (22%), Positives = 21/59 (35%), Gaps = 1/59 (1%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGSG 61
           ++FAF+EF    +   A  + +G    G  + +         PG S       P   S 
Sbjct: 51  KNFAFLEFRSVDETTQA-MAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVST 108

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 43.5 bits (103), Expect = 5e-06
 Identities = 16/59 (27%), Positives = 28/59 (47%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGSG 61
           + + FV F +  DA++A   + G+ + G +I   +A   P  P  + E   +   P SG
Sbjct: 57  KGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPSSG 115

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 42.9 bits (102), Expect = 6e-06
 Identities = 12/45 (26%), Positives = 17/45 (37%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGG 47
          +    V+F  P  A+ A   +NG  + G  I V   R       G
Sbjct: 48 KGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNASGPSSG 92

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 42.8 bits (101), Expect = 6e-06
 Identities = 12/58 (20%), Positives = 18/58 (31%), Gaps = 8/58 (13%)

Query: 2  KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPG 59
           +  AFV   +   A +A    +     G  +IV+               L  GP  G
Sbjct: 39 NKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDAL--------LCSGPSSG 88

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 43.0 bits (102), Expect = 7e-06
 Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 2/43 (4%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGP 45
           + +  VE+   ++A  A   LNG+D+ G  I V++     RGP
Sbjct: 65  KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF--VRGP 105

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 43.0 bits (102), Expect = 8e-06
 Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 2/44 (4%)

Query: 2   KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGP 45
            + +A VE+   + A  A+ +LNG ++ G  I V++     +GP
Sbjct: 67  SKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF--VKGP 108

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 43.1 bits (102), Expect = 9e-06
 Identities = 13/45 (28%), Positives = 20/45 (44%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGG 47
           + F FV + +P  A  A  S+NG  +   R+ V+  R       G
Sbjct: 67  KCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSG 111

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 43.1 bits (102), Expect = 9e-06
 Identities = 16/62 (25%), Positives = 25/62 (40%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGSGR 62
           + +  VE+   ++A  A   LNG+D+ G  I V++        G  R    R   P   R
Sbjct: 64  KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRSPDRRR 123

Query: 63  CF 64
             
Sbjct: 124 RL 125

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 14/38 (36%), Positives = 21/38 (55%)

Query: 2  KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
             + FVEF + RDA  A  ++NGR + G  + V +A 
Sbjct: 54 NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT 91

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 15/36 (41%), Positives = 19/36 (52%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
           R FAFVEF    DA  A  ++N  ++ G  I V  A
Sbjct: 105 RGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1 Length = 49

 Score = 40.7 bits (95), Expect = 1e-05
 Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 1/44 (2%)

Query: 55 GPPPGSGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 98
                 RC+NCG +GH AR C+A   +  C++CG+ GH+   C
Sbjct: 1  AQQRKVIRCWNCGKEGHSARQCRAPR-RQGCWKCGKTGHVMAKC 43

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 43.3 bits (103), Expect = 1e-05
 Identities = 11/41 (26%), Positives = 23/41 (56%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGP 45
          +AFVE+    DA+ A  +LNG+ ++ + + + +A    +  
Sbjct: 43 YAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQSS 83

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 13/47 (27%), Positives = 19/47 (40%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSR 49
           + + FVEF    DAD A   ++   + G  I V  A    +   G  
Sbjct: 57  QGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGPS 103

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 15/47 (31%), Positives = 20/47 (42%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSR 49
           + F FV FS P +A  A   +NGR V    + V  A+       G  
Sbjct: 55  KGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQSGPS 101

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 44.1 bits (103), Expect = 2e-05
 Identities = 10/37 (27%), Positives = 18/37 (48%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
          R  AFV F +   A +A  S+ G       + +++A+
Sbjct: 52 RGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK 88

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 41.4 bits (96), Expect = 2e-04
 Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 1/39 (2%)

Query: 2   KRDFAFVEFSDPRDADDARYSLNGRDVDGSRII-VEFAR 39
           + D AFVEF +   A  AR +L G  +  +  + + FA+
Sbjct: 243 RHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK 281

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 8/35 (22%), Positives = 16/35 (45%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
          + FV F     A+ A   +NG  ++  ++ V   +
Sbjct: 47 YGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK 81

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 1/46 (2%)

Query: 3   RDFAFVEFSDPRDADDARYSL-NGRDVDGSRIIVEFARGGPRGPGG 47
           R F FV+F   +DA  A  +L +   + G R+++E+A        G
Sbjct: 58  RGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSG 103

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 40.9 bits (97), Expect = 3e-05
 Identities = 12/37 (32%), Positives = 22/37 (59%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
          R + FV F+   DA +A  S+ G+D++G  + + +A 
Sbjct: 43 RGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA 79

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 12/58 (20%), Positives = 19/58 (32%), Gaps = 1/58 (1%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR-GGPRGPGGSREYLGRGPPPG 59
           R    V F    +A  A    NG+ +    + V+      P+G     E   +  P  
Sbjct: 56  RGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPSS 113

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 41.7 bits (98), Expect = 3e-05
 Identities = 12/48 (25%), Positives = 19/48 (39%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSRE 50
             A VEF +P +A  A   L         + +E+A  G  G    ++
Sbjct: 46 GITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKK 93

>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A Length = 55

 Score = 40.0 bits (93), Expect = 3e-05
 Identities = 17/37 (45%), Positives = 27/37 (72%), Gaps = 1/37 (2%)

Query: 62 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 98
          +CFNCG +GH A++C+A   K  C++CG+ GH  ++C
Sbjct: 14 KCFNCGKEGHIAKNCRAPR-KKGCWKCGKEGHQMKDC 49

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 41.2 bits (97), Expect = 3e-05
 Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 2/47 (4%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSR 49
           +  A V + DP  A  A    +G+D  GS++ V  AR   + P  S 
Sbjct: 65  KGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLAR--KKPPMNSG 109

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 11/37 (29%), Positives = 17/37 (45%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
           + + F+ FSD   A  A   LNG ++ G  + V    
Sbjct: 68  KGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVT 104

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 42.2 bits (100), Expect = 4e-05
 Identities = 11/51 (21%), Positives = 22/51 (43%), Gaps = 1/51 (1%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLG 53
           ++FAF+EF    +   A  + +G    G  + +         PG  + ++G
Sbjct: 51  KNFAFLEFRSVDETTQA-MAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIG 100

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 41.4 bits (98), Expect = 8e-05
 Identities = 11/37 (29%), Positives = 19/37 (51%)

Query: 2   KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
            + +AF E+ D    D A   LNG  +   +++V+ A
Sbjct: 135 SKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 40.2 bits (95), Expect = 4e-05
 Identities = 9/37 (24%), Positives = 12/37 (32%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41
          + FV+F  P  A  A  +L    V            G
Sbjct: 49 YGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPSSG 85

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 41.3 bits (97), Expect = 5e-05
 Identities = 19/44 (43%), Positives = 26/44 (59%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPG 46
           R FAFV F D RDA+DA  +++G  +DG  + V+ AR G     
Sbjct: 89  RGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDS 132

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 40.5 bits (95), Expect = 5e-05
 Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 2/39 (5%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDV--DGSRIIVEFAR 39
          R FAFVE+   R A  AR  L    +   G +I V++A 
Sbjct: 52 RGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAE 90

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 42.0 bits (98), Expect = 5e-05
 Identities = 5/36 (13%), Positives = 11/36 (30%)

Query: 2   KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEF 37
           +     +E+    DA +    LN   +        +
Sbjct: 164 RSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY 199

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 39.3 bits (91), Expect = 5e-04
 Identities = 14/56 (25%), Positives = 20/56 (35%)

Query: 2  KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPP 57
          K   A VE +D    D A   LN   + G ++ V  ++     PG S         
Sbjct: 41 KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCS 96

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 40.5 bits (95), Expect = 7e-05
 Identities = 17/37 (45%), Positives = 24/37 (64%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
           R FAFV F +  DA +A+   NG ++DG RI V+F+ 
Sbjct: 88  RGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSI 124

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 41.0 bits (96), Expect = 7e-05
 Identities = 11/37 (29%), Positives = 19/37 (51%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
           +  AF+   + + A  A    NG  + G  ++V+FAR
Sbjct: 92  KGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFAR 128

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 39.5 bits (93), Expect = 8e-05
 Identities = 11/50 (22%), Positives = 16/50 (32%), Gaps = 1/50 (2%)

Query: 2  KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREY 51
           + F FVE  +     +A   L+  D  G  I V  A            +
Sbjct: 42 PKGFGFVEMQEE-SVSEAIAKLDNTDFMGRTIRVTEANPKKSLEHHHHHH 90

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 39.8 bits (93), Expect = 9e-05
 Identities = 9/36 (25%), Positives = 13/36 (36%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
             A+V +    DA  A   +N   VDG  +     
Sbjct: 63 SASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLG 98

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 10/33 (30%), Positives = 18/33 (54%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEF 37
          + FVEF+D   A+   + +NG+ + G+     F
Sbjct: 54 YCFVEFADLATAEKCLHKINGKPLPGATPAKRF 86

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 41.0 bits (96), Expect = 1e-04
 Identities = 11/49 (22%), Positives = 20/49 (40%)

Query: 2  KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSRE 50
          K++ A V+ +D   A  A   LNG  + G  I +  ++          +
Sbjct: 40 KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQ 88

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 41.0 bits (96), Expect = 1e-04
 Identities = 8/39 (20%), Positives = 17/39 (43%), Gaps = 1/39 (2%)

Query: 2   KRDFAFVEFSDPRDADDARYSLNGRDVDGSRII-VEFAR 39
            R  A ++     +A  A   L+  D+  +  + V F++
Sbjct: 157 DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK 195

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 10/42 (23%), Positives = 20/42 (47%), Gaps = 2/42 (4%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRG 44
           +  A++EF    DA+       G ++DG  + + +   G +G
Sbjct: 136 KGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT--GEKG 175

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 1/43 (2%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGP 45
          R F +V+F    D + A   L G  V G+ I +E  +G     
Sbjct: 54 RKFGYVDFESAEDLEKA-LELTGLKVFGNEIKLEKPKGRDSKK 95

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 39.0 bits (92), Expect = 1e-04
 Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 3/44 (6%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPG 46
          + FA++EFSD      +  +L+     G +I V   R     PG
Sbjct: 48 KGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR--TNRPG 88

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 10/36 (27%), Positives = 14/36 (38%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
              A V F    DA  A    NG  +DG  + ++  
Sbjct: 70  LGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV 105

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 40.3 bits (94), Expect = 1e-04
 Identities = 8/60 (13%), Positives = 18/60 (30%), Gaps = 2/60 (3%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGSGR 62
           + +A V  +           L G+ ++G ++ V  A    +          +       R
Sbjct: 99  KGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPAT--RQNLSQFEAQARKRECVRVPR 156

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104

 Score = 39.5 bits (92), Expect = 1e-04
 Identities = 11/33 (33%), Positives = 15/33 (45%)

Query: 5   FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEF 37
             +V+F    DA+ A   LN R  +G  I  E 
Sbjct: 70  NVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 4/37 (10%), Positives = 12/37 (32%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
          +   F+++     A     +L      G  +   + +
Sbjct: 63 KGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK 99

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 13/61 (21%), Positives = 16/61 (26%)

Query: 1   MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGS 60
            +     VEF    D   A   L+            + R    GP        R   P S
Sbjct: 48  YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSSGPSS 107

Query: 61  G 61
           G
Sbjct: 108 G 108

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 8/30 (26%), Positives = 15/30 (50%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRII 34
          + F+E++ P  A DA  + +G  +D     
Sbjct: 49 YIFLEYASPAHAVDAVKNADGYKLDKQHTF 78

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 8/30 (26%), Positives = 15/30 (50%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRII 34
          + F+E++ P  A DA  + +G  +D     
Sbjct: 63 YIFLEYASPAHAVDAVKNADGYKLDKQHTF 92

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPG 46
           R F +V+F    D + A   L G  V G+ I +E  +G     G
Sbjct: 58  RKFGYVDFESAEDLEKA-LELTGLKVFGNEIKLEKPKGRDGTRG 100

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 9/30 (30%), Positives = 13/30 (43%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRII 34
          F FVE     DA     S +G+ +D    +
Sbjct: 56 FLFVECGSMNDAKKIIKSFHGKRLDLKHRL 85

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 4/37 (10%), Positives = 8/37 (21%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
           R   F         +      NG+ +     +     
Sbjct: 66  RGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE 102

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 10/40 (25%), Positives = 15/40 (37%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRG 44
           A V F    +A  A   LN R +   ++ +    G   G
Sbjct: 59 EAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPSSG 98

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 12/44 (27%), Positives = 20/44 (45%)

Query: 5   FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGS 48
           ++FV FS    A  A  S+NG  ++G  +   + +  P    G 
Sbjct: 63  YSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGP 106

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 38.1 bits (89), Expect = 5e-04
 Identities = 9/37 (24%), Positives = 13/37 (35%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
              A V F    DA  A     G  +DG  + ++   
Sbjct: 76  LGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA 112

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 112

 Score = 37.8 bits (88), Expect = 5e-04
 Identities = 13/36 (36%), Positives = 18/36 (50%)

Query: 5   FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40
            A V F DP +AD    +L+GR   G +I  +   G
Sbjct: 66  VASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDG 101

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 39.6 bits (92), Expect = 5e-04
 Identities = 20/77 (25%), Positives = 30/77 (38%), Gaps = 12/77 (15%)

Query: 2   KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA--------RGGPRGPGGSREYLG 53
           K++ A V+ +D   A  A   LNG  + G  I +  +        R G    G +++Y  
Sbjct: 71  KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGN 130

Query: 54  ----RGPPPGSGRCFNC 66
               R   PGS    N 
Sbjct: 131 SPLHRFKKPGSKNFQNI 147

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 38.8 bits (90), Expect = 7e-04
 Identities = 8/39 (20%), Positives = 17/39 (43%), Gaps = 1/39 (2%)

Query: 2   KRDFAFVEFSDPRDADDARYSLNGRDVDGSRII-VEFAR 39
            R  A ++     +A  A   L+  D+  +  + V F++
Sbjct: 188 DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK 226

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 39.2 bits (92), Expect = 5e-04
 Identities = 14/62 (22%), Positives = 19/62 (30%), Gaps = 2/62 (3%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGSGR 62
           + FAFVE+  P  A  A   +N   + G  I V        G                 R
Sbjct: 70  KGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS--NIGQAQPIIDQLAEEARAFNR 127

Query: 63  CF 64
            +
Sbjct: 128 IY 129

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 38.7 bits (91), Expect = 6e-04
 Identities = 7/35 (20%), Positives = 13/35 (37%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
            FV F   + A +A+ +L+   V          +
Sbjct: 49 CCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMK 83

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 36.8 bits (86), Expect = 7e-04
 Identities = 11/40 (27%), Positives = 21/40 (52%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP 42
          + + FV F +  DA++A   + G+ + G +I   +A   P
Sbjct: 48 KGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKP 87

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Length = 114

 Score = 37.3 bits (87), Expect = 7e-04
 Identities = 8/31 (25%), Positives = 13/31 (41%)

Query: 7  FVEFSDPRDADDARYSLNGRDVDGSRIIVEF 37
          +V+      A  A  +L+GR   G  I   +
Sbjct: 59 YVKCPSIAAAIAAVNALHGRWFAGKMITAAY 89

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 36.8 bits (86), Expect = 8e-04
 Identities = 11/47 (23%), Positives = 21/47 (44%)

Query: 3  RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSR 49
          + +AF+ F+    +D A  ++NG+ +    I V +A        G  
Sbjct: 48 KGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGSGPS 94

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 37.1 bits (86), Expect = 9e-04
 Identities = 9/32 (28%), Positives = 14/32 (43%)

Query: 6  AFVEFSDPRDADDARYSLNGRDVDGSRIIVEF 37
           FVEF+   D   A   L GR      ++ ++
Sbjct: 62 IFVEFTSVFDCQKAMQGLTGRKFANRVVVTKY 93

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 38.3 bits (89), Expect = 9e-04
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG-GPRGPGGSRE 50
           + +A VE+   + A  A+ +LNG ++ G  I V++    GP+    S +
Sbjct: 114 KGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKSEK 162

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	268
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	99.23
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	98.91
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	98.83
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	98.82
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	98.8
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	98.78
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	98.77
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	98.77
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	98.75
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	98.74
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	98.69
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	98.68
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	98.67
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	98.64
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	98.64
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	98.63
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	98.62
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	98.6
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	98.6
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	98.6
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	98.6
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	98.6
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	98.59
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	98.59
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	98.58
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	98.58
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	98.57
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	98.57
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	98.56
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	98.56
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	98.56
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	98.56
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	98.56
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	98.55
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	98.55
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	98.54
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	98.54
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	98.54
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	98.53
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	98.52
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	98.52
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	98.52
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	98.51
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	98.51
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	98.5
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	98.5
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	98.5
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	98.49
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	98.49
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	98.49
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	98.49
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	98.49
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	98.49
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.49
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	98.48
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	98.48
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	98.48
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	98.48
1x5p_A	97	Negative elongation factor E; structure genomics,	98.48
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	98.48
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	98.47
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	98.47
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	98.47
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	98.47
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	98.47
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	98.47
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	98.46
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.46
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	98.46
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	98.46
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	98.46
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	98.46
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	98.45
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	98.45
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	98.44
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	98.44
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	98.44
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	98.43
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	98.43
2div_A	99	TRNA selenocysteine associated protein; structural	98.42
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	98.42
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	98.42
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.42
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	98.42
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	98.42
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	98.41
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	98.41
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	98.41
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	98.41
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	98.41
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	98.41
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	98.41
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	98.41
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	98.4
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	98.4
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	98.39
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	98.39
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	98.39
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	98.38
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	98.38
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.38
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	98.37
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	98.37
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	98.37
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	98.36
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	98.36
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.36
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	98.35
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.35
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	98.34
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	98.34
2dis_A	109	Unnamed protein product; structural genomics, RRM	98.33
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	98.33
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	98.33
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	97.68
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.33
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	98.32
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	98.31
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	98.31
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.3
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	98.3
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	98.3
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	98.29
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	98.28
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	98.28
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.27
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	98.27
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	98.27
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	98.27
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	98.27
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	98.26
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	98.26
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	98.26
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	98.26
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	98.25
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.24
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	98.24
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	98.23
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	98.23
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	98.22
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	98.21
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	98.21
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	98.2
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	98.17
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	98.17
1x4e_A	85	RNA binding motif, single-stranded interacting pro	98.16
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	98.16
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	98.15
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	98.14
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	98.14
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	98.12
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.11
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	98.09
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	98.09
1x5o_A	114	RNA binding motif, single-stranded interacting pro	98.09
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	98.06
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	98.06
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	98.06
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	98.04
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	98.02
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	98.01
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	97.98
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	97.95
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	97.94
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	97.94
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	97.87
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	97.86
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	97.85
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	97.84
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	97.84
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	97.83
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	97.82
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	97.79
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	97.79
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	97.77
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	97.76
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	97.75
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	97.74
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	97.74
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	97.72
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	97.69
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	97.67
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	97.62
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	97.6
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	97.56
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	97.53
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	97.47
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	97.46
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	97.45
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	97.44
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	97.43
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	97.41
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	97.4
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	97.39
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	97.36
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	97.35
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	97.3
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	97.21
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	97.11
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	97.1
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	97.05
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	96.93
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	96.78
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	96.6
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	96.57
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	96.28
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	96.16
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	96.15
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	95.9
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	95.63
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	95.43
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	95.36
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	95.2
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	95.12
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	95.0
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	94.85
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	94.84
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	94.6
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	94.35
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	93.91
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	93.05
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	92.49
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	83.53

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*

Probab=99.23  E-value=2.9e-12  Score=105.59  Aligned_cols=46  Identities=33%  Similarity=0.711  Sum_probs=40.6

Q ss_pred             CCCCccccCCCCCCCCCcccCCCCCCccccCCCCCccccccCCCCC
Q 024424           58 PGSGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPK  103 (268)
Q Consensus        58 ~~~~rC~~CG~~GH~ardC~~~~~~~~cyrcg~~GH~~r~c~~s~~  103 (268)
                      .....||+||..|||+++|+.......||.|+..||++++|+....
T Consensus        95 ~~~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~~r~Cp~~~~  140 (148)
T 3ts2_A           95 KGGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKAQ  140 (148)
T ss_dssp             CCSCCCTTTCCSSCCGGGCCSCCCCCCCTTTCCSSCCGGGCTTTTC
T ss_pred             CCCCcccEeCCccchhhhCCCCCCCCcccccCCcCCEeccCcCCCC
Confidence            3457899999999999999987767899999999999999998543

>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=98.91  E-value=1.5e-08  Score=96.81  Aligned_cols=41  Identities=34%  Similarity=0.737  Sum_probs=38.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|+.||..|||++|+|..|.|+|+....
T Consensus       143 ~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~~~~  183 (437)
T 3pgw_S          143 PRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRT  183 (437)
T ss_pred             ccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            37999999999999999999999999999999999998643

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=98.83  E-value=2.5e-09  Score=68.38  Aligned_cols=38  Identities=39%  Similarity=0.982  Sum_probs=34.6

Q ss_pred             ccccCCCCCCCCCcccCCCCCCccccCCCCCccccccCC
Q 024424           62 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQN  100 (268)
Q Consensus        62 rC~~CG~~GH~ardC~~~~~~~~cyrcg~~GH~~r~c~~  100 (268)
                      .||+||+.||++.+|+.+. ...||.|+..||++++|++
T Consensus         2 ~C~~Cg~~GH~a~~C~~~~-~~~C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A            2 TCFNCGKPGHTARMCRQPR-QEGCWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             BCTTTCCBSSCTTTCCSCC-CSSCTTTCCSSSCTTTSCC
T ss_pred             eeeccCCCCcccccCCCCC-CCccccCCCCCCccCcCcC
Confidence            6999999999999999863 5799999999999999974

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1

Probab=98.82  E-value=4.9e-09  Score=70.37  Aligned_cols=42  Identities=40%  Similarity=1.057  Sum_probs=37.1

Q ss_pred             CCCccccCCCCCCCCCcccCCCCCCccccCCCCCccccccCCC
Q 024424           59 GSGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNS  101 (268)
Q Consensus        59 ~~~rC~~CG~~GH~ardC~~~~~~~~cyrcg~~GH~~r~c~~s  101 (268)
                      ....||+||+.|||+.+|+.+. ...||.|+..||++++|+..
T Consensus         5 r~~~C~~Cg~~GH~a~~C~~~~-~~~C~~Cg~~GH~~~~C~~~   46 (49)
T 2ec7_A            5 KVIRCWNCGKEGHSARQCRAPR-RQGCWKCGKTGHVMAKCPER   46 (49)
T ss_dssp             CCCBCTTTCCBTCCTTTCCCSS-CCSCSSSCCSSCCGGGCCSS
T ss_pred             CcCeeeecCCCCcChhhCcCCC-CCeeCcCCCcCCccCCCcCC
Confidence            3468999999999999999863 56899999999999999864

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.80  E-value=5e-09  Score=74.02  Aligned_cols=42  Identities=33%  Similarity=0.716  Sum_probs=38.2

Q ss_pred             CccccCCCCCCCCCcccCCCCCCccccCCCCCccccccCCCC
Q 024424           61 GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSP  102 (268)
Q Consensus        61 ~rC~~CG~~GH~ardC~~~~~~~~cyrcg~~GH~~r~c~~s~  102 (268)
                      ..||+||+.|||+.+|+.......||.|++.||++++|+...
T Consensus         8 ~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~ar~Cp~~~   49 (63)
T 2cqf_A            8 DRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKA   49 (63)
T ss_dssp             CCCSSSCCSSSCTTTCCSCCCSSCCTTTCCSSSCTTTCTGGG
T ss_pred             CcccccCCCCcChhhCCCCCCCCccCCcCCcCCccCcCCCcc
Confidence            679999999999999998766789999999999999999743

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}

Probab=98.78  E-value=5.4e-09  Score=76.22  Aligned_cols=43  Identities=33%  Similarity=0.692  Sum_probs=38.5

Q ss_pred             CCCccccCCCCCCCCCcccCCCCCCccccCCCCCccccccCCC
Q 024424           59 GSGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNS  101 (268)
Q Consensus        59 ~~~rC~~CG~~GH~ardC~~~~~~~~cyrcg~~GH~~r~c~~s  101 (268)
                      ....||+||..|||+.+|+.......||.|++.||++++|+..
T Consensus        23 r~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~ar~Cp~~   65 (74)
T 2li8_A           23 KGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLK   65 (74)
T ss_dssp             TTSCCTTTCCSSSCTTTCSSCCCCCCCTTTCCTTSCGGGCTTG
T ss_pred             CCCcccccCCcCcCcccCCCCCCCCccCCcCCcCCccCcCcCC
Confidence            3468999999999999999876678999999999999999863

>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=98.77  E-value=1.1e-08  Score=79.82  Aligned_cols=36  Identities=22%  Similarity=0.217  Sum_probs=32.0

Q ss_pred             CeEEEEeCCHHHHHHHHHhhCCCeecCcc-----eEEEecc
Q 024424            4 DFAFVEFSDPRDADDARYSLNGRDVDGSR-----IIVEFAR   39 (268)
Q Consensus         4 GfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~-----IrVe~a~   39 (268)
                      |||||+|++.++|++||+.|||++|+|+.     |.|..+.
T Consensus        52 g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~   92 (115)
T 3beg_B           52 GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG   92 (115)
T ss_dssp             SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC
T ss_pred             CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCC
Confidence            99999999999999999999999999998     5555543

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=98.77  E-value=4.7e-09  Score=66.30  Aligned_cols=36  Identities=36%  Similarity=1.155  Sum_probs=33.3

Q ss_pred             ccccCCCCCCCCCcccCCCCCCccccCCCCCccccccCC
Q 024424           62 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQN  100 (268)
Q Consensus        62 rC~~CG~~GH~ardC~~~~~~~~cyrcg~~GH~~r~c~~  100 (268)
                      .||+||+.||++.+|+.+   ..||.|+..||++++|++
T Consensus         2 ~C~~Cg~~GH~~~~C~~~---~~C~~Cg~~GH~a~~C~~   37 (37)
T 2bl6_A            2 TCYNCGKPGHLSSQCRAP---KVCFKCKQPGHFSKQCRS   37 (37)
T ss_dssp             CBSSSCCSSCCTTTSSCB---TTCSSCCCTTGGGGTTCC
T ss_pred             cccccCCCCcchhhCcCc---CeEccCCCcCCccCcCcC
Confidence            699999999999999976   689999999999999974

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=98.75  E-value=6.6e-09  Score=72.88  Aligned_cols=43  Identities=28%  Similarity=0.842  Sum_probs=37.3

Q ss_pred             CCccccCCCCCCCCCcccCCCC----CCccccCCCCCccccccCCCC
Q 024424           60 SGRCFNCGIDGHWARDCKAGDW----KNKCYRCGERGHIERNCQNSP  102 (268)
Q Consensus        60 ~~rC~~CG~~GH~ardC~~~~~----~~~cyrcg~~GH~~r~c~~s~  102 (268)
                      ...||+||+.|||+.+|+....    ...||.|++.||++++|+...
T Consensus         4 ~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~   50 (61)
T 2ihx_A            4 RGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRKRD   50 (61)
T ss_dssp             TTBCSSSCCBTCCGGGCTTTTSSSCCCSBCTTTCCBSSCGGGCCCCC
T ss_pred             CCcccccCCCCeehhhCcCCcCCCCCCCeeCCCCCCCCCcCCCcCCC
Confidence            4679999999999999998643    367999999999999999743

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A

Probab=98.74  E-value=3.2e-09  Score=74.17  Aligned_cols=42  Identities=33%  Similarity=0.892  Sum_probs=19.2

Q ss_pred             CccccCCCCCCCCCcccCCC-------CCCccccCCCCCccccccCCCC
Q 024424           61 GRCFNCGIDGHWARDCKAGD-------WKNKCYRCGERGHIERNCQNSP  102 (268)
Q Consensus        61 ~rC~~CG~~GH~ardC~~~~-------~~~~cyrcg~~GH~~r~c~~s~  102 (268)
                      ..||+||+.|||+++|+...       ....||.|++.||++++|+...
T Consensus         2 ~~Cf~Cg~~GH~a~~C~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~   50 (60)
T 1cl4_A            2 GSCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKSKT   50 (60)
T ss_dssp             ---------------------------CCCSCSSCSSCSSCSTTCCCTT
T ss_pred             CccccCCCCCcCHhhCcCCCCCccccCCCcceeECCCCCCccCcCCCcc
Confidence            36999999999999999763       3578999999999999999754

>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A

Probab=98.69  E-value=1.2e-08  Score=70.04  Aligned_cols=41  Identities=41%  Similarity=1.148  Sum_probs=36.6

Q ss_pred             CCccccCCCCCCCCCcccCCCCCCccccCCCCCccccccCCC
Q 024424           60 SGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNS  101 (268)
Q Consensus        60 ~~rC~~CG~~GH~ardC~~~~~~~~cyrcg~~GH~~r~c~~s  101 (268)
                      ...||+||+.|||+.+|+.+. ...||.|++.||++++|+..
T Consensus        12 ~~~C~~Cg~~GH~a~~C~~~~-~~~C~~Cg~~GH~~~~C~~~   52 (55)
T 1a1t_A           12 TVKCFNCGKEGHIAKNCRAPR-KKGCWKCGKEGHQMKDCTER   52 (55)
T ss_dssp             TCBCTTTCCBSSCGGGCSSCS-CCBCTTTCCBSSCGGGCSSS
T ss_pred             CcceeeeCCCCcChhhcCCCC-CCEeCCCCCcCCccCCCcCc
Confidence            468999999999999999863 56899999999999999874

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=98.68  E-value=1.6e-08  Score=76.13  Aligned_cols=38  Identities=18%  Similarity=0.352  Sum_probs=36.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+|||||+|.+.++|++||+.|||.+|.|+.|.|.+|.
T Consensus        42 ~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A           42 NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            58999999999999999999999999999999999984

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.67  E-value=2.4e-08  Score=75.41  Aligned_cols=41  Identities=24%  Similarity=0.633  Sum_probs=38.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      +|||||+|.+.++|+.||..|+|.+|+|+.|.|++++....
T Consensus        54 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   94 (102)
T 2fc8_A           54 KGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGE   94 (102)
T ss_dssp             EEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCCCS
T ss_pred             CcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCCCC
Confidence            58999999999999999999999999999999999986543

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=98.64  E-value=2.3e-08  Score=78.08  Aligned_cols=40  Identities=25%  Similarity=0.155  Sum_probs=37.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|++||+.|||.+|+|+.|.|+++...
T Consensus        66 ~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~  105 (111)
T 2jvr_A           66 FDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNP  105 (111)
T ss_dssp             SSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC-
T ss_pred             CCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            3799999999999999999999999999999999999754

>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=98.64  E-value=7e-08  Score=73.19  Aligned_cols=41  Identities=32%  Similarity=0.598  Sum_probs=38.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|+.||..|+|.+|+|+.|.|+++....
T Consensus        44 ~~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   84 (103)
T 2dgu_A           44 LKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPD   84 (103)
T ss_dssp             CSSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             ECCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCc
Confidence            47899999999999999999999999999999999998654

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.63  E-value=7.4e-08  Score=71.60  Aligned_cols=41  Identities=27%  Similarity=0.395  Sum_probs=38.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++.....
T Consensus        47 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   87 (95)
T 2dnz_A           47 KGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLD   87 (95)
T ss_dssp             CSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESSCCCC
T ss_pred             eeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcccccC
Confidence            68999999999999999999999999999999999986544

>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=98.62  E-value=9.5e-08  Score=74.53  Aligned_cols=40  Identities=40%  Similarity=0.704  Sum_probs=37.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++....
T Consensus        48 ~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   87 (116)
T 2fy1_A           48 RGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPS   87 (116)
T ss_dssp             CCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCCSS
T ss_pred             ccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            6999999999999999999999999999999999998654

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.60  E-value=6e-08  Score=72.97  Aligned_cols=42  Identities=45%  Similarity=0.639  Sum_probs=38.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      .+|||||+|.+.++|+.||..|+|..|+|+.|.|+++.....
T Consensus        50 ~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   91 (99)
T 2cpd_A           50 IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   91 (99)
T ss_dssp             CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             eCCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCC
Confidence            479999999999999999999999999999999999986543

>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=98.60  E-value=6.4e-08  Score=74.09  Aligned_cols=41  Identities=59%  Similarity=0.943  Sum_probs=38.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      +|||||+|.+.++|+.||+.|+|.+|+|+.|.|+++.....
T Consensus        61 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~  101 (109)
T 1x4a_A           61 PPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRG  101 (109)
T ss_dssp             SCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCCCC
T ss_pred             CcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcccCCC
Confidence            68999999999999999999999999999999999986543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.60  E-value=7.4e-08  Score=71.48  Aligned_cols=42  Identities=29%  Similarity=0.503  Sum_probs=38.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      .++||||+|.+.++|+.||..|+|.+|+|+.|.|+++.....
T Consensus        43 ~~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   84 (92)
T 2dgt_A           43 VKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLR   84 (92)
T ss_dssp             CSSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCCS
T ss_pred             ECCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCCC
Confidence            468999999999999999999999999999999999986543

>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=98.60  E-value=3.3e-08  Score=75.16  Aligned_cols=37  Identities=32%  Similarity=0.578  Sum_probs=35.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|+.||..|||..|.|+.|.|++++
T Consensus        61 kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           61 LGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             cccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            5899999999999999999999999999999999986

>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=98.60  E-value=4.2e-08  Score=79.98  Aligned_cols=41  Identities=29%  Similarity=0.452  Sum_probs=38.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      +|||||+|.+.++|+.||..|+|.+|+|..|.|+++.....
T Consensus        81 ~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  121 (156)
T 1h2v_Z           81 CGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKE  121 (156)
T ss_dssp             EEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCCT
T ss_pred             ceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            58999999999999999999999999999999999986543

>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=98.59  E-value=6.1e-08  Score=72.78  Aligned_cols=40  Identities=28%  Similarity=0.343  Sum_probs=37.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||+.|||.+|+|+.|.|+++....
T Consensus        52 rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~   91 (96)
T 2dgx_A           52 QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATGAS   91 (96)
T ss_dssp             TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCSS
T ss_pred             CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            7899999999999999999999999999999999997543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=98.59  E-value=7.9e-08  Score=76.62  Aligned_cols=41  Identities=32%  Similarity=0.519  Sum_probs=38.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      +|||||+|.+.++|+.||..|+|..|.|+.|.|+++.....
T Consensus        84 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  124 (139)
T 1u6f_A           84 RGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQ  124 (139)
T ss_dssp             EEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCC
T ss_pred             ceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            68999999999999999999999999999999999986543

>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=98.58  E-value=5.5e-08  Score=73.42  Aligned_cols=40  Identities=25%  Similarity=0.463  Sum_probs=37.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||..|+|..|+|+.|.|+++...
T Consensus        56 ~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (97)
T 2xnq_A           56 KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN   95 (97)
T ss_dssp             CSSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCC
T ss_pred             eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCC
Confidence            4799999999999999999999999999999999999754

>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=98.58  E-value=7.4e-08  Score=71.53  Aligned_cols=41  Identities=27%  Similarity=0.435  Sum_probs=38.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCC-CeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNG-RDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG-~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|+.||..|+| .+|+|+.|.|+++....
T Consensus        43 ~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~   84 (93)
T 2cqh_A           43 KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   84 (93)
T ss_dssp             ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCcc
Confidence            479999999999999999999999 99999999999998654

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.57  E-value=1.1e-07  Score=70.25  Aligned_cols=42  Identities=26%  Similarity=0.442  Sum_probs=38.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      .+|||||+|.+.++|+.||..|+|..|+|+.|.|+++.....
T Consensus        41 ~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   82 (90)
T 2dnq_A           41 IKNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSK   82 (90)
T ss_dssp             ETTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCC
T ss_pred             ECCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCC
Confidence            379999999999999999999999999999999999986543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.57  E-value=9.3e-08  Score=72.07  Aligned_cols=42  Identities=31%  Similarity=0.510  Sum_probs=38.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      .+|||||+|.+.++|+.||..|+|..|+|+.|.|+++.....
T Consensus        52 ~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   93 (101)
T 2fc9_A           52 SKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGS   93 (101)
T ss_dssp             BCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSCCC
T ss_pred             EeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCCCC
Confidence            369999999999999999999999999999999999986543

>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=98.56  E-value=6.3e-08  Score=75.91  Aligned_cols=40  Identities=28%  Similarity=0.460  Sum_probs=37.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|+|.+|+|..|.|+++....
T Consensus        64 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  103 (126)
T 3ex7_B           64 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG  103 (126)
T ss_dssp             CSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEESEESS
T ss_pred             ceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEecCCC
Confidence            7999999999999999999999999999999999997644

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.56  E-value=1.1e-07  Score=70.78  Aligned_cols=40  Identities=25%  Similarity=0.398  Sum_probs=37.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++....
T Consensus        48 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   87 (96)
T 1x5t_A           48 KGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   87 (96)
T ss_dssp             CSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEecccC
Confidence            6899999999999999999999999999999999998654

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.56  E-value=1e-07  Score=70.44  Aligned_cols=41  Identities=41%  Similarity=0.667  Sum_probs=38.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .++||||+|.+.++|+.||..|+|..|+|+.|.|+++....
T Consensus        42 ~~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   82 (90)
T 2dnp_A           42 VKDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQ   82 (90)
T ss_dssp             CSSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             ECCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCC
Confidence            46899999999999999999999999999999999998654

>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=98.56  E-value=5e-08  Score=75.28  Aligned_cols=40  Identities=23%  Similarity=0.218  Sum_probs=37.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||+.|||.+|+|+.|.|+++....
T Consensus        63 ~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           63 SASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKY  102 (111)
T ss_dssp             CEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEESCCCCS
T ss_pred             CeEEEEEECcHHHHHHHHHHhCCCEECCEEEEEEeccccc
Confidence            4899999999999999999999999999999999998654

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=98.56  E-value=5.2e-08  Score=75.60  Aligned_cols=38  Identities=24%  Similarity=0.221  Sum_probs=36.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      +|||||+|++.++|+.||+.|||.+|+|+.|.|+++..
T Consensus        48 rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~~   85 (110)
T 3s8s_A           48 LGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIK   85 (110)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECST
T ss_pred             eeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            68999999999999999999999999999999999864

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.55  E-value=5.7e-08  Score=72.46  Aligned_cols=41  Identities=20%  Similarity=0.421  Sum_probs=37.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++.....
T Consensus        53 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   93 (96)
T 1fjc_A           53 KGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             EEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             ceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCCC
Confidence            68999999999999999999999999999999999976543

>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=98.55  E-value=1.3e-07  Score=72.50  Aligned_cols=40  Identities=20%  Similarity=0.162  Sum_probs=37.4

Q ss_pred             CeEEEEeCCHHHHHHHHHhhCCCeecC-----cceEEEeccCCCC
Q 024424            4 DFAFVEFSDPRDADDARYSLNGRDVDG-----SRIIVEFARGGPR   43 (268)
Q Consensus         4 GfgFVeF~~~~dA~~Ai~~ldG~~l~G-----r~IrVe~a~~~~r   43 (268)
                      |||||+|++.++|+.||+.|||.+|+|     +.|.|+++.....
T Consensus        51 g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~~~~~   95 (108)
T 1x4c_A           51 GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSP   95 (108)
T ss_dssp             TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESSCCSC
T ss_pred             CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCCCCCC
Confidence            899999999999999999999999999     9999999986544

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.54  E-value=1.3e-07  Score=71.27  Aligned_cols=42  Identities=40%  Similarity=0.646  Sum_probs=38.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      .+|||||+|.+.++|+.||..|+|..|+|+.|.|+++.....
T Consensus        53 ~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   94 (102)
T 1x5s_A           53 SRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSD   94 (102)
T ss_dssp             CCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCC
T ss_pred             cccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            368999999999999999999999999999999999986543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.54  E-value=8.4e-08  Score=71.96  Aligned_cols=40  Identities=28%  Similarity=0.380  Sum_probs=37.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||..|+|.+|+|+.|.|+++...
T Consensus        55 ~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   94 (97)
T 2e5j_A           55 PRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ   94 (97)
T ss_dssp             TTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCC
T ss_pred             CCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            4799999999999999999999999999999999999754

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=98.54  E-value=6.4e-08  Score=72.57  Aligned_cols=42  Identities=26%  Similarity=0.476  Sum_probs=38.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      .+|||||+|.+.++|+.||..|+|..|.|+.|.|+++.....
T Consensus        44 ~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   85 (96)
T 2kvi_A           44 KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNAR   85 (96)
T ss_dssp             ETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCCC
T ss_pred             eCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCCC
Confidence            479999999999999999999999999999999999986543

>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=98.53  E-value=6.8e-08  Score=70.55  Aligned_cols=39  Identities=26%  Similarity=0.478  Sum_probs=35.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++...
T Consensus        48 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~k   86 (87)
T 3bs9_A           48 KGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK   86 (87)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC--
T ss_pred             ceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecCCC
Confidence            589999999999999999999999999999999998743

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.52  E-value=1.4e-07  Score=71.13  Aligned_cols=42  Identities=36%  Similarity=0.427  Sum_probs=38.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      .+|||||+|.+.++|+.||+.|+|..|+|+.|.|+++.....
T Consensus        53 ~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   94 (102)
T 2cqb_A           53 HRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRI   94 (102)
T ss_dssp             CSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCCC
T ss_pred             cceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeCCCCCC
Confidence            479999999999999999999999999999999999986543

>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=98.52  E-value=1e-07  Score=69.25  Aligned_cols=38  Identities=39%  Similarity=0.545  Sum_probs=35.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+|||||+|.+.++|+.||..|+|..|+|+.|.|++++
T Consensus        48 ~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~ak   85 (85)
T 3mdf_A           48 HRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   85 (85)
T ss_dssp             ECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             cccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            36899999999999999999999999999999999974

>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=98.52  E-value=1.4e-07  Score=70.73  Aligned_cols=40  Identities=28%  Similarity=0.576  Sum_probs=37.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeec--CcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVD--GSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~--Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|+|..|+  |+.|.|+++...+
T Consensus        53 ~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~~   94 (97)
T 1why_A           53 DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCCC
Confidence            689999999999999999999999999  9999999998654

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.51  E-value=1.5e-07  Score=72.30  Aligned_cols=41  Identities=34%  Similarity=0.524  Sum_probs=38.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      +|||||+|.+.++|+.||..|+|.+|+|+.|.|+++.....
T Consensus        65 ~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           65 KGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP  105 (113)
T ss_dssp             CSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCCC
T ss_pred             eeEEEEEECCHHHHHHHHHHcCCCccCCCEEEEEECCCCCC
Confidence            68999999999999999999999999999999999986543

>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=98.51  E-value=1.8e-07  Score=70.82  Aligned_cols=41  Identities=29%  Similarity=0.323  Sum_probs=38.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|+.||..|+|.+|+|+.|.|+++....
T Consensus        56 ~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   96 (105)
T 1x5u_A           56 HQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHN   96 (105)
T ss_dssp             BCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTS
T ss_pred             CCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCC
Confidence            36899999999999999999999999999999999998654

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=98.50  E-value=1.1e-07  Score=76.02  Aligned_cols=40  Identities=15%  Similarity=0.344  Sum_probs=37.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||..|||..|.|+.|.|.|+...
T Consensus        71 ~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~a~~~  110 (127)
T 2a3j_A           71 NSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETP  110 (127)
T ss_dssp             SCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEECCCC
T ss_pred             cCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEEccCc
Confidence            3699999999999999999999999999999999999754

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.50  E-value=1.2e-07  Score=71.47  Aligned_cols=40  Identities=33%  Similarity=0.546  Sum_probs=37.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|+.||+ |+|..|.|+.|.|+++....
T Consensus        57 ~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~~~~   96 (101)
T 1fj7_A           57 NRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRD   96 (101)
T ss_dssp             TTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCSCCC
T ss_pred             cCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcCCCC
Confidence            47999999999999999998 99999999999999998643

>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=98.50  E-value=1.9e-07  Score=71.88  Aligned_cols=41  Identities=27%  Similarity=0.396  Sum_probs=38.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|+.||..|+|..|+|+.|.|+++....
T Consensus        66 ~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~  106 (115)
T 2cpx_A           66 MRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKK  106 (115)
T ss_dssp             SCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCS
T ss_pred             cceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEccCCC
Confidence            36999999999999999999999999999999999998654

>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=98.49  E-value=1.2e-07  Score=70.92  Aligned_cols=39  Identities=23%  Similarity=0.353  Sum_probs=36.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++...
T Consensus        57 ~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (98)
T 2cqp_A           57 TGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGP   95 (98)
T ss_dssp             EEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEESSCS
T ss_pred             eeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEcCCC
Confidence            689999999999999999999999999999999998743

>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=98.49  E-value=1.8e-07  Score=70.92  Aligned_cols=40  Identities=30%  Similarity=0.422  Sum_probs=37.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      +|||||+|.+.++|+.|| .|+|..|+|+.|.|+++.....
T Consensus        57 ~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~   96 (104)
T 1wi8_A           57 KGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQD   96 (104)
T ss_dssp             CSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCCCCC
T ss_pred             CeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEEccCCCC
Confidence            689999999999999999 9999999999999999986543

>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=98.49  E-value=2.1e-07  Score=70.29  Aligned_cols=40  Identities=35%  Similarity=0.576  Sum_probs=37.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|+|..|.|+.|.|+++....
T Consensus        55 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   94 (103)
T 2cqi_A           55 DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPS   94 (103)
T ss_dssp             CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTT
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECCCCc
Confidence            6899999999999999999999999999999999998643

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.49  E-value=1.6e-07  Score=70.93  Aligned_cols=40  Identities=30%  Similarity=0.432  Sum_probs=37.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++....
T Consensus        57 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   96 (103)
T 2cq0_A           57 KGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPST   96 (103)
T ss_dssp             EEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCC
T ss_pred             eeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEECCCCC
Confidence            5899999999999999999999999999999999998654

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=98.49  E-value=2.8e-07  Score=69.42  Aligned_cols=42  Identities=55%  Similarity=0.886  Sum_probs=38.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      .+|||||+|.+.++|+.||..|+|..|+|+.|.|+++.....
T Consensus        36 ~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   77 (101)
T 2hvz_A           36 PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPR   77 (101)
T ss_dssp             SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCC
Confidence            379999999999999999999999999999999999987653

>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=98.49  E-value=2.7e-07  Score=69.16  Aligned_cols=41  Identities=27%  Similarity=0.302  Sum_probs=38.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|+.||..|+|..|+|+.|.|+++....
T Consensus        49 ~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   89 (99)
T 1whw_A           49 PKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKK   89 (99)
T ss_dssp             CCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCS
T ss_pred             cCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCc
Confidence            36999999999999999999999999999999999998654

>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=98.49  E-value=1.3e-07  Score=68.30  Aligned_cols=39  Identities=31%  Similarity=0.598  Sum_probs=36.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|.++...
T Consensus        43 ~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A           43 RGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             cceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            689999999999999999999999999999999999754

>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=98.48  E-value=1.1e-07  Score=73.80  Aligned_cols=39  Identities=21%  Similarity=0.394  Sum_probs=36.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|.+|+|+.|.|.++...
T Consensus        45 kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~   83 (115)
T 4f25_A           45 KGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   83 (115)
T ss_dssp             EEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCC
T ss_pred             CceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCc
Confidence            689999999999999999999999999999999998754

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.48  E-value=1.7e-07  Score=70.88  Aligned_cols=40  Identities=48%  Similarity=0.801  Sum_probs=37.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++....
T Consensus        55 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   94 (103)
T 2dnm_A           55 RGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGR   94 (103)
T ss_dssp             CSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEECSSCC
T ss_pred             CeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEECCcCC
Confidence            6999999999999999999999999999999999998643

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=98.48  E-value=3.4e-07  Score=70.57  Aligned_cols=40  Identities=28%  Similarity=0.529  Sum_probs=37.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++....
T Consensus        57 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   96 (115)
T 2dgo_A           57 KGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKP   96 (115)
T ss_dssp             EEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCC
T ss_pred             ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccCCC
Confidence            5899999999999999999999999999999999998654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.48  E-value=2.2e-07  Score=70.21  Aligned_cols=40  Identities=35%  Similarity=0.532  Sum_probs=37.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++....
T Consensus        55 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   94 (103)
T 2d9p_A           55 KGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKE   94 (103)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECSSCC
T ss_pred             CEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEecccc
Confidence            6899999999999999999999999999999999998654

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.48  E-value=1.5e-07  Score=70.53  Aligned_cols=41  Identities=37%  Similarity=0.566  Sum_probs=38.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|+.||..|+|..|+|+.|.|+++....
T Consensus        48 ~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~   88 (97)
T 1x5p_A           48 PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   88 (97)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCC
Confidence            47999999999999999999999999999999999997653

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.48  E-value=1.4e-07  Score=70.97  Aligned_cols=40  Identities=25%  Similarity=0.539  Sum_probs=37.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++....
T Consensus        58 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   97 (100)
T 2do4_A           58 KGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGP   97 (100)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCCCS
T ss_pred             EeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            5899999999999999999999999999999999998654

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.47  E-value=1.3e-07  Score=70.19  Aligned_cols=37  Identities=24%  Similarity=0.383  Sum_probs=35.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|++++
T Consensus        58 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~ak   94 (94)
T 2e5h_A           58 KGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIAI   94 (94)
T ss_dssp             TTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             ccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEecC
Confidence            6899999999999999999999999999999999974

>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=98.47  E-value=4.9e-08  Score=72.36  Aligned_cols=39  Identities=18%  Similarity=0.225  Sum_probs=34.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||+.|+|.+|+|+.|.|.++...
T Consensus        45 kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~~~   83 (90)
T 3p5t_L           45 KGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKL   83 (90)
T ss_dssp             EEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC---
T ss_pred             CcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECCCC
Confidence            689999999999999999999999999999999998754

>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=98.47  E-value=1.8e-07  Score=69.94  Aligned_cols=39  Identities=23%  Similarity=0.462  Sum_probs=37.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++...
T Consensus        44 ~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   82 (96)
T 2x1f_A           44 KGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNS   82 (96)
T ss_dssp             CSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCS
T ss_pred             ceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCCC
Confidence            699999999999999999999999999999999999754

>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=98.47  E-value=1.9e-07  Score=68.15  Aligned_cols=39  Identities=28%  Similarity=0.611  Sum_probs=36.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      .+|||||+|.+.++|+.||..|+|..|+|+.|.|+++..
T Consensus        46 ~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   84 (88)
T 4a8x_A           46 SKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLA   84 (88)
T ss_dssp             ECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             CCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECCC
Confidence            478999999999999999999999999999999999964

>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=98.47  E-value=1.1e-07  Score=70.17  Aligned_cols=39  Identities=21%  Similarity=0.315  Sum_probs=36.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      .+|||||+|.+.++|+.||+.|+|.+|+|+.|.|+++..
T Consensus        39 ~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   77 (88)
T 1wg1_A           39 NKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             GGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCC
Confidence            379999999999999999999999999999999999864

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=98.47  E-value=1.2e-07  Score=71.35  Aligned_cols=37  Identities=35%  Similarity=0.512  Sum_probs=35.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|+.||+.|+|..|.|+.|.|++++
T Consensus        63 ~G~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           63 KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT   99 (99)
T ss_dssp             EEEEEEEBSSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             eeEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEecC
Confidence            5899999999999999999999999999999999874

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=98.46  E-value=1.5e-07  Score=71.31  Aligned_cols=38  Identities=26%  Similarity=0.415  Sum_probs=36.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecC-cceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDG-SRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~G-r~IrVe~a~~   40 (268)
                      +|||||+|.+.++|+.||..|||..|.| +.|.|.++..
T Consensus        54 kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l~V~~a~~   92 (100)
T 3ns6_A           54 KGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKD   92 (100)
T ss_dssp             CSEEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEESHH
T ss_pred             ceEEEEEECCHHHHHHHHHHhCCcccCCCeEEEEEECch
Confidence            6999999999999999999999999999 9999999863

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=98.46  E-value=1.3e-07  Score=69.75  Aligned_cols=40  Identities=28%  Similarity=0.448  Sum_probs=37.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++....
T Consensus        48 ~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   87 (92)
T 2dgv_A           48 KGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNAS   87 (92)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSCCS
T ss_pred             ceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCC
Confidence            6899999999999999999999999999999999998543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=98.46  E-value=9.3e-08  Score=72.45  Aligned_cols=39  Identities=38%  Similarity=0.580  Sum_probs=35.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCC----eecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGR----DVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~----~l~Gr~IrVe~a~~   40 (268)
                      .+|||||+|.+.++|+.||+.|+|.    .|+|+.|.|++|+.
T Consensus        52 srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           52 NRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS   94 (95)
T ss_dssp             CSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEEEECCC
T ss_pred             CceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEEEEccC
Confidence            3799999999999999999999997    48999999999863

>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=98.46  E-value=1.9e-07  Score=71.61  Aligned_cols=40  Identities=30%  Similarity=0.508  Sum_probs=37.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||..|+|..|+|+.|.|+++...
T Consensus        61 ~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~  100 (110)
T 1wf1_A           61 HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP  100 (110)
T ss_dssp             ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCC
T ss_pred             eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            4799999999999999999999999999999999999754

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.46  E-value=2.2e-07  Score=69.48  Aligned_cols=40  Identities=33%  Similarity=0.598  Sum_probs=37.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|.++....
T Consensus        50 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   89 (98)
T 2cpf_A           50 MGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERAT   89 (98)
T ss_dssp             EEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCSS
T ss_pred             ccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEccCCC
Confidence            5899999999999999999999999999999999998654

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.46  E-value=1.6e-07  Score=71.51  Aligned_cols=39  Identities=31%  Similarity=0.432  Sum_probs=37.1

Q ss_pred             CeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         4 GfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      |||||+|.+.++|..||+.|+|.+|.|+.|+|.+++...
T Consensus        47 G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~~s   85 (96)
T 2diu_A           47 CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNR   85 (96)
T ss_dssp             TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCCSC
T ss_pred             CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCCCc
Confidence            899999999999999999999999999999999998654

>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=98.45  E-value=3.3e-07  Score=69.26  Aligned_cols=40  Identities=40%  Similarity=0.601  Sum_probs=37.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++....
T Consensus        55 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   94 (103)
T 2cq3_A           55 KGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV   94 (103)
T ss_dssp             CCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSC
T ss_pred             cEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcccCC
Confidence            7899999999999999999999999999999999998654

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=98.45  E-value=1.6e-07  Score=72.40  Aligned_cols=38  Identities=29%  Similarity=0.260  Sum_probs=36.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      +|||||+|.+.++|++||..|||.+|+|+.|.|.++..
T Consensus        56 ~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i~v~~a~~   93 (105)
T 2pe8_A           56 AVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNL   93 (105)
T ss_dssp             SEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             cEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcCH
Confidence            69999999999999999999999999999999999863

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.44  E-value=2.2e-07  Score=70.34  Aligned_cols=39  Identities=23%  Similarity=0.478  Sum_probs=36.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.|| .|+|.+|+|+.|.|+++....
T Consensus        56 ~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~   94 (103)
T 2dng_A           56 KGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRK   94 (103)
T ss_dssp             EEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEECCCCC
T ss_pred             ceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEecCCC
Confidence            589999999999999999 999999999999999998654

>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=98.44  E-value=2e-07  Score=71.99  Aligned_cols=40  Identities=33%  Similarity=0.439  Sum_probs=37.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|.++....
T Consensus        64 ~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           64 DGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTT  103 (112)
T ss_dssp             TCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCC
T ss_pred             CEEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCC
Confidence            7999999999999999999999999999999999997643

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.44  E-value=1.4e-07  Score=69.99  Aligned_cols=38  Identities=42%  Similarity=0.615  Sum_probs=36.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|++++.
T Consensus        57 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   94 (95)
T 2cqc_A           57 RGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPSS   94 (95)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCSC
T ss_pred             ccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecCC
Confidence            58999999999999999999999999999999999863

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.43  E-value=4.6e-07  Score=68.68  Aligned_cols=40  Identities=33%  Similarity=0.577  Sum_probs=37.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhh-CCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSL-NGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~l-dG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..| +|..|.|+.|.|+++....
T Consensus        58 ~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~~a~~~~   98 (107)
T 2cph_A           58 RGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEV   98 (107)
T ss_dssp             CSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCC
T ss_pred             CceEEEEECCHHHHHHHHHHhccCCeECCCEEEEEeCCCCC
Confidence            799999999999999999999 9999999999999998653

>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=98.43  E-value=2.5e-07  Score=70.86  Aligned_cols=40  Identities=28%  Similarity=0.558  Sum_probs=37.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|+|.+|+|+.|.|.++....
T Consensus        61 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  100 (109)
T 1x4g_A           61 KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP  100 (109)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCC
Confidence            6999999999999999999999999999999999998654

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.42  E-value=2e-07  Score=69.84  Aligned_cols=39  Identities=26%  Similarity=0.513  Sum_probs=36.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcc----eEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSR----IIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~----IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|.|..    |.|.++...
T Consensus        52 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~v~~a~~~   94 (99)
T 2div_A           52 AGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYS   94 (99)
T ss_dssp             EEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECCEEETTCC
T ss_pred             CCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEEEeecCCC
Confidence            489999999999999999999999999999    999999754

>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=98.42  E-value=1.6e-07  Score=69.70  Aligned_cols=37  Identities=22%  Similarity=0.279  Sum_probs=35.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++.
T Consensus        57 ~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           57 TGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             eeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            5899999999999999999999999999999999875

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=98.42  E-value=1.8e-07  Score=69.81  Aligned_cols=41  Identities=29%  Similarity=0.471  Sum_probs=36.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhC-CCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLN-GRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ld-G~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|+.||+.|+ +..|+|+.|.|+++...+
T Consensus        43 ~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~~~~   84 (91)
T 2lxi_A           43 SRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSDPKP   84 (91)
T ss_dssp             CSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCCSCC
T ss_pred             cCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcCCCC
Confidence            46999999999999999999875 568999999999997654

>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=98.42  E-value=1.5e-07  Score=72.41  Aligned_cols=36  Identities=31%  Similarity=0.429  Sum_probs=34.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEec
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA   38 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a   38 (268)
                      +|||||+|.+.++|++||..|||..|+|+.|.|+++
T Consensus        68 ~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~v~~s  103 (104)
T 1jmt_A           68 VGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             EEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             cEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEc
Confidence            799999999999999999999999999999999986

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.42  E-value=2e-07  Score=68.85  Aligned_cols=39  Identities=28%  Similarity=0.437  Sum_probs=36.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||. |+|..|.|+.|.|.++...+
T Consensus        50 ~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~~~~   88 (91)
T 2dgw_A           50 TGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREKSGP   88 (91)
T ss_dssp             EEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEESSCC
T ss_pred             ceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECCcCC
Confidence            6899999999999999999 99999999999999997654

>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=98.42  E-value=2.2e-07  Score=69.78  Aligned_cols=40  Identities=23%  Similarity=0.401  Sum_probs=37.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++....
T Consensus        51 kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   90 (99)
T 2cpj_A           51 KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   90 (99)
T ss_dssp             TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCC
Confidence            6999999999999999999999999999999999998543

>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=98.41  E-value=2.2e-07  Score=71.86  Aligned_cols=39  Identities=26%  Similarity=0.199  Sum_probs=36.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      .+|||||+|.+.++|+.||..|||..|+|+.|.|+|+..
T Consensus        45 ~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   83 (111)
T 1whx_A           45 GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            368999999999999999999999999999999999974

>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=98.41  E-value=2.8e-07  Score=68.72  Aligned_cols=39  Identities=26%  Similarity=0.366  Sum_probs=37.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++...
T Consensus        51 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   89 (97)
T 1nu4_A           51 RGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTD   89 (97)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSC
T ss_pred             CcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEEccCC
Confidence            699999999999999999999999999999999999754

>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=98.41  E-value=1.8e-07  Score=69.53  Aligned_cols=38  Identities=32%  Similarity=0.386  Sum_probs=36.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|++++.
T Consensus        57 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   94 (95)
T 2ywk_A           57 KSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPSS   94 (95)
T ss_dssp             EEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             ceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcCC
Confidence            68999999999999999999999999999999999863

>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=98.41  E-value=1.9e-07  Score=72.11  Aligned_cols=40  Identities=30%  Similarity=0.508  Sum_probs=37.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||+.|+|.+|+|+.|.|+++....
T Consensus        67 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~  106 (115)
T 2cpz_A           67 KCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKN  106 (115)
T ss_dssp             EEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSC
T ss_pred             CccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCC
Confidence            5899999999999999999999999999999999998543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.41  E-value=2.2e-07  Score=71.44  Aligned_cols=38  Identities=42%  Similarity=0.657  Sum_probs=36.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++..
T Consensus        69 kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  106 (109)
T 2err_A           69 KGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA  106 (109)
T ss_dssp             TTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            79999999999999999999999999999999999874

>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=98.41  E-value=2.1e-07  Score=67.73  Aligned_cols=37  Identities=30%  Similarity=0.454  Sum_probs=35.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHhh-CCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSL-NGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~l-dG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|+.||..| +|..|+|+.|.|++++
T Consensus        48 kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A           48 QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            699999999999999999999 9999999999999974

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=98.41  E-value=2.1e-07  Score=70.59  Aligned_cols=39  Identities=28%  Similarity=0.486  Sum_probs=36.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++...
T Consensus        65 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~  103 (106)
T 1p27_B           65 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVR  103 (106)
T ss_dssp             EEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEESEES
T ss_pred             eeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEeecCC
Confidence            589999999999999999999999999999999999754

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=98.41  E-value=2.5e-07  Score=71.30  Aligned_cols=40  Identities=25%  Similarity=0.435  Sum_probs=37.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++....
T Consensus        65 kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  104 (108)
T 2jvo_A           65 NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPA  104 (108)
T ss_dssp             TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCC
Confidence            7999999999999999999999999999999999998643

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.40  E-value=5.5e-07  Score=67.47  Aligned_cols=40  Identities=28%  Similarity=0.457  Sum_probs=36.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|+.||. |+|..|+|+.|.|.++....
T Consensus        51 ~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a~~~~   90 (99)
T 2dgs_A           51 PRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAEPRD   90 (99)
T ss_dssp             CCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEECCCCC
T ss_pred             CCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEECCCCc
Confidence            36999999999999999998 99999999999999998643

>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=98.40  E-value=2.6e-07  Score=71.16  Aligned_cols=37  Identities=24%  Similarity=0.405  Sum_probs=35.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|++||..|||..|+|+.|.|.++.
T Consensus        59 ~G~~fV~f~~~~~A~~Ai~~lnG~~f~GR~i~v~~~~   95 (105)
T 3v4m_A           59 CGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCD   95 (105)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             cEEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEeC
Confidence            6999999999999999999999999999999999875

>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=98.39  E-value=2.3e-07  Score=70.49  Aligned_cols=37  Identities=27%  Similarity=0.286  Sum_probs=35.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|+.||..|+|.+|+|+.|.|+++.
T Consensus        70 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           70 LGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             ceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            6899999999999999999999999999999999985

>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=98.39  E-value=2.4e-07  Score=69.98  Aligned_cols=38  Identities=32%  Similarity=0.446  Sum_probs=35.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.|| .|+|..|+|+.|.|+++...
T Consensus        61 ~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~a~~~   98 (100)
T 2j76_E           61 KGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVADQA   98 (100)
T ss_dssp             CSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEECCCS
T ss_pred             CeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEeccCC
Confidence            699999999999999999 99999999999999998753

>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=98.39  E-value=3.2e-07  Score=70.13  Aligned_cols=39  Identities=28%  Similarity=0.485  Sum_probs=37.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++...
T Consensus        68 ~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  106 (110)
T 1oo0_B           68 KGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK  106 (110)
T ss_dssp             CSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEES
T ss_pred             ceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEcccC
Confidence            699999999999999999999999999999999999754

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=98.38  E-value=2.5e-07  Score=70.63  Aligned_cols=39  Identities=23%  Similarity=0.394  Sum_probs=36.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCc-ceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGS-RIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr-~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|.|+ .|.|.++...
T Consensus        61 ~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l~V~~a~~~  100 (105)
T 2nlw_A           61 KGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDF  100 (105)
T ss_dssp             CCEEEEEECSSSHHHHHHHHCSSEECSTTCEEEEECSCCC
T ss_pred             eeEEEEEECCHHHHHHHHHHhCCcccCCCceEEEEEcchH
Confidence            69999999999999999999999999998 9999998753

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=98.38  E-value=1.9e-07  Score=70.34  Aligned_cols=39  Identities=10%  Similarity=0.272  Sum_probs=36.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      .+|||||+|.+.++|+.||..|+|..|+|+.|.|.+++.
T Consensus        62 ~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           62 EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            479999999999999999999999999999999999863

>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=98.37  E-value=3.1e-07  Score=73.05  Aligned_cols=40  Identities=43%  Similarity=0.674  Sum_probs=37.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||..|+|..|+|+.|.|+++...
T Consensus        87 ~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a~~~  126 (129)
T 2kxn_B           87 SRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK  126 (129)
T ss_dssp             CCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCCSSS
T ss_pred             cceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            3689999999999999999999999999999999999754

>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=98.37  E-value=7.9e-07  Score=67.36  Aligned_cols=41  Identities=20%  Similarity=0.256  Sum_probs=37.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCee---cCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDV---DGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l---~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|+.||..|+|..|   .|+.|.|.++....
T Consensus        54 ~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v~~a~~~~   97 (106)
T 2dgp_A           54 HKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSES   97 (106)
T ss_dssp             CCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECCCCS
T ss_pred             cceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEEEECCccc
Confidence            369999999999999999999999998   89999999998654

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.37  E-value=9e-07  Score=68.32  Aligned_cols=39  Identities=31%  Similarity=0.414  Sum_probs=36.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||..|++ +|+|+.|.|+++...
T Consensus        58 ~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~a~~~   96 (116)
T 2cqd_A           58 SRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLG   96 (116)
T ss_dssp             CCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTT
T ss_pred             cceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEEcccC
Confidence            368999999999999999999998 899999999999754

>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=98.36  E-value=3.3e-07  Score=72.09  Aligned_cols=40  Identities=18%  Similarity=0.458  Sum_probs=36.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCee-----cCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDV-----DGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l-----~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|++.++|++||+.|||.+|     .|..|.|.++...+
T Consensus        63 rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~a~~~p  107 (114)
T 2cq2_A           63 KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQ  107 (114)
T ss_dssp             CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEEESCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEecccCc
Confidence            68999999999999999999999998     68899999997544

>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=98.36  E-value=5.2e-07  Score=68.25  Aligned_cols=40  Identities=33%  Similarity=0.475  Sum_probs=37.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecC---cceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDG---SRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~G---r~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|+|..|.|   +.|.|.++....
T Consensus        56 ~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~~a~~~~   98 (105)
T 2dnh_A           56 KGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDK   98 (105)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEEESCSSC
T ss_pred             CcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEEECccCc
Confidence            6899999999999999999999999998   999999998654

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=98.36  E-value=3.1e-07  Score=72.06  Aligned_cols=37  Identities=22%  Similarity=0.247  Sum_probs=35.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|++||..|||.+|+|+.|.|+++.
T Consensus        55 ~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i~v~~~~   91 (114)
T 3s6e_A           55 QGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVP   91 (114)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             cEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEEc
Confidence            6999999999999999999999999999999999975

>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=98.35  E-value=3.3e-07  Score=69.13  Aligned_cols=39  Identities=31%  Similarity=0.521  Sum_probs=36.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|.++...
T Consensus        50 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   88 (104)
T 1p1t_A           50 KGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             EEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCT
T ss_pred             ceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCCc
Confidence            689999999999999999999999999999999999754

>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=98.35  E-value=2.7e-07  Score=71.03  Aligned_cols=39  Identities=23%  Similarity=0.194  Sum_probs=35.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCC--eecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGR--DVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~--~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|++.++|+.||+.|++.  +|.|+.|.|+++...
T Consensus        52 kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~   92 (102)
T 1x4d_A           52 INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKY   92 (102)
T ss_dssp             SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCC
T ss_pred             CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCCC
Confidence            589999999999999999998864  599999999999854

>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=98.34  E-value=3.8e-07  Score=70.15  Aligned_cols=39  Identities=28%  Similarity=0.453  Sum_probs=36.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++...
T Consensus        68 ~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~k  106 (108)
T 2jrs_A           68 KGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTER  106 (108)
T ss_dssp             EEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECSCSS
T ss_pred             ceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcccC
Confidence            589999999999999999999999999999999998743

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.34  E-value=4.9e-07  Score=68.30  Aligned_cols=40  Identities=18%  Similarity=0.301  Sum_probs=37.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCe-ecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRD-VDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~-l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|+|.. |+|+.|.|+++....
T Consensus        51 ~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~a~~~~   91 (104)
T 2dhg_A           51 KGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKA   91 (104)
T ss_dssp             EEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCBCCCCC
T ss_pred             cceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEEccCCC
Confidence            6899999999999999999999999 999999999997543

>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=98.33  E-value=4.7e-07  Score=68.97  Aligned_cols=41  Identities=37%  Similarity=0.465  Sum_probs=37.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhC--CCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLN--GRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ld--G~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|+.||..|+  +..|+|+.|.|+++....
T Consensus        51 ~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V~~a~~~~   93 (109)
T 2dis_A           51 NRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEI   93 (109)
T ss_dssp             TCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSC
T ss_pred             cCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEEEEcCCCC
Confidence            37999999999999999999996  599999999999997543

>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=98.33  E-value=9.1e-07  Score=67.46  Aligned_cols=41  Identities=22%  Similarity=0.369  Sum_probs=37.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhC------CCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLN------GRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ld------G~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|+.||..|+      |..|+|+.|.|.++....
T Consensus        56 ~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~l~v~~a~~~~  102 (111)
T 1x4h_A           56 SKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRD  102 (111)
T ss_dssp             BCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCC
T ss_pred             CccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEEEEEEECCCCc
Confidence            37999999999999999999999      999999999999998653

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=98.33  E-value=3.4e-07  Score=75.37  Aligned_cols=38  Identities=18%  Similarity=0.232  Sum_probs=36.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      +|||||+|.+.++|+.||..|||.+|+|+.|.|.++..
T Consensus        99 kGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a~~  136 (156)
T 3n9u_C           99 KGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATR  136 (156)
T ss_dssp             EEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEECCH
T ss_pred             ceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEcCC
Confidence            68999999999999999999999999999999999863

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=97.68  E-value=6.2e-08  Score=75.07  Aligned_cols=41  Identities=32%  Similarity=0.446  Sum_probs=38.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+++.....
T Consensus        57 ~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           57 KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRAD   97 (116)
Confidence            68999999999999999999999999999999999986543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.33  E-value=1.3e-06  Score=67.05  Aligned_cols=39  Identities=21%  Similarity=0.221  Sum_probs=36.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|.+|+|+.|.|+++...
T Consensus        56 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   94 (114)
T 2do0_A           56 RGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERA   94 (114)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCC
T ss_pred             eeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEcccC
Confidence            589999999999999999999999999999999998743

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.32  E-value=3.2e-07  Score=71.09  Aligned_cols=40  Identities=18%  Similarity=0.298  Sum_probs=36.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhC--CCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLN--GRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ld--G~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|++.++|+.||+.|+  +.+|+|+.|.|+++....
T Consensus        52 kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~   93 (105)
T 1sjq_A           52 KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE   93 (105)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSSS
T ss_pred             CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCCC
Confidence            6999999999999999999886  479999999999997543

>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=98.31  E-value=5.3e-07  Score=65.98  Aligned_cols=38  Identities=29%  Similarity=0.433  Sum_probs=35.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.|| .|+|..|+|+.|.|++++..
T Consensus        48 ~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~~   85 (89)
T 3ucg_A           48 KGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRTN   85 (89)
T ss_dssp             CEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTTT
T ss_pred             ceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccCC
Confidence            689999999999999999 99999999999999999753

>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=98.31  E-value=7.1e-07  Score=68.33  Aligned_cols=39  Identities=13%  Similarity=0.189  Sum_probs=35.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHhh--CCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSL--NGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~l--dG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|++.++|+.||+.|  ++.+|.|+.|.|+++...
T Consensus        51 kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~   91 (101)
T 2cq1_A           51 KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK   91 (101)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCS
T ss_pred             CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcc
Confidence            699999999999999999976  578899999999999854

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=98.30  E-value=4.7e-07  Score=71.38  Aligned_cols=37  Identities=32%  Similarity=0.398  Sum_probs=35.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|++||..|||.+|+|+.|.|.++.
T Consensus        71 ~G~~FV~F~~~e~A~~Ai~~LnGr~f~GR~i~v~~~~  107 (118)
T 3ue2_A           71 IVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  107 (118)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             eEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcC
Confidence            4899999999999999999999999999999999975

>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=98.30  E-value=6.4e-07  Score=68.30  Aligned_cols=39  Identities=18%  Similarity=0.099  Sum_probs=35.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.|| .|++.+|.|+.|.|.++....
T Consensus        55 ~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~~~~~~   93 (102)
T 1wez_A           55 TGEADVEFATHEDAVAAM-AKDKANMQHRYVELFLNSTAG   93 (102)
T ss_dssp             EEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEEEECCCC
T ss_pred             eeEEEEEECCHHHHHHHH-HhCCCeECCcEEEEEECCCCC
Confidence            689999999999999999 689999999999999887544

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=98.30  E-value=6e-07  Score=70.25  Aligned_cols=40  Identities=23%  Similarity=0.222  Sum_probs=37.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||..|+|..|+|+.|.|+++...
T Consensus        75 ~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  114 (124)
T 2kt5_A           75 SLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ  114 (124)
T ss_dssp             CCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEECCT
T ss_pred             EeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCC
Confidence            4699999999999999999999999999999999999753

>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=98.29  E-value=3.1e-07  Score=72.08  Aligned_cols=36  Identities=22%  Similarity=0.161  Sum_probs=34.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|+.||. |||.+|+|+.|.|.++.
T Consensus        67 ~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~  102 (124)
T 1wel_A           67 TGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT  102 (124)
T ss_dssp             EEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             CeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECC
Confidence            6899999999999999999 99999999999999986

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=98.28  E-value=3.2e-07  Score=66.47  Aligned_cols=33  Identities=27%  Similarity=0.513  Sum_probs=31.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCc-ceEE
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGS-RIIV   35 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr-~IrV   35 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+ .|.|
T Consensus        47 ~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A           47 KGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             eEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            69999999999999999999999999999 8876

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=98.28  E-value=5.1e-07  Score=69.34  Aligned_cols=39  Identities=26%  Similarity=0.342  Sum_probs=35.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCe--ecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRD--VDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~--l~Gr~IrVe~a~~   40 (268)
                      .+|||||+|++.++|..||+.|+|..  |.|+.|.|++++.
T Consensus        56 ~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~   96 (100)
T 3r27_A           56 KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTS   96 (100)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEeccc
Confidence            37999999999999999999999875  7899999999874

>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=98.27  E-value=8.9e-07  Score=69.31  Aligned_cols=39  Identities=18%  Similarity=0.134  Sum_probs=35.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhC--CCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLN--GRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ld--G~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|++.++|+.||+.|+  +.+|.|+.|.|+++...
T Consensus        62 kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~  102 (112)
T 1x4f_A           62 KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKY  102 (112)
T ss_dssp             TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSC
T ss_pred             CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECccc
Confidence            6999999999999999999885  46799999999999754

>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=98.27  E-value=7.9e-07  Score=68.46  Aligned_cols=38  Identities=29%  Similarity=0.405  Sum_probs=36.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      +|||||+|.+.++|+.||..|+|..|+|..|.|.++..
T Consensus        47 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   84 (115)
T 3lqv_A           47 RGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNA   84 (115)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCH
T ss_pred             CcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecC
Confidence            68999999999999999999999999999999999874

>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=98.27  E-value=5.1e-07  Score=69.53  Aligned_cols=38  Identities=29%  Similarity=0.458  Sum_probs=35.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      .+|||||+|.+.++|+.|| .|+|..|+|+.|.|+++..
T Consensus        66 ~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           66 SKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             CCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             cCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            3689999999999999999 9999999999999999874

>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=98.27  E-value=7.9e-07  Score=74.19  Aligned_cols=39  Identities=23%  Similarity=0.504  Sum_probs=36.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecC--cceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDG--SRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~G--r~IrVe~a~~~   41 (268)
                      +|||||+|++.++|+.||+.|||.+|.|  ..|+|+|++..
T Consensus        84 rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~  124 (164)
T 1sjr_A           84 QFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT  124 (164)
T ss_dssp             CEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSS
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCC
Confidence            5799999999999999999999999966  99999999854

>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=98.27  E-value=6.2e-07  Score=71.87  Aligned_cols=39  Identities=28%  Similarity=0.451  Sum_probs=36.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|.|+.|.|.++...
T Consensus        92 ~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~  130 (143)
T 3egn_A           92 KGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSA  130 (143)
T ss_dssp             EEEEEEECSSHHHHHHHHHHHTTBEETTEECEEEECCCS
T ss_pred             ccEEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            689999999999999999999999999999999999753

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=98.26  E-value=6.3e-07  Score=63.64  Aligned_cols=36  Identities=17%  Similarity=0.295  Sum_probs=33.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEec
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA   38 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a   38 (268)
                      .+|||||+|.+.++|+.||. |+|..|+|+.|.|.+|
T Consensus        40 ~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A           40 HRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             SCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             cCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            36899999999999999997 9999999999999875

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.26  E-value=8.9e-07  Score=70.51  Aligned_cols=39  Identities=33%  Similarity=0.486  Sum_probs=35.4

Q ss_pred             CCe-EEEEeCCHHHHHHHHHhhCCCeecC--cceEEEeccCC
Q 024424            3 RDF-AFVEFSDPRDADDARYSLNGRDVDG--SRIIVEFARGG   41 (268)
Q Consensus         3 rGf-gFVeF~~~~dA~~Ai~~ldG~~l~G--r~IrVe~a~~~   41 (268)
                      .|| |||+|++.++|+.||+.|||.+|.|  ..|+|++++..
T Consensus        61 ~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~  102 (124)
T 2e5i_A           61 NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPT  102 (124)
T ss_dssp             SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCS
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCC
Confidence            486 9999999999999999999999998  58999999743

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=98.26  E-value=9.9e-07  Score=68.79  Aligned_cols=39  Identities=23%  Similarity=0.393  Sum_probs=36.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.|| .|+|..|+|+.|.|+++....
T Consensus        78 ~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~  116 (124)
T 2jwn_A           78 KGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNM  116 (124)
T ss_dssp             EEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSCCC
T ss_pred             ccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCCCC
Confidence            689999999999999999 899999999999999998543

>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=98.26  E-value=7.4e-07  Score=64.89  Aligned_cols=34  Identities=24%  Similarity=0.502  Sum_probs=32.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEe
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEF   37 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~   37 (268)
                      +|||||+|.+.++|+.|| .|+|..|+|+.|.|+.
T Consensus        53 kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~r   86 (87)
T 2hzc_A           53 KNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRR   86 (87)
T ss_dssp             SSEEEEEESSHHHHHHHG-GGTTCEETTEECEEEC
T ss_pred             CcEEEEEcCCHHHHHHHH-hcCCCEECCeEEEEeC
Confidence            799999999999999999 9999999999999974

>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=98.25  E-value=6.6e-07  Score=68.80  Aligned_cols=39  Identities=15%  Similarity=0.250  Sum_probs=35.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCC--eecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGR--DVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~--~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|++.++|+.||+.|++.  +|+|+.|.|+++...
T Consensus        51 kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~   91 (104)
T 1wex_A           51 KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCc
Confidence            699999999999999999998764  599999999999754

>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=98.24  E-value=7.9e-07  Score=70.33  Aligned_cols=40  Identities=18%  Similarity=0.298  Sum_probs=36.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhC--CCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLN--GRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ld--G~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|++.++|+.||+.|+  +.+|.|+.|.|+++....
T Consensus        67 kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k~  108 (119)
T 2ad9_A           67 KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE  108 (119)
T ss_dssp             GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSSS
T ss_pred             CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCCC
Confidence            6999999999999999999987  478999999999997543

>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=98.24  E-value=6.5e-07  Score=65.82  Aligned_cols=38  Identities=29%  Similarity=0.393  Sum_probs=34.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.+ |+.||..|+|..|+|+.|.|+++...
T Consensus        43 ~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A           43 KGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             CEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             ceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            689999999999 99999999999999999999999754

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=98.23  E-value=9.7e-07  Score=70.93  Aligned_cols=39  Identities=26%  Similarity=0.622  Sum_probs=36.0

Q ss_pred             CCe-EEEEeCCHHHHHHHHHhhCCCeecC--cceEEEeccCC
Q 024424            3 RDF-AFVEFSDPRDADDARYSLNGRDVDG--SRIIVEFARGG   41 (268)
Q Consensus         3 rGf-gFVeF~~~~dA~~Ai~~ldG~~l~G--r~IrVe~a~~~   41 (268)
                      +|| |||+|.+.++|+.||+.|||.+|.|  ..|+|+|++..
T Consensus        65 ~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~  106 (130)
T 3zzy_A           65 NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT  106 (130)
T ss_dssp             TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCS
T ss_pred             CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCC
Confidence            578 9999999999999999999999998  89999999743

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=98.23  E-value=7.1e-07  Score=71.44  Aligned_cols=41  Identities=46%  Similarity=0.744  Sum_probs=37.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|+.||..|+|..|+|+.|.|+++....
T Consensus        88 ~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~  128 (135)
T 2lea_A           88 SRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  128 (135)
T ss_dssp             CCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCC
T ss_pred             cceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            36899999999999999999999999999999999998543

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=98.22  E-value=5.5e-07  Score=71.38  Aligned_cols=40  Identities=38%  Similarity=0.594  Sum_probs=37.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCC----eecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGR----DVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~----~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+. +|+.||..|+|.    +|+|+.|.|+++....
T Consensus        66 ~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~l~V~~a~~~~  109 (131)
T 2m2b_A           66 NRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKTINVEFAKGSK  109 (131)
T ss_dssp             BCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCCCCCEECCCSC
T ss_pred             cceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEEEEEEECCCCC
Confidence            479999999999 999999999999    9999999999998643

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.21  E-value=1.1e-06  Score=68.15  Aligned_cols=37  Identities=22%  Similarity=0.143  Sum_probs=34.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+|||||+|.+.++|++|| .|||.+|.|+.|.|..+.
T Consensus        55 ~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           55 NNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             CCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            4799999999999999999 799999999999998875

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.21  E-value=1.6e-06  Score=66.93  Aligned_cols=41  Identities=27%  Similarity=0.364  Sum_probs=37.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR   43 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~r   43 (268)
                      .+|||||+|.+.++|+.||.. +|..|+|+.|.|+++.....
T Consensus        68 ~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~~~~  108 (116)
T 1x4b_A           68 SRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREE  108 (116)
T ss_dssp             CCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSSCCC
T ss_pred             cCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCCCcc
Confidence            368999999999999999988 99999999999999986543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.20  E-value=9.8e-07  Score=67.56  Aligned_cols=37  Identities=16%  Similarity=0.231  Sum_probs=34.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+|||||+|.+.++|+.||. |+|.+|+|+.|.|.++.
T Consensus        51 ~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A           51 FKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   87 (103)
T ss_dssp             CCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHH
T ss_pred             CccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEch
Confidence            47999999999999999998 99999999999999875

>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=98.17  E-value=7.4e-07  Score=77.73  Aligned_cols=38  Identities=18%  Similarity=0.271  Sum_probs=35.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+|||||+|.+.++|++||..|+|.+|+|+.|.|.++.
T Consensus       111 skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a~  148 (229)
T 3q2s_C          111 SKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVN  148 (229)
T ss_dssp             EEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEECC
T ss_pred             cceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEECC
Confidence            36899999999999999999999999999999999875

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=98.17  E-value=8.2e-07  Score=69.34  Aligned_cols=36  Identities=22%  Similarity=0.106  Sum_probs=34.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|++||. |+|.+|+|+.|.|.++.
T Consensus        61 ~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~   96 (118)
T 2db1_A           61 SGEAFVELESEDDVKLALK-KDRESMGHRYIEVFKSH   96 (118)
T ss_dssp             EEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEEEEC
T ss_pred             CeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEEECC
Confidence            6899999999999999999 99999999999999875

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.16  E-value=3.3e-07  Score=66.69  Aligned_cols=37  Identities=22%  Similarity=0.355  Sum_probs=34.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|+.||..|||..|+|+.|+|.+..
T Consensus        47 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A           47 KGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             CSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             CcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            6899999999999999999999999999999887654

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=98.16  E-value=1.3e-06  Score=74.44  Aligned_cols=38  Identities=21%  Similarity=0.413  Sum_probs=36.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      +|||||+|.+.++|+.||..|||.+|+|+.|.|.++..
T Consensus       143 ~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          143 KGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            68999999999999999999999999999999999874

>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=98.15  E-value=1.7e-06  Score=73.95  Aligned_cols=39  Identities=28%  Similarity=0.265  Sum_probs=36.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      ++|||||+|.+.++|+.||+.|||.+|.|+.|.|.+++.
T Consensus        41 ~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~   79 (205)
T 3tyt_A           41 KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQ   79 (205)
T ss_dssp             STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccC
Confidence            479999999999999999999999999999999999864

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.14  E-value=1.4e-06  Score=61.98  Aligned_cols=35  Identities=29%  Similarity=0.418  Sum_probs=33.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEec
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA   38 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a   38 (268)
                      +|||||+|.+.++|+.||..|+ ..|+|+.|.|+++
T Consensus        42 ~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A           42 RGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             SSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            6899999999999999999999 9999999999987

>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=98.14  E-value=1.2e-06  Score=67.02  Aligned_cols=37  Identities=16%  Similarity=0.093  Sum_probs=34.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+|||||+|.+.++|+.||. |+|..|.|+.|.|.++.
T Consensus        54 ~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~a~   90 (107)
T 2lmi_A           54 RRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVYEIN   90 (107)
T ss_dssp             TCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCEECC
T ss_pred             EeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEEECC
Confidence            47899999999999999999 99999999999999876

>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=98.12  E-value=1.4e-06  Score=67.37  Aligned_cols=38  Identities=18%  Similarity=0.273  Sum_probs=35.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      .+|||||+|.+.++|+.||.. +|.+|+|+.|.|.++..
T Consensus        56 ~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a~~   93 (114)
T 2cpy_A           56 GLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVVTL   93 (114)
T ss_dssp             CSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEECH
T ss_pred             cceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEECCH
Confidence            479999999999999999987 99999999999999864

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.11  E-value=4.7e-06  Score=63.71  Aligned_cols=39  Identities=26%  Similarity=0.341  Sum_probs=34.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|++.++|+.||..+++  +.|+.|.|.|+...+
T Consensus        53 ~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           53 KPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQP   91 (100)
T ss_dssp             SSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCC
Confidence            579999999999999999998655  679999999998654

>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=98.09  E-value=1.3e-06  Score=70.44  Aligned_cols=36  Identities=22%  Similarity=0.117  Sum_probs=34.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|+.||. |+|.+|+|+.|.|.++.
T Consensus        88 rG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~~a~  123 (136)
T 2hgl_A           88 SGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSH  123 (136)
T ss_dssp             EEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEEECC
T ss_pred             CeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEEECC
Confidence            6899999999999999999 99999999999999875

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.09  E-value=1.8e-06  Score=65.37  Aligned_cols=39  Identities=28%  Similarity=0.368  Sum_probs=35.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||.. +|..|+|+.|.|+++....
T Consensus        58 ~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~a~~~~   96 (105)
T 2dh8_A           58 RGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCTPRG   96 (105)
T ss_dssp             EEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCCSCCSS
T ss_pred             ceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEccCCC
Confidence            58999999999999999998 9999999999999997543

>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=98.09  E-value=3e-06  Score=65.02  Aligned_cols=37  Identities=14%  Similarity=0.341  Sum_probs=34.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCee--------cCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDV--------DGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l--------~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|+.||..|+|..|        .++.|.|.|+.
T Consensus        66 ~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~~l~v~~a~  110 (114)
T 1x5o_A           66 RGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSG  110 (114)
T ss_dssp             EEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSCBEEEECC
T ss_pred             ceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCCceeEEccC
Confidence            58999999999999999999999999        56779999886

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}

Probab=98.06  E-value=1.4e-06  Score=64.64  Aligned_cols=41  Identities=27%  Similarity=0.679  Sum_probs=29.7

Q ss_pred             CccccCCCCCCCCCcccC-------------------CCCCCccccCCCCCccccccCCC
Q 024424           61 GRCFNCGIDGHWARDCKA-------------------GDWKNKCYRCGERGHIERNCQNS  101 (268)
Q Consensus        61 ~rC~~CG~~GH~ardC~~-------------------~~~~~~cyrcg~~GH~~r~c~~s  101 (268)
                      ..||+|+..||++.+|+.                   +.....||.||..||+..+|+..
T Consensus         6 ~~C~~Cg~~GH~~~~Cp~~~rcY~c~~~gh~~~~c~~p~~~~~CYnCG~~GH~~rdC~~~   65 (83)
T 3nyb_B            6 VQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEK   65 (83)
T ss_dssp             -CCSSSCCSSSCGGGCGGGTCCCCBC-------------CCCBCSSSSCBSSCGGGCSSC
T ss_pred             CCCCCCCCCCCccccCCCcccccccccCCcccccccCCCCCCeecccCCCCcCcccCCcc
Confidence            457777777777777653                   22347899999999999999973

>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=98.06  E-value=3.2e-06  Score=64.24  Aligned_cols=38  Identities=18%  Similarity=0.147  Sum_probs=34.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      .+|||||+|.+.++|+.||.. ++..|.|+.|.|..+..
T Consensus        56 ~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~~~   93 (104)
T 1wg5_A           56 STGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKSSR   93 (104)
T ss_dssp             BCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEECT
T ss_pred             cceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEECCH
Confidence            379999999999999999987 99999999999998863

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.06  E-value=5e-06  Score=61.67  Aligned_cols=38  Identities=21%  Similarity=0.258  Sum_probs=35.4

Q ss_pred             CeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         4 GfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      |.|||+|.+.++|+.||..|+|..|+|+.|.|+++...
T Consensus        55 ~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   92 (96)
T 2e44_A           55 AVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDE   92 (96)
T ss_dssp             EEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCC
T ss_pred             CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCcc
Confidence            45999999999999999999999999999999999754

>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=98.04  E-value=1.3e-06  Score=70.70  Aligned_cols=40  Identities=20%  Similarity=0.070  Sum_probs=36.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|++.++|++|| .|++.+|.|+.|.|..+....
T Consensus        85 srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~  124 (139)
T 2hgn_A           85 VTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTG  124 (139)
T ss_dssp             SSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSC
T ss_pred             CceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCC
Confidence            4799999999999999999 899999999999999887543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=98.02  E-value=4.4e-06  Score=64.14  Aligned_cols=39  Identities=26%  Similarity=0.316  Sum_probs=35.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||..| +..|+|+.|.|+++...
T Consensus        66 ~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~a~~~  104 (109)
T 2rs2_A           66 SRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKVAFPR  104 (109)
T ss_dssp             CTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEECCCC
T ss_pred             cCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEEccCC
Confidence            3689999999999999999987 59999999999999754

>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=98.01  E-value=3.4e-06  Score=61.51  Aligned_cols=35  Identities=26%  Similarity=0.366  Sum_probs=31.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEec
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA   38 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a   38 (268)
                      +|||||+|.+.++|+.||. +++.+|+|+.|.|.+|
T Consensus        53 ~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A           53 RGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             EEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEEC
T ss_pred             ccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEeC
Confidence            6899999999999999995 5888999999999875

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.98  E-value=6e-06  Score=61.27  Aligned_cols=36  Identities=22%  Similarity=0.273  Sum_probs=33.9

Q ss_pred             eEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         5 fgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      ||||+|.+.++|+.||. |+|.+|+|+.|.|.++...
T Consensus        47 ~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~   82 (94)
T 2e5g_A           47 FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQK   82 (94)
T ss_dssp             EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCS
T ss_pred             EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcC
Confidence            99999999999999999 9999999999999988643

>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1

Probab=97.95  E-value=7.9e-06  Score=52.32  Aligned_cols=26  Identities=31%  Similarity=0.765  Sum_probs=21.3

Q ss_pred             CCCCCCCccccCCCCCCCCCcccCCC
Q 024424           55 GPPPGSGRCFNCGIDGHWARDCKAGD   80 (268)
Q Consensus        55 ~~~~~~~rC~~CG~~GH~ardC~~~~   80 (268)
                      +.+.....||+||+.|||+++|+...
T Consensus         5 ~~~~~~~~C~~Cgk~GH~ardCP~~~   30 (40)
T 1a6b_B            5 RSQLDRDQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             CCSCCSSSCSSSCCTTCCTTSCSSSC
T ss_pred             cCCCCCCeeeECCCCCcchhhCcCCc
Confidence            44556689999999999999998764

>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=97.94  E-value=4.8e-06  Score=58.85  Aligned_cols=36  Identities=19%  Similarity=0.320  Sum_probs=32.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEec
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA   38 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a   38 (268)
                      .+|||||+|.+.++|+.||. +++..|+|+.|.|.++
T Consensus        40 ~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A           40 RRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             SCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             cCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            36899999999999999997 4899999999999875

>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=97.94  E-value=1.1e-05  Score=60.62  Aligned_cols=38  Identities=16%  Similarity=0.273  Sum_probs=34.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..  +..|+|+.|.|+++....
T Consensus        57 ~g~afV~f~~~~~a~~A~~~--~~~~~g~~l~v~~a~~~~   94 (103)
T 2cqg_A           57 KGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLPNSKQ   94 (103)
T ss_dssp             EEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECCCTTC
T ss_pred             cceEEEEECCHHHHHHHHHc--CCeeCCeEEEEEecCCCC
Confidence            58999999999999999984  679999999999998654

>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=97.87  E-value=1.3e-05  Score=64.42  Aligned_cols=39  Identities=38%  Similarity=0.606  Sum_probs=36.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|.|..|.|.++...
T Consensus        45 ~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~   83 (168)
T 1b7f_A           45 YGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPG   83 (168)
T ss_dssp             CSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             ceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCCC
Confidence            589999999999999999999999999999999998743

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}

Probab=97.86  E-value=1e-05  Score=64.11  Aligned_cols=41  Identities=24%  Similarity=0.555  Sum_probs=32.9

Q ss_pred             CccccCCCCCCCCCcccCCCCCCccccCCCCCccccccCCC
Q 024424           61 GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNS  101 (268)
Q Consensus        61 ~rC~~CG~~GH~ardC~~~~~~~~cyrcg~~GH~~r~c~~s  101 (268)
                      ..||+|+..||++.+|+.......||.|+..||++++|+..
T Consensus        43 ~~C~~Cg~~GH~~~~C~~~~~~~~C~~Cg~~GH~~~~Cp~~   83 (124)
T 2lli_A           43 IQCSKCDEVGHYRSQCPHKWKKVQCTLCKSKKHSKERCPSI   83 (124)
T ss_dssp             SCSSSSSCSSSSTTTSCCCCCCCSSSSSCSSCCCTTTCCCS
T ss_pred             ccccccCCCCCccccCcCcccCccCCCCCcCCcchhhCCCc
Confidence            56888888888888888765557888888888888888864

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}

Probab=97.85  E-value=1.2e-05  Score=63.72  Aligned_cols=41  Identities=27%  Similarity=0.650  Sum_probs=35.4

Q ss_pred             CCccccCCCCCCCCCcccCCC-------------------CCCccccCCCCCccccccCC
Q 024424           60 SGRCFNCGIDGHWARDCKAGD-------------------WKNKCYRCGERGHIERNCQN  100 (268)
Q Consensus        60 ~~rC~~CG~~GH~ardC~~~~-------------------~~~~cyrcg~~GH~~r~c~~  100 (268)
                      ...||+||..||++++|+...                   ....||.|+..||++.+|+.
T Consensus        64 ~~~C~~Cg~~GH~~~~Cp~~~~~y~~~~~~~~~~~~~~~~~~~~Cy~Cg~~GH~a~dCp~  123 (124)
T 2lli_A           64 KVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKE  123 (124)
T ss_dssp             CCSSSSSCSSCCCTTTCCCSTTSCCSSSCCCCCCCSCCCCCCCCTTTTSSSCTTTTTSCC
T ss_pred             CccCCCCCcCCcchhhCCCccccccccCccccccccccCCCCCCcCCCCCCCcCcccCcC
Confidence            368999999999999999642                   14689999999999999986

>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=97.84  E-value=1.3e-05  Score=70.51  Aligned_cols=39  Identities=26%  Similarity=0.366  Sum_probs=36.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|.|+.|.|.++...
T Consensus        52 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   90 (282)
T 3pgw_A           52 RGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTD   90 (282)
T ss_pred             ceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEEeccC
Confidence            699999999999999999999999999999999999643

>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=97.84  E-value=1.3e-05  Score=64.24  Aligned_cols=39  Identities=36%  Similarity=0.628  Sum_probs=36.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|.|..|.|.++...
T Consensus        44 ~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~   82 (167)
T 1fxl_A           44 LGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPS   82 (167)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCCC
Confidence            489999999999999999999999999999999998743

>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=97.83  E-value=7.4e-06  Score=65.23  Aligned_cols=37  Identities=22%  Similarity=0.124  Sum_probs=33.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+|||||+|.+.++|++||.. ++.+|.|+.|.|..+.
T Consensus        83 srGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V~~a~  119 (126)
T 2hgm_A           83 ITGEAFVQFASQELAEKALGK-HKERIGHRYIEVFKSS  119 (126)
T ss_dssp             SCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCEEEC
T ss_pred             CceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEEECC
Confidence            479999999999999999974 7799999999998774

>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=97.82  E-value=1.3e-05  Score=65.30  Aligned_cols=39  Identities=33%  Similarity=0.590  Sum_probs=35.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.|| .|+|..|.|+.|.|.++...
T Consensus        53 ~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~~~~~   91 (175)
T 1fje_B           53 NRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGR   91 (175)
T ss_dssp             TTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEECCCCS
T ss_pred             cccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEecCCCc
Confidence            4799999999999999999 59999999999999998753

>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=97.79  E-value=1.8e-05  Score=68.13  Aligned_cols=39  Identities=26%  Similarity=0.413  Sum_probs=36.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|.|+.|.|.++...
T Consensus        72 ~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  110 (229)
T 2adc_A           72 KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ  110 (229)
T ss_dssp             SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCc
Confidence            699999999999999999999999999999999998754

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=97.79  E-value=1.2e-05  Score=66.47  Aligned_cols=39  Identities=21%  Similarity=0.416  Sum_probs=36.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.|| .|+|..|.|+.|.|.++...
T Consensus        50 ~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i~v~~~~~~   88 (198)
T 2yh0_A           50 DKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDY   88 (198)
T ss_dssp             TTTEEEEEESCSHHHHHHG-GGTTEEETTEEEEEECCCCC
T ss_pred             CCCEEEEEeCCHHHHHHHH-HhcCCEEcCceEEEeCCCCC
Confidence            3799999999999999999 99999999999999998754

>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=97.77  E-value=2e-05  Score=63.72  Aligned_cols=39  Identities=21%  Similarity=0.416  Sum_probs=35.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.|| .|+|..|.|+.|.|.++...
T Consensus        50 ~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~v~~~~~~   88 (172)
T 2g4b_A           50 DKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDY   88 (172)
T ss_dssp             TTTEEEEEESSHHHHHHHG-GGTTCEETTEECEEECCSSC
T ss_pred             CCCEEEEEeCCHHHHHHHH-HhCCcEecCceeeecCCccc
Confidence            3799999999999999999 99999999999999987643

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=97.76  E-value=2.4e-05  Score=62.56  Aligned_cols=39  Identities=28%  Similarity=0.547  Sum_probs=36.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|.|..|.|.++...
T Consensus        41 ~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A           41 VNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            589999999999999999999999999999999998654

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.75  E-value=1.7e-05  Score=59.72  Aligned_cols=37  Identities=22%  Similarity=0.315  Sum_probs=34.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      .+.+||+|.+.+.|..||. |||.+|+|+.|+|.++..
T Consensus        49 ~d~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~lkt~   85 (91)
T 2dnr_A           49 EDKMWVTFLEGSSALNVLS-LNGKELLNRTITIALKSP   85 (91)
T ss_dssp             SSSEEEEESSHHHHHHGGG-GTTCEETTEEEEEEECCC
T ss_pred             cCCEEEEECChHHHHHHHh-cCCeEeCCeEEEEEeCCC
Confidence            4669999999999999998 999999999999999863

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=97.74  E-value=1.7e-05  Score=66.07  Aligned_cols=39  Identities=26%  Similarity=0.413  Sum_probs=36.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|.|+.|.|.++...
T Consensus        41 ~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~   79 (198)
T 1qm9_A           41 KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   79 (198)
T ss_dssp             SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCC
Confidence            699999999999999999999999999999999998754

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.74  E-value=7.8e-06  Score=64.75  Aligned_cols=36  Identities=19%  Similarity=0.029  Sum_probs=32.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|++||.. ++..|.|+.|.|..+.
T Consensus        68 ~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~~a~  103 (123)
T 2dha_A           68 TGDAFVLFACEEYAQNALRK-HKDLLGKRYIELFRST  103 (123)
T ss_dssp             EEEEEECCSSHHHHHHHHTT-TTEESSSCEECCEEEC
T ss_pred             eeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEEEECC
Confidence            69999999999999999986 9999999999888764

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=97.72  E-value=3e-05  Score=64.98  Aligned_cols=39  Identities=31%  Similarity=0.397  Sum_probs=35.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      .+|||||+|.+.++|+.||..|+|..|.|+.|.|.++..
T Consensus        69 ~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           69 HKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN  107 (216)
T ss_dssp             CCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSC
T ss_pred             cCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCC
Confidence            479999999999999999999999999999999988764

>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=97.69  E-value=2.7e-05  Score=68.56  Aligned_cols=39  Identities=28%  Similarity=0.548  Sum_probs=36.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|.|+.|.|.++...
T Consensus       226 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  264 (284)
T 3smz_A          226 KGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPG  264 (284)
T ss_dssp             EEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSS
T ss_pred             ccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCC
Confidence            689999999999999999999999999999999999754

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=97.67  E-value=1.2e-05  Score=60.41  Aligned_cols=37  Identities=16%  Similarity=0.269  Sum_probs=34.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||.  +|..|+|..|.|.++...
T Consensus        50 ~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~~~   86 (102)
T 2xs2_A           50 KGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAIRK   86 (102)
T ss_dssp             EEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEEEC
T ss_pred             cceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECCcC
Confidence            6999999999999999998  999999999999998743

>1dsq_A Nucleic acid binding protein P14; CCHC type zinc finger, virus/viral protein; NMR {Mouse mammary tumor virus} SCOP: g.40.1.1

Probab=97.62  E-value=2.4e-05  Score=45.31  Aligned_cols=19  Identities=53%  Similarity=1.148  Sum_probs=16.3

Q ss_pred             CccccCCCCCCCCCcccCC
Q 024424           61 GRCFNCGIDGHWARDCKAG   79 (268)
Q Consensus        61 ~rC~~CG~~GH~ardC~~~   79 (268)
                      ..||+||+.|||+++|+..
T Consensus         3 ~~Cf~CG~~GH~ardC~~~   21 (26)
T 1dsq_A            3 PVCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTCC
T ss_pred             CeeEeCCCCCcccccCCCc
Confidence            5799999999999999865

>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A

Probab=97.60  E-value=3.7e-05  Score=52.74  Aligned_cols=26  Identities=31%  Similarity=0.765  Sum_probs=20.5

Q ss_pred             CCCCCCCccccCCCCCCCCCcccCCC
Q 024424           55 GPPPGSGRCFNCGIDGHWARDCKAGD   80 (268)
Q Consensus        55 ~~~~~~~rC~~CG~~GH~ardC~~~~   80 (268)
                      +.+.....||+||+.|||++||+...
T Consensus        18 ~~~~~~~~C~~Cge~GH~ardCp~~~   43 (56)
T 1u6p_A           18 RSQLDRDQCAYCKEKGHWAKDCPKKP   43 (56)
T ss_dssp             STTCCTTBCSSSCCBSSCGGGCTTCC
T ss_pred             CCCCCCCcceeCCCCCcccccCcCCc
Confidence            44556678999999999999998753

>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=97.56  E-value=6e-05  Score=66.09  Aligned_cols=38  Identities=24%  Similarity=0.413  Sum_probs=36.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      +|||||+|.+.++|+.||..|+|..|.|+.|.|.++..
T Consensus        58 kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~   95 (261)
T 3sde_A           58 RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH   95 (261)
T ss_dssp             TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc
Confidence            79999999999999999999999999999999999863

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=97.53  E-value=6.3e-05  Score=63.90  Aligned_cols=38  Identities=24%  Similarity=0.465  Sum_probs=35.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      +|||||+|.+.++|+.||..|++..+.|+.|.|.++..
T Consensus        57 ~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~   94 (213)
T 4f02_A           57 LGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   94 (213)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cccccceeCCHHHHHHHHHHhhhhhcCCcccccccccc
Confidence            58999999999999999999999999999999998864

>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=97.47  E-value=0.0001  Score=68.28  Aligned_cols=38  Identities=21%  Similarity=0.580  Sum_probs=32.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeec---Cc--ceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVD---GS--RIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~---Gr--~IrVe~a~   39 (268)
                      .+|||||+|++.+||++||+.|||++|.   |.  .|.|.++.
T Consensus        55 ~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~~~   97 (345)
T 3tht_A           55 NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVE   97 (345)
T ss_dssp             TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEECS
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEEEee
Confidence            3799999999999999999999999884   44  46677664

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}

Probab=97.46  E-value=3.9e-05  Score=56.84  Aligned_cols=20  Identities=25%  Similarity=0.644  Sum_probs=16.3

Q ss_pred             CCccccCCCCCccccccCCC
Q 024424           82 KNKCYRCGERGHIERNCQNS  101 (268)
Q Consensus        82 ~~~cyrcg~~GH~~r~c~~s  101 (268)
                      ...||.|+..||++.+|+..
T Consensus         5 ~~~C~~Cg~~GH~~~~Cp~~   24 (83)
T 3nyb_B            5 KVQCTLCKSKKHSKERCPSI   24 (83)
T ss_dssp             --CCSSSCCSSSCGGGCGGG
T ss_pred             cCCCCCCCCCCCccccCCCc
Confidence            35799999999999999874

>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A

Probab=97.45  E-value=6.9e-05  Score=44.42  Aligned_cols=21  Identities=52%  Similarity=1.091  Sum_probs=17.6

Q ss_pred             CCccccCCCCCCCCCcccCCC
Q 024424           60 SGRCFNCGIDGHWARDCKAGD   80 (268)
Q Consensus        60 ~~rC~~CG~~GH~ardC~~~~   80 (268)
                      ...||+||+.|||+.+|+.+.
T Consensus         6 ~~~C~nCgk~GH~ar~C~~pr   26 (29)
T 1nc8_A            6 VIRCWNCGKEGHSARQCRAPR   26 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSSS
T ss_pred             CCEEEECCccccCHhHCcccc
Confidence            467999999999999998764

>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=97.44  E-value=0.00011  Score=64.93  Aligned_cols=40  Identities=23%  Similarity=0.436  Sum_probs=36.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||..|+|..|.|..|.|.++...
T Consensus       158 ~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  197 (292)
T 2ghp_A          158 SRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPL  197 (292)
T ss_dssp             -CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             cceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            3799999999999999999999999999999999998754

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.43  E-value=8.2e-05  Score=57.21  Aligned_cols=34  Identities=15%  Similarity=0.251  Sum_probs=27.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEec
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA   38 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a   38 (268)
                      +|||||+|.+.++|+.||+.|+  .|+|..|.|..+
T Consensus        52 ~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~~~   85 (114)
T 2dnl_A           52 KGYAFLLFQEESSVQALIDACL--EEDGKLYLCVSS   85 (114)
T ss_dssp             TSEEEECCSSHHHHHHHHHHSE--EETTEEEEEECC
T ss_pred             ccEEEEEECCHHHHHHHHHhhh--hcCCcEEEeccC
Confidence            7999999999999999999983  366666655543

>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=97.41  E-value=0.00011  Score=64.66  Aligned_cols=39  Identities=21%  Similarity=0.469  Sum_probs=36.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|.|+.|.|.++...
T Consensus       137 ~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~  175 (284)
T 3smz_A          137 KGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAG  175 (284)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGG
T ss_pred             ceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            589999999999999999999999999999999998753

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=97.40  E-value=7e-05  Score=60.24  Aligned_cols=38  Identities=16%  Similarity=0.149  Sum_probs=31.9

Q ss_pred             CCCeEEEEeCC----HHH----HHHHHH--hhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSD----PRD----ADDARY--SLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~----~~d----A~~Ai~--~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+|||||+|.+    +++    |..||.  .|+|..|+|+.|+|.+..
T Consensus        47 slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~I~Gr~irV~ln~   94 (136)
T 2j8a_A           47 PLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCFIMGFKFEVILNK   94 (136)
T ss_dssp             EEEEEEEECC------CCHHHHHHHHHHHTTTTCEEETTEEEEEEECC
T ss_pred             eeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCeecCcEEEEEECc
Confidence            47999999996    434    889998  899999999999999875

>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=97.39  E-value=0.00012  Score=60.37  Aligned_cols=38  Identities=26%  Similarity=0.385  Sum_probs=34.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||.. ++..|.|+.|.|.++...
T Consensus        55 ~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~~~~   92 (196)
T 1l3k_A           55 RGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSR   92 (196)
T ss_dssp             EEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCC-
T ss_pred             cceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecccCc
Confidence            58999999999999999976 899999999999998653

>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=97.36  E-value=0.00012  Score=55.38  Aligned_cols=35  Identities=20%  Similarity=0.275  Sum_probs=32.0

Q ss_pred             CeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         4 GfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +-+||+|.+.+.|..||. |||.+|+|+.|+|.+..
T Consensus        59 d~~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           59 GQMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             TEEEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             CcEEEEEcChHHHHHHHh-cCCeeeCCeEEEEeccC
Confidence            348999999999999998 99999999999998754

>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=97.35  E-value=0.00019  Score=52.88  Aligned_cols=35  Identities=37%  Similarity=0.589  Sum_probs=27.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCee--cCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDV--DGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l--~Gr~IrVe~a~~~   41 (268)
                      +|||||+|++.++|+.    |+|..+  .|..|.|.++...
T Consensus        48 rGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~~k   84 (89)
T 3d2w_A           48 RAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAEPK   84 (89)
T ss_dssp             CSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC--
T ss_pred             CCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcCCC
Confidence            7999999999999883    566654  5888888888643

>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=97.30  E-value=0.00012  Score=53.33  Aligned_cols=38  Identities=26%  Similarity=0.290  Sum_probs=28.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.|+..  ...+.|..|.|.++....
T Consensus        42 ~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~~~~   79 (88)
T 1wf0_A           42 RAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             CSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCCCC
T ss_pred             CCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCCCC
Confidence            79999999999999754321  345588889998887543

>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=97.21  E-value=0.00029  Score=56.65  Aligned_cols=39  Identities=23%  Similarity=0.243  Sum_probs=33.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeec---CcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVD---GSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~---Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..+.   +..|.|.++...
T Consensus        47 ~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~~~~~~~   88 (175)
T 3nmr_A           47 KGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSE   88 (175)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECGGG
T ss_pred             ceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEEcccccc
Confidence            589999999999999999999998876   567777776543

>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=97.11  E-value=0.00036  Score=61.53  Aligned_cols=36  Identities=28%  Similarity=0.226  Sum_probs=33.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|+.|| .|+|..|.|+.|.|.++.
T Consensus        81 ~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~v~~~~  116 (292)
T 2ghp_A           81 FRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHLT  116 (292)
T ss_dssp             SEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEECC
T ss_pred             cEEEEEEECCHHHHHHHH-HhCCcEeCCcEEEEEECC
Confidence            699999999999999999 599999999999999874

>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.10  E-value=0.00023  Score=48.58  Aligned_cols=21  Identities=33%  Similarity=1.005  Sum_probs=17.6

Q ss_pred             CCCccccCCCCCCCCCcccCC
Q 024424           59 GSGRCFNCGIDGHWARDCKAG   79 (268)
Q Consensus        59 ~~~rC~~CG~~GH~ardC~~~   79 (268)
                      ....||+||+.|||+.+|+..
T Consensus         6 ~~~~C~kCGk~GH~~k~Cp~~   26 (55)
T 2ysa_A            6 SGYTCFRCGKPGHYIKNCPTN   26 (55)
T ss_dssp             SSCCCTTTCCTTSCGGGCSGG
T ss_pred             CCCccccCCCcCcccccCCCC
Confidence            345799999999999999843

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}

Probab=97.05  E-value=0.00023  Score=51.52  Aligned_cols=33  Identities=24%  Similarity=0.602  Sum_probs=19.0

Q ss_pred             CCCCCCcccCCC---------CCCccccCCCCCccccccCCC
Q 024424           69 DGHWARDCKAGD---------WKNKCYRCGERGHIERNCQNS  101 (268)
Q Consensus        69 ~GH~ardC~~~~---------~~~~cyrcg~~GH~~r~c~~s  101 (268)
                      .||+++||+.+.         ....||+|++.||++++|+..
T Consensus         2 ~gh~~rdc~~~~~~~~~~~~~r~~~C~~Cg~~GH~a~~C~~~   43 (74)
T 2li8_A            2 SGLVPRGSHMPKGKSMQKRRSKGDRCYNCGGLDHHAKECKLP   43 (74)
T ss_dssp             ----------CCCCCCCSCCSTTSCCTTTCCSSSCTTTCSSC
T ss_pred             CccccCcCCCCCcCccccccCCCCcccccCCcCcCcccCCCC
Confidence            589999999652         446899999999999999863

>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=96.93  E-value=0.00057  Score=59.77  Aligned_cols=39  Identities=23%  Similarity=0.083  Sum_probs=33.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCC-Ceec---CcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNG-RDVD---GSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG-~~l~---Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|..||..|++ ..+.   ++.|.|.++...
T Consensus       137 ~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~  179 (261)
T 3sde_A          137 TGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQF  179 (261)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCE
T ss_pred             CcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeecccc
Confidence            68999999999999999999954 4444   899999998753

>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=96.78  E-value=0.00084  Score=53.67  Aligned_cols=36  Identities=28%  Similarity=0.422  Sum_probs=31.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+|||||+|.+.++|+.||..  +..|+|+.|.|.++.
T Consensus        44 ~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A           44 SRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             CCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             ccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            369999999999999999985  578899999888875

>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1

Probab=96.60  E-value=0.0013  Score=41.95  Aligned_cols=25  Identities=28%  Similarity=0.803  Sum_probs=21.0

Q ss_pred             CCCccccCCCCCccccccCCCCCCC
Q 024424           81 WKNKCYRCGERGHIERNCQNSPKKL  105 (268)
Q Consensus        81 ~~~~cyrcg~~GH~~r~c~~s~~~~  105 (268)
                      ....||.|++.|||+++|+....+.
T Consensus         9 ~~~~C~~Cgk~GH~ardCP~~~~~~   33 (40)
T 1a6b_B            9 DRDQCAYCKEKGHWAKDCPKKPRGP   33 (40)
T ss_dssp             CSSSCSSSCCTTCCTTSCSSSCCCT
T ss_pred             CCCeeeECCCCCcchhhCcCCcccC
Confidence            3579999999999999999865543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=96.57  E-value=0.0013  Score=57.75  Aligned_cols=27  Identities=19%  Similarity=0.415  Sum_probs=25.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCee
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDV   28 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l   28 (268)
                      .+|||||+|.+.++|+.||+.|+|..|
T Consensus       178 ~kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          178 SKNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             GGTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             CCCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            379999999999999999999999887

>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A

Probab=96.28  E-value=0.0022  Score=43.88  Aligned_cols=24  Identities=29%  Similarity=0.868  Sum_probs=20.6

Q ss_pred             CCCccccCCCCCccccccCCCCCC
Q 024424           81 WKNKCYRCGERGHIERNCQNSPKK  104 (268)
Q Consensus        81 ~~~~cyrcg~~GH~~r~c~~s~~~  104 (268)
                      ....||.||+.|||+++|+....+
T Consensus        22 ~~~~C~~Cge~GH~ardCp~~~~~   45 (56)
T 1u6p_A           22 DRDQCAYCKEKGHWAKDCPKKPRG   45 (56)
T ss_dssp             CTTBCSSSCCBSSCGGGCTTCCCS
T ss_pred             CCCcceeCCCCCcccccCcCCccc
Confidence            467999999999999999986544

>1dsq_A Nucleic acid binding protein P14; CCHC type zinc finger, virus/viral protein; NMR {Mouse mammary tumor virus} SCOP: g.40.1.1

Probab=96.16  E-value=0.0023  Score=36.76  Aligned_cols=19  Identities=42%  Similarity=1.256  Sum_probs=17.2

Q ss_pred             CccccCCCCCccccccCCC
Q 024424           83 NKCYRCGERGHIERNCQNS  101 (268)
Q Consensus        83 ~~cyrcg~~GH~~r~c~~s  101 (268)
                      ..||.||+.||++++|+..
T Consensus         3 ~~Cf~CG~~GH~ardC~~~   21 (26)
T 1dsq_A            3 PVCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTCC
T ss_pred             CeeEeCCCCCcccccCCCc
Confidence            5799999999999999864

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=96.15  E-value=0.0054  Score=48.37  Aligned_cols=36  Identities=11%  Similarity=0.157  Sum_probs=31.9

Q ss_pred             CeEEEEeCC-HHHHHHHHHhhC--CCeecCcceEEEecc
Q 024424            4 DFAFVEFSD-PRDADDARYSLN--GRDVDGSRIIVEFAR   39 (268)
Q Consensus         4 GfgFVeF~~-~~dA~~Ai~~ld--G~~l~Gr~IrVe~a~   39 (268)
                      -+|||.|.+ +.+|+.||.+|+  +.+|+|..++|+...
T Consensus        56 ~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL~   94 (121)
T 1owx_A           56 KEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE   94 (121)
T ss_dssp             SEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             CEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEECC
Confidence            379999999 899999999994  789999999998765

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=95.90  E-value=0.0017  Score=51.86  Aligned_cols=37  Identities=22%  Similarity=0.162  Sum_probs=34.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHhh-CCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSL-NGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~l-dG~~l~Gr~IrVe~a~~   40 (268)
                      +|++||+|.+.++|++||..| +|.+|+| .|.|.++..
T Consensus        13 ~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A           13 KGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             CEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             cccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            689999999999999999999 9999999 999998764

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=95.63  E-value=0.011  Score=45.88  Aligned_cols=36  Identities=25%  Similarity=0.247  Sum_probs=32.8

Q ss_pred             CeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         4 GfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +-|+|+|.+..+|.+|.-.|||.+|+|+.|++....
T Consensus        63 ~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gTv~   98 (117)
T 2l9w_A           63 NGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGTIN   98 (117)
T ss_dssp             TEEEEECSCHHHHHHHHHHHSSEEETTEEEEEECHH
T ss_pred             CceEEEEccchhhHHHHhhcCCeeecCeEEEecCHH
Confidence            558999999999999999999999999999987653

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A

Probab=95.43  E-value=0.0069  Score=41.51  Aligned_cols=21  Identities=38%  Similarity=0.953  Sum_probs=18.5

Q ss_pred             CCccccCCCCCCCCCcccCCC
Q 024424           60 SGRCFNCGIDGHWARDCKAGD   80 (268)
Q Consensus        60 ~~rC~~CG~~GH~ardC~~~~   80 (268)
                      ...||+||+.|||+++|+...
T Consensus        30 ~~~C~~Cg~~GH~ar~C~~~~   50 (60)
T 1cl4_A           30 PGLCPRCKRGKHWANECKSKT   50 (60)
T ss_dssp             CCSCSSCSSCSSCSTTCCCTT
T ss_pred             CcceeECCCCCCccCcCCCcc
Confidence            468999999999999999763

>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A

Probab=95.36  E-value=0.0076  Score=35.39  Aligned_cols=20  Identities=35%  Similarity=1.051  Sum_probs=17.6

Q ss_pred             CCccccCCCCCccccccCCC
Q 024424           82 KNKCYRCGERGHIERNCQNS  101 (268)
Q Consensus        82 ~~~cyrcg~~GH~~r~c~~s  101 (268)
                      ...||.|++.||++++|+..
T Consensus         6 ~~~C~nCgk~GH~ar~C~~p   25 (29)
T 1nc8_A            6 VIRCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSS
T ss_pred             CCEEEECCccccCHhHCccc
Confidence            35799999999999999864

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=95.20  E-value=0.012  Score=36.83  Aligned_cols=19  Identities=32%  Similarity=0.810  Sum_probs=16.9

Q ss_pred             CCccccCCCCCCCCCcccC
Q 024424           60 SGRCFNCGIDGHWARDCKA   78 (268)
Q Consensus        60 ~~rC~~CG~~GH~ardC~~   78 (268)
                      ...||+||..||++++|+.
T Consensus        21 ~~~C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A           21 QEGCWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             CSSCTTTCCSSSCTTTSCC
T ss_pred             CCccccCCCCCCccCcCcC
Confidence            4689999999999999974

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=95.12  E-value=0.013  Score=40.73  Aligned_cols=31  Identities=16%  Similarity=0.300  Sum_probs=22.7

Q ss_pred             CCCccccCCCCCCCCCcccCCCCCCccccCCC
Q 024424           59 GSGRCFNCGIDGHWARDCKAGDWKNKCYRCGE   90 (268)
Q Consensus        59 ~~~rC~~CG~~GH~ardC~~~~~~~~cyrcg~   90 (268)
                      ....||+|++.||++++|+... ...++.++.
T Consensus        28 ~~~~C~~Cg~~GH~ar~Cp~~~-~~~~~~~g~   58 (63)
T 2cqf_A           28 QPKKCHFCQSISHMVASCPLKA-QQGPSAQGS   58 (63)
T ss_dssp             CSSCCTTTCCSSSCTTTCTGGG-CSCCCCSCC
T ss_pred             CCCccCCcCCcCCccCcCCCcc-ccCCccCCC
Confidence            3478999999999999999753 334444443

>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=95.00  E-value=0.009  Score=40.60  Aligned_cols=19  Identities=42%  Similarity=1.135  Sum_probs=17.4

Q ss_pred             CCccccCCCCCccccccCC
Q 024424           82 KNKCYRCGERGHIERNCQN  100 (268)
Q Consensus        82 ~~~cyrcg~~GH~~r~c~~  100 (268)
                      ...||+||+.||++++|+.
T Consensus         7 ~~~C~kCGk~GH~~k~Cp~   25 (55)
T 2ysa_A            7 GYTCFRCGKPGHYIKNCPT   25 (55)
T ss_dssp             SCCCTTTCCTTSCGGGCSG
T ss_pred             CCccccCCCcCcccccCCC
Confidence            5689999999999999984

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=94.85  E-value=0.011  Score=40.80  Aligned_cols=21  Identities=38%  Similarity=0.738  Sum_probs=18.4

Q ss_pred             CCccccCCCCCCCCCcccCCC
Q 024424           60 SGRCFNCGIDGHWARDCKAGD   80 (268)
Q Consensus        60 ~~rC~~CG~~GH~ardC~~~~   80 (268)
                      ...||+||+.|||+++|+...
T Consensus        30 ~~~C~~Cg~~GH~ar~C~~~~   50 (61)
T 2ihx_A           30 RERCQLCNGMGHNAKQCRKRD   50 (61)
T ss_dssp             CSBCTTTCCBSSCGGGCCCCC
T ss_pred             CCeeCCCCCCCCCcCCCcCCC
Confidence            467999999999999999753

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=94.84  E-value=0.0096  Score=36.81  Aligned_cols=18  Identities=33%  Similarity=1.114  Sum_probs=16.4

Q ss_pred             CccccCCCCCCCCCcccC
Q 024424           61 GRCFNCGIDGHWARDCKA   78 (268)
Q Consensus        61 ~rC~~CG~~GH~ardC~~   78 (268)
                      ..||+||+.||++++|+.
T Consensus        20 ~~C~~Cg~~GH~a~~C~~   37 (37)
T 2bl6_A           20 KVCFKCKQPGHFSKQCRS   37 (37)
T ss_dssp             TTCSSCCCTTGGGGTTCC
T ss_pred             CeEccCCCcCCccCcCcC
Confidence            689999999999999974

>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=94.60  E-value=0.012  Score=47.12  Aligned_cols=24  Identities=13%  Similarity=0.036  Sum_probs=21.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGR   26 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~   26 (268)
                      +|||||+|.+.++|++||..+++.
T Consensus        13 ~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A           13 KGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             EEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             cchhHHHHHHHHhHHHHHHhhccc
Confidence            699999999999999999887753

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1

Probab=94.35  E-value=0.016  Score=38.11  Aligned_cols=20  Identities=30%  Similarity=0.813  Sum_probs=17.7

Q ss_pred             CCccccCCCCCCCCCcccCC
Q 024424           60 SGRCFNCGIDGHWARDCKAG   79 (268)
Q Consensus        60 ~~rC~~CG~~GH~ardC~~~   79 (268)
                      ...||+||..||++.+|+..
T Consensus        27 ~~~C~~Cg~~GH~~~~C~~~   46 (49)
T 2ec7_A           27 RQGCWKCGKTGHVMAKCPER   46 (49)
T ss_dssp             CCSCSSSCCSSCCGGGCCSS
T ss_pred             CCeeCcCCCcCCccCCCcCC
Confidence            35799999999999999864

>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A

Probab=93.91  E-value=0.02  Score=38.46  Aligned_cols=20  Identities=35%  Similarity=0.996  Sum_probs=17.8

Q ss_pred             CCccccCCCCCCCCCcccCC
Q 024424           60 SGRCFNCGIDGHWARDCKAG   79 (268)
Q Consensus        60 ~~rC~~CG~~GH~ardC~~~   79 (268)
                      ...||+||..||++.+|+..
T Consensus        33 ~~~C~~Cg~~GH~~~~C~~~   52 (55)
T 1a1t_A           33 KKGCWKCGKEGHQMKDCTER   52 (55)
T ss_dssp             CCBCTTTCCBSSCGGGCSSS
T ss_pred             CCEeCCCCCcCCccCCCcCc
Confidence            46899999999999999865

>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=93.05  E-value=0.07  Score=40.83  Aligned_cols=35  Identities=31%  Similarity=0.487  Sum_probs=32.7

Q ss_pred             EEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            6 AFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         6 gFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      ..|.|.++++|..|-..||++.|+|..|+|.|+..
T Consensus        49 irv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~   83 (104)
T 1wey_A           49 VRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             EEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             EEEEeCChHHHHHHHHHhccceecCceeEEEecCC
Confidence            47999999999999999999999999999999873

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*

Probab=92.49  E-value=0.052  Score=44.02  Aligned_cols=21  Identities=19%  Similarity=0.449  Sum_probs=18.6

Q ss_pred             CCCccccCCCCCCCCCcccCC
Q 024424           59 GSGRCFNCGIDGHWARDCKAG   79 (268)
Q Consensus        59 ~~~rC~~CG~~GH~ardC~~~   79 (268)
                      ....||+||..||++++|+..
T Consensus       118 ~~~~C~~Cg~~GH~~r~Cp~~  138 (148)
T 3ts2_A          118 QPKKCHFCQSINHMVASCPLK  138 (148)
T ss_dssp             CCCCCTTTCCSSCCGGGCTTT
T ss_pred             CCCcccccCCcCCEeccCcCC
Confidence            356899999999999999965

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=83.53  E-value=0.85  Score=31.94  Aligned_cols=37  Identities=16%  Similarity=0.262  Sum_probs=27.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      ...|.||+..... |+.++..|.+..++|+.|.|+.+.
T Consensus        39 ~d~~s~v~v~~~~-~~~~~~~l~~~~i~g~~~~v~~~~   75 (76)
T 2g0c_A           39 MDNASYVEILNGK-GPHVLKVMKNTTVKGKQLKVNKAN   75 (76)
T ss_dssp             CSSCEEEEECTTC-HHHHHHHHTTCCC---CCCEEECC
T ss_pred             eCCcEEEEECHHH-HHHHHHHhccccCcCceEEEEECC
Confidence            3468899986654 888999999999999999998764

---

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	268
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	2e-09
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	0.002
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	8e-09
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-08
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-07
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-07
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-07
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	4e-07
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-06
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-06
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	6e-06
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	8e-06
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	9e-06
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	9e-06
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-05
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-05
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-05
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-05
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-05
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	4e-05
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	8e-05
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-04
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-04
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-04
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-04
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-04
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-04
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	3e-04
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	4e-04
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	5e-04
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	6e-04
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	6e-04
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	7e-04
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	7e-04
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	7e-04
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	7e-04
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	8e-04
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	8e-04
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	8e-04
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.001
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:) 0.001
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	0.001
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	0.001
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	0.002
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	0.002
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	0.002
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	0.002
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	0.003
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	0.004

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

 Score = 49.9 bits (119), Expect = 2e-09
 Identities = 18/37 (48%), Positives = 27/37 (72%), Gaps = 1/37 (2%)

Query: 62 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 98
          +CFNCG +GH AR+C+A   K  C++CG+ GH  ++C
Sbjct: 3  KCFNCGKEGHTARNCRAPRKK-GCWKCGKEGHQMKDC 38

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

 Score = 32.9 bits (75), Expect = 0.002
 Identities = 11/25 (44%), Positives = 15/25 (60%)

Query: 84  KCYRCGERGHIERNCQNSPKKLRPR 108
           KC+ CG+ GH  RNC+   KK   +
Sbjct: 3   KCFNCGKEGHTARNCRAPRKKGCWK 27

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.9 bits (119), Expect = 8e-09
 Identities = 13/40 (32%), Positives = 18/40 (45%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40
               A V F DP +AD    +L+GR   G +I  +   G
Sbjct: 55 HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDG 94

>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 = 47.7 bits (113), Expect = 3e-08
 Identities = 12/44 (27%), Positives = 22/44 (50%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRG 44
          + + +AF E+ D    D A   LNG  +   +++V+ A  G + 
Sbjct: 41 LSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKN 84

>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 = 46.5 bits (110), Expect = 1e-07
 Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 4/51 (7%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREY 51
              F FVE+    DA++A   +NG  +D   I  ++  G   G    R+Y
Sbjct: 47 TACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEG----RQY 93

>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 = 45.8 bits (108), Expect = 2e-07
 Identities = 13/43 (30%), Positives = 19/43 (44%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR 43
          +   F FVE+  P  A  A   L G  VDG ++ V  +    +
Sbjct: 41 LSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATK 83

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 44.9 bits (106), Expect = 4e-07
 Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 2/40 (5%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGS--RIIVEFA 38
            R  AFV ++   +A +A  +LN    +G    + V  A
Sbjct: 46 RPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 85

>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 = 44.5 bits (105), Expect = 4e-07
 Identities = 10/38 (26%), Positives = 14/38 (36%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
               A V F    DA  A    NG  +DG  + ++  
Sbjct: 39 RSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV 76

>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 = 43.4 bits (102), Expect = 1e-06
 Identities = 9/39 (23%), Positives = 20/39 (51%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
              +A+V F  P DA+ A  ++N   + G  + + +++
Sbjct: 40 RSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ 78

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 2e-06
 Identities = 11/39 (28%), Positives = 19/39 (48%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
            R  A+V + D  DA +A   L+G +V    ++V +  
Sbjct: 44 ETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN 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 = 41.5 bits (97), Expect = 6e-06
 Identities = 9/39 (23%), Positives = 17/39 (43%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
            + F F+       A+ A+  L+   + G ++ V FA 
Sbjct: 42 KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC 80

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 41.1 bits (96), Expect = 8e-06
 Identities = 15/41 (36%), Positives = 21/41 (51%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41
              +AFV+F+   D+  A   LNG  V   R+ V +AR G
Sbjct: 42 YSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPG 82

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.8 bits (95), Expect = 9e-06
 Identities = 19/44 (43%), Positives = 27/44 (61%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRG 44
            RD+AFV FS+  DA +A  +LNG+ +DGS I V  A+   + 
Sbjct: 42 KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKD 85

>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 = 41.2 bits (96), Expect = 9e-06
 Identities = 10/39 (25%), Positives = 18/39 (46%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
            R  AFV F +   A +A  S+ G       + +++A+
Sbjct: 44 KMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK 82

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.9 bits (95), Expect = 1e-05
 Identities = 14/39 (35%), Positives = 21/39 (53%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
              + FV + DP+DA+ A  +LNG  +    I V +AR
Sbjct: 42 QSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR 80

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.1 bits (96), Expect = 1e-05
 Identities = 9/39 (23%), Positives = 14/39 (35%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
                FVEF+   D   A   L GR      ++ ++  
Sbjct: 56 PGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCD 94

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.7 bits (95), Expect = 1e-05
 Identities = 12/35 (34%), Positives = 21/35 (60%), Gaps = 1/35 (2%)

Query: 5  FAFVEFSDPRDADDARYSL-NGRDVDGSRIIVEFA 38
          F FV+F   +DA  A  +L +   + G R+++E+A
Sbjct: 53 FGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWA 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 = 40.9 bits (95), Expect = 2e-05
 Identities = 15/61 (24%), Positives = 22/61 (36%)

Query: 1   MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGS 60
                  + FS+P  A DAR  L+  +  G  + + FA+    G             P S
Sbjct: 44  KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKSGPSS 103

Query: 61  G 61
           G
Sbjct: 104 G 104

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.9 bits (93), Expect = 3e-05
 Identities = 12/47 (25%), Positives = 22/47 (46%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGG 47
          + + FAFV++ + R+A  A    +GR + G  + +  A        G
Sbjct: 48 VHKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVNRSG 94

>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 = 39.3 bits (91), Expect = 3e-05
 Identities = 12/44 (27%), Positives = 23/44 (52%), Gaps = 2/44 (4%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRG 44
            + +A VE+   + A  A+ +LNG ++ G  I V++     +G
Sbjct: 47 FSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF--VKG 88

>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 = 39.3 bits (91), Expect = 4e-05
 Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 2/41 (4%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDV--DGSRIIVEFAR 39
            R FAFVE+   R A  AR  L    +   G +I V++A 
Sbjct: 43 KNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAE 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 = 38.5 bits (89), Expect = 8e-05
 Identities = 15/39 (38%), Positives = 20/39 (51%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
            R FAFVEF    DA  A  ++N  ++ G  I V  A+
Sbjct: 45 KHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK 83

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 38.5 bits (89), Expect = 1e-04
 Identities = 12/46 (26%), Positives = 22/46 (47%), Gaps = 2/46 (4%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA--RGGPRG 44
            +  A++EF    DA+       G ++DG  + + +   +GG RG
Sbjct: 51 KSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTRG 96

>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 = 37.6 bits (87), Expect = 1e-04
 Identities = 7/38 (18%), Positives = 14/38 (36%), Gaps = 1/38 (2%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
           +R F F+ F +              +V  S+  ++ A
Sbjct: 39 KRRGFCFITFKEEEPVKKI-MEKKYHNVGLSKCEIKVA 75

>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 = 37.3 bits (86), Expect = 2e-04
 Identities = 9/34 (26%), Positives = 14/34 (41%), Gaps = 1/34 (2%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
          F FV F D    D    + +  ++D   I  + A
Sbjct: 44 FGFVTFMDQAGVDKVL-AQSRHELDSKTIDPKVA 76

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.9 bits (85), Expect = 2e-04
 Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 2/40 (5%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGS--RIIVEFA 38
          + R   F+ F    +A++A   LNG+   G+   I V+FA
Sbjct: 46 VSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 85

>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 = 37.3 bits (86), Expect = 2e-04
 Identities = 14/39 (35%), Positives = 21/39 (53%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
              + FVEF + RDA  A  ++NGR + G  + V +A 
Sbjct: 46 SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT 84

>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 = 36.6 bits (84), Expect = 3e-04
 Identities = 11/43 (25%), Positives = 21/43 (48%), Gaps = 2/43 (4%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGG 47
          +AF+ F+    +D A  ++NG+ +    I V +A    +   G
Sbjct: 43 YAFINFASFDASDAAIEAMNGQYLCNRPITVSYAF--KKDSKG 83

>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 = 37.0 bits (85), Expect = 3e-04
 Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 2/53 (3%)

Query: 5   FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPP 57
           + F E+ D   A  A  +LNGR+  G  + V+ A           + LG G P
Sbjct: 52  YGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA--SEKNKEELKSLGTGAP 102

>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 = 35.9 bits (82), Expect = 4e-04
 Identities = 8/33 (24%), Positives = 12/33 (36%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRI 33
            + + FV+F  P  A  A  +L    V     
Sbjct: 38 KCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA 70

>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 = 35.9 bits (82), Expect = 5e-04
 Identities = 6/38 (15%), Positives = 14/38 (36%), Gaps = 1/38 (2%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
            R F FV F      +     ++  +++   +  + A
Sbjct: 39 RHRGFGFVTFESEDIVEKVC-EIHFHEINNKMVECKKA 75

>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 = 35.9 bits (82), Expect = 6e-04
 Identities = 9/47 (19%), Positives = 15/47 (31%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGG 47
            +  AFV   +   A +A    +     G  +IV+          G
Sbjct: 38 RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDALLCSG 84

>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 = 35.8 bits (82), Expect = 6e-04
 Identities = 12/39 (30%), Positives = 17/39 (43%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
            + + FVEF    DAD A   ++   + G  I V  A 
Sbjct: 49 QHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS 87

>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 = 36.8 bits (84), Expect = 7e-04
 Identities = 15/49 (30%), Positives = 22/49 (44%)

Query: 1   MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSR 49
             R + FV+F     A  A   LNG ++   R+ V  A  G + PG + 
Sbjct: 82  QSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAG 130

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.9 bits (82), Expect = 7e-04
 Identities = 17/39 (43%), Positives = 23/39 (58%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
            R F FV F +  DA DA  ++NG+ VDG +I V+ A 
Sbjct: 45 RSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG 83

>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 = 35.7 bits (82), Expect = 7e-04
 Identities = 11/42 (26%), Positives = 21/42 (50%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP 42
           ++ ++FV FS    A  A  S+NG  ++G  +   + +  P
Sbjct: 52 PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP 93

>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 = 35.8 bits (82), Expect = 7e-04
 Identities = 16/43 (37%), Positives = 21/43 (48%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR 43
            + F FV F +  DAD AR  L+G  V+G +I V  A     
Sbjct: 49 GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVM 91

>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 = 35.9 bits (82), Expect = 8e-04
 Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 12/72 (16%)

Query: 1   MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG--------GPRGPGGSREY- 51
            K++ A V+ +D   A  A   LNG  + G  I +  ++         G    G +++Y 
Sbjct: 38  NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYG 97

Query: 52  ---LGRGPPPGS 60
              L R   PGS
Sbjct: 98  NSPLHRFKKPGS 109

>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 = 35.5 bits (81), Expect = 8e-04
 Identities = 10/41 (24%), Positives = 15/41 (36%), Gaps = 1/41 (2%)

Query: 2  KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP 42
              AF+ F +   A+ A   +N   +    I V  A   P
Sbjct: 47 NNCCAFMVFENKDSAERA-LQMNRSLLGNREISVSLADKKP 86

>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 = 35.8 bits (82), Expect = 8e-04
 Identities = 27/46 (58%), Positives = 30/46 (65%), Gaps = 1/46 (2%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPG 46
              FAFVEF DPRDA+DA Y  +G D DG R+ VEF R G RG G
Sbjct: 51 GGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG-RGTG 95

>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 = 35.0 bits (80), Expect = 0.001
 Identities = 9/38 (23%), Positives = 13/38 (34%), Gaps = 1/38 (2%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
            R F FV F +    D          ++G  I  + A
Sbjct: 39 RSRGFGFVLFKESESVDKVM-DQKEHKLNGKVIDPKRA 75

>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 = 35.4 bits (81), Expect = 0.001
 Identities = 11/35 (31%), Positives = 15/35 (42%)

Query: 3   RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEF 37
               +V+F    DA+ A   LN R  +G  I  E 
Sbjct: 68  VGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

>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 = 34.8 bits (79), Expect = 0.001
 Identities = 9/39 (23%), Positives = 19/39 (48%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
            R FA+++ +   DA      LNG  ++G  ++ + + 
Sbjct: 41 TSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN 79

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.6 bits (79), Expect = 0.001
 Identities = 12/39 (30%), Positives = 19/39 (48%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
            + FAF+ F    DA  A   ++G   D   + VE+A+
Sbjct: 48 QSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAK 86

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.1 bits (80), Expect = 0.002
 Identities = 8/41 (19%), Positives = 19/41 (46%), Gaps = 3/41 (7%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDV---DGSRIIVEFA 38
            + ++F  +    ++  A  +LNG++V    G +I +   
Sbjct: 54 PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLN 94

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.2 bits (78), Expect = 0.002
 Identities = 15/42 (35%), Positives = 20/42 (47%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP 42
            R+ AFV +     AD A   LNG  V+  ++ V  AR  P
Sbjct: 37 PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP 78

>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 = 34.7 bits (79), Expect = 0.002
 Identities = 12/35 (34%), Positives = 18/35 (51%)

Query: 5  FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39
          F FV + +P  A  A  S+NG  +   R+ V+  R
Sbjct: 62 FGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR 96

>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 = 33.9 bits (77), Expect = 0.002
 Identities = 14/38 (36%), Positives = 16/38 (42%), Gaps = 1/38 (2%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
           KR FAFV F D  D+ D         V+G    V  A
Sbjct: 42 KKRGFAFVTFDDH-DSVDKIVIQKYHTVNGHNCEVRKA 78

>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 = 33.9 bits (77), Expect = 0.003
 Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 1/38 (2%)

Query: 1  MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
            R F FV ++   + D A  +     VDG  +  + A
Sbjct: 46 RSRGFGFVTYATVEEVDAA-MNARPHKVDGRVVEPKRA 82

>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 = 33.8 bits (77), Expect = 0.004
 Identities = 14/65 (21%), Positives = 30/65 (46%), Gaps = 6/65 (9%)

Query: 1   MKRDFAFVEFSDPRDADDARYSLNGRDV--DGSRIIVEFAR----GGPRGPGGSREYLGR 54
             +  A ++++DP  A  A+ SL+G+++      + ++F++            SR+Y   
Sbjct: 43  NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRP 102

Query: 55  GPPPG 59
             P G
Sbjct: 103 DLPSG 107

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	268
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	98.9
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	98.79
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	98.64
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	98.61
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	98.6
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.6
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.59
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	98.59
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	98.58
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	98.58
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	98.58
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	98.57
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	98.57
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	98.57
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	98.57
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	98.56
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	98.56
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	98.56
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	98.55
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	98.55
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.55
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.54
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.54
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.53
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	98.53
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	98.53
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	98.52
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	98.52
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.52
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	98.51
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	98.5
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	98.49
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	98.48
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.47
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.46
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	98.46
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	98.45
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	98.45
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	98.44
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	98.44
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.43
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.43
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	98.42
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	98.42
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	98.41
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	98.4
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	98.4
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	98.4
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	98.38
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	98.37
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	98.32
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	98.32
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	98.31
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	98.31
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	98.3
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	98.27
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	98.27
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	98.26
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	98.25
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	98.23
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	98.19
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	98.17
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	98.17
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.14
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	98.13
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.11
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	98.1
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	98.1
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.09
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.08
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	98.07
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	98.07
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.06
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.05
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.01
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	97.98
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	97.98
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	97.93
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	97.91
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	97.9
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	97.9
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	97.88
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	97.87
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	97.79
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	97.67
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	97.58
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	97.24
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	96.79
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	96.58
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	96.03
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	95.49
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	94.2
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	92.73
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	91.6
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	88.89
d1cl4a_	32	Nucleocapsid protein from mason-pfizer monkey viru	85.79
d1dsva_	31	Nucleic acid binding protein p14 {Mouse mammary tu	85.48
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	84.02

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

Probab=98.90  E-value=5.1e-10  Score=71.31  Aligned_cols=39  Identities=46%  Similarity=1.199  Sum_probs=35.5

Q ss_pred             CccccCCCCCCCCCcccCCCCCCccccCCCCCccccccCC
Q 024424           61 GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQN  100 (268)
Q Consensus        61 ~rC~~CG~~GH~ardC~~~~~~~~cyrcg~~GH~~r~c~~  100 (268)
                      ++||+||..||++.+|+.+. ...||.|++.||++++|+.
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~~-~~~C~~Cg~~GH~~~~Cp~   40 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAPR-KKGCWKCGKEGHQMKDCTE   40 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSCC-CSSCSSSCCSSSCTTTCCS
T ss_pred             CccccCCCcCcCcccCcCCC-cCccccCCCCCeecccCCC
Confidence            58999999999999999874 3579999999999999986

>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=98.79  E-value=2.4e-09  Score=79.96  Aligned_cols=41  Identities=27%  Similarity=0.483  Sum_probs=38.0

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            1 MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         1 lkrGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      |.+|||||+|++.++|+.||+.|||.+|+|+.|.|+++...
T Consensus        48 i~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   88 (98)
T d1wf2a_          48 VHKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEP   88 (98)
T ss_dssp             EETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSC
T ss_pred             EeCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            35899999999999999999999999999999999999753

>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=98.64  E-value=1.5e-08  Score=72.40  Aligned_cols=38  Identities=37%  Similarity=0.564  Sum_probs=36.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      +|||||+|.+.++|+.||+.|||..|.|+.|.|++++.
T Consensus        44 ~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1          44 YGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            68999999999999999999999999999999999963

>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=98.61  E-value=2.3e-08  Score=71.34  Aligned_cols=40  Identities=35%  Similarity=0.517  Sum_probs=37.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||..|||.+|+|..|+|+|++..
T Consensus        38 ~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1          38 PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             TTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            4699999999999999999999999999999999999743

>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=98.60  E-value=2.7e-08  Score=71.28  Aligned_cols=39  Identities=26%  Similarity=0.414  Sum_probs=36.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||+.|+|..|+|+.|.|.++...
T Consensus        41 ~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1          41 KGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK   79 (83)
T ss_dssp             CSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCC
T ss_pred             CceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCC
Confidence            699999999999999999999999999999999999754

>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=98.60  E-value=1.7e-08  Score=72.66  Aligned_cols=38  Identities=34%  Similarity=0.624  Sum_probs=36.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      +|||||+|.+.++|+.||..|||..|+|+.|.|+++..
T Consensus        43 kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1          43 MGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            68999999999999999999999999999999999864

>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=98.59  E-value=2.6e-08  Score=73.43  Aligned_cols=40  Identities=60%  Similarity=0.973  Sum_probs=37.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|++.++|+.||..|||.+|+|+.|.|+|++..
T Consensus        52 ~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~~   91 (95)
T d1x4aa1          52 GPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG   91 (95)
T ss_dssp             SSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccCC
Confidence            3689999999999999999999999999999999999753

>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=98.59  E-value=1.7e-08  Score=73.47  Aligned_cols=38  Identities=29%  Similarity=0.507  Sum_probs=36.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      +|||||+|.+.++|+.||..|||..|+|+.|.|+|+..
T Consensus        49 ~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~~   86 (88)
T d1rk8a_          49 KGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV   86 (88)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEE
T ss_pred             ccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEecC
Confidence            68999999999999999999999999999999999974

>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=98.58  E-value=3.1e-08  Score=72.75  Aligned_cols=40  Identities=40%  Similarity=0.617  Sum_probs=37.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||..|+|.+|+|+.|.|++|+.+
T Consensus        50 ~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~r   89 (93)
T d2cq3a1          50 SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR   89 (93)
T ss_dssp             TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSS
T ss_pred             CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCcC
Confidence            3689999999999999999999999999999999999854

>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=98.58  E-value=2e-08  Score=73.28  Aligned_cols=38  Identities=32%  Similarity=0.450  Sum_probs=36.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      +|||||+|.+.++|+.||+.|+|..|.|+.|.|++++.
T Consensus        50 rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~akp   87 (90)
T d2cq0a1          50 KGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKP   87 (90)
T ss_dssp             EEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSC
T ss_pred             ccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeeeC
Confidence            68999999999999999999999999999999999974

>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=98.58  E-value=1.5e-08  Score=73.93  Aligned_cols=40  Identities=20%  Similarity=0.308  Sum_probs=37.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||..|||++|+|+.|.|+++...
T Consensus        39 ~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~   78 (88)
T d1wg1a_          39 NKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             GGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             cCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            4799999999999999999999999999999999999643

>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=98.57  E-value=2.9e-08  Score=70.60  Aligned_cols=38  Identities=26%  Similarity=0.280  Sum_probs=35.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+|||||+|.+.++|+.||..|||..|+|+.|.|+++.
T Consensus        40 ~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_          40 SLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             SCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             cceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            36899999999999999999999999999999999985

>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=98.57  E-value=3.2e-08  Score=72.79  Aligned_cols=41  Identities=29%  Similarity=0.323  Sum_probs=37.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|+.||..|+|+.|.|+.|+|.+|....
T Consensus        50 ~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~~~   90 (93)
T d1x5ua1          50 HQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHN   90 (93)
T ss_dssp             BCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTS
T ss_pred             cccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCC
Confidence            46899999999999999999999999999999999997543

>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=98.57  E-value=4.5e-08  Score=76.86  Aligned_cols=40  Identities=33%  Similarity=0.520  Sum_probs=37.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||+.|||.+|+|+.|.|+++....
T Consensus        84 rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~~~  123 (139)
T d1u6fa1          84 RGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGH  123 (139)
T ss_dssp             EEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCC
T ss_pred             cceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            6899999999999999999999999999999999997543

>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=98.57  E-value=2.9e-08  Score=72.97  Aligned_cols=40  Identities=30%  Similarity=0.460  Sum_probs=37.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|||..|+|+.|.|+|+.+..
T Consensus        49 kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~~~~   88 (93)
T d1h2vz_          49 CGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK   88 (93)
T ss_dssp             EEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCC
T ss_pred             cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            5899999999999999999999999999999999997543

>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=98.56  E-value=3e-08  Score=73.43  Aligned_cols=40  Identities=35%  Similarity=0.545  Sum_probs=37.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|||.+|+|+.|.|.+++..+
T Consensus        58 ~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~a~~~~   97 (101)
T d2cpea1          58 KGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP   97 (101)
T ss_dssp             CSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCC
T ss_pred             cceeeEEecCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            5899999999999999999999999999999999998643

>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=98.56  E-value=3.5e-08  Score=69.79  Aligned_cols=39  Identities=15%  Similarity=0.227  Sum_probs=37.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      .+|||||+|.+.++|+.||+.|||.+|.|+.|.|+++..
T Consensus        32 ~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~   70 (75)
T d1wi6a1          32 YKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPT   70 (75)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCS
T ss_pred             cceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCC
Confidence            579999999999999999999999999999999999964

>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=98.56  E-value=1.3e-08  Score=74.22  Aligned_cols=39  Identities=21%  Similarity=0.394  Sum_probs=36.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|++.++|+.||+.|||..|+|+.|.|++++..
T Consensus        48 kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2          48 KGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             CSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             cceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            699999999999999999999999999999999999753

>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=98.55  E-value=2.6e-08  Score=71.05  Aligned_cols=37  Identities=38%  Similarity=0.672  Sum_probs=35.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|+.||..|+|..|.|+.|.|++++
T Consensus        44 ~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~Ak   80 (82)
T d1fxla1          44 LGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (82)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             eeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            5899999999999999999999999999999999986

>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=98.55  E-value=3.4e-08  Score=73.13  Aligned_cols=39  Identities=26%  Similarity=0.508  Sum_probs=37.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|.+|.|+.|+|.|++..
T Consensus        54 kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~   92 (96)
T d1x4ga1          54 KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            799999999999999999999999999999999998754

>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=98.55  E-value=6e-08  Score=71.86  Aligned_cols=41  Identities=27%  Similarity=0.302  Sum_probs=37.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|+.||..|||..|+|+.|.|.++....
T Consensus        49 ~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~~~   89 (99)
T d1whwa_          49 PKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKK   89 (99)
T ss_dssp             CCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCS
T ss_pred             cCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            36899999999999999999999999999999999998643

>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=98.54  E-value=4.1e-08  Score=72.28  Aligned_cols=40  Identities=33%  Similarity=0.597  Sum_probs=37.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhh-CCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSL-NGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~l-dG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||..| +|..|+|+.|.|+|+...
T Consensus        50 ~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~A~~~   90 (94)
T d2cpha1          50 HRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSE   90 (94)
T ss_dssp             SCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCC
T ss_pred             cccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEEcCCC
Confidence            3699999999999999999998 899999999999999753

>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=98.54  E-value=3.2e-08  Score=73.05  Aligned_cols=40  Identities=20%  Similarity=0.440  Sum_probs=37.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      +|||||+|.+.++|+.||..|+|..|+|+.|.|+|+....
T Consensus        53 ~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~   92 (96)
T d1fjca_          53 KGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG   92 (96)
T ss_dssp             EEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSC
T ss_pred             ccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            6899999999999999999999999999999999998543

>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=98.53  E-value=3.9e-08  Score=70.14  Aligned_cols=38  Identities=24%  Similarity=0.511  Sum_probs=35.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+|||||+|.+.++|+.||..|||..|+|+.|.|.++.
T Consensus        42 ~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~   79 (81)
T d2ghpa1          42 SRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN   79 (81)
T ss_dssp             -CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcc
Confidence            46999999999999999999999999999999999986

>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=98.53  E-value=4.4e-08  Score=70.68  Aligned_cols=41  Identities=46%  Similarity=0.633  Sum_probs=37.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|..||..|+|..|.|+.|.|.|++...
T Consensus        43 ~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1          43 IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCC
Confidence            47999999999999999999999999999999999997543

>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=98.53  E-value=4.1e-08  Score=71.39  Aligned_cols=40  Identities=43%  Similarity=0.678  Sum_probs=37.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||..|+|..|.|+.|.|+++...
T Consensus        46 ~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~~   85 (90)
T d1x5sa1          46 SRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKS   85 (90)
T ss_dssp             CCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECC
T ss_pred             ccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCC
Confidence            4789999999999999999999999999999999999754

>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=98.52  E-value=3.3e-08  Score=73.92  Aligned_cols=39  Identities=31%  Similarity=0.529  Sum_probs=36.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|||.+|.|+.|.|+++...
T Consensus        60 kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~~k   98 (102)
T d2cpza1          60 KCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSK   98 (102)
T ss_dssp             EEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCS
T ss_pred             ccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeCCC
Confidence            589999999999999999999999999999999999754

>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=98.52  E-value=4e-08  Score=73.71  Aligned_cols=39  Identities=28%  Similarity=0.449  Sum_probs=36.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      ++|||||+|++.++|+.||+.|+|..|+|+.|.|++++.
T Consensus        39 ~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~   77 (109)
T d2adca1          39 KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH   77 (109)
T ss_dssp             TSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            479999999999999999999999999999999999864

>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=98.52  E-value=2.8e-08  Score=72.11  Aligned_cols=40  Identities=18%  Similarity=0.160  Sum_probs=36.6

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            1 MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         1 lkrGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      +++|||||+|.+.++|+.||..|||.+|.|+.|.|.++..
T Consensus        33 ~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~   72 (87)
T d3begb1          33 YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   72 (87)
T ss_dssp             CTTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             cccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEec
Confidence            3579999999999999999999999999999999988753

>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=98.51  E-value=2.7e-08  Score=71.01  Aligned_cols=37  Identities=24%  Similarity=0.486  Sum_probs=35.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.++++|+.||+.|+|..|.|+.|+|.+++
T Consensus        42 ~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1          42 LGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             CCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            5899999999999999999999999999999999985

>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=98.50  E-value=5.3e-08  Score=69.54  Aligned_cols=40  Identities=28%  Similarity=0.490  Sum_probs=36.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCC-eecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGR-DVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~-~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||+.|+|. +|+|+.|.|+++...
T Consensus        36 ~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k   76 (80)
T d2cqha1          36 KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   76 (80)
T ss_dssp             ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCc
Confidence            4799999999999999999999996 699999999999753

>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=98.49  E-value=5.6e-08  Score=73.63  Aligned_cols=38  Identities=29%  Similarity=0.371  Sum_probs=36.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      +|||||+|.+.++|..||+.|+|..|.|+.|.|+++..
T Consensus        46 kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1          46 RGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             CCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            69999999999999999999999999999999999853

>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=98.48  E-value=5.2e-08  Score=70.87  Aligned_cols=39  Identities=38%  Similarity=0.518  Sum_probs=36.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      .+|||||+|.+.++|+.||..|||..|+|+.|.|+++..
T Consensus        46 ~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p   84 (89)
T d2cqba1          46 HRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKP   84 (89)
T ss_dssp             CSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             ccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            479999999999999999999999999999999999974

>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=98.47  E-value=4.8e-08  Score=70.69  Aligned_cols=39  Identities=23%  Similarity=0.259  Sum_probs=35.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||. |||.+|.|+.|.|.++...
T Consensus        47 ~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a~~k   85 (86)
T d2ghpa3          47 NNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLADKK   85 (86)
T ss_dssp             CCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEECCCC
T ss_pred             cceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEcCCC
Confidence            36899999999999999995 9999999999999999754

>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=98.46  E-value=7.7e-08  Score=69.47  Aligned_cols=41  Identities=29%  Similarity=0.494  Sum_probs=37.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|+.||..|+|.+|.|+.|.|+++....
T Consensus        42 ~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~~   82 (85)
T d2u2fa_          42 SKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA   82 (85)
T ss_dssp             CCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCCC
T ss_pred             cceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            36999999999999999999999999999999999997543

>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=98.46  E-value=8.1e-08  Score=71.20  Aligned_cols=40  Identities=28%  Similarity=0.410  Sum_probs=37.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||..|||..|.|+.|.|+|++..
T Consensus        59 ~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak~k   98 (102)
T d2cpxa1          59 MRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNK   98 (102)
T ss_dssp             SCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCC
T ss_pred             ccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCCCc
Confidence            3689999999999999999999999999999999999754

>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=98.45  E-value=6.9e-08  Score=71.73  Aligned_cols=40  Identities=18%  Similarity=0.171  Sum_probs=37.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      ++|||||+|.+.++|+.||+.|||.+|+|+.|.|.+++..
T Consensus        49 ~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~   88 (98)
T d1wg4a_          49 KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVY   88 (98)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEE
T ss_pred             ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecC
Confidence            5799999999999999999999999999999999998754

>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=98.45  E-value=1e-07  Score=69.43  Aligned_cols=40  Identities=35%  Similarity=0.579  Sum_probs=37.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||..|+|..|.|+.|+|.|+...
T Consensus        47 ~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~   86 (90)
T d2cqia1          47 NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTP   86 (90)
T ss_dssp             SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCT
T ss_pred             cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCC
Confidence            4689999999999999999999999999999999999743

>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=98.44  E-value=1.6e-07  Score=70.58  Aligned_cols=40  Identities=28%  Similarity=0.331  Sum_probs=37.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      ++||||+|.+.++|+.||..|+|+.|+|+.|.|+|++...
T Consensus        46 ~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~   85 (104)
T d1weya_          46 FKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLH   85 (104)
T ss_dssp             TTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCSS
T ss_pred             CCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecccCC
Confidence            5899999999999999999999999999999999997543

>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=98.44  E-value=7.7e-08  Score=69.69  Aligned_cols=38  Identities=24%  Similarity=0.416  Sum_probs=36.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      +|||||+|++.++|+.||..|+|..|+|+.|.|++|..
T Consensus        44 k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~   81 (86)
T d2cpja1          44 KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   81 (86)
T ss_dssp             TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            68999999999999999999999999999999999974

>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=98.43  E-value=8.9e-08  Score=71.90  Aligned_cols=40  Identities=28%  Similarity=0.249  Sum_probs=37.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||..|||..|.|+.|.|+|+...
T Consensus        45 ~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_          45 GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            3689999999999999999999999999999999998643

>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=98.43  E-value=7.5e-08  Score=70.54  Aligned_cols=38  Identities=34%  Similarity=0.589  Sum_probs=35.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      .+|||||+|.+.++|+.||+ |+|.+|.|+.|.|++++.
T Consensus        53 ~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak~   90 (91)
T d1fjeb1          53 NRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKG   90 (91)
T ss_dssp             TTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCC
T ss_pred             ccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecCC
Confidence            36999999999999999995 999999999999999874

>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=98.42  E-value=1.2e-07  Score=69.18  Aligned_cols=39  Identities=26%  Similarity=0.366  Sum_probs=36.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|++.++|..||..|+|.+|+|+.|.|.|++..
T Consensus        46 ~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak~~   84 (91)
T d1nu4a_          46 RGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTD   84 (91)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSC
T ss_pred             CCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeCCC
Confidence            699999999999999999999999999999999999753

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.42  E-value=1.3e-07  Score=70.40  Aligned_cols=41  Identities=32%  Similarity=0.423  Sum_probs=37.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|++.++|..||..|||..|+|+.|.|+++.+..
T Consensus        56 ~~G~~fV~f~~~e~A~~A~~~lng~~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          56 PDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTT   96 (99)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCC
T ss_pred             CccEEEEEECCHHHHHHHHHHhCCcEECCEEEEEEEeCCcC
Confidence            36999999999999999999999999999999999987643

>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=98.41  E-value=9.7e-08  Score=68.73  Aligned_cols=37  Identities=22%  Similarity=0.323  Sum_probs=34.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEec
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA   38 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a   38 (268)
                      .+|||||+|.+.++|+.||.+|||..|.|+.|.|.++
T Consensus        50 ~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1          50 PTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             EEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             cceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3689999999999999999999999999999999875

>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=98.40  E-value=1.4e-07  Score=68.23  Aligned_cols=38  Identities=21%  Similarity=0.454  Sum_probs=35.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCee-cCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDV-DGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l-~Gr~IrVe~a~~   40 (268)
                      +|||||+|++.++|+.||..|+|..| +|+.|+|.|++.
T Consensus        48 ~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2          48 RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             cceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCC
Confidence            68999999999999999999999988 689999999874

>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=98.40  E-value=1.4e-07  Score=67.65  Aligned_cols=38  Identities=29%  Similarity=0.561  Sum_probs=34.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeec-CcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVD-GSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~-Gr~IrVe~a~   39 (268)
                      ++|||||+|.+.++|+.||..|+|..|. |..|.|.|++
T Consensus        44 ~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1          44 RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            4689999999999999999999999984 6899999986

>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=98.40  E-value=1e-07  Score=71.16  Aligned_cols=39  Identities=31%  Similarity=0.521  Sum_probs=36.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..|+|..|.|+.|.|+++...
T Consensus        50 ~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~~   88 (104)
T d1p1ta_          50 KGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             EEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCT
T ss_pred             CCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            589999999999999999999999999999999998643

>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=98.38  E-value=9.5e-08  Score=71.88  Aligned_cols=37  Identities=30%  Similarity=0.399  Sum_probs=35.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEec
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA   38 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a   38 (268)
                      .+|||||+|.+.++|+.||..|||.+|+|+.|.|++.
T Consensus        67 ~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          67 LVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             SEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             EeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            3699999999999999999999999999999999985

>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=98.37  E-value=1.3e-07  Score=67.98  Aligned_cols=36  Identities=31%  Similarity=0.468  Sum_probs=33.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecC--cceEEEec
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDG--SRIIVEFA   38 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~G--r~IrVe~a   38 (268)
                      +|||||+|.+.++|+.||+.|||..|.|  +.|.|.||
T Consensus        48 ~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2          48 RGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             ceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            5899999999999999999999999987  77999986

>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=98.32  E-value=1.8e-07  Score=68.03  Aligned_cols=33  Identities=27%  Similarity=0.291  Sum_probs=31.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEE
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIV   35 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrV   35 (268)
                      .|||||+|++.++|+.||+.|||..|+|+.|+|
T Consensus        56 ~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lkv   88 (89)
T d2cpia1          56 SASAYVTYIRSEDALRAIQCVNNVVVDGRTLKA   88 (89)
T ss_dssp             CEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             ceEEEEecccchhHHHHHHHhCCCEECCEEEEE
Confidence            489999999999999999999999999999987

>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=98.32  E-value=2.1e-07  Score=66.97  Aligned_cols=36  Identities=36%  Similarity=0.637  Sum_probs=33.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCc--ceEEEec
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGS--RIIVEFA   38 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr--~IrVe~a   38 (268)
                      +|||||+|.+.++|+.||..|||..|.|.  .|.|.||
T Consensus        48 kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2          48 RGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            58999999999999999999999999985  5888886

>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=98.31  E-value=1.6e-07  Score=67.11  Aligned_cols=33  Identities=48%  Similarity=0.753  Sum_probs=31.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEE
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIV   35 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrV   35 (268)
                      +|||||+|.+.++|+.||..|||.+|+|+.|+|
T Consensus        51 ~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1          51 RGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             ccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            589999999999999999999999999999987

>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=98.31  E-value=2e-07  Score=69.43  Aligned_cols=40  Identities=18%  Similarity=0.055  Sum_probs=36.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|+.||+ ||+.+|.|+.|.|.++....
T Consensus        54 ~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~~~~   93 (102)
T d1weza_          54 VTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAG   93 (102)
T ss_dssp             EEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECCCC
T ss_pred             ceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcCCCC
Confidence            36899999999999999985 89999999999999987543

>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=98.30  E-value=3.4e-07  Score=63.86  Aligned_cols=36  Identities=17%  Similarity=0.295  Sum_probs=33.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEec
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA   38 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a   38 (268)
                      .+|||||+|.+.++|+.||+ |+|..|+|+.|.|.+|
T Consensus        40 ~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_          40 HRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             SCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             cCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            46899999999999999995 9999999999999875

>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=98.27  E-value=5.4e-07  Score=66.37  Aligned_cols=40  Identities=30%  Similarity=0.635  Sum_probs=36.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCc--ceEEEeccCCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGS--RIIVEFARGGP   42 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr--~IrVe~a~~~~   42 (268)
                      ++||||+|.+.++|+.||+.|+|.+|.|.  .|+|+|++..+
T Consensus        53 ~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~~   94 (97)
T d1whya_          53 DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCCC
Confidence            68999999999999999999999999874  79999998544

>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=98.27  E-value=4.9e-07  Score=66.18  Aligned_cols=41  Identities=22%  Similarity=0.369  Sum_probs=36.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhC------CCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLN------GRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ld------G~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|+.||..|+      |..|+|+.|.|+++..+.
T Consensus        49 ~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~v~~a~~k~   95 (98)
T d1x4ha1          49 SKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRD   95 (98)
T ss_dssp             BCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCC
T ss_pred             ccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEEEEEECCCCC
Confidence            47999999999999999999886      678999999999997543

>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=98.26  E-value=2.5e-07  Score=69.02  Aligned_cols=37  Identities=30%  Similarity=0.466  Sum_probs=34.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+|||||+|.+.++|+.|| .|||..|.|+.|.|.++.
T Consensus        59 ~kG~afV~F~~~e~a~~A~-~l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          59 SKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             CCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHH
T ss_pred             ccceEEEEECCHHHHHHHH-HHCCCEECCEEEEEEECC
Confidence            4789999999999999999 599999999999999875

>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=98.25  E-value=6e-07  Score=66.70  Aligned_cols=40  Identities=30%  Similarity=0.407  Sum_probs=34.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP   42 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~~   42 (268)
                      .+|||||+|.+.++|+.|+ .|+|.+|+|+.|+|.++....
T Consensus        56 ~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a~~~~   95 (104)
T d1wi8a_          56 LKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQ   95 (104)
T ss_dssp             BCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCCCC
T ss_pred             cceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEECCCCC
Confidence            3689999999999997665 799999999999999987543

>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=98.23  E-value=8.4e-07  Score=66.06  Aligned_cols=39  Identities=31%  Similarity=0.414  Sum_probs=35.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||+.|++ .|+|+.|.|.++...
T Consensus        51 ~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~~~   89 (103)
T d2cqda1          51 SRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLG   89 (103)
T ss_dssp             CCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTT
T ss_pred             cCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcCCC
Confidence            379999999999999999999876 799999999998754

>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=98.19  E-value=2.5e-07  Score=68.72  Aligned_cols=37  Identities=11%  Similarity=0.182  Sum_probs=34.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|+.||+.|||.+|.|+.|.|.++.
T Consensus        59 ~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~   95 (101)
T d1x5oa1          59 RGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE   95 (101)
T ss_dssp             EEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             ccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCC
Confidence            5899999999999999999999999999998887664

>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=98.17  E-value=7.4e-07  Score=62.57  Aligned_cols=36  Identities=25%  Similarity=0.363  Sum_probs=32.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEec
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA   38 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a   38 (268)
                      .+|||||+|.+.++|+.||. +++..|+|+.|.|..|
T Consensus        40 ~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_          40 SRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             cCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            36999999999999999996 8999999999998643

>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=98.17  E-value=5.3e-07  Score=63.82  Aligned_cols=36  Identities=28%  Similarity=0.407  Sum_probs=33.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEec
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA   38 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a   38 (268)
                      .+|||||+|.+.++|+.||. |++..|+|+.|.|..|
T Consensus        41 ~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_          41 SRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             ccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            47999999999999999996 7999999999999876

>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=98.14  E-value=8.3e-07  Score=62.54  Aligned_cols=36  Identities=36%  Similarity=0.435  Sum_probs=32.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEec
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA   38 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a   38 (268)
                      .+|||||+|.+.++|+.|| +|+|.+|+|+.|.|..|
T Consensus        43 ~~g~afV~f~~~e~~~~al-~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2          43 KRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             EEEEEEEEESSHHHHHHHH-HCSCCEETTEECEEEEC
T ss_pred             cccEEEEEEcCHHHHHHHH-HhCCCEECCEEEEEEEC
Confidence            3689999999998888887 69999999999999876

>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=98.13  E-value=1.2e-06  Score=64.26  Aligned_cols=40  Identities=38%  Similarity=0.493  Sum_probs=34.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCC--CeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNG--RDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG--~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.||+.|++  ..+.|+.|.|.||...
T Consensus        44 ~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~A~p~   85 (96)
T d2disa1          44 NRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPE   85 (96)
T ss_dssp             TCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSS
T ss_pred             CCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEEcCCC
Confidence            368999999999999999999964  5667999999999753

>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=98.11  E-value=7.3e-07  Score=66.19  Aligned_cols=37  Identities=22%  Similarity=0.374  Sum_probs=34.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+|||||+|.+.++|+.||. |+|..|+|+.|.|.++.
T Consensus        49 ~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1          49 GLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             cCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            47999999999999999995 99999999999999875

>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=98.10  E-value=1.4e-06  Score=65.15  Aligned_cols=39  Identities=28%  Similarity=0.392  Sum_probs=35.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|+.|| +|+|..|+|+.|.|.+|...
T Consensus        61 ~kg~aFV~f~~~~~a~~al-~~~~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          61 SRGFGFVTFSSMAEVDAAM-AARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             CCSEEEEECSSHHHHHHHH-TSCSEEETTEEEEEECCSSC
T ss_pred             ccCeEEEEECCHHHHHHHH-HhCCCeECCEEEEEEECccc
Confidence            4699999999999999998 58999999999999998754

>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=98.10  E-value=9.1e-07  Score=66.31  Aligned_cols=38  Identities=24%  Similarity=0.528  Sum_probs=34.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCee--cCcceEEEeccC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDV--DGSRIIVEFARG   40 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l--~Gr~IrVe~a~~   40 (268)
                      +|||||+|.+.++|+.||+.|+|..|  .+..|.|.+++.
T Consensus        45 ~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~   84 (108)
T d2adba1          45 QFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL   84 (108)
T ss_dssp             EEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSS
T ss_pred             CCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCC
Confidence            68999999999999999999999998  467888888864

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.09  E-value=1.5e-06  Score=64.92  Aligned_cols=37  Identities=24%  Similarity=0.405  Sum_probs=35.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .|++||+|.+.++|.+|+..|+|..|+|+.|.|.++.
T Consensus        58 ~g~vfV~f~~~e~A~~A~~~l~Gr~f~gR~v~v~f~~   94 (104)
T d1o0pa_          58 CGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCD   94 (104)
T ss_dssp             CCEEEEEESCHHHHHHHHHHHSSCCSSSSCCEEEEEC
T ss_pred             ceEEEEEECCHHHHHHHHHHHCCCEECCeEEEEEEcC
Confidence            4899999999999999999999999999999999975

>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=98.08  E-value=1.6e-06  Score=60.91  Aligned_cols=35  Identities=29%  Similarity=0.234  Sum_probs=32.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEec
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA   38 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a   38 (268)
                      ++||||+|.+.++|+.|| .|++..|+|+.|.|+.+
T Consensus        40 ~~~afV~F~~~~~a~~Al-~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2          40 FRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             SEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             ceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            579999999999999998 69999999999999875

>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=98.07  E-value=4e-07  Score=63.19  Aligned_cols=33  Identities=24%  Similarity=0.433  Sum_probs=30.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceE
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRII   34 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~Ir   34 (268)
                      .+|||||+|.+.++|+.||..|||..|+|+.|+
T Consensus        39 ~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1          39 CKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             CCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             ccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            469999999999999999999999999998764

>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=98.07  E-value=1.6e-06  Score=64.53  Aligned_cols=39  Identities=18%  Similarity=0.147  Sum_probs=35.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.++++|+.|| .|++..|.|+.|.|.++...
T Consensus        56 ~kG~afV~F~~~e~a~~a~-~~~~~~i~gR~i~V~~~~~~   94 (104)
T d1wg5a_          56 STGEAFVQFASQEIAEKAL-KKHKERIGHRYIEIFKSSRA   94 (104)
T ss_dssp             BCSEEEEEESSHHHHHHHH-TTTTCCSSSSCCEEEEECTT
T ss_pred             cceEEEEEeCCHHHHHHHH-hhCCCEEcceEEEEEECCHH
Confidence            4799999999999999888 59999999999999998753

>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=98.06  E-value=1.7e-06  Score=62.08  Aligned_cols=37  Identities=27%  Similarity=0.381  Sum_probs=33.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+|||||+|.+.++|+.||. +++..|+|+.|.|..|.
T Consensus        47 ~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1          47 SRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             EEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             cccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            36999999999999999996 68999999999998874

>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=98.05  E-value=1.6e-06  Score=62.29  Aligned_cols=36  Identities=17%  Similarity=0.295  Sum_probs=33.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|+.|| .++|.+|.|+.|.|.+..
T Consensus        47 kG~afV~f~~~e~a~~al-~~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2          47 KGSIFVVFDSIESAKKFV-ETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             EEEEEEEESCHHHHHHHH-TCCCCEETTEECEEEEGG
T ss_pred             ceEEEEEEcCHHHHHHHH-HHCCCEECCEEEEEEEcC
Confidence            589999999999999999 589999999999999864

>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=98.01  E-value=4.2e-07  Score=65.89  Aligned_cols=37  Identities=22%  Similarity=0.474  Sum_probs=33.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      .+|||||+|.+.++|+.|| .|||++|+|+.|.|..++
T Consensus        47 ~kg~afV~f~~~e~a~~a~-~l~g~~~~Gr~l~V~r~k   83 (90)
T d1u2fa_          47 DKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPH   83 (90)
T ss_dssp             TTTEEEEEESSCTTTTTGG-GGSSCCSSSSCCCCBCTT
T ss_pred             CceEEEEEeCCHHHHHHHH-hhCCcEECCEEEEECCCC
Confidence            4799999999999999998 599999999999997654

>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=97.98  E-value=1.6e-06  Score=48.94  Aligned_cols=22  Identities=50%  Similarity=1.025  Sum_probs=18.9

Q ss_pred             CCCccccCCCCCCCCCcccCCC
Q 024424           59 GSGRCFNCGIDGHWARDCKAGD   80 (268)
Q Consensus        59 ~~~rC~~CG~~GH~ardC~~~~   80 (268)
                      ....|||||++||++++|.++.
T Consensus         5 ~~ikCfNCGkeGH~ar~CrAPR   26 (29)
T d1nc8a_           5 KVIRCWNCGKEGHSARQCRAPR   26 (29)
T ss_dssp             CCCBCTTTSCBSSCGGGCCSSS
T ss_pred             ceeEeecCCccchhhhhccCcc
Confidence            3468999999999999999885

>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=97.98  E-value=3.9e-06  Score=61.99  Aligned_cols=40  Identities=18%  Similarity=0.130  Sum_probs=35.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHH--hhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARY--SLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~--~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|.+.++|..||+  ++++..|.|+.|.|.+++..
T Consensus        54 ~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~~   95 (99)
T d1x4fa1          54 MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKY   95 (99)
T ss_dssp             TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSC
T ss_pred             cCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCCc
Confidence            36999999999999999998  58899999999999999643

>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=97.93  E-value=5.2e-06  Score=59.66  Aligned_cols=39  Identities=13%  Similarity=0.189  Sum_probs=34.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhh--CCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSL--NGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~l--dG~~l~Gr~IrVe~a~~   40 (268)
                      .+|||||+|.+.++|+.||..|  ++..|.|+.|+|.|++.
T Consensus        43 ~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~   83 (88)
T d2cq1a1          43 GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH   83 (88)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSC
T ss_pred             cceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCC
Confidence            3689999999999999999865  67899999999999863

>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=97.91  E-value=3.1e-06  Score=61.55  Aligned_cols=37  Identities=16%  Similarity=0.276  Sum_probs=32.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      +|||||+|.+.++|+.||..++  .|+|+.|.|.++...
T Consensus        50 rG~aFV~f~~~~~a~~al~~~~--~l~Gr~i~v~~a~~k   86 (90)
T d2cqga1          50 KGFGFVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSK   86 (90)
T ss_dssp             EEEEEEEESSHHHHHHHHHSCE--EETTEEEEEECCCTT
T ss_pred             CCEEEEEECCHHHHHHHHhcCC--ccCCEEeEEEeCCCC
Confidence            6899999999999999998654  899999999998753

>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=97.90  E-value=6.8e-06  Score=59.47  Aligned_cols=39  Identities=26%  Similarity=0.248  Sum_probs=35.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhh--CCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSL--NGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~l--dG~~l~Gr~IrVe~a~~   40 (268)
                      .++||||+|++.++|+.||+.|  ++..|.|+.|.|.|++.
T Consensus        44 ~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~   84 (89)
T d1x4da1          44 KINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   84 (89)
T ss_dssp             SSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             cceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCC
Confidence            3689999999999999999965  78899999999999974

>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=97.90  E-value=2.8e-06  Score=61.28  Aligned_cols=38  Identities=26%  Similarity=0.277  Sum_probs=34.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccCC
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG   41 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~~   41 (268)
                      .+|||||+|++.++|+.||.  ++.+|+|+.|.|.++...
T Consensus        41 ~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k   78 (88)
T d1wf0a_          41 FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPK   78 (88)
T ss_dssp             CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCC
T ss_pred             cCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCC
Confidence            47999999999999999984  788999999999999754

>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=97.88  E-value=2.8e-06  Score=64.07  Aligned_cols=36  Identities=22%  Similarity=0.167  Sum_probs=33.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|+.|| .|||..|+|+.|.|..+.
T Consensus        60 ~G~afVeF~~~e~a~~al-~~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          60 TGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             EEEEEEEBSSSHHHHHHH-TSCSBCSTTSCBEEEEEC
T ss_pred             eeEEEEEECCHHHHHHHH-HcCCCcCCCEEEEEEEcC
Confidence            589999999999999888 599999999999998764

>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=97.87  E-value=7.2e-06  Score=60.85  Aligned_cols=39  Identities=15%  Similarity=0.200  Sum_probs=34.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhh--CCCeecCcceEEEeccC
Q 024424            2 KRDFAFVEFSDPRDADDARYSL--NGRDVDGSRIIVEFARG   40 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~l--dG~~l~Gr~IrVe~a~~   40 (268)
                      .+|||||+|++.++|+.||..|  ++..|.|+.|.|.|+..
T Consensus        50 ~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~   90 (104)
T d1wexa_          50 FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTS   90 (104)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSS
T ss_pred             cceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCC
Confidence            4789999999999999999987  56778999999999864

>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=97.79  E-value=4.7e-06  Score=58.52  Aligned_cols=36  Identities=19%  Similarity=0.320  Sum_probs=31.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEec
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA   38 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a   38 (268)
                      .+|||||+|.+.++|+.||+ +++.+|+|+.|.|..|
T Consensus        40 ~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1          40 RRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             TTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             cccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            47999999999999999996 4778899999988764

>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=97.67  E-value=2.1e-05  Score=56.08  Aligned_cols=35  Identities=23%  Similarity=0.230  Sum_probs=30.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcc-eEEEec
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSR-IIVEFA   38 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~-IrVe~a   38 (268)
                      +|||||+|.+.++|++|| .|||..|+|+. |.|..+
T Consensus        39 ~~~~fV~f~~~~~A~~Al-~~nG~~~~g~~~vgV~~~   74 (81)
T d1wwha1          39 GNWMHIRYQSKLQARKAL-SKDGRIFGESIMIGVKPC   74 (81)
T ss_dssp             SSEEEEEESSHHHHHHHH-TTTTCEETTTEECEEEEC
T ss_pred             CCEEEEEEcccHHHHHHH-hcCCCeECCcEEEEEEeC
Confidence            699999999999999999 59999999975 456554

>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=97.58  E-value=3.3e-05  Score=57.10  Aligned_cols=27  Identities=22%  Similarity=0.619  Sum_probs=25.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHhhCCCee
Q 024424            2 KRDFAFVEFSDPRDADDARYSLNGRDV   28 (268)
Q Consensus         2 krGfgFVeF~~~~dA~~Ai~~ldG~~l   28 (268)
                      .++||||+|.+.++|+.||..|+|.+|
T Consensus        55 ~k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          55 NKPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            368999999999999999999999987

>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=97.24  E-value=0.00011  Score=55.19  Aligned_cols=37  Identities=11%  Similarity=0.101  Sum_probs=32.0

Q ss_pred             CCeEEEEeCCH-HHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDP-RDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~-~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||.|.+. ++|..||..|++..|.+..+.|.++.
T Consensus        47 kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          47 AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            68999999985 78999999999999988877777654

>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=96.79  E-value=0.00028  Score=39.57  Aligned_cols=21  Identities=33%  Similarity=0.987  Sum_probs=18.2

Q ss_pred             CCccccCCCCCccccccCCCC
Q 024424           82 KNKCYRCGERGHIERNCQNSP  102 (268)
Q Consensus        82 ~~~cyrcg~~GH~~r~c~~s~  102 (268)
                      .-.||+||++||++++|....
T Consensus         6 ~ikCfNCGkeGH~ar~CrAPR   26 (29)
T d1nc8a_           6 VIRCWNCGKEGHSARQCRAPR   26 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSSS
T ss_pred             eeEeecCCccchhhhhccCcc
Confidence            468999999999999998643

>d1dsqa_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=96.58  E-value=0.0004  Score=37.35  Aligned_cols=18  Identities=56%  Similarity=1.241  Sum_probs=14.3

Q ss_pred             ccccCCCCCCCCCcccCC
Q 024424           62 RCFNCGIDGHWARDCKAG   79 (268)
Q Consensus        62 rC~~CG~~GH~ardC~~~   79 (268)
                      .||.||+.||+..||+..
T Consensus         4 vcfscgktghikkdck~e   21 (26)
T d1dsqa_           4 VCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             BCTTTCCBSSCTTTTTCC
T ss_pred             EEEecCCcccchhhhhhh
Confidence            688888888888888754

>d1dsqa_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=96.03  E-value=0.0012  Score=35.42  Aligned_cols=19  Identities=42%  Similarity=1.256  Sum_probs=17.1

Q ss_pred             CccccCCCCCccccccCCC
Q 024424           83 NKCYRCGERGHIERNCQNS  101 (268)
Q Consensus        83 ~~cyrcg~~GH~~r~c~~s  101 (268)
                      -.||.||+.|||.++|.+.
T Consensus         3 pvcfscgktghikkdck~e   21 (26)
T d1dsqa_           3 PVCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTCC
T ss_pred             CEEEecCCcccchhhhhhh
Confidence            4799999999999999874

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

Probab=95.49  E-value=0.0039  Score=38.46  Aligned_cols=18  Identities=39%  Similarity=1.123  Sum_probs=16.6

Q ss_pred             CccccCCCCCCCCCcccC
Q 024424           61 GRCFNCGIDGHWARDCKA   78 (268)
Q Consensus        61 ~rC~~CG~~GH~ardC~~   78 (268)
                      ..||.||..|||+.+|+.
T Consensus        23 ~~C~~Cg~~GH~~~~Cp~   40 (42)
T d2exfa1          23 KGCWKCGKEGHQMKDCTE   40 (42)
T ss_dssp             SSCSSSCCSSSCTTTCCS
T ss_pred             CccccCCCCCeecccCCC
Confidence            579999999999999985

>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Zinc finger protein ncp10
species: Moloney murine leukemia virus, MoMLV [TaxId: 11801]

Probab=94.20  E-value=0.02  Score=34.13  Aligned_cols=20  Identities=40%  Similarity=1.076  Sum_probs=11.5

Q ss_pred             CCCccccCCCCCCCCCcccC
Q 024424           59 GSGRCFNCGIDGHWARDCKA   78 (268)
Q Consensus        59 ~~~rC~~CG~~GH~ardC~~   78 (268)
                      ....|.-|-..|||+.||+.
T Consensus         9 ~kDQCAyCke~GHW~~dCPk   28 (40)
T d1a6bb_           9 DRDQCAYCKEKGHWAKDCPK   28 (40)
T ss_dssp             CSSSCSSSCCTTCCTTSCSS
T ss_pred             cchhhHHHhhcCchhhhCcc
Confidence            34456666666666666653

>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=92.73  E-value=0.047  Score=42.39  Aligned_cols=36  Identities=28%  Similarity=0.411  Sum_probs=29.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHhhCCCeecCcceEEEecc
Q 024424            3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR   39 (268)
Q Consensus         3 rGfgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~   39 (268)
                      +|||||+|.+.++|+.|+.. .+..|.+..|.+....
T Consensus        48 ~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~   83 (183)
T d1u1qa_          48 RGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAV   83 (183)
T ss_dssp             EEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECC
T ss_pred             cCceecccCCHHHHHHHHHh-cCCcccccchhhhhhh
Confidence            58999999999999999864 5666777777776654

>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Zinc finger protein ncp10
species: Moloney murine leukemia virus, MoMLV [TaxId: 11801]

Probab=91.60  E-value=0.074  Score=31.59  Aligned_cols=24  Identities=29%  Similarity=0.908  Sum_probs=20.5

Q ss_pred             CCccccCCCCCccccccCCCCCCC
Q 024424           82 KNKCYRCGERGHIERNCQNSPKKL  105 (268)
Q Consensus        82 ~~~cyrcg~~GH~~r~c~~s~~~~  105 (268)
                      ++-|-.|.+.|||.++|+..+...
T Consensus        10 kDQCAyCke~GHW~~dCPkkprg~   33 (40)
T d1a6bb_          10 RDQCAYCKEKGHWAKDCPKKPRGP   33 (40)
T ss_dssp             SSSCSSSCCTTCCTTSCSSSCCCT
T ss_pred             chhhHHHhhcCchhhhCccCCCCC
Confidence            578999999999999999866543

>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=88.89  E-value=0.28  Score=33.18  Aligned_cols=36  Identities=31%  Similarity=0.396  Sum_probs=33.6

Q ss_pred             eEEEEeCCHHHHHHHHHhhCCCeecCcceEEEeccC
Q 024424            5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG   40 (268)
Q Consensus         5 fgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a~~   40 (268)
                      .|.|...+..||..||..|+-..|.+++|.|.++.+
T Consensus        37 ~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          37 KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            588999999999999999999999999999999864

>d1cl4a_ g.40.1.1 (A:) Nucleocapsid protein from mason-pfizer monkey virus (MPMV) {Mason-pfizer monkey virus [TaxId: 11855]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleocapsid protein from mason-pfizer monkey virus (MPMV)
species: Mason-pfizer monkey virus [TaxId: 11855]

Probab=85.79  E-value=0.31  Score=27.62  Aligned_cols=19  Identities=42%  Similarity=1.046  Sum_probs=15.4

Q ss_pred             CccccCCCCCCCCCcccCC
Q 024424           61 GRCFNCGIDGHWARDCKAG   79 (268)
Q Consensus        61 ~rC~~CG~~GH~ardC~~~   79 (268)
                      +.|-+|.+.-||+.+|..-
T Consensus         3 ~lCPrC~kG~HWa~~Crsk   21 (32)
T d1cl4a_           3 GLCPRCKRGKHWANECKSK   21 (32)
T ss_dssp             CSCSSCSSCSSCSTTCCCT
T ss_pred             ccCccccCcchHHHHhhhh
Confidence            5688898888999888754

>d1dsva_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=85.48  E-value=0.18  Score=28.49  Aligned_cols=19  Identities=37%  Similarity=0.943  Sum_probs=15.9

Q ss_pred             CccccCCCCCCCCCcccCC
Q 024424           61 GRCFNCGIDGHWARDCKAG   79 (268)
Q Consensus        61 ~rC~~CG~~GH~ardC~~~   79 (268)
                      ..|-+|.+.-||+.+|..-
T Consensus         3 ~lCPrC~kG~HWa~~Crsk   21 (31)
T d1dsva_           3 GLCPRCKKGYHWKSECKSK   21 (31)
T ss_dssp             CBCTTTCSSBSCTTTCCCS
T ss_pred             ccCccccCcchHHHHhhhh
Confidence            5789999999999999753

>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=84.02  E-value=0.31  Score=34.58  Aligned_cols=33  Identities=21%  Similarity=0.326  Sum_probs=28.5

Q ss_pred             eEEEEeCCHHHHHHHHHhhCCCeecCcceEEEec
Q 024424            5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA   38 (268)
Q Consensus         5 fgFVeF~~~~dA~~Ai~~ldG~~l~Gr~IrVe~a   38 (268)
                      --.|+|.+-+.|..|+ .|+|++|+|+.|.|...
T Consensus        60 ~mwVTF~dG~SAL~al-~l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          60 QMLVTFADSHSALSVL-DVDGMKVKGRAVKISGP   92 (95)
T ss_dssp             EEEEECSCSHHHHHHH-HGGGSEETTEEEEEECC
T ss_pred             eEEEEECCcHHHHHHh-ccCCeEEcceEEEEecC
Confidence            4579999999999998 69999999999988643